title: PARENT_HDAC4_nodox_biol rep 2

city: STANFORD

first: Joydeb

last: Sinha

address: 443 VIA ORTEGA

institute: Stanford University

data_processing:
library strategy: EMseq
Make genome file with synthetic reporter integration
For CUT&RUN: Align reads to genome with Bowtie 2 version 2.3.4.1 with command 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x {reference genome} -p 16 -1 {first mate of pair} -2 {second mate of pair} -S {output SAM file name}'
For CUT&RUN: Convert SAM files to BAM files and subsequently sort and index BAM files with Samtools version 1.7
For CUT&RUN: Quantify and mark duplicates with Picard version 11.0.7 with command 'java -jar {picard tool} MarkDuplicates -I {input sorted BAM file} -O {output deduplicated BAM file} -M {output metrics file} --REMOVE_DUPLICATES true'
For CUT&RUN: Normalize by reads per million with bamCoverage version 3.3.1 with command 'bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file}  --outFileFormat bedgraph --extendReads --centerReads -p 12 --binSize 10 --normalizeUsing CPM' for files unless stated otherwise. For H3K9me3 Scaling factors for normalization were calculated as the inverse of the percentage of uniquely aligned reads in each sample that mapped to the E. coli K12 MG1655 reference genome, as defined in the EpiCypher manual, and normalization used the following bamCoverage command: bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file} -- outFileFormat bedgraph --extendReads --centerReads --binSize 10 --scaleFactor {E. coli spike-in DNA scale factor}. For H3K36me3 Scaling factors for normalization were calculated using barcoded spike-in nucleosomes (EpiCypher 19-1002)  as the inverse of the percentage of reads in each sample containing DNA barcodes for the expected histone modification, and normalization used the following bamCoverage command: bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file} -- outFileFormat bedgraph --extendReads --centerReads --binSize 10 --scaleFactor {K-MetStat scale factor}.
For Emseq: BWAmeth was used for methylation-specific alignment to the reporter
For Emseq: samtools was used to convert raw alignment files to indexed .bam.
For Emseq: Bulk CpG methylation levels were calculated per site using MethylDackel (https://github.com/dpryan79/MethylDackel)
Assembly: hg19
Supplementary files format and content: bedgraph files

growth_protocol: DMEM-GlutaMAX media (10566024, Gibco) supplemented with 1x Penicillin-Streptomycin-Glutamine (10378016, Gibco) and 10 % FBS (FB-15, Omega Scientific)

extract_protocol:
For CUT&RUN: Cells were permeabilized by 0.025% digitonin followed by incubation with antibody and Mnase excision using CUTANA ChIC/CUT&RUN Kit (14-1048, EpiCypher)
For EMseq: Genomic DNA was extracted from roughly 500,000 HEK293T cells using the Monarch Genomic DNA Purification Kit (NEB T3010L) and fragmented by digestion with XbaI and AccI to excise and release the genomic DNA region corresponding to the AAVS1 reporter. The DNA was then size selected using 1x volume SPRI bead clean up (Beckman Coulter B23317). 200ng of cleaned DNA was used as an input for conversion using a Enzymatic Methyl-seq Kit (NEB E7120S) according to the manufacturer’s recommended protocol.
For CUT&RUN: Library was prepared using  CUTANA™ CUT&RUN Library Prep Kit with Primer Set 1 (14-1001, EpiCypher) or Primer Set 2 (14-1002, EpiCypher)  Library fragment sizes were checked with Agilent 2100 Bioanalyzer.
For EMseq: Briefly, APOBEC converted DNA was PCR amplified using 22x cycles with Q5U master mix (NEB M0597S) with primer pairs cTF378+cTF381 for the promoter and oSA021+oSA023 for the gene body. Amplified DNA was then size enriched using 0.9X volume SPRI beads and subject to another round of PCR using 10x cycles with NEBNext Ultra II (NEB M0544S) using primers pairs cTF383+cTF399 for the promoter and oSA021+oSA023 for the gene body to add Illumina Read1 and Read2 overhangs. DNA was cleaned up using 0.9X volume SPRI beads. The above PCR and clean up steps were repeated for a third PCR reaction with indexing primers to append Illumina indices for sequencing.

value: Human embryonic kidney


title: K36M_HDAC4_nodox_biol rep 1

status: Public on Aug 01 2024

type: SRA

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: cardiomyocyte,AAV_CTRL, replicate1-63, scRNAseq

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

description:
smartseq2
CTRL_AAV_1.xlsx

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: heart

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

value: cardiomyocyte

tag: tissue

value: heart

tag: strain

tag: age

value: 6-8 weeks old

tag: treatment


title: cardiomyocyte,AAV_CTRL, replicate1-62, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PARENT_HDAC4_nodox_biol rep 1


title: K36M_HDAC4_20DAYMEM_biol rep 2


title: K36M_HDAC4_20DAYMEM_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-61, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-70, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-60, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-59, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PGP1 +AM580 sorted CD38+

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

library_source: other

data_processing:
Barcode amplicon reads were processed using a custom pipeline available at: https://github.com/mpiersonsmela/barcode-matching
Assembly: n/a
Supplementary files format and content: barcode_counts_GEO.csv: barcode counts for each sample
Library strategy: Amplicon sequencing

molecule: other

growth_protocol: Plasmids for doxycycline-inducible expression of TFs were integrated into reporter hiPSCs. Pooled PiggyBac plasmid libraries (Figure 3A/B) were integrated into 1 million hiPSCs per replicate, using a Lonza nucleofector with 100 µL of P3 buffer. 250 fmol transposon pool and 2.5 µg transposase plasmid were used for each nucleofection. Puromycin selection was performed between days 2-7 post-nucleofection. Subsequently, DDX4+ iOLCs were induced using the protocol described above. In follow-up rounds of screening, cells were treated with 5 µM GSK-3484862, and some replicates were additionally treated with the retinoic acid receptor agonist AM580 (1 µM).

extract_protocol:
DNA was extracted from sorted DDX4+ cells using the Qiagen DNEasy Micro kit, and from unsorted and pre-induction cells using the Qiagen DNEasy kit.
Barcode amplification and sequencing was performed as previously described (Smela et al., eLife 2023). For fold-change calculations, barcode abundances in the DDX4+ cells were separately compared to unsorted cells and to pre-induction cells.

value: Sorted CD38+ cells

tag: genotype

value: iOLC induction, + 1 µM AM580


title: PARENT_HDAC4_20DAYMEM_biol rep 2


title: cardiomyocyte,AAV_CTRL, replicate1-58, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PARENT_HDAC4_20DAYMEM_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-57, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PARENT_KRAB_6DAY_DMSO_biol rep 2


title: cardiomyocyte,AAV_CTRL, replicate1-56, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PARENT_KRAB_6DAY_SETD2IN1_biol rep 2


title: K36M_HDAC4_nodox_biol rep 2


title: PARENT_KRAB_6DAY_DMSO_biol rep 1


title: PARENT_KRAB_6DAY_SETD2IN1_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-65, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PARENT_KRAB_6DAY_siNSD1_biol rep 2


title: PARENT_KRAB_6DAY_siNSD1_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-51, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PARENT_KRAB_6DAY_siControl_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-50, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PARENT_KRAB_6DAY_siControl_biol rep 2


title: PARENT_KRAB_18DAY_biol rep 2


title: cardiomyocyte,AAV_CTRL, replicate1-49, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-53, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-48, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-46, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-47, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-55, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-54, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PARENT_KRAB_No Dox _biol rep 1


title: HEK293T_K36M_KRAB_GENEBODY_6_14_DOX_biol rep 1


title: HEK293T_PARENT_KRAB_GENEBODY_6_14_DOX_biol rep 2


title: HEK293T_K36M_KRAB_GENEBODY_6_14_DOX_biol rep 2


title: cardiomyocyte,AAV_CTRL, replicate1-45, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-78, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-44, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PARENT_KRAB_No Dox _biol rep 2


title: cardiomyocyte,AAV_CTRL, replicate1-42, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-41, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_PARENT_KRAB_GENEBODY_6_14_DOX_biol rep 1


title: HEK293T_K36M_KRAB_GENEBODY_ND_DOX_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-43, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_K36M_KRAB_GENEBODY_ND_DOX_biol rep 2


title: cardiomyocyte,AAV_CTRL, replicate1-52, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-40, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_PARENT_KRAB_GENEBODY_ND_DOX_biol rep 2


