title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, H3K4me3, rep2

description:
Library name: dKOert_Eth_H3K4me3_rep2
H3K4me3


title: P7_Ctrl_IHC_31

status: Public on Mar 28 2026

type: SRA

city: Beijing

first: Zhiyong

last: Liu

address: Kexueyuan Road

country: China

institute: National Institute of Biological Sciences, Beijing

description: Library name: Sample 31

library_source: transcriptomic single cell

data_processing:
Reads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.2.1) with default parameters.
The resulting alignment files were converted, sorted, and indexed using Samtools.
Raw counts were calculated by featureCounts (v2.0.1) software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Cochlear

extract_protocol:
Cochlear samples were incubated in choline chloride solution containing 20 U/mL papain (Cat# LK003178, Worthington) and 100 U/mL DNase I (Cat# LK003172, Worthington) for 20 min at 37°C, and this was followed by digestion with a protease (Cat# P5147, Sigma; 1 mg/mL) and dispase (Cat# LS02104, Worthington; 1 mg/mL) for 20 min at 25°C. The components of the choline chloride solution contained 92 mM choline chloride, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 mM sodium ascorbate, 2 mM thiourea, 3 mM sodium pyruvate, 10 mM MgSO4.7H2O, 0.5 mM CaCl2.2H2O, and 12 mM N-acetyl-L-cysteine. Next, the post-digested cochlear samples were gently triturated using fire-polished glass Pasteur pipettes (13-678-20b; Fisher) with 4 different pore sizes (largest size the first, and smallest one the last). The picked endogenous IHCs and iOHCs were immediately subjected to reverse-transcription and cDNA amplification using a Smart-Seq HT kit (Cat# 634437, Takara).
Smart-Seq HT kit (Cat# 634437, Takara) was used to generate full-length cDNA. The cDNAs (1 ng each) were tagmented using a TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD503-02, Vazyme) and a TruePrep Index Kit V2 for Illumina (Cat# TD202, Vazyme).

tag: tissue

value: Cochlear

tag: genotype


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, H3K4me3, rep1

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

country: USA

institute: UCSF

description:
Library name: dKOert_Tam_H3K4me3_rep1
H3K4me3

library_source: genomic

data_processing:
Fastq files for CUT&RUN samples were processed using Nextflow and the nf-core CUT&RUN pipeline v3.1. In brief, adapters were trimmed using Trim Galore. Paired-end alignment was performed using Bowtie2 and peaks were called using SEACR with a peak threshold of 0.05 using spike in calibration performed using the E.coli genome K12.
Assembly: mm10
Supplementary files format and content: bigWig files generated from merging replicates together post processing and used as input into all metagene analyses
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: Mouse ESCs were cultured in Knockout DMEM (Thermo Fisher, CAT#10829018) supplemented with 15% FBS, L-Glutamine, Penicillin/Streptomycin, NEAA, LIF (1000U/mL), and 2i (1uM MEK inhibitor PD0325901 and 3uM GSK3 inhibitor CHIR99021). GRHL2-ERT proof of principle tests were conducted in WT V6.5 ESCs. Clones used to conduct RNA-seq are derived from WT R1 ESCs. CKO ESCs (KMT2C-/-; KMT2Dfl/fl) and KMT2C/D dKO (KMT2C-/-; KMT2D-/-) are derived from a mixed background of C57BL/6J and 129 strains. The plasmid expressing GRHL2-ERT from the hPGK promoter was integrated into CKO and dKO genomes using cotransfection with a transient plasmid expressing PiggyBac transposase. Transfected cells were treated with blasticidin to select for GRHL2-ERT integration and plated at single cell density in 10cm2 plates to isolate and characterize colonies. Formative cells were generated by removal of LIF and 2i. Briefly, 5e4 ESCs were plated per well of a 6 well plate on day −1 in LIF+2i media. To initiate differentiation, LIF and 2i were removed 24 hours after seeding (Day 0). Formative cells were collected on day 3 of differentiation, 63 hours after removal of LIF and 2i. To overcome proliferation defects 7.5e4 KMT2C/D dKO cells were plated per well of a 6 well. Naive cells were passaged and staged appropriately for simultaneous harvest. Lines consistently tested negative for mycoplasm.

extract_protocol:
Following treatment or differentiations, cells were harvested using trypsinization and normalized cell counts were used as input into CUT&Tag protocols
CUT&TAG was conducted using the protocol from Kaya-Okur et al. 2020 with the following modifications: freshly trypsinized cells were bound to Concanavalin A beads at a ratio of 2e5 cells/7ul beads in CR wash at room temp. We used 2e5 cells as input per sample. Bead-bound cells were then incubated rotating overnight at 4C in CT Antibody buffer (CR Wash with 0.05% Digitonin, 2mM EDTA, 1mg/mL BSA) containing primary antibody. We used the following primary antibodies for CUT&TAG: 1:100 Rabbit anti-HA (Abcam, abxxx), 1:100 1:100 Rabbit anti-H3K4me1 (Abcam, ab8895), 1:100 Rabbit anti-H3K4me2 (Abcam, abxxx), 1:100 Rabbit anti-H3K27ac (Abcam, ab4729), 1:100 Rabbit anti-KAT2B (Abcam, ab), 1:100 Rabbit anti-H3.3 (Active Motif, xxxx), and 1:100 Rabbit IgG isotype control (Abcam, ab171870). After primary, samples were washed 3 times for 5 minutes each using CR Dig-wash buffer and resuspended in 1:100 secondary antibody (Guinea pig anti-rabbit, Antibodies Online #ABIN101961) in CR Dig-wash buffer at 4C for 1 hour rotating at 4C. Samples were then incubated for 1 hour at 4C with 50ul of approximately 25nM homemade pA-Tn5 in CT Dig300 wash buffer (20mM HEPES, 300mM NaCl, 0.01% Digitonin, 0.5mM Spermidine with Roche cOmplete protease inhibitors added). Recombinant Tn5 was purified and loaded with adapters as previously described (Kaya-Okur et al. 2019). After Tn5 incubation, samples were washed 3 times for 5 minutes each with CT Dig300 wash buffer. Tagmentation was then initiated for 1hr at 37C in a thermocycler by adding MgCl2 to 10mM final concentration in 50uL volume. The tagmentation reaction was quenched immediately afterwards by adding 1.6ul of 0.5M EDTA, 1ul of 10mg/mL Proteinase K, and 1ul of 5% SDS. Samples were then incubated at 55C for 2 hours in a thermocycler to denature Tn5 and solubilize tagmented chromatin. After incubation, samples were magnetized and the supernatant was transferred to new wells where SPRI bead purification was performed using homemade beads to select all DNA fragment lengths larger than 100bp. Samples were eluted in 0.1X TE and approximately half of each sample was used for library preparation using NEBNext HIFI Polymerase with custom indices synthesized by IDT. An appropriate number of cycles for each target was chosen to prevent overamplification bias. After amplification, libraries were purified with 1.2x homemade SPRI beads to select for fragments >250bp and eluted in 0.1X TE. Quality and concentration of libraries were determined by an Agilent 4200 Tapestation with D1000 reagents before pooling for sequencing. CUT&TAG samples were processed similarly to CUT&RUN samples using the same Nextflow pipeline.

tag: cell line

tag: cell type

value: Naive ESC

value: Kmt2cKO; Kmt2dKO;GRHL2-ERT

tag: treatment

value: Tam 8 hours

tag: antibody


title: P7_Ctrl_IHC_32

description: Library name: Sample 32


title: P7_Ctrl_IHC_30

description: Library name: Sample 30


title: P7_Ctrl_IHC_29

description: Library name: Sample 29


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, H3K4me3, rep1

description:
Library name: dKOert_Eth_H3K4me3_rep1
H3K4me3

value: EtOH 8 hours


title: Synovium, FAI, FAI007

city: Rochester

first: Gulzada

last: Kulzhanova

state: NY

address: 310 University Park

department: Biomedical Engineering

institute: University of Rochester

description: Library name: Sample 5

data_processing:
Paired-end sequencing reads were processed by Cell Ranger (10x Genomics software, version 2.0.0). Reads were aligned to the GRCh38 (version 90) for genome annotation, demultiplexing, barcode filtering, and gene quantification. Cell Ranger also removes any barcode that has less than 10% of the 99th percentile of total unique molecular identifiers (UMI) counts per barcode as these barcodes are considered to be associated with empty droplets. After this quality control, gene barcode matrices for each sample were generated by counting the number of UMIs for a given gene (as row) in individual cell (as column). For each sample, ~5000-10000 cells were captured.
Assembly: GRCh38 (version 90)
Supplementary files format and content: gene list (_genes.tsv) and cell barcodes (_barcodes.tsv) as well as gene/barcode matrices (_matrix.mtx) are provided for each time sample

molecule: total RNA

organism: Homo sapiens

source_name: synovium

extract_protocol:
Human FAI and hip OA synovium samples (3 samples per disease condition per sex) were harvested for scRNA-seq analysis. The FAI synovium samples were minced by hand and digested in 0.3% collagenase medium (DMEM/F-12, GlutaMAX™ supplement, #10-565-018, Gibco™ with 3 ug/mL collagenase II, #LS004177, Worthington Biochemical Corporation, and 10% Fetal Bovine Serum, #F0926-100, Sigma-Aldrich) for three hours at 37C while shaking continuously. The samples were thoroughly vortexed every hour. The OA synovium samples were digested in 0.4% collagenase medium (DMEM/F-12, GlutaMAX™ supplement, #10-565-018, Gibco™ with 4 ug/mL collagenase II, #LS004177, Worthington Biochemical Corporation, and 10% Fetal Bovine Serum, #F0926-100, Sigma-Aldrich) at 37C overnight. Cells were then resuspended in ACK lysing buffer (#A1049201, Gibco) for 1-2 minutes to lyse red blood cells. Afterwards, cells were filtered through 70um (#130-110-916, Miltenyi Biotec) and 30um MACS® SmartStrainers (#130-110-915, Miltenyi Biotec). The cell suspension was later frozen down in freezing medium (DMEM/F-12, GlutaMAX™ supplement, #10-565-018, Gibco™ with 10% Pierce™ Dimethylsulfoxide (DMSO), LC-MS Grade, #85190, ThermoFischer, and 80% Fetal Bovine Serum, #F0926-100, Sigma-Aldrich) until submitted for scRNA-seq.
Samples with greater than 70% viability were submitted to UR Genomics Research Center for scRNA-Seq library preparation using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR. The final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Sequence data was generated using the Illumina NovaSeq 6000 platform.

