title: Sorted tumor-associated macrophages from Grp65-knockout high-fat-diet-fed mouse 2

extract_protocol:
RNA was harvested using Rneasy mini  kit (QIAGEN). >200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Takara SMART-seq kit following the manufacturer's protocol.

value: Mouse genotype is Gpr65-knockout


title: Sorted MC38 tumor cells from control-diet-fed mouse 1

status: Public on Oct 18 2024

type: SRA

city: San Mateo

first: Sreya

last: Bagchi

state: CA

address: 1202 S Claremont Street

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequences/low-quality sequences using Cutadapt v1.15 and quality was evaluated using FastQC v0.11.5.
Trimmed sequence reads were mapped to GrCM38/mm10 using bwa v0.7.12 and filtered for MAPQ < 5.
Read count extraction performed using DESeq2 v1.24.0 in R.
Assembly: mm10
Supplementary files format and content: Comma-delimited text file includes raw counts for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini  kit (QIAGEN). >200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep kit following the manufacturer's protocol.

tag: tissue

value: Tumor

tag: cell line

tag: cell type

value: Tumor cell (CD45-negative)

tag: treatment

value: Control-diet-fed


title: LOAD15 H PM024

city: New York

first: John

last: Tuddenham

state: NY

institute: Columbia University

description:
LOAD15 H
polyA RNA

library_source: transcriptomic single cell

data_processing:
Fastq files were run through 10x Genomics Cellranger v3.1.0.
Assembly: hg38.91
Supplementary files format and content: Counts tables for all barcodes, filtered by CellRanger, in standard hdf5 output from CellRanger. For samples with cell hashing, HTO count library is also included.

organism: Homo sapiens

source_name: H

extract_protocol:
CD45+ cells were isolated from autopsy tissue or surgical resections using a cold mechanical dissociation protocol, as described in our publication. (Tuddenham, Taga, Haage, et al. 2022)
10x Genomics Chromium 3' v2 and v3 chemistry

value: H


title: unrupture_nohCG_rep14

city: Somerville

first: Daniela

middle: Dolores

last: Russo

state: Massachusetts

address: 5 Russell Rd

institute: Ragon Institute of MGH, MIT and Harvard

description:
Smart-seq2
Rupture_Unrupture_G04

data_processing:
Raw sequencing data were demultiplexed and aligned to the GRCm38 genome using publicly available scripts on Terra (github.com/broadinstitute/TAG-public)
Cells expressing less than 500 genes were excluded from further analysis and genes were filtered to contain only those that were protein coding.
To filter for high-quality cells for each category, we utilized the AddModuleScore function in Seurat v4 (Hao et al., 2021) for scoring marker gene expression modules established from published datasets (Wang et al., 2020, Tharp et al., 2020, Zhang et al., 2018, Pangas et al., 2006) (Supplementary Table 1). Oocytes that scored highly for somatic cell gene expression (>2 standard deviations above the mean somatic cell module score) were removed. Similarly, somatic cells that scored highly for oocyte gene expression were also excluded.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated counts and tpm files

molecule: total RNA

source_name: Cumulus-oocyte complex

extract_protocol:
Mouse secondary follicles were isolated from the ovaries of 14-16 day-old CD-1 female mice enzymatically using L15 media (Thermo Fisher Scientific, Waltham, MA) with 1% penicillin-streptomycin (Thermo Fisher Scientific), 25 μg/ml liberase (Sigma-Aldrich, St. Louis, MO), and 200 μg/mlDNase I (Qiagen, Hilden, Germany). Ovary pieces were manually dispersed using a P1000 pipette to release follicles. Follicles with intact morphology were encapsulated in an alginate hydrogel (Sigma-Aldrich) for the preservation of the 3D structure of follicles throughout folliculogenesis. Follicles were cultured for 8 days, then antral follicles were removed, washed, and transferred to maturation media with or without human chorionic gonadotropin (Sigma-Aldrich for 12 hours to allow for ovulation and follicle rupture.
Bulk RNA-seq libraries were generated using SMART-Seq2 protocol (Trombetta et al., 2014). Briefly, cDNA was reversed transcribed from single cells using Maxima RT (Thermo Fisher Scientific) and whole transcriptome amplification (WTA) was performed. WTA products were purified using the Agencourt AMPure XP beads (Beckman Coulter, IN, USA) and used to prepare paired-end libraries with Nextera XT  (Illumina, CA, USA).

value: Cumulus-oocyte complex

tag: group


title: unrupture_nohCG_rep13

description:
Smart-seq2
Rupture_Unrupture_G03


title: unrupture_nohCG_rep12

description:
Smart-seq2
Rupture_Unrupture_G02


title: LOAD15 GM PM023

description:
LOAD15 GM
polyA RNA


title: Sorted MC38 tumor cells from control-diet-fed mouse 2


title: Sorted tumor-associated macrophages from Grp65-knockout high-fat-diet-fed mouse 1

value: Tumor model is MC38

tag: genotype

value: High-fat-diet-fed


title: Sorted tumor-associated macrophages from Grp65-wild-type high-fat-diet-fed mouse 4

value: Mouse genotype is Gpr65-wild-type


title: S. indica, 40FC, biol rep 1

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovía M-40 (km 38)

department: Centro de Biotecnología y Genómica de Plantas

country: Spain

institute: Universidad Politécnica de Madrid

data_processing:
Novogene Co., LTD Genomics Service (Cambridge, UK)
Original image data files from the Illumina platform were transformed to sequenced reads by CASAVA base recognition.
Sequence reads were trimmed for the adaptor sequence/low-quality reads were deleted using a Novogene in-house script (quality parameter limit: 0.05)
Trimmed sequence reads were mapped against the TAIR10 Arabidopsis genome using hisat2 v2.0.5.
Read count extraction and normalization was performed using HTSeq v0.6.1 with ‐m union parameter.
Assembly: ensemblplants_solanum_lycopersicum_sl3_0_gca_000188115_3
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

organism: Solanum lycopersicum

source_name: Roots

growth_protocol: Per 25 cm diameter pot, filled with mixtures of peat:vermiculite (3:1), one tomato seedling was transferred at 100% FC. The 100% FC condition pots were readjusted to 100% FC every 2 days; whereas the 40% FC condition pots were not watered until they reached 40% FC. Thereafter, the FC of the 40% FC condition was also readjustment every 2 days.. Plants were grown for 8 weeks.

extract_protocol:
DNA-free total RNA was extracted by employing the phenol/chloroform method described by Oñate-Sánchez & Vicente-Carbajosa, 2008, BMC Res. Notes.
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations.

treatment_protocol: Each tomato seedling was either mock-infected (100 ml water) or inoculated with 100 ml of a solution containing 2 x 105 spores/ml, once directly after the tranfer and a second time after 2 weeks.

value: Roots

value: Moneymaker


title: S. indica, 40FC, biol rep 2


title: Sorted tumor-associated macrophages from Grp65-wild-type high-fat-diet-fed mouse 2


title: Sorted tumor-associated macrophages from Grp65-wild-type high-fat-diet-fed mouse 3


title: S. indica, 40FC, biol rep 3


title: LOAD14 GM PM020

description:
LOAD14 GM
polyA RNA


title: S. indica, 100FC, biol rep 3


title: LOAD14 SN PM022

description:
LOAD14 SN
polyA RNA


title: unrupture_nohCG_rep9

description:
Smart-seq2
Rupture_Unrupture_F09


title: LOAD14 H PM021

description:
LOAD14 H
polyA RNA

source_name: SN

value: SN


title: Sorted tumor-associated macrophages from Grp65-knockout high-fat-diet-fed mouse 3


title: LOAD13 SN PM018

description:
LOAD13 SN
polyA RNA


title: unrupture_nohCG_rep11

description:
Smart-seq2
Rupture_Unrupture_G01


title: LOAD11 GM DeJager_MO_LOAD11_GM

description:
LOAD11 GM
polyA RNA


title: Sorted tumor-associated macrophages from Grp65-wild-type high-fat-diet-fed mouse 1


title: unrupture_nohCG_rep8

description:
Smart-seq2
Rupture_Unrupture_F08


title: S. indica, 100FC, biol rep 1


title: S. indica, 100FC, biol rep 2


title: P. miniolutem, 40FC, biol rep 3


title: unrupture_nohCG_rep7

description:
Smart-seq2
Rupture_Unrupture_F07


title: unrupture_nohCG_rep10

description:
Smart-seq2
Rupture_Unrupture_F10


title: unrupture_nohCG_rep6

description:
Smart-seq2
Rupture_Unrupture_F06


title: unrupture_nohCG_rep5

description:
Smart-seq2
Rupture_Unrupture_F05


title: P. miniolutem, 40FC, biol rep 2


title: unrupture_nohCG_rep4

description:
Smart-seq2
Rupture_Unrupture_F04


title: LOAD13 H PM017

description:
LOAD13 H
polyA RNA


title: P. miniolutem, 40FC, biol rep 1


title: LOAD13 GM PM016

description:
LOAD13 GM
polyA RNA


title: P. miniolutem, 100FC, biol rep 3


title: DLBD-PD1 SN PM007

description:
DLBD-PD1 SN
polyA RNA


title: LOAD12 GM PM013

description:
LOAD12 GM
polyA RNA


title: P. miniolutem, 100FC, biol rep 2


title: unrupture_nohCG_rep2

description:
Smart-seq2
Rupture_Unrupture_F02


title: unrupture_nohCG_rep3

description:
Smart-seq2
Rupture_Unrupture_F03


title: DLBD-PD2 GM PM004

description:
DLBD-PD2 GM
polyA RNA


title: DLBD-PD1 GM PM006

description:
DLBD-PD1 GM
polyA RNA


title: DLBD-PD2 SN PM005

description:
DLBD-PD2 SN
polyA RNA


title: P. chrysogenum, 40FC, biol rep 3


title: P. miniolutem, 100FC, biol rep 1


title: HMC3 w50 n3

type: RNA

city: örebro

first: isak

last: demirel

address: campus usö

country: Sweden

institute: örebro University

description: Gene expression after 24 hours of stimulated HMC3

hyb_protocol: Labelled samples were hybridised onto G4851C SurePrint G3 Human Gene Expression v3 8x60K Microarray glass slides (Agilent)

scan_protocol: Microarrays were scanned with a G2565 CA array laser scanner (Agilent) followed by image analysis and data extraction with Feature Extraction Software version 10.7.3.1 (Agilent).