title: HEK293T_K36M_KRAB_GENEBODY_6_0_DOX_biol rep 2


title: cardiomyocyte,AAV_CTRL, replicate1-39, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_K36M_KRAB_GENEBODY_6_0_DOX_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-38, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_PARENT_KRAB_GENEBODY_ND_biol rep 1


title: PARENT_KRAB_18DAY_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-37, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-35, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-36, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_K36M_KRAB_PROMOTER_6_14_DOX_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-31, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_K36M_KRAB_PROMOTER_6_14_DOX_biol rep 2


title: HEK293T_K36M_KRAB_PROMOTER_ND_DOX_biol rep 2


title: cardiomyocyte,AAV_CTRL, replicate1-34, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-29, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_PARENT_KRAB_PROMOTER_6_14_DOX_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-32, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-30, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_PARENT_KRAB_GENEBODY_6_0_DOX_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-33, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_PARENT_KRAB_PROMOTER_ND_DOX_biol rep 2


title: HEK293T_PARENT_KRAB_PROMOTER_6_14_DOX_biol rep 2


title: cardiomyocyte,AAV_CTRL, replicate1-27, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-28, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_PARENT_KRAB_PROMOTER_ND_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-26, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_K36M_KRAB_PROMOTER_6_0_DOX_biol rep 2


title: HEK293T_K36M_KRAB_PROMOTER_6_0_DOX_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-23, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-24, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-25, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_PARENT_KRAB_PROMOTER_6_0_DOX_biol rep 2


title: HEK293T_PARENT_KRAB_GENEBODY_6_0_DOX_biol rep 2


title: HEK293T_PARENT_KRAB_PROMOTER_6_0_DOX_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-21, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-22, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-20, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HEK293T_K36M_KRAB_PROMOTER_ND_DOX_biol rep 1


title: cardiomyocyte,AAV_CTRL, replicate1-19, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-18, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-17, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-14, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-16, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-13, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HCT116 with distal enhancer deletion biological replicate1

city: Memphis

first: Chunliang

last: Li

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
RNA-Seq reads from each species were aligned using Bowtie2  2.3.4
FPKM value were obtained using cufflinks v2.2.1
Genome_build: hg19

source_name: colon

growth_protocol: HCT116 cells (ATCC, CCL-247) were maintained with DMEM (Lonza) supplemented with 10% FBS (Hyclone). SEM cells (DSMZ, ACC-546) were grown in RPMI 1640 with L-glutamine (Thermo Fisher Scientific). All cells were maintained at 37 °C in a 5% CO2 atmosphere and 95% humidity.

extract_protocol:
Total RNA was extracted by Trizol (Invitrogen)
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Cat. No. RS-122-2301) was used for library construction.

treatment_protocol: Distal Enhancer was deleted by CRISPR/Cas9.

value: colon cancer cell

value: colon

tag: genotype/variation

value: distal enhancer deletion


title: wild type HCT116 biological replicate2

value: wild type


title: HCT116 with distal enhancer deletion biological replicate2


title: wild type HCT116 biological replicate1


title: IMR90_CDKN2B.IMR90.Combined_reads_Redig_CC3_CDKN2B

data_processing:
Library strategy: Capture-C
The paired-end reads were reconstructed into single reads with FLASH1.2.11
Digested in silico with the DpnII2E.pl script
aligned to the human genome using Bowtie 1.0.0 (http://bowtie-bio.sourceforge.net/index.shtml).
Interaction frequencies were determined using CCanalyser2.pl (https://github.com/telenius/captureC/releases).
Genome_build: hg19, mm9
Supplementary_files_format_and_content: bigwig

source_name: fibroblast

growth_protocol: Wildtype MEFs were prepared from mouse embryos of C57Bl/6 strain at 13.5 days post coitum (dpc) as described previously [2]. Primary MEFs were maintained in DMEM (Lonza) supplemented with 10% FBS (Hyclone), 2mM glutamine (Invitrogen), 0.1mM non-essential amino acids (Invitrogen), and 55 uM b-mercaptoethanol (Invitrogen). HCT1116 cells (ATCC, CCL-247) IMR90 cells (ATCC, CCL-186) were maintained with DMEM (Lonza) supplemented with 10% FBS (Hyclone). SEM cells (DSMZ, ACC-546) were grown in RPMI 1640 with L-glutamine (Fisher Scientific). All cells were maintained at 37 °C in a 5% CO2 atmosphere and 95% humidity.

extract_protocol:
Suspension cells (SEM) cells were collected at 1X10^7 cells per reaction while adherent cells (IMR90, HCT116 and human iPS) were trypsinized before collection. Cells were fixed and lysed in 15 mL conical tubes before storage in -80°C for up to 1 month before library construction. Cells were thawed on ice and spun down for 5 minutes at 4000rpm, 4°C. The remaining lysis buffer was removed and discarded. The pellets were re-suspended in 1 mL of 1x DpnII buffer and transferred to a 2 mL tube for homogenization with a pestle. The homogenized samples were then centrifuged for 14,000 rpm at 5 mins in 4°C. The supernatant was removed and discarded. After decrosslinking, phenol-chloroform-isoamylalcohol DNA extraction, and sodium acetate precipitation, a small portion of DNA was run on a gel to check for digest and ligation efficiency. Once the 3C library was construction was complete, 5-6ug of the 3C DNA in a total volume of 130ug per covaris tube (microTUBE AFA Fiber Crimp-Cap 6X16mm, catalog). Each 2ug of 3C library generated one Capture.NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles.The Nimblegen SeqCap EZ Hybridization and Wash Buffer Kit (Roche) was used for subsequent hybridization and wash steps. Constructed library was sequenced on Miseq for paired-end 150bp.
NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles. Agencourt AMPure XP beads were used at 0.8x for all cleanup steps.

value: Human Caucasian foetal lung fibroblast

tag: subline

value: fibroblast

value: CDKN2b promoter probe


title: IMR90_ARF_P14.IMR90.Combined_reads_Redig_CC3_ARF

value: ARF promoter probe


title: ips_HumanMale-IPS-CDKN2B_S2.bait_CDKN2B

description: BJ-iPS

value: human-induced pluripotent stem cells


title: IMR90_CDKN2A.IMR90.Combined_reads_Redig_CC3_CDKN2A

value: CDKN2a promoter probe


title: IMR90_CTCF

value: CTCF probe


title: ips_HumanMale-IPS-hCTCF_S4.bait_HCTCF

description: BJ-iPS


title: cardiomyocyte,AAV_CTRL, replicate1-12, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: ips_HumanMale-IPS-CDKN2A_S3.bait_CDKN2A

description: BJ-iPS


title: cardiomyocyte,AAV_CTRL, replicate1-11, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: ips_HumanMale-IPS-ARF_S1.bait_ARF

description: BJ-iPS


title: SMW11_47KO_p14Rep_Combined_reads_Redig_CC3_ARF_Probes


title: SMW10_47KO_CTCF_Combined_reads_Redig_CC3_hCTCF


title: cardiomyocyte,AAV_CTRL, replicate1-7, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: HCT116_distal_enhancer_probe

value: Distal enhancer probe


title: HCT116_ARF_probe_SMW9_WT_ARF_probe


title: cardiomyocyte,AAV_CTRL, replicate1-8, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx

value: cardiomyocyte


title: cardiomyocyte,AAV_CTRL, replicate1-6, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx

value: heart


title: cardiomyocyte,AAV_CTRL, replicate1-15, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx

value: 6-8 weeks old


title: 6_dset1-2

city: Chuncheon-si

first: Shinae

last: Park

address: Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

description: MAT alpah his3d1 leu2d0 ura3d0 lysd0 set1Δ::HIS3

data_processing:
The Illumina Hiseq generates raw images utilizing HCS(HiSeq Control Software v2.2) for system control
Base calling through an integrated primary analysis software called RTA(Real Time Analysis. v1.18)
The BCL(base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq(v1.8.4)
Adapters are not trimmed away from the reads.
bedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cells are cultured at 10ml YPD(1% Yeast extract, 2% Peptone, 2% Glucose) in 100ml flask (30℃, 230rpm) and harvested at OD600=1.0

extract_protocol:
RNA was harvested according to the MN RNA-isolation kit(MN;#7409555.50) standard protocols. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina(NEB #E7420S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Yeast cells

value: MAT alpah his3d1 leu2d0 ura3d0 lysd0 set1delta::HIS3


title: cardiomyocyte,AAV_CTRL, replicate1-5, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: 5_dset1-1


title: cardiomyocyte,AAV_CTRL, replicate1-4, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: 4_dleo1-2

description: MATa his3∆0 leu2∆0 met15∆0 ura3∆0 leo1Δ::KanMX

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 leo1delta::KanMX


title: 3_dleo1-1


title: cardiomyocyte,AAV_CTRL, replicate1-2, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-1, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: 1_BY4741-1

description: MATa his3∆0 leu2∆0 met15∆0 ura3∆0

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0


title: 5_dset1-1-H3K4me3

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
For normalization, S. pombespike-in reads in each sample was calculated.
We assumed that the amount of spike-in added to each sample is same, and the normalization ratio was calculated as "1000000/spike-in reads" for each sample.
The normalized bedGraph was produced by using 'bamCoverage --scaleFactor' and calculated normalization ratio.
bedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: fastq, bigwig

source_name: cells

growth_protocol: Cells were prepared from exponentially growing at OD600 = 1.0. Harvested cells were resuspended with 4ml of 1XTBS and evenly divided into 4 eppendorf tubes. Cell is harvested by centrifuge 3000 rpm 5min and supernatant was removed. After one more wash step, samples were stored at -80℃.