value: synovium

value: human primary cells

value: FAI synoviocytes

tag: disease state

value: FAI

tag: batch

tag: patient

value: Human hip synoviocytes from FAI patient #5


title: Synovium, FAI, FAI008

description: Library name: Sample 6

value: Human hip synoviocytes from FAI patient #6


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, H3K4me3, rep2

description:
Library name: CKOert_Eth_H3K4me3_rep2
H3K4me3

value: Kmt2cKO; Kmtd fl/fl;GRHL2-ERT


title: P7_Ctrl_IHC_28

description: Library name: Sample 28


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, H3K4me3, rep1

description:
Library name: CKOert_Tam_H3K4me3_rep1
H3K4me3


title: Synovium, FAI, FAI004

description: Library name: Sample 4

value: Human hip synoviocytes from FAI patient #4


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, H3K4me3, rep2

description:
Library name: CKOert_Tam_H3K4me3_rep2
H3K4me3


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, H3K27ac, rep1

description:
Library name: CKOert_Tam_H3K27ac_rep1
H3K27ac


title: P7_Ctrl_IHC_27

description: Library name: Sample 27


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, H3K4me2, rep1

description:
Library name: dKOert_Tam_H3K4me2_rep1
H3K4me2


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, H3K4me2, rep2

description:
Library name: dKOert_Tam_H3K4me2_rep2
H3K4me2


title: Synovium, FAI, FAI002

description: Library name: Sample 2

value: Human hip synoviocytes from FAI patient #2


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, H3K4me2, rep2

description:
Library name: CKOert_Tam_H3K4me2_rep2
H3K4me2


title: P7_Ctrl_IHC_26

description: Library name: Sample 26


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, H3K4me2, rep2

description:
Library name: dKOert_Eth_H3K4me2_rep2
H3K4me2


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, H3K4me2, rep1

description:
Library name: dKOert_Eth_H3K4me2_rep1
H3K4me2


title: Synovium, FAI, FAI003

description: Library name: Sample 3

value: Human hip synoviocytes from FAI patient #3


title: P7_Ctrl_IHC_25

description: Library name: Sample 25


title: Synovium, hip OA, OA001

description: Library name: Sample 7

value: OA synoviocytes

value: hip OA

value: Human hip synoviocytes from OA patient #1


title: Synovium, FAI, FAI001

description: Library name: Sample 1

value: Human hip synoviocytes from FAI patient #1


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, H3K4me2, rep2

description:
Library name: CKOert_Eth_H3K4me2_rep2
H3K4me2

value: Naive ESC


title: P7_Ctrl_IHC_24

description: Library name: Sample 24

value: Cochlear


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, H3K4me2, rep1

description:
Library name: CKOert_Eth_H3K4me2_rep1
H3K4me2

value: EtOH 8 hours


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, H3K4me3, rep1

description:
Library name: CKOert_Eth_H3K4me3_rep1
H3K4me3


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, H3K4me2, rep1

description:
Library name: CKOert_Tam_H3K4me2_rep1
H3K4me2

value: Tam 8 hours


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, H3K4me1, rep1

description:
Library name: dKOert_Tam_H3K4me1_rep1
H3K4me1

value: Kmt2cKO; Kmt2dKO;GRHL2-ERT


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, H3K4me1, rep2

description:
Library name: dKOert_Tam_H3K4me1_rep2
H3K4me1


title: CAMP46LC

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

description: Library name: CAMP46LC

library_source: transcriptomic

data_processing:
The raw sequence reads were aligned to the GRCh38 reference genome using STAR.
RSEM was used for transcript quantification based on the STAR alignment.
Assembly: CRCh38
Supplementary files format and content: tab-delimited text file FPKM counts for each samples
Supplementary files format and content: tab-delimited text file Cufflinks counts for each samples

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The clean RNA samples were used for library preparation in the Genomic and RNA Profling Core, Baylor College of Medicine. Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions.

value: Tumor


title: P7_Ctrl_IHC_23

description: Library name: Sample 23


title: P7_Ctrl_IHC_22

description: Library name: Sample 22


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, H3K4me1, rep2

description:
Library name: dKOert_Eth_H3K4me1_rep2
H3K4me1


title: CAMP45LC

description: Library name: CAMP45LC


title: P7_Ctrl_IHC_21

description: Library name: Sample 21


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, H3K4me1, rep2

description:
Library name: CKOert_Tam_H3K4me1_rep2
H3K4me1


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, H3K4me1, rep1

description:
Library name: CKOert_Tam_H3K4me1_rep1
H3K4me1


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, H3K4me1, rep1

description:
Library name: dKOert_Eth_H3K4me1_rep1
H3K4me1


title: P7_Ctrl_IHC_20

description: Library name: Sample 20


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, H3K4me1, rep2

description:
Library name: CKOert_Eth_H3K4me1_rep2
H3K4me1


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, HA, rep2

description:
Library name: dKOert_Tam_HA_rep2
HA

value: HA


title: CAMP42KC

description: Library name: CAMP42KC


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, HA, rep1

description:
Library name: dKOert_Tam_HA_rep1
HA


title: CAMP44LC

description: Library name: CAMP44LC


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, HA, rep1

description:
Library name: dKOert_Eth_HA_rep1
HA


title: CAMP43JC

description: Library name: CAMP43JC


title: P7_Ctrl_IHC_18

description: Library name: Sample 18


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, HA, rep2

description:
Library name: dKOert_Eth_HA_rep2
HA


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, HA, rep2

description:
Library name: CKOert_Tam_HA_rep2
HA


title: P7_Ctrl_IHC_17

description: Library name: Sample 17


title: P7_Ctrl_IHC_16

description: Library name: Sample 16


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, IgG control, rep1

description:
Library name: dKOert_igg_Tam_rep1
IgG control

value: IgG control


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, HA, rep2

description:
Library name: CKOert_Eth_HA_rep2
HA


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, H3K4me1, rep1

description:
Library name: CKOert_Eth_H3K4me1_rep1
H3K4me1


title: CAMP36KC

description: Library name: CAMP36KC


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, HA, rep1

description:
Library name: CKOert_Tam_HA_rep1
HA


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, HA, rep1

description:
Library name: CKOert_Eth_HA_rep1
HA


title: CAMP41JC

description: Library name: CAMP41JC


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, IgG control, rep2

description:
Library name: dKOert_igg_Eth_rep2
IgG control


title: P7_Ctrl_IHC_15

description: Library name: Sample 15


title: CAMP35JC

description: Library name: CAMP35JC


title: P7_Ctrl_IHC_19

description: Library name: Sample 19


title: P7_Ctrl_IHC_14

description: Library name: Sample 14


title: P7_Ctrl_IHC_13

description: Library name: Sample 13


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, IgG control, rep2

description:
Library name: CKOert_igg_Tam_rep2
IgG control


title: CAMP31KC

description: Library name: CAMP31KC


title: CAMP39KC

description: Library name: CAMP39KC


title: CAMP32KC

description: Library name: CAMP32KC


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, IgG control, rep1

description:
Library name: CKOert_igg_Tam_rep1
IgG control


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, IgG control, rep2

description:
Library name: CKOert_igg_Eth_rep2
IgG control


title: P7_Ctrl_IHC_12

description: Library name: Sample 12


title: CAMP30KC

description: Library name: CAMP30KC


title: CAMP29LC

description: Library name: CAMP29LC


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, IgG control, rep1

description:
Library name: CKOert_igg_Eth_rep1
IgG control


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, IgG control, rep1

description:
Library name: dKOert_igg_Eth_rep1
IgG control


title: P7_Ctrl_IHC_11

description: Library name: Sample 11


title: CAMP38KC

description: Library name: CAMP38KC


title: Form ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep2, techrep2

description:
Library name: dKO_form_GRHL2_rep2_t2
anti-GRHL2

data_processing:
Fastq files for CUT&RUN samples were processed using Nextflow and the nf-core CUT&RUN pipeline v3.1. In brief, adapters were trimmed using Trim Galore. Paired-end alignment was performed using Bowtie2 and peaks were called using SEACR with a peak threshold of 0.05 using spike in calibration performed using the E.coli genome K12.
Assembly: mm10
Supplementary files format and content: bigwig files generated by merging technical and biological replicates.
Library strategy: CUT&Run

growth_protocol: Mouse ESCs were cultured in Knockout DMEM (Thermo Fisher, CAT#10829018) supplemented with 15% FBS, L-Glutamine, Penicillin/Streptomycin, NEAA, LIF (1000U/mL), and 2i (1uM MEK inhibitor PD0325901 and 3uM GSK3 inhibitor CHIR99021).

extract_protocol:
Following treatment or differentiations, cells were harvested using trypsinization and normalized cell counts were used as input into CUT&Tag protocols
CUT&RUN was conducted using the protocol from Skene et al. 2018(Skene, Henikoff, and Henikoff 2018) with the following modifications: Freshly trypsinized cells were bound to activated Concanavalin A beads (Bang Laboratories, #BP531) at a ratio of 2e5 cells/10ul beads in CR Wash buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine with protease inhibitors added) at room temp. An input of 2e5 cells were used per target. Bead-bound cells were then incubated rotating overnight at 4C in CR Antibody buffer (CR Wash with 0.05% Digitonin, 2mM EDTA) containing primary antibody. We used the following antibodies for CUT&RUN: Rabbit anti-GRHL2 1:100 (Sigma, CAT#HPA004820) and 1:100 Rabbit IgG isotype control (Abcam, ab171870). After primary, we washed 3 times 5 minutes each with cold CR Dig-wash buffer (CR Wash with 0.05% Digitonin) and incubated with pA-MNase (1:100 of 143ug/mL stock provided by Steve Henikoff) for 1 hour rotating at 4C. After MNase binding, we washed 3 times 5 each with cold CR Dig-wash buffer, and chilled cells down to 0C using a metal tube rack partially submerged in an ice water slurry. MNase digestion was induced by adding CaCl2 at a final concentration of 2mM. After 30 minutes of digestion, the reaction was quenched using Stop Buffer containing 340mM NaCl, 20mM EDTA, 4mM EGTA, 0.05% Digitonin, 100ug/mL RNAse A, 50ug/mL Glycogen, and approximately 2pg/mL Yeast spike-in DNA (provided by Steve Henikoff). The digested fragments for each sample were then extracted using a phenol chloroform extraction. Library preparation on samples was conducted using manufacturer’s protocols for NEBNext Ultra II Dna Library Prep Kit (New England BioLabs, CAT#E7645) and NEB Multiplex Dual Index oligos (New England BioLabs, CAT#E7600, #E7780) with the following modifications. We input approximately 10ng of sample for half reactions, we diluted the NEBNext Illumina adaptor 1:25, we used the following PCR cycling conditions: 1 cycle of Initial Denaturation at 98C for 30 seconds, 12+ cycles of Denaturation at 98C for 10 seconds then Annealing/Extension at 65C for 10 seconds, and 1 final cycle of extension at 65C for 5 minutes. Following library preparation, double size selection was performed using Ampure beads and quality and concentration of libraries were determined by an Agilent 4200 Tapestation with High-Sensitivity D1000 reagents before pooling for sequencing.