data_processing: 75th percentile shift normalisation and baseline adjusted

source_name: HMC3 w50

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the low input quick amp labeling kit,one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The immortalized human microglial cell line HMC3 (American Type Culture Collection (ATCC), Manassas, VA, USA) was cultured in Dulbecco´s Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS), 1mM non-essential amino acids and 2mM L-glutamine (all from Thermo Fisher Scientific, Waltham, MA, USA) in 37°C in 5% CO2 atmosphere. 18 hours prior to and during experiments, the culture medium was changed to DMEM without FBS.

extract_protocol: Total RNA was isolated using the E.Z.N.A. Total RNA Kit I. RNA quality and integrity were evaluated using Agilent TapeS  tation 2200 platform (Agilent Technologies, Palo Alto, CA, USA) according to manufacturer in-structions. The RNA integrity number (RIN) was 10 for all RNA samples.

treatment_protocol: HMC3 cells were stimulated with P. gingivalis strains W50, E8 and K1A (MOI 10) for 24 hours and the gene expression was evaluated.

value: W50 for 24 h


title: HMC3 K1A n3

source_name: HMC3 K1A

value: K1A for 24 h


title: P. chrysogenum, 40FC, biol rep 1


title: unrupture_nohCG_rep1

description:
Smart-seq2
Rupture_Unrupture_F01


title: HMC3 w50 n4


title: HMC3 K1A n4


title: rupture_hCG_rep11

description:
Smart-seq2
Rupture_Unrupture_D06


title: LOAD12 AH PM014

description:
LOAD12 AH
polyA RNA


title: HMC3 E8 n4

source_name: HMC3 E8

value: E8 for 24 h


title: P. chrysogenum, 40FC, biol rep 2


title: rupture_hCG_rep13

description:
Smart-seq2
Rupture_Unrupture_D09


title: ALS4 GM MA002

description:
ALS4 GM
polyA RNA


title: HMC3 E8 n3


title: rupture_hCG_rep12

description:
Smart-seq2
Rupture_Unrupture_D08


title: HMC3 unstimulated n3

description: Gene expression after 24 hours of unstimulated HMC3

source_name: HMC3 unstimulated

value: unstimulated


title: HMC3 K1A n2


title: P. chrysogenum, 100FC, biol rep 3


title: ALS4 SC MA004

description:
ALS4 SC
polyA RNA

source_name: SC

value: SC


title: HMC3 unstimulated n4


title: ALS4 FN MA003

description:
ALS4 FN
polyA RNA

source_name: FN

value: FN


title: HMC3 w50 n2


title: rupture_hCG_rep10

description:
Smart-seq2
Rupture_Unrupture_D05


title: P. chrysogenum, 100FC, biol rep 1


title: ALS4 GM MA001

description:
ALS4 GM
polyA RNA


title: P. chrysogenum, 100FC, biol rep 2


title: Mock, 40FC, biol rep 3


title: rupture_hCG_rep9

description:
Smart-seq2
Rupture_Unrupture_D04


title: Mock, 40FC, biol rep 1


title: HMC3 unstimulated n2


title: HMC3 E8 n2


title: Torin2 biological replicate 3

data_processing:
Picard version 1.83
RSeQC version 2.6.1
STAR version 2.5.2a was used to align reads to the GRCh38 genome, using Gencode v25 annotation.
Bowtie2 version 2.1.0 was used to measure rRNA abundance.
Annotated genes were quantified with featureCounts version 1.4.3-p1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file include un-normalized counts for each sample.

growth_protocol: HMC3 cells were grown in ATCC EMEM + 10% FBS and antibiotics in a humidified atmosphere with 5% CO2 at 37C. They were passaged 2-3x weekly at 80% confluence with trypsin-EDTA.

extract_protocol:
RNA was extracted with the Qiagen Rneasy Plus Mini Kit. RNA quality was assessed using the 2100 Bioanalyzer G2938C using an Agilent RNA 6000 Nano Kit and the Qubit 4 Fluorometer using Qubit 1XdsDNA HS assay
mRNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols and using IDT for Illumina TruSeq DNA UD Indices for adapters

treatment_protocol: Cells were treated with drugs as noted above for 24 hours, trypsinized for counting and assessment of cell viability, then harvested for RNA extraction.

value: microglia

value: WT

value: 10uM Torin-2


title: rupture_hCG_rep8

description:
Smart-seq2
Rupture_Unrupture_D03


title: rupture_hCG_rep7

description:
Smart-seq2
Rupture_Unrupture_D02


title: HMC3 w50 n1


title: Torin2 biological replicate 1


title: Torin2 biological replicate 2


title: HMC3 unstimulated n1


title: rupture_hCG_rep3

description:
Smart-seq2
Rupture_Unrupture_C08


title: Narciclasine biological replicate 3

value: 0.1uM Narciclasine


title: Methanosarcina_acetivorans_WWM204_-Tet_48h_rep2

city: Lincoln

first: Nicole

last: Buan

state: NE

address: 1901 Vine St N200 Beadle N200 Beadle

department: Biochemistry

institute: University of Nebraska-Lincoln

description: 48h HdrED depleted

hyb_protocol: Hybridization was performed by NBuan following manufacturer's standard operating protocol. See NimbleGen Systems Inc., Madison, WI USA, www.nimblegen.com.

scan_protocol: Scanning was performed by NBuan following manufacturer's standard operating protocol. See NimbleGen Systems Inc., Madison, WI USA, www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.).

organism: Methanosarcina acetivorans

source_name: M.acetivorans WWM204 -Tet tube2 48h

label_protocol: Labeling was performed by NBuan following manufacturer's standard operating protocol. See NimbleGen Systems Inc., Madison, WI USA, www.nimblegen.com.

growth_protocol: Methanosarcina strain WWM204 (Dhpt att::PmcrB-tetR/PhiC31 int/attB::hdrED::PmcrB-tetR frt/pac hpt/frt PmcrB(tet01)hdrED )(doi:10.1111/j.1365-2958.2009.06990.x) was grown at 37C under strictly anaerobic conditions in HS mineral salts medium in 15ml anaerobic culture tubes.(doi:DOI: https://doi.org/10.1128/aem.47.5.971-978.1984, doi:https://doi.org/10.1128/aem.59.11.3832-3839.1993). The following anaerobic additions were added when appropriate: MeOH (125mM), Tetracycline (100ug/ml, +Tet), and Puromycin (2ug/ml). WWM204 was maintained with tetracycline at all times until commencing the experiment. Growth was measured every 6 hours by reading the optical density at 600nm (OD600) in a Spectronic 21 spectrophotometer (Milton Roy Company)

extract_protocol: Harvested cells were directly lysed in 15ml Qiagen RNEasy buffer RLT and frozen at -80C until RNA extraction. A total of 17 RNA samples were collected. Total RNA was extracted using the Qiagen RNEasy midiprep kit and DNA contamination was removed by digestion with TurboDNAfree DNAse (Ambion) and confirmed by lack of product after 40 cycles of PCR amplification.

treatment_protocol: Ptet-hdrED strain WWM204 was grown on MeOH in standard HS medium in the presence or absence of inducer (tetracycline). Total RNA was harvested from +Tet culture during exponential growth and at stationary phase, and from matched cultures which had been inoculated without inducer (-Tet) every 6 hours between 24-48h after start of innoculation. Transcripts were compared to identify differentially expressed genes between exponential vs stationary phase, and as growth rate decreased due to transcriptional repression of hdrED genes.

tag: strain

value: del-hpt::PmcrB-tetR/phiC31 int/attB hdrED::PmcrB-tetR frt/pac hpt/frt PmcrB(tetO1)-hdrE

tag: phenotype

value: tetracycline-induced expression of essential HdrED

tag: c source

value: MeOH

value: w/o Tet


title: rupture_hCG_rep6

description:
Smart-seq2
Rupture_Unrupture_D01

value: Cumulus-oocyte complex


title: HMC3 E8 n1


title: HMC3 K1A n1


title: Methanosarcina_acetivorans_WWM204_-Tet_42h_rep2

description: 42h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube7 42h


title: Mock, 100FC, biol rep 3

value: Roots

value: Moneymaker


title: rupture_hCG_rep1

description:
Smart-seq2
Rupture_Unrupture_C06


title: Methanosarcina_acetivorans_WWM204_-Tet_42h_rep1

description: 42h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube5 42h


title: Methanosarcina_acetivorans_WWM204_-Tet_48h_rep3

description: 48h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube8 48h


title: Narciclasine biological replicate 2


title: rupture_hCG_rep5

description:
Smart-seq2
Rupture_Unrupture_C10


title: Narciclasine biological replicate 1


title: rupture_hCG_rep4

description:
Smart-seq2
Rupture_Unrupture_C09


title: Mock, 100FC, biol rep 1


title: Mock, 100FC, biol rep 2


title: H55F7CCX2_1_adt

city: Cambridge

first: Simon

last: Mages

state: MA

address: 415 Main St.

institute: Broad Institute

description: HTO library: R1 file contains cell barcode and UMI; R2 file contains Hashtag Antibody Derived Tag reads

library_source: other

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the 10x Genomics Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) within the Cumulus feature barcoding workflow v0.2.0
Assembly: mm10-3.0.0
Supplementary files format and content: XXX_matrix.mtx.gz is the raw gene count matrix
Supplementary files format and content: XXX_barcodes.tsv.gz is the list of barcodes associated with XXX_matrix.mtx.gz
Supplementary files format and content: XXX_features.tsv.gz is the list of genes associated with XXX_matrix.mtx.gz
Supplementary files format and content: XXX_adt.csv give the HTO counts per sample

molecule: protein

source_name: Hashtag oligo (HTO) library

extract_protocol:
Single-cell suspensions from healthy colon or dysplastic lesions were processed using a modified version of a previously published protocol40. Tissue samples were rinsed in 30ml of ice-cold PBS (ThermoFisher 10010-049), chopped to small pieces and washed twice in 25 ml PBS, 5mM EDTA (ThermoFisher AM9261), 1%FBS (ThermoFisher 10082-147). To prime tissue for enzymatic digestion, samples were incubated for 10 minutes at 37°C, placed on ice for 10 minutes before shaking vigorously 15 times followed by supernatant removal. Tissues were placed into a large volume of ice-cold PBS to rinse prior to transferring to 5ml of enzymatic digestion mix (Base: RPMI1640, 10 mM HEPES (ThermoFisher 15630-080), 2% FBS), freshly supplemented immediately before use with 100 mg/mL of Liberase TM (Roche 5401127001) and 50 mg/mL of DNase I (Roche 10104159001), and incubated at 37°C with 120 rpm rotation for 30 minutes. After 30 minutes, enzymatic dissociation was quenched by addition of 1ml of 100% FBS and 10mM EDTA. Samples were then filtered through a 40 mM cell strainer into a new 50 mL conical tube and rinsed with PBS to 30 mL total volume. Tubes were spun down at 400 g for 7 minutes, at 4°C. Resulting cell pellets were resuspended in 1ml PBS, placed on ice and counted.
10XV3, following the manufacturer protocol for the v3 kit (10X Genomics, Pleasanton, CA).