extract_protocol:
Cells were resuspended with lysis buffer and homogenized with glass beads at cold room. Lysed cells were sonicated and centrifuged to obtain soluble chromatin fraction. S. cerevisiae chromatin lysates, containing 5% of Schizosaccharomyces pombe chromatin extract for control of sample-to-sample normalization, were incubated with antibody and antibody-protein-chromatin complex was captured by Protein A/G agarose. After sequential washing steps and reverse crosslinking, remaining DNA is purified by phenol-chloroform extraction and washing.
ChIP-Seq DNA samples were quantified by Quant-iT PicoGreen dsDNA Assay kit and their quality were assessed Bioanalyzer 2100. ChIP-Seq library was constructed with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: Before wash the cells with 1XTBS, cells were treated with 1% formaldehyde for 5mins and quenched with 2.5M Glycine for 20mins

value: cells

tag: chip antibody


title: cardiomyocyte,TAC2w, replicate2, scRNAseq

description:
10x Genomics
TAC2w_2_barcodes.tsv
TAC2w_2_matrix.mtx

value: non cardiomyocyte


title: cardiomyocyte,AAV_CTRL, replicate1-10, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: 3_dleo1-1-H3K4me3


title: cardiomyocyte,TAC2w+CDK-i, replicate2, scRNAseq

description:
10x Genomics
TAC2w_CDK_2_barcodes.tsv
TAC2w_CDK_2_matrix.mtx


title: cardiomyocyte,AAV_CTRL, replicate1-9, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: non cardiomyocyte,sham, replicate2, scRNAseq

description:
10x Genomics
Sham_2_barcodes.tsv
Sham_2_matrix.mtx

value: sham


title: cardiomyocyte,TAC2w+CDK-i, replicate1, scRNAseq

description:
10x Genomics
TAC2w_CDK_1_barcodes.tsv
TAC2w_CDK_1_matrix.mtx


title: 4_dleo1-2-H3K4me3


title: cardiomyocyte,TAC2w, replicate1, scRNAseq

description:
10x Genomics
TAC2w_1_barcodes.tsv
TAC2w_1_matrix.mtx


title: non cardiomyocyte,sham, replicate1, scRNAseq

description:
10x Genomics
Sham_1_barcodes.tsv
Sham_1_matrix.mtx


title: 1_BY4741-1-H3K4me3


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-91, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: BrdU_ChIP_mrc1dHBS

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

data_processing:
reads were mapped to the genome with bowtie2 (v2.5.0)
duplicate reads were removed with rmDup from samtools (version 2.0.1)
For ChIP-seq, Bam files were converted to bigwig and input normalized using deeptools bamCompare (--normalizeUsing CPM --centerReads --maxFragmentLength 1000 --scaleFactorsMethod None --pseudocount 1). Replicates were merged using wiggletools and converted to bigwig using UCSC BedGraphToBigWig. For BrdU-seq, bedgraphs were generated using MACS2 (version 2.2.7.1) and converted to bigwig using USCS BedGraphToBigWig.
bigWig files normalized to Input and counts per million. Text files containing the genome assembly of h90 fission yeast and gff3 file for gene annotations.
Assembly: S.pombe h90
Supplementary files format and content: bigwig files, genome.fa file for reference genome, gff3 for genome annotations.
Library strategy: BrdU-seq

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

growth_protocol: S. pombe cell cultures were grown exponentially in YES media at 30°C, shifted to 20°C for 5h, shifted to 30°C for 60min with addition of 200ug/mL BrdU and 25mM HU(BrdU-seq) or 30 min with addition of 500uM EdU (ChIP-seq). For more details see Methods section in Charlton et al. (2023).

extract_protocol:
See Charlton et al, 2023 for details. For BrdU-seq, gDNA was extracted, sonicated, and incubated with anti-BrdU antibody (2B1, MBL, Cat# MI-11-3). Bound BrdU-labelled DNA was washed and purified. For ChIP-seq, cells were fixed for 15min in 1% formaldehyde, lysed using bead-beating, sonicated, and incubated with anti-H3K9me2 antibody (MABI0307). Bound H3K9me2 chromatin was washed, extracted, and decrosslinked overnight. Then, decrosslinked DNA was incubated with Protease K and RNase A before clean up with Ampure XP beads.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit (BrdU-Seq) or the KAPA Roche Library Prep Kit (H3K9me2-ChIP).

treatment_protocol: See growth protocol

value: yeast cell

value: h90 nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mrc1{delta}(782-879) leu1-32

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add BrdU (200 ug/ml) and HU (25 mM)

tag: antibody


title: BrdU_Input_mrc1dHBS


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-90, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: BrdU_ChIP_WT

value: h90 nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 leu1-32

value: anti-BrdU antibody (2B1, MBL, Cat# MI-11-3)


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-89, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-88, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-3, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: Input

city: RTP

first: Wendy

last: Jefferson

state: NC

address: 105 T. W. Alexander Drive

institute: NIEHS

data_processing:
The raw ChIP-Seq reads were initially processed by filtering with average quality scores greater than 20.
Then the reads were aligned to the mouse reference genome (mm10; Genome Reference Consortium Mouse Build 38 from December 2011) using Bowtie version 1.1.2 with unique mapping and up to 2 mismatches for each read (-m 1 -v 2)
The duplicated reads with the same sequence were discarded
Assembly: mm10
Supplementary files format and content: biWig files were generated from normalized bedgraph files using bedGraphToBigWig

source_name: mouse uterus

growth_protocol: Adult mouse uterine tissues were colleclted from control diestrus, control estrus or DES treatment groups.

extract_protocol:
Frozen pooled uterine samples were sent to ACTIVE MOTIF for all ChIP-seq experiments.
Library construction for all ChIP-seq was performed at Active Motif.

treatment_protocol: Hif2a uterine conditional knock out mice were generated by crossing Hif2a (Epas2) floxed mice with PgR-cre mice.

value: mouse uterus

value: Input


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-87, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

value: cardiomyocyte


title: 2_BY4741-2

description: MATa his3∆0 leu2∆0 met15∆0 ura3∆0


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-86, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

value: heart


title: 2_BY4741-2-H3K4me3


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-85, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

value: 6-8 weeks old


title: Adult CoD PgR ChIP-seq

source_name: Adult Co diestrus PgR, uterus

value: 2 months

tag: Stage

value: diestrus

value: PgR, Active Motif; cat#61023


title: Adult CoE PgR ChIP-seq

source_name: Adult Co estrus PgR, uterus

value: estrus


title: Adult CoE ERalpha ChIP-seq

source_name: Adult Co estrus ERalpha, uterus

value: ERalpha, Santa Cruz; cat# sc-543


title: Adult CoD Hif2a ChIP-seq

source_name: Adult Co diestrus Hif2a, uterus

value: Hif2a, Active Motif, cat# 39665


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-80, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-83, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-84, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-81, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: Adult CoE Hif2a ChIP-seq

source_name: Adult Co estrus Hif2a, uterus


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-82, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: Adult CoD ERalpha ChIP-seq

source_name: Adult Co diestrus ERalpha, uterus


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-78, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: Adult CoE ATAC-seq

data_processing:
The raw reads were trimmed by trim_galore (v0.4.4) (quality score < 20).
Then the reads were aligned to the mouse reference genome (mm10; Genome Reference Consortium Mouse Build 38 from December 2011) using Bowtie version 1.1.2 with unique mapping and up to 2 mismatches for each read (-m 1 -v 2)
After removing the mitochondria and duplicated reads, only 9bp at the terminal of the fragment was saved for following analysis.
Assembly: mm10
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig.

source_name: Adult control estrus, uterus

growth_protocol: Adult mouse uterine tissues were collected from control diestrus, control estrus.