value: Form ESC

value: Kmt2cKO; Kmt2dKO


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, IgG control, rep2

description:
Library name: dKOert_igg_Tam_rep2
IgG control


title: Form ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep1, techrep2

description:
Library name: dKO_form_GRHL2_rep1_t2
anti-GRHL2


title: P7_Ctrl_IHC_10

description: Library name: Sample 10


title: Form ESC, WT, GRHL2, rep1, techrep2

description:
Library name: dKO_naive_GRHL2_rep1_t2
anti-GRHL2

value: WT


title: Naive ESC, WT, GRHL2, rep2, techrep2

description:
Library name: WT_naive_GRHL2_rep2_t2
anti-GRHL2


title: Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep2, techrep2

description:
Library name: WT_form_GRHL2_rep2_t2
anti-GRHL2


title: Naive ESC, WT, GRHL2, rep1, techrep2

description:
Library name: WT_naive_GRHL2_rep1_t2
anti-GRHL2


title: CAMP27KC

description: Library name: CAMP27KC


title: P7_Ctrl_IHC_7

description: Library name: Sample 7


title: P7_Ctrl_IHC_9

description: Library name: Sample 9


title: CAMP25KC

description: Library name: CAMP25KC


title: Form ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep2

description:
Library name: dKO_form_GRHL2_rep2_t1
anti-GRHL2


title: Form ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep1

description:
Library name: dKO_form_GRHL2_rep1_t1
anti-GRHL2


title: CAMP22KC

description: Library name: CAMP22KC


title: Form ESC, WT, GRHL2, rep2

description:
Library name: dKO_naive_GRHL2_rep2_t1
anti-GRHL2


title: Form ESC, WT, GRHL2, rep1

description:
Library name: dKO_naive_GRHL2_rep1_t1
anti-GRHL2


title: Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep1, techrep2

description:
Library name: WT_form_GRHL2_rep1_t2
anti-GRHL2


title: CAMP26KC

description: Library name: CAMP26KC


title: Form ESC, WT, GRHL2, rep2, techrep2

description:
Library name: dKO_naive_GRHL2_rep2_t2
anti-GRHL2


title: P7_Ctrl_IHC_8

description: Library name: Sample 8


title: Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep2

description:
Library name: WT_form_GRHL2_rep2_t1
anti-GRHL2


title: P7_Ctrl_IHC_5

description: Library name: Sample 5


title: CAMP20KC

description: Library name: CAMP20KC


title: Naive ESC, WT, GRHL2, rep2

description:
Library name: WT_naive_GRHL2_rep2_t1
anti-GRHL2


title: Naive ESC, Kmt2cKO; Kmt2dKO, GRHL2, rep1

description:
Library name: WT_form_GRHL2_rep1_t1
anti-GRHL2


title: CAMP19LC

description: Library name: CAMP19LC


title: Whole kidneys of proximal tubules-specific conditional knockout mice(CKO) mice (Reg-2)

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

country: Japan

institute: Tokushima University Graduate School of Biomedical Sciences

description: Library name: CKO

data_processing:
Sequencing was conducted on a NovaSeq sequencer (Illumina), resulting in an average read length of 100 bp.
The STAR aligner (version 2.7.3a) was used for sequence alignment; HTSeq for raw read counting; DESeq2 for normalization; Cufflinks (version 2.2.1) for estimating gene expression levels, which were reported as fragments per kilobase of transcript per million mapped reads (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/); and FastQC for data quality assessment, excluding low-quality reads from further analysis.
Filtering criteria exclude genes with at least one zero count.
In order to reduce systematic bias, size factors were estimated from the read count data (calcNormFactors method). Using them, the read count data was normalized with Trimmed mean of M-values (TMM) method in edgeR library. Then, statistical test was performed with the normalized data.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file containing TMM-normalized counts for the 19,550 filtered genes.

source_name: Kidneys

growth_protocol: Mice were fed ad libitum with the standard chow diet with constant access to water under a 12:12 h light/dark cycle as previously described.

extract_protocol:
RNA was extracted from RNAeasy Kit
Library preparation was performed using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA).

treatment_protocol: No treatment

value: Kidneys


title: Naive ESC, WT, GRHL2, rep1

description:
Library name: WT_naive_GRHL2_rep1_t1
anti-GRHL2


title: CAMP17LC

description: Library name: CAMP17LC


title: CAMP15LC

description: Library name: CAMP15LC


title: Whole kidneys of control mice (WT)

description: Library name: WT+AKI


title: P7_Ctrl_IHC_6

description: Library name: Sample 6


title: Whole kidneys of proximal tubules-specific conditional knockout mice(CKO) mice (Inmt TG)

description: Library name: TG+AKI


title: CAMP14KC

description: Library name: CAMP14KC


title: Whole kidneys of control mice (Reg-2)

description: Library name: Control


title: KO_sgRNA4, unstimulated, donor3, batch1

city: Oslo

first: Pu

last: Chen

address: Gaustadalléen 21

department: Norwegian Center for Molecular Biosciences and Medicine

country: Norway

institute: University of Oslo

description: Library name: KO_S4_UT_D3

data_processing:
Raw reads were filtered using Novogene’s in-house filtering pipeline to remove low-quality reads (i.e., adapter-contaminated reads).
Reads were aligned to the GRCh38 reference genome using the Subread package (version 2.0.6) and gene-level counts were quantified using featureCounts (Subread package), assigning reads to annotated genes.
Assembly: GRCh38
Supplementary files format and content: featureCounts_raw_counts.txt

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: Healthy donors’ PBMCs were stimulated in ImmunoCult-XF T cells Expansion Medium (Stemcell) for three days before the CRISPR-Cas9 KO by electroporation. Cells were then cultured and collected at 7 days post electroporation for treatment and RNA sequencing.

extract_protocol:
RNA extraction was conducted using a total RNA purification kit (Norgen Biotek Corp).
Library preparations were conducted by Novogene using an in-house kit.

treatment_protocol: Cells were stimulated with 200 ng/ml anti-CD3 (Hit3a, Thermofisher) or left unstimulated for 2 hours before proceeding to RNA extraction

value: Peripheral Blood Mononuclear Cells

value: Primary cells

value: SIT1 KO

value: unstimulated


title: P7_Ctrl_IHC_4

description: Library name: Sample 4


title: P7_Ctrl_IHC_2

description: Library name: Sample 2


title: P7_Ctrl_IHC_1

description: Library name: Sample 1


title: PIA+IL-27 rep2

city: jinan

first: 兴慧

last: 乔

address: 山东大学

institute: 山东大学

description: Library name: IL27_2

data_processing:
Data were processed using the Dr.Tom platform (BGI Genomics). Standard pipelines for quality control, read alignment, and gene expression quantification were applied automatically through the platform.
Assembly: not provided
Supplementary files format and content: FPKM

source_name: hippocampus

extract_protocol:
RNA extraction
Total RNA was extracted and sent to BGI Genomics (Shenzhen, China) for library preparation and sequencing.

value: hippocampus


title: PIA+IL-27 rep1

description: Library name: IL27_1


title: CAMP13KC

description: Library name: CAMP13KC


title: KO_sgRNA4, unstimulated, donor2, batch1

description: Library name: KO_S4_UT_D2


title: CAMP12LC

description: Library name: CAMP12LC


title: PIA rep2

description: Library name: lps_2

value: PIA


title: P7_Ctrl_IHC_3

description: Library name: Sample 3

value: Cochlear


title: CAMP11KC

description: Library name: CAMP11KC


title: C2C12 cells, 10 kPa, 12h, rep2

city: Shenzhen

first: Qin

last: Peng

address: Gaoke Innovation Center

institute: Shenzhen Bay Laboratory

description: Library name: 10 kPa_12h_rep2

data_processing:
The raw data underwent quality control using fastp (v2.0) to remove adapters, trim low-quality reads (score < 20), and discard reads with an N content exceeding 10%. The resulting processed data is referred to as clean data.
Clean reads were aligned to the reference genome using HISAT2 (v2.1.0), and alignment quality was assessed using RSeQC (v3.0.1).
Assembly: mm39
Supplementary files format and content: CSV file of CMD samples includes TPM values and count value for each sample.
Supplementary files format and content: CSV file of C2C12 on PAA gel samples includes FKPM values and count value for each sample.

growth_protocol: C2C12 cells differentiated with DMEM containing 2% heat-inactivated horse serum, and cultured at 37 °C with 5% CO2. C2C12 myoblasts on PAA gel were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 20%  fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
Total RNAs were extracted from cultured C2C12 cells using E.Z.N.A. Total RNA Kit I reagent (Omegabiotek, R6834-01) according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit according to the manufacturer's instructions.

value: myoblast

value: 10 kPa PAA gel


title: KO_sgRNA4, unstimulated, donor1, batch1

description: Library name: KO_S4_UT_D1


title: KO_sgRNA4, anti-CD3 stimulated for 2 hours, donor3, batch1

description: Library name: KO_S4_2H_D3

value: anti-CD3 stimulated


title: CAMP10KC

description: Library name: CAMP10KC

value: Tumor


title: C2C12 cells, 10 kPa, 12h, rep1

description: Library name: 10 kPa_12h_rep1


title: C2C12 cells, 0.2 kPa, 12h, rep3

description: Library name: 0.2 kPa_12h_rep3

value: 0.2 kPa PAA gel


title: CAMP09JC

description: Library name: CAMP09JC


title: PIA rep1

description: Library name: lps_1


title: KO_sgRNA4, anti-CD3 stimulated for 2 hours, donor1, batch1

description: Library name: KO_S4_2H_D1


title: C2C12 cells, 0.2 kPa, 12h, rep1

description: Library name: 0.2 kPa_12h_rep1


title: CAMP08KC

description: Library name: CAMP08KC


title: KO_sgRNA4, anti-CD3 stimulated for 2 hours, donor2, batch1

description: Library name: KO_S4_2H_D2


title: CAMP05JC

description: Library name: CAMP05JC


title: NSK IRF1 KO, pig IRF1, PRU infected, rep 2

city: Edinburgh

first: Marzuq

last: Ungogo

state: Midlothian

address: Easter Bush Campus, Easter Bush Campus

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

description: Library name: 17_pIRF1_PRU

data_processing:
Reads were pseudoaligned to the Ensembl porcine and Toxoplasma genomes using Kallisto v0.51.1 with 100 bootstraps to generate transcript-level expression estimates as transcripts per million (TPM).
Assembly: Ensembl Sscrofa11, ToxoDB release 68
Supplementary files format and content: txt. files containing count matrix

organism: Sus scrofa

source_name: NSK

extract_protocol:
RNA was extracted using Qiagen RNA extraction kit
Libraries were prepared using the NEBNEXT Ultra II Directional RNA Library Prep kit (NEB) and the Poly-A mRNA magnetic isolation module (NEB) according to the provided protocol. Poly-A containing mRNA molecules were purified, fragmented and reverse transcribed into cDNA and adapters were ligated to the fragments. Purified, adapter-ligated DNA was then multiplexed and sequenced on NextSeq 2000 platform (Illumina Inc) using the NextSeq 2000 P3 XLEAP-SBS Reagent Kit (100 cycles) to yield ~60 million 50 bp high quality strand-specific paired reads per sample.

treatment_protocol: IRF1-depleted cells were transduced with lentivirus expressing human IRF1, pig IRF1 or the empty RFP vector. At 72 h post-transduction, cells were left uninfected or infected with Toxoplasma PruA7 and incubated for further 48 h.