treatment_protocol: Mice were injected to the submucosal layer of the colon with 4-hydroxytamoxifen (EMD Millipore # 579002) dissolved in ethanol at a concentration of 100 mM.  Tumors and matching colon tisuuea were resected at  3 weeks after 4-hydroxytamoxifen injection.

value: Hashtag oligo (HTO) library

tag: library type

value: HTO


title: unrupture_hCG_rep12

description:
Smart-seq2
Rupture_Unrupture_C05


title: Methanosarcina_acetivorans_WWM204_-Tet_36h_rep2

description: 36h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube6 36h


title: H55F7CCX2_1_rna

description: GEX (3' mRNA) library: R1 file contains cell barcode and UMI; R2 file contains transcript

source_name: 2 normal colon tissue, 2 Colorectal pre-malignant and 4 malignant lesions

value: Unsorted cells

value: Apcfl/flVillincreERT2  mice and Apcfl/fl; LSL-KrasG12D; Trp53fl/fl;Rosa26LSL-tdTomato/+; VillinCreERT2  mice

value: Mice were injected to the submucosal layer of the colon with 4-hydroxytamoxifen (EMD Millipore # 579002) dissolved in ethanol at a concentration of 100 mM (for the mice that were kept for 3 weeks after injection) or 30 mM (for the mice that were kept for 9 weeks after injection).  Tumors were resected at either 3 or 9 weeks after 4-hydroxytamoxifen injection

value: mRNA


title: Methanosarcina_acetivorans_WWM204_-Tet_36h_rep1

description: 36h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube4 36h


title: Camptothecin biological replicate 2

value: microglia

value: 1uM Camptothecin


title: Mock, 40FC, biol rep 2


title: Control biological replicate 3

value: WT

value: 10uM DMSO


title: unrupture_hCG_rep11

description:
Smart-seq2
Rupture_Unrupture_C04

source_name: Cumulus-oocyte complex


title: Camptothecin biological replicate 1


title: Methanosarcina_acetivorans_WWM204_-Tet_48h_rep1

description: 42h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube9 42h

value: del-hpt::PmcrB-tetR/phiC31 int/attB hdrED::PmcrB-tetR frt/pac hpt/frt PmcrB(tetO1)-hdrE


title: RNAseq_EC_10ng

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description:
Ecoli RNA (10ng)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx

data_processing:
quality control with FastQCv0.12.1
adapter removal with Cutadatv4.4 (bulk, SPE) and seqtkv1.2-r122 (MIP)
alignment with BWA-MEMv0.7.12-r1188
read extraction and filtering with bamtoolsv2.5.2 (MAPQ >30, NM<4)
count tables generated with SAMtoolsv0.7.17-r1188
Assembly: GCF_017329165.1 (Sa M2872), GCF_006094375.1 (Se ATCC 14990), GCF_002993865.1 (Sa USA300)
Supplementary files format and content: Supp_Table_06_Bulk_data_expdb.xlsx: table of bulk RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_05_Bulk_data_refdb.xlsx: table of bulk RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_08_MIP_data_expdb.xlsx: table of MIP RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_07_MIP_data_refdb.xlsx: table of MIP RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_10_SPE_data_expdb.xlsx: table of SPE RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_09_SPE_data_refdb.xlsx: table of SPE RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.

organism: Escherichia coli

source_name: bacterial culture

extract_protocol:
RNA was extracted using RNeasy 96 QIAcube HT kit (Qiagen, Hilden, Germany) according to the manufacturer’s directions. Samples were eluted in nuclease-free water (Qiagen, Hilden, Germany) and frozen at -80°C until sequencing preparation.
The sequencing libraries were prepared with NEBNext rRNA Depletion Kit v2 (New England Biolabs, Ipswich, MA) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) following the manufacturer’s directions.

treatment_protocol: S. aureus and S. epidermidis were grown in TSB, TSB pH 4.8 or on reconstructed human epidermidis for bulk and targted RNA-seq with and without ribo-depletion and/or SPIA.

value: bacterial culture

tag: seqeuncing appraoch

value: bulk RNA-Seq

tag: experimental batch

value: batch 1

tag: treatment rrna

value: ribo-depletion

tag: treatment spia

value: SPIA

tag: treatment media

value: TSB


title: rupture_hCG_rep2

description:
Smart-seq2
Rupture_Unrupture_C07

value: Cumulus-oocyte complex


title: Control biological replicate 2


title: HY2Y2CCXY_7_rna

source_name: 2 Colorectal pre-malignant and 4 malignant lesions

extract_protocol:
Single-cell suspensions from healthy colon or dysplastic lesions were processed using a modified version of a previously published protocol40. Tissue samples were rinsed in 30ml of ice-cold PBS (ThermoFisher 10010-049), chopped to small pieces and washed twice in 25 ml PBS, 5mM EDTA (ThermoFisher AM9261), 1%FBS (ThermoFisher 10082-147). To prime tissue for enzymatic digestion, samples were incubated for 10 minutes at 37°C, placed on ice for 10 minutes before shaking vigorously 15 times followed by supernatant removal. Tissues were placed into a large volume of ice-cold PBS to rinse prior to transferring to 5ml of enzymatic digestion mix (Base: RPMI1640, 10 mM HEPES (ThermoFisher 15630-080), 2% FBS), freshly supplemented immediately before use with 100 mg/mL of Liberase TM (Roche 5401127001) and 50 mg/mL of DNase I (Roche 10104159001), and incubated at 37°C with 120 rpm rotation for 30 minutes. After 30 minutes, enzymatic dissociation was quenched by addition of 1ml of 100% FBS and 10mM EDTA. Samples were then filtered through a 40 mM cell strainer into a new 50 mL conical tube and rinsed with PBS to 30 mL total volume. Tubes were spun down at 400 g for 7 minutes, at 4°C. Resulting cell pellets were resuspended in 1ml PBS, placed on ice and counted.
10XV2, following the manufacturer protocol for the v2 kit (10X Genomics, Pleasanton, CA).


title: unrupture_hCG_rep9

description:
Smart-seq2
Rupture_Unrupture_C02


title: RNAseq_EC_100ng

description:
Ecoli RNA (100ng)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx

value: no SPIA


title: Methanosarcina_acetivorans_WWM204_-Tet_30h_rep1

description: 30h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube2 30h

value: tetracycline-induced expression of essential HdrED

value: MeOH

value: w/o Tet


title: unrupture_hCG_rep8

description:
Smart-seq2
Rupture_Unrupture_B10


title: H55F7CCX2_2_rna

value: 2 normal colon tissue, 2 Colorectal pre-malignant and 4 malignant lesions

value: Unsorted cells

value: Apcfl/flVillincreERT2  mice and Apcfl/fl; LSL-KrasG12D; Trp53fl/fl;Rosa26LSL-tdTomato/+; VillinCreERT2  mice

value: Mice were injected to the submucosal layer of the colon with 4-hydroxytamoxifen (EMD Millipore # 579002) dissolved in ethanol at a concentration of 100 mM (for the mice that were kept for 3 weeks after injection) or 30 mM (for the mice that were kept for 9 weeks after injection).  Tumors were resected at either 3 or 9 weeks after 4-hydroxytamoxifen injection

value: mRNA


title: unrupture_hCG_rep7

description:
Smart-seq2
Rupture_Unrupture_B09


title: Control biological replicate 1

value: microglia

value: WT

value: 10uM DMSO


title: SAHA+sonidedgib_2

city: Shanghai

first: Min

last: Huang

address: 555, Zuchongzhi Road

country: China

institute: Shanghai Institute of Materia Medica

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie2 v2.4.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with TPM for every gene and every sample

source_name: Breast Cancer

extract_protocol:
Total RNA was extracted with TRIzol reagent following the recommendations of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-468 cells were treated with SAHA (10 μM, 12 hr) alone or in combination with sonidegib (10 μM, pretreatment for 72 hr).

value: SAHA and sonidegib


title: Camptothecin biological replicate 3

value: 1uM Camptothecin


title: Methanosarcina_acetivorans_WWM204_+Tet_exp_rep1B

description: exponential

source_name: M.acetivorans WWM204 +Tet exp

value: del-hpt::PmcrB-tetR/phiC31 int/attB hdrED::PmcrB-tetR frt/pac hpt/frt PmcrB(tetO1)-hdrE

value: w/Tet


title: Methanosarcina_acetivorans_WWM204_+Tet_sta_rep1B

description: stationary

source_name: M.acetivorans WWM204 +Tet sta


title: sonidedgib_3

value: sonidegib (10 uM, pretreatment for 72 hr)


title: unrupture_hCG_rep10

description:
Smart-seq2
Rupture_Unrupture_C03

value: Cumulus-oocyte complex


title: unrupture_hCG_rep5

description:
Smart-seq2
Rupture_Unrupture_B07


title: cont4_V2

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the 10x Genomics Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-3.0.0
Supplementary files format and content: XXX_matrix.mtx.gz is the raw gene count matrix
Supplementary files format and content: XXX_barcodes.tsv.gz is the list of barcodes associated with XXX_matrix.mtx.gz
Supplementary files format and content: XXX_features.tsv.gz is the list of genes associated with XXX_matrix.mtx.gz

source_name: normal colon

value: normal colon

value: injection with 4-hydroxytamoxifen to the submucosal layer of the colon, monitoring for 3 weeks


title: HY2Y2CCXY_7_adt

value: Hashtag oligo (HTO) library

value: HTO


title: Methanosarcina_acetivorans_WWM204_-Tet_24h_rep2

description: 24h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube7 24h

value: tetracycline-induced expression of essential HdrED

value: MeOH

value: w/o Tet


title: Methanosarcina_acetivorans_WWM204_-Tet_24h_rep3

description: 24h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube9 24h


title: unrupture_hCG_rep4

description:
Smart-seq2
Rupture_Unrupture_B06


title: unrupture_hCG_rep3

description:
Smart-seq2
Rupture_Unrupture_B05


title: SAHA+sonidedgib_1


title: unrupture_hCG_rep6

description:
Smart-seq2
Rupture_Unrupture_B08


title: Methanosarcina_acetivorans_WWM204_-Tet_30h_rep2

description: 30h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube8 30h


title: cont3_V2

value: Unsorted cells


title: SAHA_3

value: SAHA (10 uM, 12 hr)