extract_protocol:
DNA was isolated using Qiagen Blood and Tissue DNA isolation kit
ATAC libraries were generated using the Nextera DNA Library Prep Kit

treatment_protocol: Mice were unexposed control CD-1 mice


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-77, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-79, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-76, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: P56 Extracellular vesicles secreted by inguinal adipocytes of mice.3 [miRNA-Seq]

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

country: Germany

institute: University of Ulm

description: ATMs isolated from the inguinal adipose tissue

data_processing:
Firstly,we remove the reads mapped to rRNA and get raw data.
Then the sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads, should be processed to be removed before downstream analyses.
reads mapped to reference genome were compared with specific sequences in the miRBase to obtain detail information of mapped reads, including the secondary structure of the mapped miRNAs, the sequence of miRNAs in each sample, length, the number of occurrences and other information. Mature miRNA is developed from precursor through Dicer enzyme digestion. Specificity of enzyme digestion sites makes the first base of the mature miRNA sequence highly biased, so we have also analyzed first base distribution analysis of miRNAs with different lengths , as well as distribution of other bases.
Small RNA reads are annotated with sequences from the non-coding transcript sequences of the species with reference. For those species without reference, small RNA reads are annotated with sequences from Rfam. The matched reads from rRNA, tRNA, snRNA, and snoRNA are removed. Lastly we calculate gene expression level for each sample with  RSEM.
The expression of known and unique miRNAs in each sample are statistically analyzed and normalized by TPM. The normalized expression = (read count*1,000,000)/libsize. Libsize is the sample miRNA read count.
processed data files format and content: Excel showing DEGs.
log2 (P6 / P56)
Transcripts Ids, Gene names, Read ounts

source_name: extracellular vesicles

growth_protocol: Primary adipocytes were cultured in L-15 media. To avoid contamination with bovine EVs, we used EV-depleted fetal calf serum throughout the study (Gibco). EVs were precipitated with the EPStep exosome precipitation solution (Immunostep, Centro de Investigación del Cáncer, Campus Miguel de Unamuno, Salamanca, Spain) and concentrated by centrifugation. EVs were analyzed with FACS using capture beads and labeling for CD63 (Immunostep). EV pellets were used to extract RNA. Fractions of EV pellets were also fixed in paraformaldehyde/glutaraldehyde, and processed for transmission electron microscopy analysis.

extract_protocol: TRIZOL extraction from tissue

tag: developmental stage

value: postnatal day 56 (P56)

tag: Sex

value: male


title: Adult CoD ATAC-seq

source_name: Adult control diestrus, uterus


title: P56 Extracellular vesicles secreted by inguinal adipocytes of mice.2 [miRNA-Seq]


title: Adult CoE HiC-seq

data_processing:
Those raw reads were mapped to mouse reference genome (mm10), truncated, deduplicated using HiCUP version 0.7.1.
The uniquely mapped di-tag passing quality filtering with distance larger than 10Kb were used for downstream analyses.
The BAM file was converted to .hic file using juicer tools.
Assembly: mm10
Supplementary files format and content: Chromatin loops were identified by Juicer using hiccups function.

growth_protocol: Adult mouse uterine tissues were colleclted from control diestrus, control estrus.

extract_protocol:
DNA was isolated using Qiagen Blood and Tissue DNA isolation kit
Libraries were constructed using Arima HiC kit


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-75, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: P56 Extracellular vesicles secreted by inguinal adipocytes of mice.1 [miRNA-Seq]


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-73, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-74, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: P6 Extracellular vesicles secreted by inguinal adipocytes of mice.3 [miRNA-Seq]

value: postnatal day 6 (P6)


title: Adult CoD HiC-seq


title: P6 Extracellular vesicles secreted by inguinal adipocytes of mice.2 [miRNA-Seq]


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-72, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-71, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: P6 Extracellular vesicles secreted by inguinal adipocytes of mice.1 [miRNA-Seq]


title: P56 Extracellular vesicles secreted by inguinal adipocytes of mice.2

data_processing:
Firstly,we remove the reads mapped to rRNA and get raw data.
Then the sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads, should be processed to be removed before downstream analyses.
We map clean reads to reference transcripts using Bowtie2.
Lastly we calculate gene expression level for each sample with  RSEM.
Genome_build: Based on the gene expression level, we can identify  DEGs (Differentially expression genes) between P6 and P56 samples. We used DEseq2 algorithms to detect the DEGs.
Supplementary_files_format_and_content: Excel showing DEGs.
Supplementary_files_format_and_content: log2 (P6 / P56)
Supplementary_files_format_and_content: Transcripts Ids, Gene names, Read ounts
Supplementary_files_format_and_content: P6 is an infant animal, P56 is an adult animal


title: P6 Extracellular vesicles secreted by inguinal adipocytes of mice.2


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-69, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-67, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-66, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: P6 Extracellular vesicles secreted by inguinal adipocytes of mice.1


title: BrdU_Input_WT

value: yeast cell

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add BrdU (200 ug/ml) and HU (25 mM)


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-65, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-70, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: P56 Extracellular vesicles secreted by inguinal adipocytes of mice.1


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-64, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: 2a_CKO_D19

city: Los Angeles

first: Kindra

middle: M

last: Kelly-Scumpia

address: 615 Charles E Young Dr Rm 246

institute: UCLA

data_processing:
RNA-seq libraries were sequenced, single end 50bp on an Illumina HiSeq 3000.
RNA-seq fastq files were mapped using Hisat2. Only the uniquely mapped reads were kept for further analysis.
Uniquely aligned reads were used to quantify against exon in seqmonk to generated read counts matrix
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each file

source_name: skin

extract_protocol:
RNA was harvested using RNAeasy kit (Qiagen)
RNA libraries for RNA-seq were prepared using Illumina's  TruSeq stranded RNA Sample Preparation Kit

treatment_protocol: Mouse skin was wounded and harvested 14 and 19 days later

value: skin

value: Col5a1 CKO

value: wounded+WT fibroblasts

tag: time

value: Day 19


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-63, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

source_name: heart

value: cardiomyocyte

value: heart


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-62, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

value: 6-8 weeks old


title: 2c_CKO_D19


title: 2c_WT_D19

value: WT

value: wounded


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-61, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: 2b_WT_D19


title: CKO_c_fibro_D14

value: Day 14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-60, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-59, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: 2a_WT_D19


title: P56 Extracellular vesicles secreted by inguinal adipocytes of mice.3


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-58, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: CKO_b_fibro_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-57, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-68, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: CKO_a_fibro_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-56, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: P6 Extracellular vesicles secreted by inguinal adipocytes of mice.3


title: 2b_CKO_D19


title: CKO_g_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-55, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: CKO_f_D14


title: CKO_d_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-52, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: CKO_e_D14


title: CKO_c_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-51, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-54, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-53, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: CKO_b_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-49, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-48, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: CKO_a_D14


title: WT_g_D14


title: WT_f_D14


title: WT_e_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-47, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-46, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-45, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: WT_d_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-44, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: WT_b_D14


title: WT_c_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-43, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: WT_a_D14


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-42, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: C4-2, PARP1 WT, replicate2

city: CHICAGO

first: Qingshu

last: Meng

state: Illinois

address: 303 E. Superior Street

institute: Northwestern University

data_processing:
The RNA-seq reads were mapped to the human genome GRCh38 and assigned to the reference genes using HISAT2 version 2.1.0
Read counts for each gene were calculated by featureCounts v1.6.1
Differential gene expression analysis was performed between the two groups of cells by R packages edgeR and limma
Assembly: hg38
Supplementary files format and content: featureCounts output file (raw counts of reads)

extract_protocol:
RNA was extracted from C4-2 cells using RNeasy Plus Kit (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using BGI Stranded Total RNA Prep Kit following manufacturer's protocols.

value: epithelial cell

value: endogenous PARP1 knockdown and stably expressing PAPR1  -WT


title: C4-2, PARP1 WT, replicate3


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-41, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-40, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: C4-2, PARP1 K607A, replicate3

value: endogenous PARP1 knockdown and stably expressing PAPR1  -K607A


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-38, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: C4-2, PARP1 K607A, replicate2


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-39, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: C4-2, PARP1 WT, replicate1