value: NSK

value: Kidney cells, epithelial-like

value: IRF1 knockout

value: RFP and pig IRF1 expression, Toxoplasma PRU infection


title: KO_sgRNA2, unstimulated, donor3, batch2

description: Library name: KO_S2_UT_D3


title: C2C12 cells, 0.2 kPa, 12h, rep2

description: Library name: 0.2 kPa_12h_rep2

value: WT


title: C2C12 cells, 10 kPa, 12h, rep3

description: Library name: 10 kPa_12h_rep3


title: NSK IRF1 KO, pig IRF1, PRU infected, rep 1

description: Library name: 16_pIRF1_PRU


title: Control rep2

description: Library name: Control_2

value: Control


title: C2C12 cells, myogenic differentiation, 7 days, rep 3

description: Library name: CMD-7days-3

value: myogenic differentiation


title: NSK IRF1 KO, human IRF1, PRU infected, rep 3

description: Library name: 15_hIRF1_PRU

value: RFP and human IRF1 expression, Toxoplasma PRU infection


title: KO_sgRNA2, unstimulated, donor2, batch2

description: Library name: KO_S2_UT_D2

value: Peripheral Blood Mononuclear Cells

value: Primary cells

value: SIT1 KO

value: unstimulated


title: C2C12 cells, myogenic differentiation, 7 days, rep 2

description: Library name: CMD-7days-2

value: myoblast


title: CAMP01KC

description: Library name: CAMP01KC


title: Control rep1

description: Library name: Control_1

value: hippocampus


title: NSK IRF1 KO, human IRF1, PRU infected, rep 2

description: Library name: 14_hIRF1_PRU


title: KO_sgRNA2, unstimuated, donor1, batch2

description: Library name: KO_S2_UT_D1


title: NSK IRF1 KO, pig IRF1, PRU infected, rep 3

description: Library name: 18_pIRF1_PRU


title: CAMP02KC

description: Library name: CAMP02KC


title: C2C12 cells, myogenic differentiation, 7 days, rep 1

description: Library name: CMD-7days-1


title: NSK IRF1 KO, human IRF1, PRU infected, rep 1

description: Library name: 13_hIRF1_PRU


title: CAMP03KC

description: Library name: CAMP03KC


title: KO_sgRNA2, anti-CD3 stimulated for 2 hours, donor2, batch2

description: Library name: KO_S2_2H_D2

value: anti-CD3 stimulated


title: KO_sgRNA2, anti-CD3 stimulated for 2 hours, donor3, batch2

description: Library name: KO_S2_2H_D3


title: C2C12 cells, myogenic differentiation, 24 hours, rep 2

description: Library name: CMD-24hours-2


title: NSK IRF1 KO, EmptyVector, PRU infected, rep 2

description: Library name: 12_EMP_PRU

value: RFP expression, Toxoplasma PRU infection


title: KO_sgRNA2, anti-CD3 stimulated for 2 hours, donor1, batch2

description: Library name: KO_S2_2H_D1


title: ccRCC5,replicate1, scRNA-seq

first: Pavlos

last: Msaouel

state: Texas

address: 1155 Pressler Street, Unit 1374

department: Genitourinary Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description: Library name: 2640201

data_processing:
Sequence data was put through the 10X genomic cell ranger 6.0.1 pipeline. QC and Fastq files were obtained and checked for data quality, and Fastq files were used to do further analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and matrix files

source_name: Lymph node

extract_protocol:
Tumor biopsy samples were thoroughly minced to size < 1mm and transferred to 2.0ml Eppendorf tube containing 0.1 mg/ml Liberase TM and 0.2 mg/ml DNase I (MillieporeSigma) in RPMI1640/0.1% BSA. Tubes were then incubated at 37 degrees Celsius for 15 minutes with gentle rotation. Samples were filtered through 70 µm filters, spun down, and red blood cell lysis was performed with ACK lysis buffer (ThermoFisher, catalog #A1049201). Cell viability will be determined with Trypan blue exclusion assay.
Samples with >60% viability were further processed on Chromium iX (10x Genomics) to generate 5' v2 gel beads-in-emulsions (GEMs). The barcoded cDNA was purified and amplified for the final generation of 10x single cell RNA sequencing (scRNAseq) libraries. After quantification with a high sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent), the libraries were sequenced as recommended by the manufacturer (approximately 50,000 reads per cell) on a NovaSeq 6000 system.

value: Lymph node

tag: subject status

value: ccRCC


title: ccRCC4,replicate1, scRNA-seq

description: Library name: 576Ex1201

source_name: Colon

value: Colon


title: AAVS1_sgRNA(control), unstimulated, donor3, batch1

description: Library name: A1_S4_UT_D3

value: AAVS1 KO


title: C2C12 cells, myogenic differentiation, 24 hours, rep 1

description: Library name: CMD-24hours-1


title: NSK IRF1 KO, EmptyVector, PRU infected, rep 1

description: Library name: 11_EMP_PRU

value: NSK

value: Kidney cells, epithelial-like

value: IRF1 knockout


title: C2C12 cells, myogenic differentiation, 24 hours, rep 3

description: Library name: CMD-24hours-3

value: WT

value: myogenic differentiation


title: C2C12 cells, myogenic differentiation, 6 hours, rep 3

description: Library name: CMD-6hours-3


title: ccRCC1,replicate1, scRNA-seq

description: Library name: GB080101

source_name: Kidney

value: Kidney


title: NSK IRF1 KO, pig IRF1, Uninfected, rep 3

description: Library name: 9_pIRF1

value: RFP and pig IRF1 expression


title: C2C12 cells, myogenic differentiation, 6 hours, rep 2

description: Library name: CMD-6hours-2


title: ccRCC2,replicate1, scRNA-seq

description: Library name: 264T10101


title: NSK IRF1 KO, pig IRF1, Uninfected, rep 2

description: Library name: 8_pIRF1


title: AAVS1_sgRNA(control), unstimulated, donor1,batch1

description: Library name: A1_S4_UT_D1

value: Peripheral Blood Mononuclear Cells

value: Primary cells


title: RMC71, replicate1, scRNA-seq

description: Library name: 0650801

value: RMC


title: NSK IRF1 KO, pig IRF1, Uninfected, rep 1

description: Library name: 7_pIRF1


title: AAVS1_sgRNA(control), unstimulated, donor2,batch1

description: Library name: A1_S4_UT_D2

value: unstimulated


title: AAVS1_sgRNA(control), anti-CD3 stimulated for 2 hours, donor3, batch1

description: Library name: A1_S4_2H_D3

value: anti-CD3 stimulated


title: C2C12 cells, myogenic differentiation, 6 hours, rep 1

description: Library name: CMD-6hours-1

value: myoblast


title: RMC66, replicate1, scRNA-seq

description: Library name: 0650901

source_name: Liver

value: Liver


title: AAVS1_sgRNA(control), anti-CD3 stimulated for 2 hours, donor1, batch1

description: Library name: A1_S4_2H_D1


title: C2C12 cells, myogenic differentiation, 0 hours, rep 3

description: Library name: CMD-0hour-3


title: NSK IRF1 KO, human IRF1, Uninfected, rep 2

description: Library name: 6_hIRF1

value: RFP and human IRF1 expression


title: ccRCC3,replicate1, scRNA-seq

description: Library name: 576Ex3701

value: ccRCC


title: NSK IRF1 KO, human IRF1, Uninfected, rep 1

description: Library name: 4_hIRF1


title: C2C12 cells, myogenic differentiation, 0 hours, rep 2

description: Library name: CMD-0hour-2


title: RMC53, replicate1, scRNA-seq

description: Library name: 2010101


title: C2C12 cells, myogenic differentiation, 0 hours, rep 1

description: Library name: CMD-0hour-1


title: AAVS1_sgRNA(control), unstimulated, donor3, batch2

description: Library name: A1_S2_UT_D3

value: AAVS1 KO


title: AAVS1_sgRNA(control), unstimulated, donor2, batch2

description: Library name: A1_S2_UT_D2


title: NSK IRF1 KO, EmptyVector, Uninfected, rep 3

description: Library name: 3_EMP

value: NSK

value: RFP expression


title: RMC46, replicate1, scRNA-seq

description: Library name: 0650101

value: Lymph node


title: Mouse heart RNA-seq ISO+1 µm PS (C6)

first: Yilin

last: Pan

address: Anzhen Road #2, Chaoyang District

institute: Beijing Anzhen Hospital

description:
Library name: C6
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch2.txt

data_processing:
Adapters/low-quality bases removed using fastp; quality metrics (Q20/Q30/GC) computed.
Paired-end reads were aligned to the mouse reference genome using HISAT2 (v2.0.5) with splice-aware mapping and the corresponding gene annotation (GTF).
Aligned reads were assembled with StringTie (v1.3.3b) in reference-guided mode.
Gene-level counts generated using featureCounts (v1.5.0-p3).
Gene-level raw counts were used for downstream differential expression analyses. Count matrices were harmonized to a common Entrez Gene ID space and merged; low-abundance genes were filtered (counts ≥5 in at least two samples). Differential expression was performed using DESeq2 with sequencing batch included as a covariate (design: ~ batch + group). FPKM values were generated only for descriptive purposes/visualization.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Processed data include gene-level raw count tables provided separately for Batch 1 and Batch 2 (tab-delimited text; rows=genes, columns=samples).

source_name: heart

growth_protocol: Male C57BL/6 mice were housed under a 12-hour light/dark cycle with ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from mouse heart tissue using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent Bioanalyzer 2100.
mRNA-seq libraries were prepared by Novogene (Batch 1) and Majorbio Bio-Pharm Technology (Batch 2) using a standard poly(A)+ mRNA enrichment protocol with oligo(dT) beads, followed by RNA fragmentation, cDNA synthesis, end repair/A-tailing, adapter ligation, size selection, and PCR amplification. Libraries were sequenced on an Illumina platform as paired-end reads (instrument model/read configuration as reported in the raw sequencing metadata).

treatment_protocol: Mice were assigned to ISO (A1–A6), ISO+100 nm PS-NPs (B1–B6), or ISO+1 µm PS-NPs (C1–C6). ISO was administered by daily subcutaneous injection (2.5 mg/kg/day in PBS) for 21 days. PS-NPs were administered by daily oral gavage (50 mg/kg/day) for 21 days (water gavage for ISO-only group). Hearts were collected at the protocol endpoint for RNA extraction.

value: heart

value: ISO+1 µm PS

value: Batch 2 (Majorbio)


title: RMC49, replicate1, scRNA-seq

description: Library name: 0650201


title: Mouse heart RNA-seq ISO+1 µm PS (C5)

description:
Library name: C5
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch2.txt


title: AAVS1_sgRNA(control), anti-CD3 stimulated for 2 hours, donor3, batch2

description: Library name: A1_S2_2H_D3


title: IMR32-ASCL1-induced-5

city: Cambridge

first: Lidiya

last: Mykhaylechko

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way,

institute: University of cambridge

data_processing:
TrimGalore 0.6.4 for adapter and quality trimming
STAR 2.6.1d alignment to hg38 genome
STAR quant mode reverse to obtain gene counts
DESeq2 1.32.0 for differential expression analysis
Assembly: hg38
Supplementary files format and content: tsv file includes raw counts and counts per million (CPM) for each sample

growth_protocol: IMR32, SK-N-BE(2)-C, and SH-EP were cultured in DMEM-F12 with GlutaMAX (Gibco) supplemented with 10% FBS (Sigma) and 1% Penicillin-Streptomycin (Sigma).