title: SAHA+sonidedgib_3


title: SAHA_2


title: Methanosarcina_acetivorans_WWM204_-Tet_24h_rep1

description: 24h HdrED depleted

source_name: M.acetivorans WWM204 -Tet tube6 24h


title: unrupture_hCG_rep1

description:
Smart-seq2
Rupture_Unrupture_B01


title: H55F7CCX2_2_adt

source_name: Hashtag oligo (HTO) library


title: sonidedgib_2


title: AV5_V2

source_name: Colorectal pre-malignant lesion

value: Colorectal pre-malignant lesion

value: Apcfl/flVillincreERT2  mice


title: cont1_V2

value: WT


title: Con_2

value: control


title: SAHA_1


title: unrupture_hCG_rep2

description:
Smart-seq2
Rupture_Unrupture_B04


title: WT

first: Delphine

last: Larrieu

address: CIMR Hills Road

country: United Kingdom

institute: University of Cambridge

data_processing:
FastQC (v0.11.4) was used to assess sequence quality and nucleotide content of paired-end fastq files and enabled trimming of low quality bases from the 3’ end, using TrimGalore (v0.5.0). Trimmed reads were then aligned with STAR (v2.7.9) and HISAT2 (v2.1.0), for genome and transcript level analyses respectively, using Ensembl’s Homo sapiens GRCh38 (release 109) reference files. Uniquely aligned genomic reads, with a mapping score of 10 or greater, were quantified using HTSeq (v0.6.1), while StringTie (v1.3.4) was used to assemble and estimate transcript expression levels of HISAT2 alignments. Read counts were then read into R statistical software (v 3.6.1) and used as input to the edgeR package (v3.26.5) for pairwise comparisons, to identify differentially expressed genes and transcripts between Wild type cells and NGPS1/NGPS2 cells. A ‘5 CPM (Counts Per Million) in at least half of the samples’ filter was applied to the counts, which were then normalised before differential tests were performed. The CQN Bioconductor package (v1.30.0) was also used to correct for any Guanine-Cytosine or gene-length biases, prior to pairwise comparisons.
Assembly: Ensembl’s Homo sapiens GRCh38 (release 109)
Supplementary files format and content: csv file with differential analysis results

source_name: skin

extract_protocol:
Total RNA was extracted using the RNA miniprep kit from Zymo Research
The library was prepared with the Illumina TruSeq Stranded mRNA library prep kit.

value: skin

value: immortalised fibroblasts

value: wild-type


title: AV4_V2


title: NGPS_87

value: BANF1 p.Ala12Thr


title: sonidedgib_1

value: sonidegib (10 uM, pretreatment for 72 hr)


title: cont2_V2

value: normal colon

value: injection with 4-hydroxytamoxifen to the submucosal layer of the colon, monitoring for 3 weeks


title: AV1_V2


title: proQ-3XFLAG_hcd_rep2

city: Jena

first: Rabea

last: Ghandour

address: Winzerlaer Straße 2

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University

description:
proQ_hcd_2
Dataset_S2.xlsx

data_processing:
*library strategy: RIL-seq
demultiplexing of raw fastq files using custom script
reads trimming and barcode removal using fastp version 0.23.1. Default parameters were used except for the following: --umi-loc=read1 –umi-length=9 –cut-front –cut-tail –cut-mean-quality=25 –trim-poly-x
Analysis with "ChimericFragments" (doi: 10.5281/zenodo.8376810)
default parameters, exept: min_seed_length=15; autocomplete_utrs=false; bp_shift_weight=0.0; max_bp_fdr=0.4; max. fisher fdr:0.05; min_reads=5
Assembly: NC_002505, NC_002506
Supplementary files format and content: xlsx file including reads and FDR values for identified chimeras for each of the samples

molecule: other

organism: Vibrio cholerae

growth_protocol: Vibrio cholerae C6706  WTand proQ::3XFLAG were grown overnight in LB media. The following day bacteria were diluted 1:1000 in fresh media. At OD 0.2 and OD 2.0, cells were collected.

extract_protocol:
first strand cDNA synthesis using SuperScript III and Primer AR2, RNA degradation, cDNA cleanup, ligation of second adaptor(3Tr3) to cDNA 3' ends, cDNA cleanup and PCR enrichment using P5_Enr primer and P7_BC1_Enr primer
RIL-seq (doi: 10.1038/nprot.2017.115)

treatment_protocol: RNA-protein crosslinking, cell lysis, CoIP using anti-FLAG-antibody, RNA ends trimmed using RNase A/T1, ligation of neighboring RNAs, Protein digestion using Proteinase K, RNA extraction, fragmentaton and DNase digestion, ribosomal RNA depletion and purification with AMPure XP beads

value: crosslinking + CoIP


title: proQ-3XFLAG_hcd_rep1

description:
proQ_hcd_1
Dataset_S2.xlsx


title: Progenitorcells2

status: Public on Oct 17 2024

city: Nan Jing

first: Chuancheng

last: Gao

address: 163 Xianlin Avenue, Qixia Distric

institute: Nanjing University

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 was applied to align the clean reads to the gene set,  in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.26_GRCm38.p6.v2201
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Bone Marrow

extract_protocol:
Total RNA was extracted from the cells of different groups using TRIzol reagent according to the manufacturer’s protocol. To avoid the contamination of genomic DNA, RNA samples were treated with RNase-free DNase.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE 100/150 bases reads are generated on G400/T7/T10 platform (BGI-Shenzhen, China).

value: Bone Marrow

value: primary cell

value: Progenitors

value: untreated


title: proQ-3XFLAG_lcd_rep2

description:
proQ_lcd_2
Dataset_S2.xlsx


title: Methanosarcina_acetivorans_WWM204_+Tet_exp_rep1A

description: exponential

value: del-hpt::PmcrB-tetR/phiC31 int/attB hdrED::PmcrB-tetR frt/pac hpt/frt PmcrB(tetO1)-hdrE

value: tetracycline-induced expression of essential HdrED

value: MeOH

value: w/Tet


title: Progenitorcells3

value: WT


title: ControlM3

value: Macrophages

value: Control-CAR expression

value: Control-CAR treated


title: proQ-3XFLAG_lcd_rep1

description:
proQ_lcd_1
Dataset_S2.xlsx


title: Hoxb8macrophage2


title: NGPS_96

value: skin

value: immortalised fibroblasts

value: BANF1 p.Ala12Thr


title: Progenitorcells1


title: ControlM2


title: Hoxb8macrophage3


title: Hoxb8macrophage1


title: CAR2

value: CAR expression

value: CAR treated


title: BMDM3

value: Bone Marrow


title: Con_3

value: control


title: CAR3

value: primary cell


title: BMDM1

value: untreated


title: AV3_V2

value: Colorectal pre-malignant lesion

value: Unsorted cells

value: Apcfl/flVillincreERT2  mice

value: injection with 4-hydroxytamoxifen to the submucosal layer of the colon, monitoring for 3 weeks


title: ControlM1


title: BMDM2

value: WT


title: CAR1

value: Macrophages


title: 293T cells DMSO control day a INPUT

city: San Diego

first: Gudrun

last: Stengel

address: 11535 Sorrento Valley Rd Suite 407

institute: AlidaBio

data_processing:
Basecalling (BCL convert v00.000.000.4.2.4)
Read cleaning and barcode extraction (EpiScout)
Spike-in control and genome mapping (Bowtie v2.4.4, STAR v2.7.10a)
Barcode demultiplexing and deduplication (EpiScout)
Spike-in control quantification and normalization (EpiScout)
Signal-processing peak calling (EpiScout)
Peak scaling and normalization (EpiScout)
Noise filtering and qualiry score assignment (EpiScout)
Peak genomic annotations and statistic calculation (EpiScout)
Differential analysis (when applicable) (EpiScout)
Summary statistic generation (EpiScout)
Assembly: GRCh38.p14
Supplementary files format and content: Peak files -- BED6+ format. Flag indicates pass/fail of high-confidence measure
Library strategy: EpiPlex

extract_protocol:
Epitranscriptomic profiling was conducted using AlidaBio’s EpiPlex RNA library preparation kit (#EP100100) using 50 ng of purified, polyA-selected RNA as input. Poly-A selection was performed using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L).
In brief, purified RNA is mixed with spike-in controls, fragmented to ~ 140bp, end-repaired and ligated to the P7 adapter. RNA fragments are captured by specific RNA modification binders. The captured RNA fragments are random primed by bead-anchored P5 adapters. The immobilized P5 adapters comprise the MBC, which is transferred to the cDNA during reverse transcription. PCR amplification concludes the library preparation and paired-end sequencing is used to read the UMI, MBC along with the RNA sequence. A solution control is processed in parallel, skipping the bead exposure

value: Kidney

value: DMSO control


title: 293T cells DMSO control day b INPUT


title: dTAG-ADAR p110 dTAG-13 treatment_A INPUT

value: ADAR p110 KO

value: dTAG-ADAR p110 dTAG-13 treatment


title: siEIF4A3_A INPUT


title: dTAG-ADAR p110 dTAG-13 treatment_B INPUT


title: 5uM EIF4A3 inhibitor_B INPUT

value: 5uM EIF4A3 inhibitor


title: siControl_A INPUT

value: siControl


title: siEIF4A3_B INPUT


title: Con_1


title: 293T cells DMSO control day c INPUT


title: 20uM STM2457_B INPUT

value: METTL3 KO


title: 20uM STM2457_A INPUT


title: 5uM EIF4A3 inhibitor_A INPUT


title: 10uM STM2457_B INPUT


title: 10uM STM2457_A INPUT


title: 2.5uM STM2457_A INPUT


title: 1uM STM2457_B INPUT

value: 1uM STM2457


title: 293T cells DMSO control_B INPUT


title: 293T cells DMSO control_A INPUT


title: 5uM STM2457_A INPUT

value: 5uM STM2457


title: 1uM STM2457_A INPUT


title: 5uM STM2457_B INPUT


title: 2.5uM STM2457_B INPUT


title: dTAG-ADAR p110 dTAG-13 treatment_B1


title: dTAG-ADAR p110 dTAG-13 treatment_B2


title: siControl_B INPUT


title: dTAG-ADAR p110 dTAG-13 treatment_A2


title: dTAG-ADAR p110 dTAG-13 treatment_A1


title: siEIF4A3_B2


title: siControl_B1


title: siEIF4A3_A1


title: siEIF4A3_B1


title: siEIF4A3_A2


title: siControl_A1


title: 5uM EIF4A3 inhibitor_B2


title: siControl_B2


title: siControl_A2


title: 5uM EIF4A3 inhibitor_B1


title: 5uM EIF4A3 inhibitor_A1


title: 20uM STM2457_B


title: AV2_V2


title: 20uM STM2457_A


title: 10uM STM2457_B


title: 5uM EIF4A3 inhibitor_A2


title: 293T cells DMSO control_B


title: Methanosarcina_acetivorans_WWM204_+Tet_sta_rep1A

description: stationary

value: del-hpt::PmcrB-tetR/phiC31 int/attB hdrED::PmcrB-tetR frt/pac hpt/frt PmcrB(tetO1)-hdrE

value: tetracycline-induced expression of essential HdrED

value: MeOH

value: w/Tet


title: 293T cells DMSO control day b


title: 5uM STM2457_B


title: 5uM STM2457_A


title: 2.5uM STM2457_B


title: Liver, cthko+betaine, rep2

city: Changsha

first: wei

last: zhang

address: 87 Xiangya Road, Changsha, Hunan, China

institute: Xiangya Hospital Central South University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 and |log2(foldchange)| >= 1 found by DESeq2 were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: Tab-delimited file includes FPKM values for each Sample

source_name: liver

extract_protocol:
RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H -). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 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 m in 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.