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-50, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-35, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-37, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: C4-2, PARP1 K607A, replicate1


title: In-vitro treated PBMCs

city: Shanghai

first: Huaxin

last: Song

address: Shanghai Jiao Tong University School of Medicine

country: China

data_processing:
The CellRanger (10x Genomics, default settings, Version 6.0.0) pipelines were used to process Chromium single-cell data to align reads, generate feature-barcode matrices.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: Peripheral blood

growth_protocol: In-vitro treated PBMCs were cultured at 37 ℃ in RPMI 1640 Medium, supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
Cellular suspensions were copartitioned with barcoded gel beads to generate single-cell gel bead-in-emulsion (GEM) and poly-adenylated transcripts were reverse-transcribed using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1
RNA libraries were prepared with Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the standard manufacturer’s protocol (PN-1000121, 10x Genomics)

treatment_protocol: In-vitro treated PBMCs were treated with  0.2 μg/mL ATO for 24 h in dish.

tag: disease state

value: AML

value: PBMC

value: Treatment with 0.2 ug/mL ATO for 24 h in vitro


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-36, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-34, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-33, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: In-patient treated PBMCs

institute: Shanghai Jiao Tong University School of Medicine

value: Treatment with 10 mg/kg ATO for 12 days in patient


title: Untreated PBMCs

value: untreated


title: HS_C10

city: Aurora

first: Christophe

last: Langouët-Astrié

state: CO

department: Pulmonary Sciences and Critical Care

institute: University of Colorado Denver, Anschutz

data_processing:
CLC Genomics Workbench (v.21.0.5)
Illumina reads were trimmed for adaptor sequence and for quality
Trimmed sequences were mapped to to the reference genome sequence of USA400 assembly NC_007795.1, with the parameters: mismatch cost, 2; insertion and deletion cost, 3; length and similarity fraction, 0.8.
Uniquely mapped transcripts from each sample were exported from CLC Genomics Workbench and used for normalization and differential gene expression analysis with an R package, DESeq2 version 1.34.0
Assembly: NC_007795.1
Supplementary files format and content: tab-delimited text files include uniquely mapped transcript values for each sample and time point

organism: Staphylococcus aureus subsp. aureus NCTC 8325

source_name: NCTC 8325

growth_protocol: USA400 was grown in TSB for 18-24 hours at 37°C with 200 rpm of shaking. Bacterial suspensions were diluted to a final dilution of 1:1000 and were cultured for 3 or 10hrs at 37°C with 1000 rpm of shaking

extract_protocol:
RNA isolated using RNeasy Mini Kit (Qiagen) following manufacturer’s recommendations followed by DNase treatment using the TURBO DNA-free Kit (Invitrogen)
RNA samples were rRNA depleted using the Ribo-Zero Plus rRNA Removal kit (Illumina) and libraries were prepared using the Illumina Stranded Total RNA Prep

treatment_protocol: USA400 was grown in the presence or absence of unfractionated heparin (2 ug/mL)

value: NCTC 8325

value: Heparin


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-32, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: HS_B10


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-31, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: Ctrl_C10

value: Saline


title: HS_A10


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-30, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

value: cardiomyocyte


title: Ctrl_B10


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-28, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

value: heart


title: Ctrl_A10


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-27, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

value: 6-8 weeks old


title: HS_C3


title: HS_B3


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-25, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-23, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-24, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: HS_A3


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-26, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: Ctrl_C3


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-22, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: Ctrl_A3


title: Ctrl_B3


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-19, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-20, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: ATACseq_sticklebackPrimarySpermatocytesGenomicControl_FreshwaterPool1

city: Tuebingen

first: Felicity

middle: C

last: Jones

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory of the Max Planck Society

description:
nakedDNAcontrol
ATACseq_sticklebackPrimarySpermatocytesGenomicControl_MarineAndFreswaterPoolsMerged.processedData.bdg

data_processing:
Reads were mapped to the reference genome BROAD/GasAcu1, mitochondrial reads and PCR duplicates removed, and the files downsampled to 20M read pairs using samtools.
Macs2 was used to call peaks by contrasting the pooled ATACseq libraries made from chromatin relative to pooled naked genomic DNA (parameters --shift -100 --extsize 200 --tsize 150) generating normalized signal and control bedgraph files, and narrowPeak files (except for naked genomic input).
Assembly: Broad/gasAcu1
Supplementary files format and content: bedGraph (MACS2 normalized files for chromatin "treatment" and naked genomic DNA "control" files), narrowPeak (except for naked genomic DNA controls)

organism: Gasterosteus aculeatus

source_name: primary spermatocytes

growth_protocol: Wild-derived strains of marine and freshwater sticklebacks from the River Tyne, East Lothian, Scotland under a seasonally varying day length (3 months of 16 hours light, 8 hours dark, followed by 3 months of winter 8 hours dark, 16 hours light).  Testes were collected for ATACseq from adult males during the last three weeks of the 3-month winter light regime, and processed immediately after dissection.

extract_protocol:
For each ATAC-seq replicate (Buenrostro et al (2015) 109:2191-99), the testes of three males were pooled and dissociated with 0.07U/ml Liberase (Sigma). The isolation of 50000 primary spermatocytes per lysate was carried out by flow cytometry using a BD FACSMelody Cell Sorter (BD Biosciences) based on FSC-A and SSC-A (separating 4C primary spermatocytes, 2C secondary spermatocytes, 1C spermatids/sperm by size and complexity). Cell membranes were lysed with cold 10mM Tris pH8; 10mM NaCl; 3mM MgCl2; 0.1% NP-40 and nuclei were isolated by centrifugation.
Tn5 was applied onto the nuclei in standard TAPS-DMF buffer for 30min +37’C with shaking (1000rpm), the tagged DNA was cleaned with the Min Elute kit (Qiagen) and processed to a sequencing library. A control library of naked genomic DNA was also made from each testes pool.  The libraries were paried-end sequenced on an Illumina platform.

value: primary spermatocytes

value: wild-derived freshwater strain


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-21, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: ATACseq_sticklebackPrimarySpermatocytesGenomicControl_FreshwaterPool3


title: ATACseq_sticklebackPrimarySpermatocytesGenomicControl_FreshwaterPool2


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-29, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: ATACseq_sticklebackPrimarySpermatocytesGenomicControl_MarinePool3

value: wild-derived marine strain


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-17, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: ATACseq_sticklebackPrimarySpermatocytesATAC_FreshwaterPool3

description:
ATACseq
ATACseq_sticklebackPrimarySpermatocytesATAC_MarineAndFreshwaterPoolsMerged.processedData.bdg
ATACseq_sticklebackPrimarySpermatocytesATAC_MarineAndFreshwaterPoolsMerged.processedData.narrowPeak


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-15, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-18, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-16, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-14, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: ATACseq_sticklebackPrimarySpermatocytesATAC_FreshwaterPool1


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-13, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-12, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: ATACseq_sticklebackPrimarySpermatocytesATAC_MarinePool2


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-10, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: ATACseq_sticklebackPrimarySpermatocytesATAC_MarinePool3


title: ATACseq_sticklebackPrimarySpermatocytesATAC_FreshwaterPool2


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-9, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-8, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-7, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-6, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: P0D-2, miRNA

city: Guangzhou

first: Chen

last: Yaqing

state: Guangdong

address: South China Normal University

department: School of Life Sciences

institute: South China Normal University

description: The testes were dissected from 0-day-old pupae

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N); 2) Removing reads without 3’adapters; 3) Removing reads containing 5' adapters; 4) Removing reads containing 3' and 5' adapters but no small RNA fragment between them; 5) Removing reads containing ployA in small RNA fragment; 6) Removing reads shorter than 18 nt (not include adapters).
For miRNA-seq clean data, all of the clean tags were aligned with small RNAs in both GeneBank database (Release 209.0) and Rfam database (Release 11.0) to identify and remove rRNA, scRNA, snoRNA, snRNA and tRNA.
For miRNA-seq clean data, all of the clean tags were also aligned with reference genome. Those mapped to exons or introns might be fragments from mRNA degradation, so these tags were removed. The tags mapped to repeat sequences were also removed.
For miRNA-seq clean data, all of the clean tags were then searched against miRBase database (Release 22) to identify known miRNAs. The unannotated tags were aligned with reference genome, according to their genome positions and hairpin structures predicted by software mirdeep2 (Friedländer et al., 2012), the novel miRNA candidates were identified.
For miRNA expression analysis,the miRNA expression level was calculated and normalized to transcripts per million (TPM).The formula is as follows: TPM=Actual miRNA counts/Total counts of clean tags*106
MiRNAs differential expression (DE) analysis was performed by edgeR software between two different groups or samples.We identified miRNAs with a fold change ≥2 and P value <0.05 in a comparison as significant DE miRNAs.
For miRNA target prediction, two softwares Miranda (Version 3.3a) and TargetScan (Version 7.0) were used to predict targets. The intersection of the results were more credible to be chosen as predicted miRNA target genes. The default parameters of software Miranda were as follows:  1) The set score threshold is 140; 2) The set energy threshold is -10 kcal/mol; 3) Demand strict 5’ seed pairing; 4) The gap-open penalty is -4.0; 5) The gap-extend penalty is -9.0. The default parameters of software TargetScan were as follows: The 2-8 nt sequences which start from 5’small RNA were choose as seed sequences to predict with 3’-UTR of transcripts.
Assembly: Spodoptera litura genome sequence (assembly ASM270686v1).
Supplementary files format and content: Tab-delimited text file (.txt) includes raw read counts for the miRNA-seq data of all samples. In addition, the sequences for the counted genes of the miRNA-seq data are provided by a FASTA file (.fa).