extract_protocol:
Cells were lysed using RLT buffer and RNA extracted following the RNeasy Protocol Part I (Qiagen).
QIAseq Stranded mRNA Select Kit (180775), 100bp paired-end sequencing

treatment_protocol: Cells were plated and left to attach for 24 hours. Cell were either collected for RNA extraction after 24 hours of plating, or treated with 1µg/ml doxycycline for a further 24 hours before collection and RNA extraction

value: neuroblastoma cell

value: 24h ASCL1 induction with dox treatment


title: NSK IRF1 KO, EmptyVector, Uninfected, rep 1

description: Library name: 1_EMP

value: Kidney cells, epithelial-like

value: IRF1 knockout


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 16 hours, rep2

description: Library name: dKOert_16h_Tam_rep2

data_processing:
Fastq files for RNA-seq samples were processed using Nextflow(Ewels et al. 2020) and the nf-core RNA-seq pipeline v3.9 with default settings. The gene count output from the pipeline was filtered for genes greater than 1 cpm in at least two total samples. Samples were normalized using TMM. Next, Log2 CPM averages were calculated for replicates of each sample for scatterplot visualization and nearest neighbor TSS analysis. All transcriptomics analyses were conducted using CPM values from TMM normalization of all samples except for nearest neighbor analysis where WT and dKO were TMM normalized together. To conduct differential gene expression we performed DESeq2 v1.34.0 analysis using the raw gene count matrix as input for each desired comparison. Gene ontology was performed using ClusterProfiler 4.2.2. Custom R code for other downstream transcriptomics analyses and visualization provided on Github.
Assembly: mm10
Supplementary files format and content: csv file containing raw counts as determined by Salmon.

extract_protocol:
Total RNA was extracted and purified from cells using Trizol followed by ethanol precipitation
RNA-seq libraries were generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, CAT#A01172) according to their protocol using 200ng of total RNA for input. We utilized the PCR Add-on kit for Illumina (Lexogen, CAT#M02096) to determine an appropriate number of PCR cycles to amplify libraries. Amplified libraries were quantified using Agilent Tapestation 4200. Libraries were pooled and sequenced using a HiSeq 4000 to obtain single end 50bp reads. At least 10 million mapped reads or more per sample were obtained.

value: Naive ESC

value: Kmt2cKO; Kmt2dKO;GRHL2-ERT

value: Tam 16 hours


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 16 hours, rep1

description: Library name: dKOert_16h_Tam_rep1


title: AAVS1_sgRNA(control), anti-CD3 stimulated for 2 hours, donor2, batch2

description: Library name: A1_S2_2H_D2

value: Peripheral Blood Mononuclear Cells

value: Primary cells

value: anti-CD3 stimulated


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 16 hours, rep3

description: Library name: dKOert_16h_Tam_rep3


title: Mouse heart RNA-seq ISO+1 µm PS (C3)

description:
Library name: C3
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt

value: Batch 1 (Novogene)


title: IMR32-ASCL1-induced-2


title: AAVS1_sgRNA(control), unstimulated, donor1, batch2

description: Library name: A1_S2_UT_D1

value: AAVS1 KO

value: unstimulated


title: Mouse heart RNA-seq ISO+1 µm PS (C4)

description:
Library name: C4
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt


title: AAVS1_sgRNA(control), unstimulated, donor2, batch3

description: Library name: A1_NA_UT_D2


title: Mouse heart RNA-seq ISO+1 µm PS (C2)

description:
Library name: C2
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt


title: IMR32-ASCL1-induced-3


title: NSK IRF1 KO, EmptyVector, Uninfected, rep 2

description: Library name: 2_EMP

value: NSK

value: RFP expression


title: AAVS1_sgRNA(control), anti-CD3 stimulated for 2 hours, donor2, batch3

description: Library name: A1_NA_2H_D2


title: Mouse heart RNA-seq ISO+1 µm PS (C1)

description:
Library name: C1
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt

value: heart

value: ISO+1 µm PS


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 16 hours, rep3

description: Library name: dKOert_16h_Eth_rep3

value: EtOH 16 hours


title: IMR32-ASCL1-induced-4

value: neuroblastoma cell

value: 24h ASCL1 induction with dox treatment


title: IMR32-ASCL1-induced-1


title: Mouse heart RNA-seq ISO+100 nm PS (B6)

description:
Library name: B6
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch2.txt

value: ISO+100 nm PS

value: Batch 2 (Majorbio)


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 16 hours, rep2

description: Library name: dKOert_16h_Eth_rep2

value: Naive ESC

value: Kmt2cKO; Kmt2dKO;GRHL2-ERT


title: IMR32-uninduced-5

value: uninduced


title: Line 4- stressed

type: RNA

city: Giza

first: Marwa

last: Sanad

address: 33 El Bohouth St, Dokki

department: Genetics and Cytology

country: Egypt

institute: National Research Centre

description: Heat Treatment (stressed)

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package for each plate , and then the final normallization for the plates done manually in the excel sheets
For the normalization it uses the average of the housekeeping genes: ACTIN 7
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

organism: Triticum aestivum

source_name: leaves during anthesis stage

label_protocol: PCR assays were performed using synthesized cDNA using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems) following the Manufacturer’s instructions. Reverse transcription was performed from 50 ng total RNA using the and PowerUp™ SYBR™ Green Master Mix (ThermoFisher). Quantitative real-time PCR were performed (Applied Biosystem Light Cycler 7500 Fast) with 40 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with GeneJET™ Plant RNA Purification Mini Kit followed by DNase I treatment.

value: heat stressed

tag: passive reference

value: ROX included


title: Mouse heart RNA-seq ISO+100 nm PS (B5)

description:
Library name: B5
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt

value: Batch 1 (Novogene)


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 16 hours, rep1

description: Library name: dKOert_16h_Eth_rep1


title: IMR32-uninduced-4


title: IMR32-uninduced-3


title: Line 4- nonstressed

description: Heat Treatment (stressed)


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 16 hours, rep2

description: Library name: CKOert_16h_Tam_rep2

value: Kmt2cKO; Kmtd fl/fl;GRHL2-ERT

value: Tam 16 hours


title: Misr 2- stressed

description: Control (non-stressed)

value: non-stressed


title: Mouse heart RNA-seq ISO+100 nm PS (B1)

description:
Library name: B1
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt


title: Misr 2- nonstressed

description: Control (non-stressed)


title: Mouse heart RNA-seq ISO+100 nm PS (B2)

description:
Library name: B2
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt


title: Mouse heart RNA-seq ISO+100 nm PS (B4)

description:
Library name: B4
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt


title: Mouse heart RNA-seq ISO+100 nm PS (B3)

description:
Library name: B3
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 16 hours, rep3

description: Library name: CKOert_16h_Tam_rep3


title: BE2C-ASCL1-induced-5


title: siRNA Agrin rep 1

city: Singapore

first: Pierre-alexis

last: Goy

state: Singapore

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore (GIS-ASTAR)

data_processing:
Raw reads from fastq files were aligned to the hg38 genome using STAR 2.6.1d (using options --sjdbGTFfile gencode.v29.annotation.gtf --sjdbOverhang 75 --outSAMtype BAM   Unsorted --outSAMstrandField intronMotif  --twopassMode Basic).
Bam files were sorted with samtools sort and indexed with samtools index.
The number of reads mapping to each gene was quantified with htseq-count (using options --format=bam --order=pos --stranded=reverse  --idattr=gene_name --nonunique=all) on features from the gtf file gencode.v29.annotation.gtf.
The raw counts of reads were then imported into EdgeR in R to perform the differential expression analyses.
Assembly: hg38
Supplementary files format and content: Counts per million (CPM) from EgdeR in excel format

source_name: BJ

growth_protocol: BJ cells were cultured in RPMI (Roswell Park Memorial Institute) media supplemented with 10% (v/v) FBS. All cells were grown at 37°C in an atmosphere of 5% CO2.

extract_protocol:
RNA was isolated from the cells after compound treatment using Quick-RNA Miniprep kit (Zymo Research)
Total RNA, 2.5μg, was used for RNASequencing library preparation with the TruSeq Stranded mRNA Library Prep kit (Illumina) largely according to manufacturer’s instructions.

treatment_protocol: BJ cells were treated with siRNA knockdown against Agrin.

value: BJ

value: human fibroblasts cells

value: WT

value: siRNA Agrin knockdown


title: Mouse heart RNA-seq ISO (A6)

description:
Library name: A6
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch2.txt

value: heart

value: ISO


title: siRNA Agrin rep 3


title: IMR32-uninduced-2

value: neuroblastoma cell


title: IMR32-uninduced-1


title: siRNA Agrin rep 2


title: BE2C-ASCL1-induced-4

value: 24h ASCL1 induction with dox treatment


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 16 hours, rep1

description: Library name: CKOert_16h_Tam_rep1

value: Naive ESC


title: Mouse heart RNA-seq ISO (A5)

description:
Library name: A5
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch2.txt

value: Batch 2 (Majorbio)


title: siRNA control rep 3

value: siRNA control


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 16 hours, rep2

description: Library name: CKOert_16h_Eth_rep2

value: EtOH 16 hours


title: BE2C-ASCL1-induced-3


title: Mouse heart RNA-seq ISO (A4)

description:
Library name: A4
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch2.txt


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 16 hours, rep1

description: Library name: CKOert_16h_Eth_rep1


title: BE2C-ASCL1-induced-2


title: Mouse heart RNA-seq ISO (A3)

description:
Library name: A3
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, Tam 16 hours, rep3

description: Library name: CKO_16h_Tam_rep3

value: Kmt2cKO; Kmtd fl/fl


title: BE2C-ASCL1-induced-1


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, Tam 16 hours, rep1

description: Library name: CKO_16h_Tam_rep1


title: BE2C-uninduced-5

value: uninduced


title: Mouse heart RNA-seq ISO (A1)

description:
Library name: A1
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt

value: Batch 1 (Novogene)


title: siRNA control rep 1


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 16 hours, rep3

description: Library name: CKOert_16h_Eth_rep3

value: Kmt2cKO; Kmtd fl/fl;GRHL2-ERT


title: Mouse heart RNA-seq ISO (A2)

description:
Library name: A2
ISO injury model ± PS-NPs (co-exposure); heart tissue collected at endpoint.
mouse_gene_count_batch1.txt


title: siRNA control rep 2


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, rep1

description: Library name: dKOert_8h_Tam_rep1

value: Kmt2cKO; Kmt2dKO;GRHL2-ERT

value: Tam 8 hours


title: IRX3 cl1 +/+ 2 (hiPSC-CM Day 4 of differentiation)

city: Sao Paulo

first: Jose

middle: E

last: Krieger

state: SP

address: Av Dr Eneas C Aguiar 44 10ofl

department: Cardiology

country: Brazil

institute: Heart Institute (InCor)/Univ Sao Paulo Med Sch

description:
Total RNA extracted from hPSC commited to cardiomyocytes differentiation protocol in differentiation day 4 of development
Wt_D4.2

hyb_protocol: Samples were hybridized with GeneChipTM    WT PLUS Reagent Kit (Affymetrix) and scanned at  GeneTitan ™ Microarray System

scan_protocol: The entire protocol for processing, running and scanning the samples followed the manufacturer's instruction [GeneChip ™ WT PLUS Reagent Kit Manual] at GeneTitan ™ Microarray System

data_processing: The .CEL files were analyzed using the R software with oligo package, and RMA normalization.