value: liver

value: Cth knockout

value: betaine at 1% in drinking water


title: Liver, cthko+betaine, rep3


title: 10uM STM2457_A


title: 1uM STM2457_A


title: 293T cells DMSO control_A

value: WT


title: 1uM STM2457_B

value: Kidney


title: Liver, cthko, rep1

value: drinking water


title: Liver, cthko+betaine, rep1


title: 293T cells DMSO control day c

value: DMSO control


title: Liver, cthko, rep3


title: Liver, wt, rep3


title: Liver, cthko, rep2


title: Liver, wt, rep1


title: Liver, wt, rep2


title: 2.5uM STM2457_A


title: Quadriceps, wild type mice3, HFD

city: Buk-gu, Gwangju

first: Suhyeon

last: Park

state: Gwangju

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호

country: South Korea

institute: GIST

data_processing:
kallisto
Assembly: GRCm39
Supplementary files format and content: Excel file includes estimated counts for each sample

source_name: Quadriceps

growth_protocol: 8 weeks aged wild type and Tph1 KO mice were fed 60 HFD for 12 weeks.

extract_protocol:
Total RNA was harvested usging Trizol (Invitrogen,15596018)
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Sample Prep Kit following manufacturer's protocols.

value: Quadriceps

value: skeletal muscle cells

value: HFD


title: Quadriceps, wild type mice4, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: Quadriceps, Tph1 ko mice5, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호

value: Tph1 knockout


title: Quadriceps, Tph1 ko mice2, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: Quadriceps, Tph1 ko mice3, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: Quadriceps, wild type mice2, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: 293T cells DMSO control day a


title: Quadriceps, wild type mice1, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: WT2

city: sinjuku-ku

first: Sho

last: Ishigaki

state: Tokyo

address: 35 shinanomachi

department: Division of Rheumatology

country: Japan

institute: Keio University

data_processing:
RaNA-seq web tool
Assembly: GRCm38
Supplementary files format and content: raw couns for each sample

source_name: Effector memory CD4+ T cells

extract_protocol:
Total RNA from were extracted using RNeasy Micro kit (Qiagen).The integrity and quantity of the total RNA was measured with an Agilent 2100 Bioanalyzer RNA 6000 Pico kit (Agilent Technologies, Santa Clara, CA, USA). A 10-ng aliquot of the total RNA obtained from each sample was used to construct a sequencing library with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA, USA) with the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s protocols. The quality of the libraries was assessed using the
Agilent 2200 TapeStation High Sensitivity D1000 (Agilent Technologies). The pooled libraries of the samples were sequenced using the NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA) in 150-base pair (bp) paired-end reads.

value: Effector memory CD4+ T cells

value: Lymphocyte


title: WT3


title: Il1rnKO2


title: ATAC_Tel_HFSC_Setdb1_cKO_rep1

city: Houston

first: Yejing

last: Ge

state: Texas

department: Cancer Biology

institute: The University of Texas, MD Anderson Cancer Center

library_source: genomic

data_processing:
Raw sequencing 150-bp paired-end reads were aligned to mus musculus genome mm10 using STAR.
Reads mapped to a single genomic location were kept for peak identification using the Model based Analysis of Chip-seq 2 (MACS2) pipeline with the parameter --nomodel.
Assembly: mm10
Supplementary files format and content: narrowPeak files include peak informations for each Sample

molecule: genomic DNA

growth_protocol: Mice were maintained on a mixed C57BL/6J background in a specific pathogen-free barrier facility on a standard light-dark cycle, housed in groups, and monitored for health status every other day.

extract_protocol:
Freshly FACS-sorted cells were subjected to tagmentation reactions with 10ul Tn5 transposase (Illumina Cat#20034198) and cleaned up with MinElute PCR Purification Kit (Qiagen Cat#28004)
DNA fragments were PCR-amplified for 8-12 cycles. Libraries were purified by Beckman Coulter AMPureXP beads (Fisher Cat#NC9959336) and run on D1000 High Sensitivity Tape Station (Agilent Cat# 5067-5584) for quality control (QC) prior to sequencing.

treatment_protocol: Following euthanasia, back skin at second telogen stage was removed and fat on the dermal side was scraped off using blunt scalpel. Then skin was placed dermis side down on trypsin-EDTA (Gibco) at 37 °C for 30 min, neutralized by cold PBS containing 2% calcium chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Single-cell suspensions were incubated with the appropriate antibodies and sorted using a 70-μm nozzle on a BD FACSAria equipped with FACSDiva software (BD Biosciences), gating on DAPI-CD45-YFP+ITGA6+Sca1-CD34+ to isolate hair follicle stem cells.

value: skin

value: Hair follicle stem cell

value: Setdb1 fl/fl; R26YFP fl/+; K14Cre +/-


title: Tel_HFSC_Setdb1_cKO_rep1

description:
"R5" column in two processed data files
R5-R8_ensembl_gene_counts.txt
R5-R8_retrotransposon_counts.txt

data_processing:
Raw 150-bp pair-end reads were aligned to the mus musculus reference genome mm10 (GRCm38) using STAR (v2.7.2b) with default setting.
FeatureCounts (v. 2.0.3) was then used to quantify gene or transponson expression by counting fragments overlapped with Ensemble genes and transponsons in RepeatMasker, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

extract_protocol:
Total RNA was extracted from back skin epithelium using Direct-zol RNA Miniprep Kit (Zymo, R2051).
Use NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit NEB #E7760) for library preparation.


title: WT uninfected, sample 3

city: Saint Louis

first: Alina

last: Ulezko Antonova

state: MO

address: 660 S. Euclid Ave

department: Path/Immuno

institute: WUSM

data_processing:
Data was processed with the DeSeq2 package
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: Excel table with sample names as columns and gene information in rows

source_name: Colon

extract_protocol:
Total RNA was extracted from samples using a RNeasy Micro Plus Kit (Qiagen). Total RNA integrity was determined using Agilent Bioanalyzer or 4200 TapeStation.
Library preparation was performed with 10 ng total RNA with a Bioanalyzer RNA integrity number score greater than 8. Double standard complementary DNA (cDNA) was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, and cycles per burst 50 for 120 s. cDNA was blunt ended, had an A base added to the 3′ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 to 15 cycles using primers, incorporating unique dual index tags.

value: Colon

value: lineage negative (CD3- CD19- NK1.1- KLRG1-), positive for Thy1.2, and intermediate for CD45

tag: infection

value: uninfected


title: Quadriceps, Tph1 ko mice1, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: Quadriceps, Tph1 ko mice4, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: ATAC_Tel_HFSC_Setdb1_Het_rep2

value: Setdb1 fl/+; R26YFP fl/+; K14Cre +/-


title: Il1rnKO1


title: WT infected, sample 2

value: Clostridioides difficile


title: WT uninfected, sample 2


title: KO8_stim

city: Graz

first: Johannes

last: Breithofer

state: Styria

address: Heinrichstraße, 31/3

department: Institute for molecular Biosciences

country: Austria

institute: University of Graz

data_processing:
Quality assessment was carried out using FastQC
Sequencing reads were aligned to the mouse mm39 reference genome using the splice-aware aligner STAR (v 2.7.10b)
Read quantitation at the gene level was performed using FeatureCounts (v2.0.6) and genecode annotation (vM31)
Differentially expressed genes were determined using DESeq2 based on raw counts and a negative binomial distribution
Data were normalized using DESeq2 and log-transformed
Assembly: mm39
Supplementary files format and content: tab delimited txt file include raw counts for each sample (raw_counts.txt)
Supplementary files format and content: tab delimited txt file include log2 transformed normalized counts adding a pseudocount of 1 (DESeq2) for each sample (log2_normalized_counts_1.txt)

source_name: primary keratinocytes

growth_protocol: Primary keratinocytes were isolated from two days old neonatal wild-type (n=5)  and  Pla2g4d-deficient (n=8) C57BL/6NJ mice. Cells were cultured for four days in an EpiLife growth medium containing HKGS growth supplement, 0.06 mM CaCl2 and primocin. Cells were grown under standard conditions (37°C; 95% humidified atmosphere; 7% CO2) with medium change every other day.

extract_protocol:
Total RNA was isolated using the TRIZol reagent according to manufacturer's instructions
Illumina TruSeq Stranded mRNA Library Prep

treatment_protocol: Cells were stimulated with 20 ng/ml IL17A and 20 ng/ml TNFα for 24h.