organism: Spodoptera litura

source_name: Testis

growth_protocol: The S. litura larvae were reared on artificial diet with soybean powder, wheat powder, yeast powder under the condition of 27 ± 1 ◦C with 70 ± 5% relative humidity, and the light:dark = 16 h:8 h photoperiod after egg hatching as the described previously (Luo et al., 2006).

extract_protocol:
Total RNA from the testes of S. litura was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
The RNA molecules in a size range of 18-30 nt were enriched by polyacrylamide gel electrophoresis (PAGE). Then the 3’adapters were added and the 36-44 nt RNAs were enriched. The 5’adapters were then ligated to the RNAs as well. The ligation products were reverse transcribed by PCR amplification and the 140-160 bp size PCR products were enriched to generate a cDNA library and sequenced using an Illumina Novaseq6000 platform by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: The testes were dissected from 9 male individuals at L6D4,L6D6 and P0D stages and there were three repeats for each stage.

value: Testis

value: 0-day-old pupae

tag: culture environment

value: under condition 27 ± 1 ◦C with 70 ± 5% relative humidity, and light:dark = 16 h:8 h photoperiod

tag: replicate


title: P0D-1, miRNA


title: ATACseq_sticklebackPrimarySpermatocytesGenomicControl_MarinePool2

tag: cell type


title: ATACseq_sticklebackPrimarySpermatocytesGenomicControl_MarinePool1


title: L6D6-3, miRNA

description: The testes were dissected from 6-day-old sixth instar larvae

tag: tissue

value: 6-day-old sixth instar larvae

value: fed on artificial diet, under condition 27 ± 1 ◦C with 70 ± 5% relative humidity, and light:dark = 16 h:8 h photoperiod


title: L6D6-2, miRNA


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-3, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

tag: strain


title: L6D6-1, miRNA


title: L6D4-3, miRNA

description: The testes were dissected from 4-day-old sixth instar larvae

value: 4-day-old sixth instar larvae


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-1, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

tag: age


title: L6D4-1, miRNA


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-4, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx

tag: treatment


title: L6D4-2, miRNA


title: cardiomyocyte,KLH_TAC4w, replicate1-89, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-2, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-11, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-88, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: ATACseq_sticklebackPrimarySpermatocytesATAC_MarinePool1


title: cardiomyocyte,KLH_TAC4w, replicate1-87, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: P0D-3, miRNA


title: P0D-1, RNA

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows:1)removing reads containing adapters;2) removing reads containing more than 10% of unknown nucleotides (N);3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
For RNA-seq data, short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database (Langmead and Salzberg, 2012). The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
For RNA-seq clean data, an index of the reference genome was built, and paired-end clean reads were mapped to the reference genome   Spodoptera litura (assembly ASM270686v1) using HISAT2 (version 2.1.0) with “-rna-strandness RF” and other parameters set as a default (Kim et al., 2015).
For RNA-seq clean data, after detecting transcriptome library was eligible, the library preparations were sequenced on an Illumina Novaseq6000 platform. The FPKM（Fragments Per Kilobase of transcript per Million fragments mapped）value representing the expression level of transcripts was calculated. The reconstruction of transcripts was carried out with software Stringtie (version 1.3.4), which together with HISAT2, allow biologists to identify new genes and new splice variants of known ones.
For RNA-seq clean data, lncRNA prediction: Two softwares CNCI (version 2) and CPC (version 0.9-r2) ( http://cpc.cbi.pku.edu.cn/) were used to assess the non protein-coding potential of novel transcripts by default parameters. The intersection of both non protein-coding potential results were chosen as long non-coding RNAs.
For RNA-seq clean data, the differentially expressed transcripts of coding RNAs and lncRNAs were analyzed respectively. RNAs and lncRNAs differential expression analysis was performed by DESeq2 (version 1.6.3) software between two different groups. The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts. Differentially expressed coding RNAs were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Spodoptera litura genome sequence (assembly ASM270686v1).
Supplementary files format and content: Tab-delimited text file (.txt) includes raw read counts for the RNA-seq data of all samples. In addition, the sequences for the counted genes of the RNA-seq data are provided by a FASTA file (.fa).

extract_protocol:
Total RNA from the testes of S. litura was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.After total RNA was extracted, rRNAs were removed to retain mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then UNG (Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using an Illumina Novaseq6000 platform by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: cardiomyocyte,KLH_TAC4w_vac, replicate1-5, scRNAseq

description:
smartseq2
TAC4w_vac_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-85, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-84, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: L6D6-2, RNA


title: cardiomyocyte,KLH_TAC4w, replicate1-83, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-82, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: B6-Abx-Colon feces, IL-22Fc, replicate 6

city: San Diego

first: Peng

last: Zhang

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
Sequence data were analyzed using QIIME 2 pipeline and R.
Assembly: Greengenes 13.8 and the non-eukaryotic fraction of Silva 128 databases
Supplementary files format and content: Relative abundance files and richness files
Library strategy: 16s rDNA-seq

organism: feces metagenome

source_name: Mouse feces

extract_protocol:
The UC San Diego Microbiome Core performed nucleic acid extractions from feces utilizing previously published protocols6. Briefly, samples were purified using the MagMAX Microbiome Ultra Nucleic Acid Isolation Kit (Thermo Fisher Scientific, USA) and automated on KingFisher Flex robots (Thermo Fisher Scientific, USA). Blank controls and mock communities (Zymo Research Corporation, USA) were included and carried through all downstream processing steps.
16S rRNA gene amplification was performed according to the Earth Microbiome Project protocol7. Briefly, Illumina primers with unique forward primer barcodes8 were used to amplify the V4 region of the 16S rRNA gene (515fB-806r9). Amplification was performed as single reactions per sample10, then equal volumes of each amplicon were pooled and the libraries sequenced on the Illumina NovaSeq 6000 sequencing platform with paired-end 150 bp cycles at the Institute for Genomic Medicine (IGM, UC San Diego).

tag: host tissue

value: Colon

tag: host

value: Mouse

tag: host strain

tag: host genotype

value: HFD+30% fructose water for 16 weeks, Abx for last 5 weeks and i.p. injected with IL-22Fc for last 4 weeks


title: B6-Abx-Colon feces, IL-22Fc, replicate 5


title: cardiomyocyte,KLH_TAC4w, replicate1-78, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-80, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: L6D4-1, RNA


title: cardiomyocyte,KLH_TAC4w, replicate1-79, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: B6-Abx-Colon feces, IL-22Fc, replicate 4


title: L6D4-3, RNA


title: L6D6-1, RNA


title: L6D4-2, RNA


title: P0D-2, RNA


title: P0D-3, RNA


title: cardiomyocyte,KLH_TAC4w, replicate1-76, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: L6D6-3, RNA


title: B6-Abx-Colon feces, IL-22Fc, replicate 2


title: cardiomyocyte,KLH_TAC4w, replicate1-86, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-75, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: B6-Abx-Colon feces, IL-22Fc, replicate 3


title: B6-Abx-Colon feces, IL-22Fc, replicate 1


title: B6-Abx-Colon feces, Fc, replicate 6

value: HFD+30% fructose water for 16 weeks, Abx for last 5 weeks and i.p. injected with Fc for last 4 weeks


title: B6-Abx-Colon feces, Fc, replicate 5


title: cardiomyocyte,KLH_TAC4w, replicate1-72, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: B6-Abx-Colon feces, Fc, replicate 4


title: cardiomyocyte,KLH_TAC4w, replicate1-71, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-73, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-81, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: B6-Abx-Colon feces, Fc, replicate 2


title: B6-Abx-Colon feces, Fc, replicate 3


title: cardiomyocyte,KLH_TAC4w, replicate1-70, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-68, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔIEC-Colon feces, IL-22Fc, replicate 5