label: biotin

source_name: hiPSC-derived cardiac progenitor cell (CPC)

label_protocol: Samples were enzymatically fragmented and biotinylated using RNA samples for whole  transcriptome  expression analysis with GeneChipTM Whole Transcript (WT) Expression Arrays (appliedbiosystems)

growth_protocol: Prior to cardiac differentiation hiPSC cells were maintained in StemFlex medium (Gibco) at 37ºC and 5% CO2 with daily change. Stablished hiPSC-CM were cultivated with RPMI-1640 supplemented with B27 and insulin until the end of protocol.

extract_protocol: We used the RNeasy Micro Kit (Qiagen) for total RNA isolation

treatment_protocol: Cardiac cell differentiation protocol followed Burridge et al., 2014 specifications. No treatment was applied after cell differentiation.

tag: age

value: Differentiation day 4

tag: cell lineage

value: SS109 - in house developed hiPSC lineage


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, rep3

description: Library name: dKOert_8h_Eth_rep3

value: EtOH 8 hours


title: KO_3

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

description: Library name: 6

data_processing:
Reads were aligned to GRCm39 mouse genome with “Rbowtie2”
counts extracted with featureCounts function from “Rsubread” and gencode annotation release 32 (gencode.vM32.annotation.gtf)
Gene set enrichment analyses were conducted with GSEA (version 4.1.0) software 74, using the normalized count values.
Assembly: GRCm39
Supplementary files format and content: normalized counts

source_name: MEFs

growth_protocol: MEFs were cultured in Dulbecco´s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin at 37ºC in a humidified 5% CO2-95% air incubator.

extract_protocol:
Total RNA from WT and GαqKO mouse embrionary fibroblasts extracted and purified with RNeasy Mini Kit (Qiagen), and genomic DNA was removed using the RNase-Free DNase Set (Qiagen).
cDNA library was constructed using Stranded mRNA Library Preparation Kit and sequenced in the Illumina Novaseq platform, using 150bp paired-end sequencing reads.

value: MEFs

value: Mouse embryonic fibroblasts

value: GalfaqKO


title: BE2C-uninduced-1

value: neuroblastoma cell


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, Tam 16 hours, rep2

description: Library name: CKO_16h_Tam_rep2

value: Naive ESC

value: Tam 16 hours


title: KO_2

description: Library name: 5


title: IRX3 cl1 -/- 2 (hiPSC-CM Day 4 of differentiation)

description:
Total RNA extracted from hPSC commited to cardiomyocytes differentiation protocol in differentiation day 4 of development
KO_D4.2


title: WT_3

description: Library name: 3

value: WT


title: BE2C-uninduced-2


title: BE2C-uninduced-4


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, rep2

description: Library name: dKOert_8h_Eth_rep2


title: IMRC12-Rep4-Ascl1_S29

data_processing:
Fastq trimming with trim_galore v0.6.4_dev -q 20 --paired
Mapped to hg38 with bowtie2 v2.4.1 snakemake wrapper 0.71.1/bio/bowtie2/align
Mapped reads filtered for paired end = True, mismatch NM:<=4, min fragment size >=-2000 max fragment size <=2000
Duplicate reads marked but not removed, peaks called with macs2 v2.2.7.1, snakemake wrapper 0.66.0/bio/macs2/callpeak  -f BAMPE -g hs --SPMR --qvalue 0.05 --keep-dup all
Bigwig files generated with deeptools bamCoverage v3.4.3 with CPM normalisation
Assembly: hg38
Supplementary files format and content: Macs2 narrowpeak files
Supplementary files format and content: Bigwig

extract_protocol:
Cells were fixed with 1 % PFA, lysed, and sheared to 100-300 bp fragments, before immunoprecipitating with ASCL1 antibody (ab74065). DNA was purified using the QIA Quick PCR purification kit and quantified with the Qubit HS assay kit, for library preparation.
NEBNext Ultra II DNA library prep kit, Illumina

treatment_protocol: Cells were plated and left to attach for 24 hours. Cell were treated with 1µg/ml doxycycline for a further 24 hours before collection and RNA or genomic DNA extraction

value: 24h ASCL1 induction with dox treatment

tag: chip antibody

value: ASCL1 (Abcam:ab74065)


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, rep3

description: Library name: dKOert_8h_Tam_rep3


title: BE2C-uninduced-3

value: uninduced


title: AD2

city: Wuhan

first: chen

last: cheng

address: No. 169 Donghu Road, Wuchang District, Wuhan City, Hubei Province

institute: Wuhan University

description:
Library name: sample11
Column name in gene.counts.matrix.add_info.txt: AD2

data_processing:
Raw FASTQ data were processed using fastp (v0.21.0) with a length filter of 30 bp (-l 30) to remove adapter sequences and low-quality reads, yielding high-quality clean reads.
The clean reads were aligned to the Drosophila melanogaster reference genome (Release 6/dm6) using STAR (v2.7.9a) with default parameters.
Gene and transcript expression levels were quantified using RSEM. For paired-end sequencing, reads originating from the same fragment were counted as a single entity.
Read counts were normalized to FPKM (Fragments Per Kilobase per Million mapped reads) to represent gene expression levels.
Assembly: Flybase genome annotation version r6.47
Supplementary files format and content: gene.counts.matrix.add_info.txt

organism: Drosophila melanogaster

source_name: whole-body

growth_protocol: Flies were maintained on food containing 5.5 g agar, 65 g sucrose, 25 g yeast powder, 65 g cornmeal, 4 mL propionic acid, and 1.25 g Methylparaben (dissolved in 95% ethanol) per liter at constant temperature of 25°C with a 12 h:12 h light / dark cycle.

extract_protocol:
For each biological replicate, five whole adult flies were collected and homogenized in 1 mL of TRIzol Reagent (Invitrogen/Thermo Fisher Scientific) using  bead-based homogenizer. Total RNA was extracted following the standard acid guanidinium thiocyanate-phenol-chloroform method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies of the indicated genotypes (w1118 and Akh mutant: AkhA) were subjected to PBS or Drosophila C Virus (DCV) infection. Whole fly bodies were collected at 5.5 day post-infection(dpi) for w1118 and 3.5 dpi for AkhA

value: whole-body

value: Akh mutant

value: DCV injection


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, Tam 8 hours, rep2

description: Library name: dKOert_8h_Tam_rep2

value: Kmt2cKO; Kmt2dKO;GRHL2-ERT

value: Tam 8 hours


title: AD3

description:
Library name: sample12
Column name in gene.counts.matrix.add_info.txt: AD3


title: KO_1

description: Library name: 4


title: AD1

description:
Library name: sample10
Column name in gene.counts.matrix.add_info.txt: AD1


title: IRX3 cl1 +/+ 1 (hiPSC-CM Day 4 of differentiation)

description:
Total RNA extracted from hPSC commited to cardiomyocytes differentiation protocol in differentiation day 4 of development
Wt_D4.1

value: Differentiation day 4

value: SS109 - in house developed hiPSC lineage


title: AP2

description:
Library name: sample8
Column name in gene.counts.matrix.add_info.txt: AP2

value: PBS injection


title: Naive ESC, Kmt2cKO; Kmt2dKO;GRHL2-ERT, EtOH 8 hours, rep1

description: Library name: dKOert_8h_Eth_rep1

value: EtOH 8 hours


title: WT_2

description: Library name: 2

value: MEFs

value: Mouse embryonic fibroblasts


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, rep3

description: Library name: CKOert_8h_Tam_rep3

value: Naive ESC

value: Kmt2cKO; Kmtd fl/fl;GRHL2-ERT


title: IMRC12-Rep1-Ascl1_S26

value: neuroblastoma cell


title: AP3

description:
Library name: sample9
Column name in gene.counts.matrix.add_info.txt: AP3


title: AP1

description:
Library name: sample7
Column name in gene.counts.matrix.add_info.txt: AP1


title: YF+HDI ChIP

city: Suzhou

first: Hang

last: Ruan

state: Jiangsu

address: 199 Ren'ai Road

department: IBMS

institute: Soochow University

data_processing:
The raw ChIP-Seq reads were trimmed using fastp v0.23.2 and aligned to the mouse reference genome (mm39) using bwa version 0.7.17-r1188. Only the uniquely mapped reads were retained. The bam files were sorted using samtools version 0.1.19-44,428 cd. The peaks were called using macs2 version 2.2.7.1. The HOMER toolkit was used to produce "BigWig" files.
Assembly: mm39
Supplementary files format and content: bigWig

source_name: liver

extract_protocol:
Cells were homoginised and cross-linked in 1% formaldehyde for 20 min at room temperature. Whole-cell extracts were sonicated followed by immunoprecipitation with antibodies for H3k27ac (Abcam, ab4729) and Protein A Sepharose CL-4B (GE, 17-0780-01). After the immunoprecipitation, beads were washed by ChIP dilution buffer (50 mM HEPES (pH 7.5]), 155 mM NaCl, 1.1% TritonX-100, 0.11% NaDeoxycholate, 1 mM EDTA) three times followed by a wash with ChIP wash buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 0.5% NaDeoxycholate, 250 mM LiCl, and 0.5% NP-40). Sepharose beads were further washed once by TE buffer (Promega, E260A). DNA were enriched with phenol–chloroform extraction and dissolved in 20 µl TE buffer followed by RNA degradation by RNase (Roche, 11119915001) for 30 min at 37 °C.
Four HDAC3 ChIP reactions were performed with each reaction containing samples from three mice. The ChIP reactions were then pooled to be sequenced as one sample, together with the pooled total input DNA as the control. The precipitated DNA was then pooled and amplified according to the manufacturer's guide of Illumina (Ilumina TruSeq ChIP Library Preparation Kit), followed by 50 bp single-end deep sequencing on Illumina NovaSeq 6000.

value: liver

value: hepatocytes


title: IMRC12-Rep3-Ascl1_S28

value: 24h ASCL1 induction with dox treatment

value: ASCL1 (Abcam:ab74065)


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, rep2

first: Robert

last: Blelloch

address: 35 Medical Center Way

institute: UCSF

description: Library name: CKOert_8h_Tam_rep2


title: WT_1

description: Library name: 1

value: WT


title: WD3

description:
Library name: sample6
Column name in gene.counts.matrix.add_info.txt: WD3

value: whole-body

value: DCV injection


title: YF ChIP


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, rep3

description: Library name: CKOert_8h_Eth_rep3


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, Tam 8 hours, rep1

description: Library name: CKOert_8h_Tam_rep1

value: Tam 8 hours


title: IMRC12-Rep2-Ascl1_S27


title: WD2

description:
Library name: sample5
Column name in gene.counts.matrix.add_info.txt: WD2


title: WD1

description:
Library name: sample4
Column name in gene.counts.matrix.add_info.txt: WD1