value: primary keratinocytes

value: KO


title: KO6_stim


title: KO4_stim


title: WT infected, sample 3


title: KO7_stim


title: KO3_stim


title: Il1rnKO3


title: ATAC_Tel_HFSC_Setdb1_Het_rep1


title: ATAC_Tel_HFSC_Setdb1_cKO_rep2


title: KO5_stim


title: WT infected, sample 1


title: KO2_stim


title: KO1_stim


title: WT1


title: Tel_HFSC_Setdb1_Het_rep1

description:
"R7" column in two processed data files
R5-R8_ensembl_gene_counts.txt
R5-R8_retrotransposon_counts.txt


title: KO6_bas

value: basal


title: KO8_bas


title: KO7_bas


title: KO5_bas


title: Tel_HFSC_Setdb1_cKO_rep2

description:
"R6" column in two processed data files
R5-R8_ensembl_gene_counts.txt
R5-R8_retrotransposon_counts.txt


title: KO2_bas


title: KO1_bas


title: WT4_stim

value: WT


title: WT3_stim


title: WT2_stim


title: WT1_stim


title: WT3_bas


title: WT2_bas


title: WT5_bas


title: Pseudomonas chlororphis 200B-1; infected with Pseudomonas phage 201phi2-1; control

city: Heverlee

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

data_processing:
Real time basecalling and demultiplexing by the Guppy software (v3.2.10) in high accuracy mode.
read processing, mapping and identification of the viral transcription start sites (TSS) and termination sites (TTS) was performed according to the ONT-cappable-seq2 automated data-analysis workflow (https://github.com/LoGT-KULeuven/ONT-cappable-seq2)
Assembly: Submitted as SAMN37853578 to NCBI
Supplementary files format and content: .txt files contain information on the location and efficiency of transcription start and termination sites of 201f2-1
Library strategy: ONT-cappable-seq2

organism: Pseudomonas phage 201phi2-1

source_name: P. chlororaphis 200B-1 infected with phage 201f2-1

growth_protocol: An overnight culture of P. chlororaphis 200B-1 was diluted in 30 ml of fresh LB medium and grown to an OD600 of 0.3. 201f2-1 was added at a multiplicity of infection (MOI) of 1. Over a period of 90 min, samples were taken every 15 min

extract_protocol:
All samples were pooled together and homogenized. The resulting sample was subjected to hot phenol treatment and ethanol precipitation to extract and purify  the RNA
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In parallel, control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded accoriding to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCB109). The amplified cDNA samples were pooled together in a final library

treatment_protocol: Total RNA was extracted using hot-phenol extraction, followed by DNAse treatment. The enriched samples were subjected to an enrichment procedure based on streptavidin beads to enrich for primary transcripts. For the control samples the enrichment steps were omitted.

tag: host

value: Pseudomonas chlororphis

value: bacterial cell

value: no enrichment

tag: infection stage

value: infected with phage 201phi2-1


title: WT1_bas


title: WT, thymocyte, CD4(-)/CD8(-), replicate1 [B6-1_DN-1]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Demultiplexing of raw base call files into FASTQ files was completed with 10X Genomics Cell Ranger (v.3.0.2) mkfastq coupled with mouse reference version mm10. The results from Cell Ranger were processed using DoubletFinder and Seurat, following standard procedures (42-44). DoubletFinder was used on each sample individually to remove doublets. One WT and one ΔEPE3 sample were paired together and integrated with a second pair of WT and ΔEPE3 samples to remove experimental batch effect. Integrated data were clustered with a resolution of 0.4. Clusters comprising less than 5% were removed from further analysis, as were NKT cells. Differentially expressed genes between genotypes were identified with the FindMarkers function of Seurat
Assembly: mm10
Supplementary files format and content: .h5 file contains barcodes, features and matrix files

source_name: thymus

extract_protocol:
Thymocytes were depleted using CD8α microbeads. The CD8-depleted fraction was incubated with lineage marking antibodies (TCRβ, CD4, and CD8, CD11c, CD11b, Gr1, CD19, B220, Ter119) and then lineage- cells were sorted in RPMI-1640 medium supplemented with 10% FBS. Post-sorting, a small fraction of sorted cells was used to check the purity (>98%). 200,000 cells per sample were provided for the library preparation.
Using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1  and the Chromium Next GEM Chip H Single Cell Kit v1.1 , thymocyte nuclei, at 7,000 nuclei per µl, were loaded onto a Chromium controller  to generate single-nuclei GEMs after which library construction is performed according to the manufacturer’s protocol
Approximately 10,000 cells per sample were added to chip G to create GEMs. Cells were lysed, and the bead captured poly(A) RNA was barcoded during reverse transcription in a thermal cycler at 53 °C for 45 min, followed by 85 °C for 5 min. cDNA was generated and amplified. Quality control and quantification of the cDNA were conducted using Agilent’s High Sensitivity DNA Kit in the 2100 Bioanalyzer. scRNA-seq libraries were constructed using a Chromium Single Cell 3ʹ Library Kit v3.1 and indexed with Single Index Kit T Set A. The libraries were sequenced using an Illumina NovaSeq 6000 sequencer with single-indexing strategy consisting of 28 cycles for read 1 and 91 cycles for read 2.

tag: tissue

value: thymus


title: C57BL/6J-ΔEPE3, thymocyte, CD4(-)/CD8(-), replicate2 [pk3-2_DN-2]

tag: cell type


title: C57BL/6J-ΔEPE3, thymocyte, CD4(-)/CD8(-), replicate1 [pk3-1_DN-1]


title: Monosomes_DMSO2

city: Wako-shi

first: Tilman

last: Schneider-Poetsch

email: tilman@cal.berkeley.edu, tsp@riken.jp

state: Saitam

address: 2-1 Hirosawa

department: Center for Sustainable Resource Science

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: Human Genome hg38
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling

source_name: HEK294T flip in

growth_protocol: HEK294T flip in cells grown in DMSO with 10% FBS and antibiotics at 37 deg C under 5% CO2

extract_protocol:
Cells were collected in lysis buffer, cleared of debris and lysates were snap frozen with liquid nitrogen and stored at -80 deg C
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq, Poly(A) selection and cDNA synthesis were performed using Illumina Stranded mRNA Prep, Ligation (Illumina) and subsequent steps were performed by TruSeq Stranded Total RNA Library Prep Gold (Illumina).

treatment_protocol: Cells were treated with DMSO solvent or indicated concentration of girolline for 2 hrs

value: wild type

tag: treatment

value: HEK294T flip in


title: WT, thymocyte, CD4(-)/CD8(-), replicate2 [B6-2_DN-2]


title: Monosomes_DMSO1


title: Pseudomonas chlororphis 200B-1; infected with Pseudomonas phage 201phi2-1; enriched

value: enriched for primary RNAs


title: Monosomes_CHX2

value: CHX 2 uM


title: WT, thymocyte, CD4(-)/CD8(-), replicate2

description: scATAC

library_source: genomic single cell

data_processing:
Demultiplexing of raw base call files into FASTQ files was completed with 10X Genomics Cell Ranger-ATAC MKFASTQ coupled with mouse reference version mm10. The results from Cell Ranger were processed using Seurat V3 and Signac V0.2.1 and 1.0.0, following standard procedures (46). Genomic traces were generated from single-cell ATAC data that has been converted to pseudo-bulk tracks of DN cells
Assembly: mm10
Supplementary files format and content: .h5 matrix files containing peaks, barcodes and

extract_protocol:
100,000 cells were centrifuged at 500 g for 5 minutes at 4°C.  Cell pellet was washed with 50 μl ice-cold PBS. Cell pellet was gently resuspended in 50 μl cold lysis buffer (10mM Tris-Cl, pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% IGAPAL CA-630) and centrifuged at 500 g for 10 minutes at 4°C. Isolated nuclei were passed through Flowmi Cell Strainer (40 μM)
Using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1  and the Chromium Next GEM Chip H Single Cell Kit v1.1 , thymocyte nuclei, at 7,000 nuclei per µl, were loaded onto a Chromium controller  to generate single-nuclei GEMs after which library construction is performed according to the manufacturer’s protocol
nuclear DNA is fragmented at open regions of the chromatin with transposase while adapter sequences are added at the ends.  The fragmented nuclear DNA is then loaded on H chips and partitioned into nanoliter-scale GEMS (Gel Beads-in-emulsion). Illumina P5 sequence, a barcode and read 1 sequence are added by PCR amplification. Unused primers and reagents are removed from the sample by SPRI beads.  The library construction is completed by the addition of both P7 and a sample index. The libraries were sequenced using an Illumina NovaSeq 6000 sequencer with a paired-end, dual-index strategy consisting of 50 cycles for read 1, 50 cycles for read 2, 8 cycles for the i7 index and 16 for the i5.


title: C57BL/6J-ΔEPE3, thymocyte, CD4(-)/CD8(-), replicate2

description: scATAC


title: KO4_bas


title: C57BL/6J-ΔEPE3, thymocyte, CD4(-)/CD8(-), replicate1

description: scATAC


title: KO3_bas


title: WT5_stim


title: Monosomes_CHX1

value: CHX 1 uM


title: WT4_bas


title: EMseq_P0_Dnmt1_cKO_rep2

data_processing:
The Illumina adapters and low-complexity adapters were removed from the reads by Trim Galore! (version 0.4.1), cutadapt (version 1.7.1) and an in-house bash script. Then the reads were mapped to the mouse genome mm10 by the bisulfite converted read mapper Bismark (version v0.16.3) and Bowtie2 (version 2.1.0).
The methylation percentages for the CpG sites were calculated by the bismark_methylation_extractor script from Bismark and an in-house Perl script. Then the methylation percentages for the CpG sites with read coverage ≥ 8 were written in wiggle format and displayed using Integrative Genomics Viewer (IGV). The differential methylation on CpG sites was statistically assessed by R/Bioconductor package methylKit (version 0.9.5). The CpG sites with read coverage ≥ 8 in all the samples were qualified for the test and the cutoffs used to call differential CpG sites is methylation difference >= 25% and Q-value <= 0.01.
Assembly: mm10
Supplementary files format and content: bed file containing detected CpGs with coverage >= 8 in the library
Library strategy: Enzymatic Methyl-seq (EM-seq)

extract_protocol:
Isolated cells were subjected to genomic DNA extraction with Qiagen DNeasy Blood & Tissue Kit (Cat# 69504) following the manufacturer’s instructions.
Enzymatic Methyl-seq (EM-seq) libraries were prepared using NEBNext Enzymatic Methyl-seq Kit following manufacturer's protocols

treatment_protocol: Back skin from P0 mouse was dissected and submerged dermis side down on 2.5 U/mL Dispase (Gibco) in PBS overnight at 4°C. The epidermis was then peeled off and incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37°C, minced, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Cells were spun down at 300 g for 10 min at 4°C and washed once with cold PBS containing 2% FBS(-).