value: HFD+30% fructose water for 16 weeks, and i.p. injected with IL-22Fc for last 4 weeks


title: cardiomyocyte,KLH_TAC4w, replicate1-67, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx

value: cardiomyocyte


title: cardiomyocyte,KLH_TAC4w, replicate1-77, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx

value: heart


title: cardiomyocyte,KLH_TAC4w, replicate1-69, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx

value: 6-8 weeks old


title: cardiomyocyte,KLH_TAC4w, replicate1-65, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-63, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔIEC-Colon feces, IL-22Fc, replicate 3


title: Il22ra1ΔIEC-Colon feces, IL-22Fc, replicate 2


title: cardiomyocyte,KLH_TAC4w, replicate1-66, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔIEC-Colon feces, Fc, replicate 8

value: HFD+30% fructose water for 16 weeks, and i.p. injected with Fc for last 4 weeks


title: cardiomyocyte,KLH_TAC4w, replicate1-64, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: B6-Abx-Colon feces, Fc, replicate 1


title: cardiomyocyte,KLH_TAC4w, replicate1-74, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔIEC-Colon feces, IL-22Fc, replicate 4


title: Il22ra1ΔIEC-Colon feces, IL-22Fc, replicate 1


title: Il22ra1ΔIEC-Colon feces, Fc, replicate 7


title: cardiomyocyte,KLH_TAC4w, replicate1-60, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-61, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔIEC-Colon feces, Fc, replicate 6


title: cardiomyocyte,KLH_TAC4w, replicate1-59, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔIEC-Colon feces, Fc, replicate 4


title: cardiomyocyte,KLH_TAC4w, replicate1-62, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔIEC-Colon feces, Fc, replicate 5


title: cardiomyocyte,KLH_TAC4w, replicate1-57, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔIEC-Colon feces, Fc, replicate 3


title: Il22ra1ΔIEC-Colon feces, IL-22Fc, replicate 6


title: Il22ra1ΔIEC-Colon feces, Fc, replicate 1


title: cardiomyocyte,KLH_TAC4w, replicate1-55, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔIEC-Colon feces, Fc, replicate 2


title: Il22ra1ΔHep-Colon feces, IL-22Fc, replicate 8


title: Il22ra1ΔHep-Colon feces, IL-22Fc, replicate 7


title: cardiomyocyte,KLH_TAC4w, replicate1-53, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-54, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔHep-Colon feces, IL-22Fc, replicate 6


title: cardiomyocyte,KLH_TAC4w, replicate1-52, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-51, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-50, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔHep-Colon feces, IL-22Fc, replicate 5


title: Il22ra1ΔHep-Colon feces, IL-22Fc, replicate 3


title: Il22ra1ΔHep-Colon feces, IL-22Fc, replicate 4


title: Il22ra1ΔHep-Colon feces, IL-22Fc, replicate 2


title: cardiomyocyte,KLH_TAC4w, replicate1-49, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-47, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-58, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔHep-Colon feces, IL-22Fc, replicate 1


title: cardiomyocyte,KLH_TAC4w, replicate1-46, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-45, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔHep-Colon feces, Fc, replicate 7


title: cardiomyocyte,KLH_TAC4w, replicate1-44, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔHep-Colon feces, Fc, replicate 6


title: Il22ra1ΔHep-Colon feces, Fc, replicate 5


title: cardiomyocyte,KLH_TAC4w, replicate1-56, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-43, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-42, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔHep-Colon feces, Fc, replicate 4


title: cardiomyocyte,KLH_TAC4w, replicate1-40, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 12


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 11


title: Il22ra1ΔHep-Colon feces, Fc, replicate 1


title: cardiomyocyte,KLH_TAC4w, replicate1-41, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-39, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-48, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-36, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔHep-Colon feces, Fc, replicate 2


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 9


title: cardiomyocyte,KLH_TAC4w, replicate1-38, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-37, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-35, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 7


title: cardiomyocyte,KLH_TAC4w, replicate1-34, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-33, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 6


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 8


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 5


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 4


title: cardiomyocyte,KLH_TAC4w, replicate1-32, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1ΔHep-Colon feces, Fc, replicate 3


title: cardiomyocyte,KLH_TAC4w, replicate1-31, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 1


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 3


title: cardiomyocyte,KLH_TAC4w, replicate1-29, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-28, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-27, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 10


title: Il22ra1f/f-Colon feces, IL-22Fc, replicate 2


title: Il22ra1f/f-Colon feces, Fc, replicate 10


title: Il22ra1f/f-Colon feces, Fc, replicate 9


title: cardiomyocyte,KLH_TAC4w, replicate1-26, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, Fc, replicate 8


title: cardiomyocyte,KLH_TAC4w, replicate1-22, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, Fc, replicate 6


title: cardiomyocyte,KLH_TAC4w, replicate1-21, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, Fc, replicate 4


title: cardiomyocyte,KLH_TAC4w, replicate1-19, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, Fc, replicate 3


title: cardiomyocyte,KLH_TAC4w, replicate1-24, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-30, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, Fc, replicate 2


title: cardiomyocyte,KLH_TAC4w, replicate1-23, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-18, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, Fc, replicate 1


title: cardiomyocyte,KLH_TAC4w, replicate1-17, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-20, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-16, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-13, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-14, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, Fc, replicate 7


title: cardiomyocyte,KLH_TAC4w, replicate1-15, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-25, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: Il22ra1f/f-Colon feces, Fc, replicate 5


title: pat 14 non-Vd1Vd2 cells

type: RNA

city: Goteborg

first: Marianne

last: Quiding Jarbrink

address: Box 435

department: Microbiology and Immunology

country: Sweden

institute: University of Gothenburg

description:
14.3
NS_Immunology_v2_C2328

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Data was normalized to adjust for platform-associated variations (positive control normalization) and sample input variations (CodeSet content variations/housekeeping gene normalization) using nSolver analysis software

label: not provided

source_name: pat 14 non-Vd1Vd2 cells

label_protocol: Single cell suspensions were lysed in 1 part RLT lysis buffer and 2 parts nuclease free water

extract_protocol: Single cells were isolated from human colon adenocarcinomas by enzymatic extraction, and Vd1, Vd2, and non-Vd1Vd2 cells sorted by flow cytometry, generating 3 samples per patient

value: colon adenocarcinoma

value: non-Vd1Vd2 cells

tag: microsatellite status

value: MSS

tag: differentiation

value: low grade tumor

value: IIIA

tag: subject id

value: pat 14


title: cardiomyocyte,KLH_TAC4w, replicate1-11, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: pat 14 Vd1 cells

description:
14.1
NS_Immunology_v2_C2328

source_name: pat 14 Vd1 cells

value: Vd1 cells

tag: Stage


title: pat 14 Vd2 cells

description:
14.2
NS_Immunology_v2_C2328

source_name: pat 14 Vd2 cells

value: Vd2 cells


title: cardiomyocyte,KLH_TAC4w, replicate1-9, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: cardiomyocyte,KLH_TAC4w, replicate1-10, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: pat 13 non-Vd1Vd2 cells

description:
13.3
NS_Immunology_v2_C2328

source_name: pat 13 non-Vd1Vd2 cells

value: IIIC

value: pat 13


title: pat 13 Vd2 cells

description:
13.2
NS_Immunology_v2_C2328

source_name: pat 13 Vd2 cells


title: cardiomyocyte,KLH_TAC4w, replicate1-8, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: pat 13 Vd1 cells

description:
13.1
NS_Immunology_v2_C2328

source_name: pat 13 Vd1 cells


title: pat 12 Vd2 cells

description:
12.2
NS_Immunology_v2_C2328

source_name: pat 12 Vd2 cells

value: MSI-H

value: IIA

value: pat 12


title: cardiomyocyte,KLH_TAC4w, replicate1-6, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx

value: cardiomyocyte


title: cardiomyocyte,KLH_TAC4w, replicate1-5, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx

value: heart


title: pat 11 non-Vd1Vd2 cells

description:
11.3
NS_Immunology_v2_C2328

source_name: pat 11 non-Vd1Vd2 cells

value: high grade tumor

value: pat 11


title: cardiomyocyte,KLH_TAC4w, replicate1-7, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx

value: 6-8 weeks old


title: pat 11 Vd2 cells

description:
11.2
NS_Immunology_v2_C2328

source_name: pat 11 Vd2 cells

value: colon adenocarcinoma


title: pat 11 Vd1 cells

description:
11.1
NS_Immunology_v2_C2328

source_name: pat 11 Vd1 cells


title: GEX-34_pre_PBMC

city: Philadelphia

first: Alexander

last: Huang

state: PA

address: 421 Curie Boulevard

department: Department of Hematology/Oncology

institute: University of Pennsylvania

description: 10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)

data_processing:
CellRanger v7.0.0 count was run on GEX fastqs.
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files containing GEX data: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: peripheral blood

extract_protocol:
PBMCs were sorted on Live CD3+CD8+ and Live CD3+CD4+ T cells. TILs were sorted on Live CD45+ cells.
Library was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 5’, 10x Genomics).