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, rep2

description: Library name: CKOert_8h_Eth_rep2


title: IMRC12-Input_S25


title: YF input


title: Naive ESC, Kmt2cKO; Kmtd fl/fl;GRHL2-ERT, EtOH 8 hours, rep1

description: Library name: CKOert_8h_Eth_rep1


title: BE2CA1-Rep3-Ascl1_S18


title: YF+HDI input


title: BE2CA1-Rep2-Ascl1_S17


title: WP3

description:
Library name: sample3
Column name in gene.counts.matrix.add_info.txt: WP3


title: IRX3 cl1 -/- 1 (hiPSC-CM Day 4 of differentiation)

description:
Total RNA extracted from hPSC commited to cardiomyocytes differentiation protocol in differentiation day 4 of development
KO_D4.1

value: Differentiation day 4


title: HDI ChIP


title: HDI input


title: BE2CA1-Rep1-Ascl1_S16


title: WP2

description:
Library name: sample2
Column name in gene.counts.matrix.add_info.txt: WP2


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, Tam 8 hours, rep3

description: Library name: CKO_8h_Tam_rep3

value: Kmt2cKO; Kmtd fl/fl


title: Control ChIP


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, Tam 8 hours, rep2

description: Library name: CKO_8h_Tam_rep2


title: BE2CA1-Input_S15


title: Naive ESC, Kmt2cKO; Kmtd fl/fl, Tam 8 hours, rep1

description: Library name: CKO_8h_Tam_rep1


title: BE2CA1-Rep4-Ascl1_S19


title: WP1

description:
Library name: sample1
Column name in gene.counts.matrix.add_info.txt: WP1

value: PBS injection


title: RNA-Seq of Rhodococcus opacus 1CP D123 pheA1 triple knockout mutant, 2mM p-cresol, replicate 2

status: Public on Mar 27 2026

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

country: Germany

institute: Bielefeld University

description:
Library name: Ropa_123_pCresol_B
D123_pCresol_B

data_processing:
Basecalls were performed using RTA v 1.18.66.3
Sequenced reads were mapped to CP009111.1-CP009113.1 using bowtie2 v2.3.2 with parameters -X 600
Raw counts and TPM values were determined/calculated using ReadXplorer v.2.2.3
Assembly: CP009111.1-CP009113.1
Supplementary files format and content: tab-delimited matrix table with TPM values for every gene and every sample

organism: Rhodococcus opacus

source_name: bacterial cell

growth_protocol: For the cultivation of cells for tetradecane, phenol and p-cresol studies, the procedure was as follows. Precultures of R. opacus 1CPWT and R. opacus 1CP Δ123 were grown in 20 ml minimal medium (doi:10.1007/BF00696222) containing 4 mM benzoate as sole carbon source at 30 °C under continuous shaking. After four days the cultures were fed with 5 mM benzoate. After five and seven days of growth, 2 mM of the above-mentioned carbon sources were added.

extract_protocol:
Prior to harvesting the cells, a 10% ice-cold stop solution (10% buffered phenol in ethanol) was added to the culture, followed by centrifugation at 11,000 × g for 5 min at 4°C. The supernatant was discarded, and the pellet was stored until RNA isolation at −80°C. To break up the cells, 150 μl of a 5-mg ml−1 lysozyme solution was added to the pellet, mixed, and incubated at room temperature for 5 min. Next, 450 μl of buffer RLT (Qiagen) and 50 mg of 0.1-mm glass beads were added to resuspend and break the cells by repeated vortexing at 4°C. The suspension was applied to a QIAshredder column for homogenization and to remove particles from the sample. Extraction of total RNA was done by applying an RNeasy minikit, including on-column DNA digestion (Qiagen). Isolated RNA was stored at −80°C, and the quality was controlled on a 2100 Bioanalyzer using an RNA 6000 Nano kit (Agilent Technologies, Böblingen, Germany).
To construct whole transcriptome cDNA libraries, 2.5 μg of total RNA each was depleted of rRNA (Ribo-Zero rRNA Removal Kit (Bacteria), Illumina, San Diego, CA, USA). Successful rRNA removal was validated (Agilent RNA Pico 6000 kit, Agilent 2100 Bioanalyzer, Agilent Technologies). The obtained mRNA was converted into a cDNA library according to the TruSeq Stranded mRNA Sample Preparation guide (Illumina). Appropriate cDNA quality and quantity was validated (Agilent High Sensitivity DNA kit, Agilent 2100 Bioanalyzer, Agilent Technologies). Sequencing was performed on an Illumina NextSeq 500 instrument using 75 bases read length (Illumina).

treatment_protocol: After eight days, cultures were divided into 4 shaking flasks for each substrate containing 100 ml of fresh minimal medium and 2 mM of the respective carbon source. Afterwards, for three days the cultures were fed daily with two times 2 mM of the respective carbon source.

tag: strain

value: bacterial cell

value: pheA1 triple knockout mutant

value: 2mM p-cresol


title: Control input


title: RNA-Seq of Rhodococcus opacus 1CP wildtype, 2mM phenol, replicate 1

description:
Library name: Ropa_WT_Phenol_A
WT_Phenol_A

value: wildtype

value: 2mM phenol


title: RNA-Seq of Rhodococcus opacus 1CP wildtype, 2mM styrol, replicate 4

description:
Library name: Ropa_WT_Styrol_D
WT_Styrol_D

value: 2mM styrol


title: RNA-Seq of Rhodococcus opacus 1CP D123 pheA1 triple knockout mutant, 2mM p-cresol, replicate 4

description:
Library name: Ropa_123_pCresol_D
D123_pCresol_D


title: RNA-Seq of Rhodococcus opacus 1CP wildtype, 2mM styrol, replicate 2

description:
Library name: Ropa_WT_Styrol_B
WT_Styrol_B


title: RNA-Seq of Rhodococcus opacus 1CP wildtype, 2mM styrol, replicate 1

description:
Library name: Ropa_WT_Styrol_A
WT_Styrol_A


title: RNA-Seq of Rhodococcus opacus 1CP wildtype, 2mM phenol, replicate 4

description:
Library name: Ropa_WT_Phenol_D
WT_Phenol_D


title: RNA-Seq of Rhodococcus opacus 1CP wildtype, 2mM styrol, replicate 3

description:
Library name: Ropa_WT_Styrol_C
WT_Styrol_C


title: RNA-Seq of Rhodococcus opacus 1CP wildtype, 2mM phenol, replicate 3

description:
Library name: Ropa_WT_Phenol_C
WT_Phenol_C


title: RNA-Seq of Rhodococcus opacus 1CP wildtype, 2mM phenol, replicate 2

description:
Library name: Ropa_WT_Phenol_B
WT_Phenol_B


title: RNA-Seq of Rhodococcus opacus 1CP wildtype, 2mM tetradecane, pool of replicates 1-4

description:
Library name: Ropa_WT_TD_Pool
WT_Tetradecane_Pool

value: 2mM tetradecane


title: salmonella exposed to tryptophan 10 minutes rep 2

city: Rehovot

first: Erez

last: Mills

address: Hertzel 229

country: Israel

institute: The Hebrew University

description: Library name: batch2_TRP.1.fastq

library_source: other

data_processing:
quality check using fastqc
Cutadapt v4.7 (py-cutadapt) (Martin, 2011) for adapter removal and quality filtering — trimming reads with Phred scores < 30 and lengths < 80 bp in pool1 and pool3 samples including combining R1 and r2 reads. For batch2 samples, R1 and R2 were not combined and are in seperated files as submitted.
Assembly: ASM2216v1
Supplementary files format and content: raw gene-level read counts

molecule: other

organism: Salmonella enterica

source_name: Salmonella enterica serovar Typhimurium stain SL14028

growth_protocol: Mills, E., Petersen, E., Kulasekara, B.R., Miller, S.I., 2015. A direct screen for c-di-GMP modulators reveals a Salmonella Typhimurium periplasmic ʟ-arginine–sensing pathway. Sci Signal 8, ra57–ra57. https://doi.org/10.1126/scisignal.aaa1796

extract_protocol:
Total RNA purification was performed using Norgen kits for the rapid purification of total RNA, including microRNA without the use of phenol (Norgen Biotek, Cat no. SKU 17200). Chemical and mechanical lysis was performed using 1mg/ml of lysozyme and vertexing as described in section 1E of the kit protocol, suitable for gram negative bacteria.
Avraham, R., Haseley, N., Fan, A., Bloom-Ackermann, Z., Livny, J., Hung, D.T., 2016. A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes. Nat. Protoc. 11, 1477–1491. https://doi.org/10.1038/nprot.2016.090

treatment_protocol: Bacterial cultures were treated with one of the following compounds, each added at a final concentration as specified: Acetic acid (1 mM), propionic acid (400 µM), isobutyric acid (100 µM), glycine (20 µM), gamma aminobutyric acid (GABA, 25 µM), taurine (50 µM), cysteine (5 µg/mL or 41.3 µM), proline (20 µM), 5-oxoproline (10 mM), D-arabinose (50 µM), L-arabinose (50 µM), salicylic acid (400 µM), p-aminobenzoic acid (PABA, 4 µM), tyramine (100 µM), dopamine (500 µM), tyrosine (200 µM), tryptophan (100 µM), melatonin (2 µg/mL or 8.61 µM), and α-tocopherol (8 µM). Concentrations were chosen according to the literature to represent physiological concentrations. Double-distilled water (DDW) was used as the control treatment. Each treatment had 3 biological replicates. Compounds were administered in a 1:4 ratio (compound to bacterial culture), with a total final volume of 1 mL per sample. The exposure time for all treatments was 10 minutes. Exposure was done in a shaker incubator at 37C.