value: skin

tag: cell line

value: P0 skin epithelia

value: Dnmt1 fl/fl; K14Cre +/-


title: WT, thymocyte, CD4(-)/CD8(-), replicate1

description: scATAC

tag: genotype


title: Monosomes_Anisomycin2

value: Anisomycin 0.01 ug/ml


title: Monosomes_Anisomycin1


title: EMseq_P0_Dnmt1_cKO_rep1


title: EMseq_P0_Dnmt1_WT_rep2


title: Disomes_DMSO2


title: Disomes_CHX2


title: EMseq_P0_Dnmt1_WT_rep1


title: Disomes_DMSO1


title: Disomes_CHX1


title: Tlr3-/-_Setdb1_cKO_rep3

description: "R113" column in two processed data files

data_processing:
Raw 150-bp pair-end reads were aligned to the mus musculus reference genome mm10 (GRCm38) using STAR (v2.7.2b) with default setting.
FeatureCounts (v. 2.0.3) was then used to quantify gene or transponson expression by counting fragments overlapped with Ensemble genes and transponsons in RepeatMasker or gEVE database, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

treatment_protocol: For antiviral treatment, Tenofovir disoproxil fumarate (Fisher Scientific AC461250010, 100 mg/kg) was dissolved in DMSO and Emtricitabine (Fisher Scientific AC462070010, 60 mg/kg) were dissolved in water and administered via oral gavage daily starting postnatal two weeks until analysis. For ATRi treatment, Ceralasertib (AZD6738, Selleckchem S7693, 50 mg/kg) was dissolved in DMSO and administered with vehicle (5% DMSO, 40% propylene glycol, and 50% dH2O) via oral gavage daily upon anagen entry until analysis.

value: skin epithelia

value: Setdb1 fl/fl; K14Cre +/-; Tlr3-/-


title: Tlr3-/-_Setdb1_cKO_rep4

description: "R114" column in two processed data files


title: Disomes_Anisomycin 2


title: Disomes_Anisomycin 1


title: Tlr3-/-_Setdb1_cKO_rep1

description: "R109" column in two processed data files


title: Tlr3-/-_Setdb1_Ctrl_rep2

description: "R112" column in two processed data files

value: Setdb1 fl/fl; K14Cre -/-; Tlr3-/-


title: OHT_FOS DN batch4

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Sample normalization was carried out using the median-ratio normalization method from DESeq2 R package (v1.30.1)
Assembly: mm10 (GRCm38 GENCODE release M25)
Supplementary files format and content: .csv, salmon counts and median-ratios-normalized salmon counts for all samples

source_name: Epithelial inestinal tumoroids

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit . 1 ug of total RNA was used for library prepration.
RNA libraries for RNA-seq were prepared usingNEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®  following manufacturer's protocol.

value: Epithelial inestinal tumoroids

value: A/APC flox/flox +OHT

value: Dominant negative FOS


title: OHT_FOS DN batch3


title: OHT_FOS DN batch2


title: Sting-/-_Setdb1_cKO_rep2

description: "R78" column in two processed data files

value: skin hair follicle cells

value: Setdb1 fl/fl; K14Cre +/-; Sting-/-


title: OHT_EV batch4

value: Empty Vector


title: Tlr3-/-_Setdb1_cKO_rep2

description: "R110" column in two processed data files


title: OHT_EV batch3


title: OHT_FOS DN batch1


title: Sting-/-_Setdb1_cKO_rep3

description: "R123" column in two processed data files


title: Sting-/-_Setdb1_Ctrl_rep1

description: "R42" column in two processed data files

value: Setdb1 fl/+; K14Cre +/-; Sting-/-


title: OHT_EV batch1


title: Sting-/-_Setdb1_Ctrl_rep2

description: "R58" column in two processed data files


title: WT_EV batch4

source_name: Epithelial inestinal organoids

value: Epithelial inestinal organoids

value: WT_APC flox/flox


title: Aim2-/-_Setdb1_cKO_rep2

description: "R45" column in two processed data files

value: Setdb1 fl/fl; K14Cre +/-; Aim2-/-


title: Aim2-/-_Setdb1_cKO_rep1

description: "R43" column in two processed data files

value: skin


title: WT_EV batch3


title: WT_EV batch1


title: Aim2-/-_Setdb1_Ctrl_rep2

description: "R94" column in two processed data files

value: Setdb1 fl/+; K14Cre +/-; Aim2-/-


title: Dnmt1_cKO_rep3

description: "DT6" column in two processed data files

value: P0 skin epithelia

value: Dnmt1 fl/fl; K14Cre +/-


title: Tlr3-/-_Setdb1_Ctrl_rep1

description: "R111" column in two processed data files

value: skin epithelia


title: Aim2-/-_Setdb1_Ctrl_rep1

description: "R41" column in two processed data files


title: AKPS_scr_yap_sh2_b3

source_name: AKPS tumoroids

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit . 1 ug of total RNA was used for library prepration.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®  following manufacturer's protocol.

value: AKPS tumoroids

value: VAKSP


title: Dnmt1_cKO_rep4

description: "DT8" column in two processed data files


title: AKPS_scr_yap_sh2_b2

value: Epithelial inestinal tumoroids


title: Dnmt1_cKO_rep2

description: "DT4" column in two processed data files


title: Sting/-_Setdb1_cKO_rep1

description: "R61" column in two processed data files


title: OHT_EV batch2

value: A/APC flox/flox +OHT


title: AKPS_scr_yap_sh1_b4


title: AKPS_scr_yap_sh2_b1


title: Dnmt1_Het_rep3

description: "DT5" column in two processed data files

value: Dnmt1 fl/+; K14Cre +/-


title: Dnmt1_Het_rep4

description: "DT7" column in two processed data files


title: Dnmt1_cKO_rep1

description: "DT1" column in two processed data files


title: Dnmt1_Het_rep1

description: "DT2" column in two processed data files


title: AKPS_scr_yap_sh1_b3


title: AKPS_scr_yap_sh1_b2


title: WT_EV batch2


title: AKPS_scr_yap_sh2_b4


title: hMedIP_Ana_HF_Setdb1cKO_hMeDIP_rep2

description: hMeDIP

data_processing:
Raw sequencing150-bp paired-end reads were aligned to mus musculus genome mm10 using STAR.
Reads mapped to a single genomic location were kept for peak identification using the Model based Analysis of Chip-seq 1 (MACS1) or Model based Analysis of Chip-seq 2 (MACS2) pipeline.
Assembly: mm10
Supplementary files format and content: bed or broadPeak files include peak informations for each Sample (except for control sample)
Library strategy: hMeDIP

growth_protocol: C57BL/6J mice cultured in a specific pathogen-free barrier facility on a standard light-dark cycle.

extract_protocol:
Freshly FACS-sorted cells were fixed with 1% formaldehyde for 10 minutes. For IgG and H3K9me3 ChIP, after quenching and cell lysis, chromatin was sonicated using Bioruptor Sonicator; for Setdb1 ChIP, use CST SimpleChIP protocol following manufacture recommendation.
For ChIPseq, the DNA extract was incubated overnight at 4°C with primary antibody. 10 μl of Dynal Protein G magnetic beadswas added to each sample the following day, incubated at 4°C for 2-4 h, followed by washes for several times. Bound complexes were treated with 5ul Tn5 transposase at 37°C for 5min, eluted and crosslinking was reversed by 6-10h incubation at 65°C, cleaned up with MinElute PCR Purification Kit and PCR-amplified for 10-12 cycles. Libraries were purified by Beckman Coulter AMPureXP beads and submitted to Novogene for library quality control (QC). For hMeDIP, fragmented DNA was used for end-repair, A-tailing and ligation of adapters using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs).  10% of the ligated material was saved as input reference and the remaining material was immunoprecipitated using Diagenode’s hMeDIP kit (Diagenode, Denville, NJ). Final libraries from input and 5hmC-immunoprecipitate were obtained by PCR amplification using barcoded primers, followed by clean-up using magnetic beads.

treatment_protocol: For hair follicle cell isolation from P30 mice, back skin at anagen stage was removed and submerged in 0.25% collagenase/HBSS (Gibco) containing DNase I for 1hr at 37°C. Release cells were scraped off, resuspended in cold PBS, and the remaining skin was then incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37C, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Cells were spin down at 400g for 10 min at 4°C, and washed once with cold PBS containing 2% FBS(-). Freshly isolated cells were incubated with conjugated antibodies and sorted using a 70-μm nozzle on a BD FACSAria equipped with FACSDiva software (BD Biosciences), gating on DAPI-CD31-CD140A-CD45-ITGA6+ to isolate epithelial cells, and further separated into epidermal (Sca1+) and hair follicle (Sca1-) cells. For epithelia cells islolation from P0 mice, back skin was dissected and submerged dermis side down on 2.5 U/mL Dispase (Gibco) in PBS overnight at 4°C. The epidermis was then peeled off and incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37°C, minced, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Cells were spun down at 300 g for 10 min at 4°C and washed once with cold PBS containing 2% FBS(-).

value: anagen hair follicle cells


title: hMedIP_Ana_HF_Setdb1cKO_hMeDIP_rep1_input

description: hMeDIP


title: AKPS_scr_b2

value: Control ShRNA


title: AKPS_scr_yap_sh1_b1


title: AKPS_scr_b1


title: AKPS_fos_kd_b3

value: Fos-ShRNA


title: hMedIP_Ana_HF_Setdb1cKO_hMeDIP_rep1

description: hMeDIP


title: hMedIP_Ana_HF_Setdb1Het_hMeDIP_rep2

description: hMeDIP


title: hMedIP_Ana_HF_Setdb1Het_hMeDIP_rep1_input

description: hMeDIP


title: AKPS_fos_kd_b2


title: AKPS_scr_b4


title: hMedIP_Ana_HF_Setdb1Het_hMeDIP_rep2_input

description: hMeDIP


title: AKPS_fos_kd_b1


title: hMedIP_Ana_HF_Setdb1Het_hMeDIP_rep1

description: hMeDIP


title: Dnmt1_Het_rep2

description: "DT3" column in two processed data files


title: WT_YAP_FOS_batch3

source_name: organoids

value: organoids

value: WT

value: YAP--FOS overexpression


title: SNU-6625-TO treated with Lenvatinib

city: Seoul

first: JA-LOK

last: KU

address: 101 Daehak-ro, Jongno-gu

department: Cancer Research Institute

institute: Seoul National University College of Medicine

data_processing:
Paired end sequencing reads of cDNA libraries (101 bp) verified with FastQC v 0.11.7. For data preprocessing, low quality bases and adapter sequences in reads were trimmed using Trimmomatic 0.38. The trimmed reads were aligned to the genomic reference (mm10) using HISAT2 v2.1.0 through Bowtie2 aligner (v2.3.4.1). Then, transcript assembly of known transcripts and genes was processed by StringTie v2.1.3b. Based on the result, expression abundance of transcript and gene were calculated as read count or fragments per kilobase of exon per million fragments mapped (FPKM) and Transcripts Per Kilobase Million (TPM) value per sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw read-counts for each sample

source_name: Organoid

extract_protocol:
Total RNA was isolated from cell lysate using Trizol (Qiagen) and Qiagen RNeasy Kit (Qiagen).
Sequencing libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit.

value: Organoid

value: MASH-related HCC organoid treated with Lenvatinib

value: Lenvatinib


title: WT_YAP_FOS_batch2


title: WT_YAP_FOS_batch1


title: WT_YAP_FOS_batch4


title: SNU-6624-TO treated with Lenvatinib


title: SNU-6624-TO-LEN

value: Lenvatinib-resistant MASH-related HCC organoid

value: control


title: WT uninfected, sample 1

value: Colon

value: lineage negative (CD3- CD19- NK1.1- KLRG1-), positive for Thy1.2, and intermediate for CD45

value: uninfected


title: WT_YAP_EV_batch4

value: Epithelial inestinal tumoroids

value: YAP overexpression


title: AKPS_scr_b3

value: AKPS tumoroids

value: VAKSP


title: hMedIP_Ana_HF_Setdb1cKO_hMeDIP_rep2_input

description: hMeDIP

value: skin

value: anagen hair follicle cells


title: SNU-6625-TO

value: MASH-related HCC organoid


title: WT_YAP_EV_batch3

value: organoids

value: WT


title: SNU-6624-TO

value: Organoid


title: WT_YAP_EV_batch2


title: SNU-6622-TO


title: WT_YAP_EV_batch1


title: WT_EV_batch3

value: Empty vector


title: WT_EV_batch2


title: H3K27ac HiChIP of wilde-type DN3 cells, biological replicate 1.

data_processing:
HiChIP reads were processed using Juicer to generate .hic files . Juicer was run with the flags “-g mm10 -s Arima”. To compare multiple experiments, Hi-ChIP data were normalized by down-sampling to the same number of total reads. Contacts within 2,000 bp and reads with mapping quality scores below 30 were removed prior to down-sampling. To quantify the interaction frequency between specific regions, such as EPE sites and promoters, the number of contacts was counted after the experiments had been down-sampled to the same number of total reads.
Assembly: mm10
Library strategy: HiChIP

source_name: E14 fetal liver precursors

growth_protocol: E14 fetal liver precursors from WT and ΔEPE3 were cultured on OP9-DL1 monolayers for 7 days, following which DN3 cells were isolated by flow cytometry

extract_protocol:
The Arima HiC+ kit (Arima Genomics, Cat. #A101020) was employed, strictly following the manufacturer's protocol as outlined in Arima-HiC documents A160168 v00 (HiChIP)
HiChIP libaries were prepared accrording to the Arima protocol A160169 v00 using a Swift Biosciences Accel-NGS 2S Plus DNA Library Kit.

value: E14 fetal liver precursors

value: DN3 cell

value: Wilde type


title: H3K27ac HiChIP of ΔEPE3 DN3 cells, biological replicate 2.

value: EPE3 deletion mutant


title: WT_EV_batch1


title: H3K27ac HiChIP of ΔEPE3 DN3 cells, biological replicate 1.


title: H3K27ac HiChIP of wilde-type DN3 cells, biological replicate 2.


title: AKSP_RXRi_3

source_name: AKSP tumoroids

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit . 1 ug of total RNA was used for library prepration.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following manufacturer's protocol.

value: AKSP tumoroids

value: RXRi

tag: time


title: WT/A-Fos KD3

source_name: WT/A

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit . 1 ug of total RNA was used for library prepration.
RNA libraries for RNA-seq were prepared using RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following manufacturer's protocol.

value: WT/A

value: Epithelial inestinal tumoroids

value: A (Apc flox/flox+OHT)

value: Fos_ShRNA +OHT


title: WT/A-Fos KD2


title: AKSP_RXRi_1

value: VAKSP


title: AKSP_RXRi_2


title: Tibia, PMLGH, C2-4

city: Nanjing

first: Liu

last: Xu

address: No.138,Xianlin Avenue,Qixia District,Nanjing City

institute: Nanjing University of Chinese medicine

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Differential expression analysis was performed using the DESeq2 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs) .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. Thetranscriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

organism: Rattus norvegicus

source_name: tibia

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min. B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube. C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through. E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min. G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3. I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at –70°C.
1. Purify and Fragment mRNA a. Add 50 μL RNA Purification Beads to each well with 50 μL total RNA (4μg) and mix thoroughly. b. Incubate at 65°C for 5 min, remove at 4°C, and then place at room temperature for 5 min. c. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. d. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly. e. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. f. Add 50 μL of Elution Buffer in each well and mix thoroughly. g. Incubate at 80°C for 2 min, remove at 25°C, and then place at room temperature. h. Add 50 μL of Beads Binding Buffer in each well and mix thoroughly. The mixture was placed at room temperature for 5 min. i. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. j. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly. k. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. l. Remove the magnetic stand, add 19.5 μL of Elute, Primer,Fragment Mix in each well and mix thoroughly. m. Incubate at 94°C for 8 min, remove at 4°C, and then centrifuge. 2. Synthesize First Strand cDNA a. Add 8 μL First Strand Synthesis Act D Mix and SuperScript II Reverse Transcriptase in each well and mix thoroughly. b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C. 3. Synthesize Second Strand cDNA a. Add 5 μL End Repair Control (2 μL End Repair Control + 98 μL Resuspension Buffer) in each well. b. Add 20 μL Second Strand Marking Master Mix and mix thoroughly. The mixture was incubated at 16°C for 60 min. 3.1 Purification a. Add 90 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 5 min. c. Remove and discard all of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 17.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. i. Transfer 15 μL the supernatant from each well into the new PCR plate. 4. Adenylate 3’Ends a. Add 2.5 μL diluted A-Tailing Control (1 μL A-Tailing Control + 99 μL Resuspension Buffer) in each well. b. Add 12.5 μL A-Tailing Mix and mix thoroughly. c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C. 5. Ligate Adapters a. Add 2.5 μL diluted Ligation Control (1 μL Ligation Control + 99 μL Resuspension Buffer) in each well. b. Add 2.5 μL Ligation Mix. c. Add 2.5 μL RNA Adapter Index and mix thoroughly. d. The mixture was incubated at 30°C for 10 min. e. Add 5 μL Stop Ligation Buffer in each well and mix thoroughly. 5.1 Purification a. Add 42 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 15 min. c. Remove and discard 79.5 μL of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 52.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. i. Transfer 50 μL the supernatant from each well into the new PCR plate. j. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. k. Place it on the magnetic stand at room temperature for 15 min. l. Remove and discard 95 μL of the supernatant from each well. m. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. n. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. o. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. p. Add 22.5 μL Resuspension Buffer and mix thoroughly. q. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. r. Transfer 20 μL the supernatant from each well into the new PCR plate. 6. Enrich DNA Fragments a. Add 5 μL PCR Primer Cocktail. b. Add 25 μL PCR Master Mix and mix thoroughly. c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 sec; 15 cycles 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; 1 cycle 72°C for 5 min; hold at 10°C. 7. Purification a. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 15 min. c. Remove and discard 95 μL of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 32.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. i. Transfer 30 μL the supernatant from each well into the new PCR plate. 8. Validate library a. Load 1 μL sample on an Agilent 2100 Bioanalyzer. b. Check the size and purity of the library.

value: tibia

tag: strain

value: Sprague Dawley

tag: Sex

value: male

value: PMLGH


title: Tibia, PMLGH, C2-3


title: AKSP_DMSO_3

value: DMSO


title: Tibia, PMLGH, C2-2


title: AKSP_DMSO_2


title: AKSP_DMSO_1


title: Tel_HFSC_Setdb1_Het_rep2

description:
"R8" column in two processed data files
R5-R8_ensembl_gene_counts.txt
R5-R8_retrotransposon_counts.txt

source_name: skin

value: skin

value: Hair follicle stem cell

value: Setdb1 fl/+; R26YFP fl/+; K14Cre +/-


title: WT/A-YAPsh2-3

value: Yap_shRNA2 + OHT


title: WT_EV_batch4

value: organoids

value: WT

value: Empty vector


title: WT/A-Fos KD1

value: WT/A


title: Tibia, GelMA, C1-4

value: GelMA


title: SNU-6621-TO

value: Organoid

value: MASH-related HCC organoid

value: control


title: WT/A-YAPsh2-2

value: Epithelial inestinal tumoroids

value: A (Apc flox/flox+OHT)


title: MMA 3

city: Tampa

first: Ana

middle: P

last: Da Silva Gomes

state: Florida

address: 12902 Magnolia Drive

department: Molecular Oncology

institute: H Lee Moffitt Cancer Center

data_processing:
Raw data cleanedby removing reads containing adapters or ploy-N and low quality reads using Novogene in-houseperlscripts.
Index of the reference genome was built using Hisat2 v2.0.5
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCountsv1.5.0-p3 was used to count the reads numbers mapped to each gene
FPKM was calculated based on gene length and reads count mapped to this gene.
Assembly: GRCm39/mm39
Supplementary files format and content: tab delimited text file including raw counts for each sample
Supplementary files format and content: tab delimited text file including FPKM values for each sample

source_name: CD8 T cells

growth_protocol: Mouse CD8+ T cells were cultured in RPMI-1640 media supplemented with 10% FBS, 1% penicillin/streptomycin, 50 μM β-mercaptoethanol, 1 mM sodium pyruvate, and 1% MEM nonessential amino acids in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and contaminant DNA was digested on column with RNase-free DNase (Qiagen)
Libraries were preapared using NEB ultra kit following it's instructions

treatment_protocol: Cells were treated with water or 5 mM methylmalonic acid (Sigma) for three days

value: CD8 T cells

value: 5 mM MMA


title: MMA 2


title: Tibia, GelMA, C1-3

value: tibia

value: Sprague Dawley

value: male


title: SNU-6625-TO-LEN

value: Lenvatinib-resistant MASH-related HCC organoid


title: MMA 1


title: WT/A-YAPsh2-1

value: Yap_shRNA2 + OHT


title: WT/A-YAPsh1-4

value: Yap_shRNA1 + OHT


title: Vehicle 1

value: Water


title: Tibia, GelMA, C1-2


title: Vehicle 2


title: Tibia, Model, M5

value: Model