title: RNA-Seq of Rhodococcus opacus 1CP D123 pheA1 triple knockout mutant, 2mM p-cresol, replicate 3

description:
Library name: Ropa_123_pCresol_C
D123_pCresol_C


title: salmonella exposed to tyrosine 10 minutes rep 2

description: Library name: batch2_TYR.1.fastq

value: Salmonella enterica serovar Typhimurium stain SL14028


title: salmonella exposed to propionic acid 10 minutes rep 2

description: Library name: batch2_poropionicacid.1.fastq


title: salmonella exposed to tairine 10 minutes rep 2

description: Library name: batch2_TAURINE.1.fastq


title: salmonella exposed to salicylic acid 10 minutes rep 2

description: Library name: batch2_SA.1.fastq


title: salmonella exposed to tyramine 10 minutes rep 2

description: Library name: batch2_TYRAMINE.1.fastq


title: RNA-Seq of Rhodococcus opacus 1CP D123 pheA1 triple knockout mutant, 2mM p-cresol, replicate 1

description:
Library name: Ropa_123_pCresol_A
D123_pCresol_A


title: salmonella exposed to PABA 10 minutes rep 2

description: Library name: batch2_PAMINOBENZOICACID.1.fastq


title: salmonella exposed to proline 10 minutes rep 2

description: Library name: batch2_PRO.1.fastq


title: salmonella exposed to melatonine  10 minutes rep 2

description: Library name: batch2_Melatonine.1.fastq


title: salmonella exposed to l-arabinose  10 minutes rep 2

description: Library name: batch2_LARABINOSE.1.fastq


title: salmonella exposed to glycine 10 minutes rep 2

description: Library name: batch2_glycine.1.fastq


title: salmonella exposed to dopamine  10 minutes rep 2

description: Library name: batch2_dopamin.1.fastq


title: salmonella exposed to GABA  10 minutes rep 2

description: Library name: batch2_GABA.1.fastq


title: salmonella exposed to isobutyric  acid 10 minutes rep 2

description: Library name: batch2_isobutyricacid.1.fastq


title: salmonella exposed to ddw  10 minutes rep 2

description: Library name: batch2_ddw.1.fastq


title: salmonella exposed to a-tocopherol  10 minutes rep 2

description: Library name: batch2_atocopherol.1.fastq


title: salmonella exposed to acetic acid 10 minutes rep 2

description: Library name: batch2_ACETICACID.1.fastq


title: salmonella exposed to cysteiene 10 minutes rep 2

description: Library name: batch2_CYS.1.fastq


title: salmonella exposed to d-arabinose  10 minutes rep 2

description: Library name: batch2_DARABINOSE.1.fastq


title: Feces_EAE_KU_biol_rep2

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

institute: Forth Military Medicial University

description: Library name: Feces_EAE_KU_biol_rep2

data_processing:
Raw sequencing reads were processed to obtain valid reads for further analysis. First, sequencing adapters were removed from sequencing reads using cutadapt v1.9. Secondly, low quality reads were trimmed by fqtrim v0.94 using a sliding-window algorithm. Thirdly, reads were aligned to the host genome using bowtie2 v2.2.0 to remove host contamination. Once quality-filtered reads were obtained, they were de novo assembled to construct the metagenome for each sample by IDBA-UD v1.1.1. All coding regions (CDS) of metagenomic contigs were predicted by MetaGeneMark v3.26. CDS sequences of all samples were clustered by CD-HIT v4.6.1 to obtain unigenes. Unigene abundance for a certain sample were estimated by TPM based on the number of aligned reads by bowtie2 v2.2.0. The lowest common ancestor taxonomy of unigenes were obtained by aligning them against the NCBI NR database by DIAMOND v 0.9.14. Similarly, the functional annotation (GO, KEGG, eggnog, CAZy, CARD, PHI, MGEs, VFDB) of unigenes were obtained. Based on the taxonomic and functional  annotation of unigenes, along with the abundance profile of unigenes, the differential analysis were carried out at each taxonomic or functional or gene-wise level by Fisher's exact test(non-replicated groups) or Kruskal-Wallis test (replicated groups).
Assembly: Host genome: Mus musculus (mm10/GRCm38) was used for host read removal.
Supplementary files format and content: 1. Clean sequencing reads: FASTQ format (adapter-trimmed, quality-filtered, host-depleted). 2. Assembled contigs: FASTA format (de novo metagenomic contigs per sample). 3. Unigene sequences: FASTA format (non-redundant gene catalog). 4. Gene abundance table: TXT format (TPM-normalized unigene abundance across all samples). 5. Taxonomic annotations: TXT format (LCA-based taxonomy for unigenes against NCBI NR). 6. Functional annotations: TXT format (GO, KEGG, eggNOG, CAZy, CARD, PHI, MGEs, VFDB annotations for unigenes).

organism: metagenome

source_name: Feces

growth_protocol: Female C57BL/6 mice aged 6-8 weeks were purchased from GemPharmatech and maintained in the Laboratory Animal Center of Fourth Military Medical University. All mice were maintained under SPF conditions and housed under a 12:12-h light-dark cycle, with humidity of 40-70%, ambient temperature of 26 °C, and sufficient food and water. Mice were group-housed with cage rotation for 2 weeks before the experiments. All animal experimental procedures were approved by the Institutional Animal Care and Use Committee of Fourth Military Medical University.

extract_protocol:
Feces were collected under sterile conditions and promptly stored at -80 °C. DNA from different samples was extracted using The E.Z.N.A.® Stool DNA Kit (D4015-02, Omega, Inc., USA) according to manufacturer’s instructions. The reagent which was designed to uncover DNA from trace amounts of sample has been shown to be effective for the preparation of DNA of most bacteria. Sample blanks consisted of unused swabs processed through DNA extraction and tested to contain no DNA amplicons. The total DNA was eluted in 50 µl of Elution buffer by a modification of the procedure de-scribed by manufacturer (QIAGEN) and stored at -80°C until measurement in the PCR by LC-BIO TECHNOLOGIES (HANGZHOU) CO., LTD., Hang Zhou, Zhejiang Province, China.
DNA Library Construction DNA library was constructed by TruSeq Nano DNA LT Library.

treatment_protocol: The mice were inoculated with an emulsion comprising incomplete Freund’s adjuvant, MOG35-55 (200 μg) and H37RA (500 μg) at 3 subcutaneous locations on the dorsal surface of the mice. The mice were intraperitoneally injected with 200 ng of pertussis toxin (PTX) on the induction day and 48 h later. EAE clinical scores were assessed daily: 0 (no symptoms), 1 (tail limpness), 2 (hindlimb weakness), 3 (hindlimb paralysis), 4 (tetraplegia), and 5 (moribund/death). On 11 dpi, the KU group was orally administered 100 mg/kg of KU treatment, and the EAE group received PBS until 21 dpi.

value: Feces

value: MOG35-55 peptide-induced EAE, KU treatment


title: Feces_EAE_KU_biol_rep7

description: Library name: Feces_EAE_KU_biol_rep7


title: salmonella exposed to 5oxoproline 10 minutes rep 2

description: Library name: batch2_5oxoproline.1.fastq


title: Feces_EAE_KU_biol_rep3

description: Library name: Feces_EAE_KU_biol_rep3


title: Feces_EAE_KU_biol_rep8

description: Library name: Feces_EAE_KU_biol_rep8


title: Feces_EAE_KU_biol_rep6

description: Library name: Feces_EAE_KU_biol_rep6


title: Feces_EAE_biol_rep8

description: Library name: Feces_EAE_biol_rep8

value: MOG35-55 peptide-induced EAE


title: Feces_EAE_KU_biol_rep5

description: Library name: Feces_EAE_KU_biol_rep5


title: Feces_EAE_biol_rep7

description: Library name: Feces_EAE_biol_rep7


title: Feces_EAE_KU_biol_rep1

description: Library name: Feces_EAE_KU_biol_rep1


title: Feces_EAE_biol_rep1

description: Library name: Feces_EAE_biol_rep1


title: Feces_EAE_biol_rep5

description: Library name: Feces_EAE_biol_rep5


title: Feces_EAE_biol_rep3

description: Library name: Feces_EAE_biol_rep3


title: Feces_Control_biol_rep8

description: Library name: Feces_Control_biol_rep8


title: Feces_EAE_biol_rep4

description: Library name: Feces_EAE_biol_rep4


title: Feces_Control_biol_rep6

description: Library name: Feces_Control_biol_rep6


title: Feces_EAE_biol_rep2

description: Library name: Feces_EAE_biol_rep2


title: Feces_EAE_KU_biol_rep4

description: Library name: Feces_EAE_KU_biol_rep4


title: Feces_Control_biol_rep5

description: Library name: Feces_Control_biol_rep5


title: Feces_Control_biol_rep4

description: Library name: Feces_Control_biol_rep4


title: Feces_Control_biol_rep2

description: Library name: Feces_Control_biol_rep2


title: Feces_Control_biol_rep3

description: Library name: Feces_Control_biol_rep3


title: Feces_EAE_biol_rep6

description: Library name: Feces_EAE_biol_rep6


title: Feces_Control_biol_rep1

description: Library name: Feces_Control_biol_rep1


title: Feces_Control_biol_rep7

description: Library name: Feces_Control_biol_rep7


title: WT3

city: beijing

first: Hongyue

last: Wang

state: Beijing

address: Mentougou District Fuwai Hospital Western Hills scientific research base

institute: Fuwai Hospital

description: Library name: sample6

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke [1] 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). Structure variation detection The clean reads were mapped to the reference genome using HISAT2 [2]. After that, Ericscript (v0.5.5) [3] and rMATS (V4.1.2) [4] were used to detect fusion genes and differential splicing genes (DSGs), respectively
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: RNA identification Bowtie2[5] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) [6]. The heatmap was drawn by pheatmap (v1.0.12) [7] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) [8] (or DEGseq （v1.48.0）[9] or PoissonDis[10])with Q value ≤ 0.05 (or FDR ≤ 0.001). Gene Annotation 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) [11].
Supplementary files format and content: all-gene.xls

extract_protocol:
Add the equal volume of 70% ethanol to the collection tube, mix by pipetting.Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow.Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube.Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
1. Introduction RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts. Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly. 2.Experimental Procedure 2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: embryonic stem cell


title: WT2

description: Library name: sample5


title: napM-deleted biol rep 2

city: Wrocław

first: Kornel

last: Milcarz

address: Fryderyka Joliot-curie 14a

department: Faculty of Biotechnology

country: Poland

institute: University of Wrocław

data_processing:
Unzipping the .gz file with gunzip function with Ubuntu Linux command line
seqencing adapter removal with Cutadapt software v.2.8 with parameters set cutadapt -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -g TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -G AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -A TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15 && cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -g GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -G TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15
Quality trimming was done with Sickle v.1.33 -pe script setting variable parameters as -t sanger -q 20 -l 20
Mapping reads to the reference genome with bowtie2 v.2.3.5.1 in pair end mode -1 -2
Sorting and indexing of the alignemnt files with Samtools v.1.10
Counting reads to features with HTSeq.count v.0.11.2 -t CDS -i Locus -m intersection-nonempty
Count matrix was build in excel by merging the HTSeq.count output files
Assembly: Assembly: NC_008596.1 (Mycolicibacterium smegmatis, MC2_v4.fasta) were used for mapping.
Supplementary files format and content: This file contains a tabular format with genes (MSMEG annotation) as rows and samples as columns. Each cell represents the number of reads mapped to a specific gene in a sample, providing a quantitative measurement of gene expression across all samples.

organism: Mycolicibacterium smegmatis

source_name: Bacterial culture

growth_protocol: 7H9 medium supplemented with 10% ADC and 0,05% Tween 80

extract_protocol:
RNA was isolated with the standard RNA isolation protocol, ribodepletion was performed using riboPools Pan-Bacteria (siTools Biotech GmbH), followed by sequencing library preparation using a KAPA-stranded RNA Seq kit (Roche Diagnostics).
Sequencing libraries were generated with a KAPA-stranded RNA Seq kit, according to the manufacturer's protocol.

value: Bacterial culture

value: napM deletion


title: napM-deleted biol rep 3


title: KO1

description: Library name: sample1


title: KO3

description: Library name: sample3