value: peripheral blood

value: CD4+ and CD8+ T cells

tag: disease

value: melanoma

tag: patient

tag: timepoint

value: baseline

tag: type

value: GEX


title: GEX-34_pre_TIL

source_name: tumor

value: tumor

tag: cell type

value: CD45+ cells


title: cardiomyocyte,KLH_TAC4w, replicate1-4, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx

source_name: heart

tag: tissue


title: cardiomyocyte,KLH_TAC4w, replicate1-12, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx

tag: strain


title: GEX-32_pre_TIL


title: cardiomyocyte,KLH_TAC4w, replicate1-3, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx

tag: age


title: GEX-31_pre_TIL


title: GEX-32_pre_PBMC


title: cardiomyocyte,KLH_only, replicate1-66, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

tag: treatment


title: pat 12 non-Vd1Vd2 cells

description:
12.3
NS_Immunology_v2_C2328

source_name: pat 12 non-Vd1Vd2 cells

value: non-Vd1Vd2 cells

value: low grade tumor


title: cardiomyocyte,KLH_TAC4w, replicate1-2, scRNAseq

description:
smartseq2
KLH_TAC4w_1.xlsx


title: GEX-31_pre_PBMC


title: cardiomyocyte,KLH_only, replicate1-65, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-63, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-64, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: AG09429 untreated

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

description: naive/untreated

data_processing:
Low quality reads from the RNA -seq dataset were removed via FastQC (sickle with default setting). A HISAT2 index was built for the GRCh38 genome assembly using HISAT2 version 2.1.0. RNA -sequencing reads of each sample was mapped using HISAT2 supplied by Ensembl annotation file; GRCh38.78.gtf. For the count call, HTseq-count version 0.10.0 was used.
Assembly: GRCh38
Supplementary files format and content: Raw read count (HTseq-count output)

source_name: iPSC derived neural progenitor cells (AG09429)

growth_protocol: The cells were maintained in culture plate coated first with poly-L-ornithine then mouselaminin. The cells were lifted using TrypLE (Gibco) and passaged at 1 to 3 ratio in medium containing DMEM/F12, antibiotic/antimyotic, N2 supplement, B27 without vitamin A, GlutaMax and FGF2 (20ng/mL,Peprotech)

extract_protocol:
The NPCs (GM03440 passaged at P7-12, AG09429 passaged at 8) were trypsinized and pelleted in 1X PBS.
The cDNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instruction.
The libraries were pooled and diluted to 3 nM using 10 mM Tris - HCl, pH 8.5, and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read.

tag: passages


title: GM03440 untreated

description: naive/untreated

source_name: iPSC derived neural progenitor cells (GM03440)


title: cardiomyocyte,KLH_TAC4w, replicate1-1, scRNAseq

city: Bunkyo-ku

first: Manami

last: Katoh

institute: The University of Tokyo

description:
smartseq2
KLH_TAC4w_1.xlsx


title: BaselineCART_RNA-seq Biorep3

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

data_processing:
Fastq files were first evaluated for quality using FASTQC. Then, Cutadapt was used to remove Illumina adapters before FASTQC was run again to evaluate quality after adapter removal. Next, the paired end reads for each condition were aligned with STAR using the genome reference consortium human build 38 patch release 13 (GRCh38.p13) downloaded from NCBI. HTSeq was used to generate expression counts for each gene.
Assembly: genome reference consortium human build 38 patch release 13 (GRCh38.p13) downloaded from NCBI
Supplementary files format and content: tab-delimited text files contain the gene expression counts for each sample

source_name: T-cell

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA INC., California, USA)

treatment_protocol: CART19-28ζ cells from three biological replicates were collected before (baseline) or after chronic stimulation (exhausted) in our in vitro model for CART cell exhaustion. In this model, CART cells were chronically stimulated with JeKo-1 cells.

value: T-cell

value: Baseline


title: cardiomyocyte,KLH_only, replicate1-61, scRNAseq

address: 7-3-1 Hongo

description:
smartseq2
KLH_4w_1.xlsx

value: cardiomyocyte


title: ExhaustedCART_RNA-seq Biorep2

value: Exhausted


title: ExhaustedCART_RNA-seq Biorep3


title: cardiomyocyte,KLH_only, replicate1-60, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: heart


title: BaselineCART_RNA-seq Biorep2


title: cardiomyocyte,KLH_only, replicate1-62, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-59, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: BaselineCART_RNA-seq Biorep1


title: cardiomyocyte,KLH_only, replicate1-58, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-57, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: HMC3, Input

city: Soochow

first: Hao

last: Wang

state: Jiangsu

address: 899 Pinghai Road

department: Department of Neurosurgery & Brain and Nerve Research Laboratory

institute: The First Affiliated Hospital of Soochow University

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
Sequence quality was examined using the FastQC software.
After passing Solexa CHASTITY quality filter, the clean reads were aligned to human genome (UCSC HG19) using BOWTIE software (V2.2.7).
Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2.
Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-4.The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database.
Assembly: hg37
Supplementary files format and content: bed, Genomic alignment result for the reads which pass Solexa CHASTITY quality filter

source_name: microglia

growth_protocol: The HMC3 cell line was cultured in MEM (including NEAA) supplemented with 10% FBS (VivaCell) and 1% PS. All cells were maintained at 37 ℃ and 5% CO2.

extract_protocol:
cells were fasten in 1% formaldehyde at 37◦C for 15 min and terminated with glycine (125 mM) for 10 min, then completed cell cross-linking, then prepared nuclei, and sonic fragmented chromatin by Bioruptor (Diagenode).
10 ng of our DNA samples were prepared for Illumina sequencing as the following steps: 1) DNA samples were blunt-ended; 2) A dA base was added to the 3' end of each strand; 3) Illumina's genomic adapters were ligated to the DNA fragments; 4) PCR amplification was performed to enrich ligated fragments; 5) Size selection of ~200-1500bp enriched product using AMPure XP beads. The completed libraries were quantified by Agilent 2100 Bioanalyzer. The libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cell, amplified in situ. The libraries were then sequenced on the Illumina NovaSeq 6000 following the NovaSeq 6000 S4 Reagent Kit (300 cycles) protocol.

value: microglia

tag: cell line

value: HMC3 cells

value: Human microglia cells

tag: genotype

value: WT

value: No treatment


title: HMC3, NFκB, CHIP


title: SHG143 GSCs, β-catenin, CHIP

source_name: Glioblastoma

growth_protocol: The GSCs culture medium consisted of DMEM/F12 (Corning), B27 (Gibco), 20 ng ml-1 recombinant human epidermal growth factor and 20 ng/ml basic fibroblast growth factor. All cells were maintained at 37 ℃ and 5% CO2.

value: Glioblastoma

value: SHG143 GSCs

value: Human glioblastoma


title: SHG143 GSCs, Input


title: cardiomyocyte,KLH_only, replicate1-54, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: 6-8 weeks old


title: shPRRG1-3_3

first: zheng

last: wu

address: 800 Dongchuan Road

institute: School of Medicine, Shanghai Jiao Tong University

data_processing:
1_quality_control, The raw sequencing data is stored in fastq format files for each sample in this project, which involves paired-end sequencing. Therefore, each sample consists of two fastq files. For each individual fastq file, the sequencing results are assessed for quality using FastQC software.
2_clean_statistic, Using the fastp software to filter sequences, the main objectives are to exclude the following sequences: 1. Remove sequencing adapter sequences contained in the reads. 2. Trim bases with a quality score (Q) lower than 20 from the 3’ end of the reads. 3. Discard reads shorter than 25 bases in length. 4. Remove ribosomal RNA reads from the target sequencing species.
3_mapping_statistic, The software used for sequence alignment is Hisat2. Its alignment algorithm is called the spliced mapping algorithm, which can split reads that cannot be fully matched and then map them. This is suitable for aligning eukaryotic genomes that contain introns.
4_gene_expression_and_differential_expression_genes, Based on the physical location information of genes aligned to the reference genome, the number of reads covering each gene (including newly predicted genes) from start to end is counted. The Stringtie software is used to count the fragments within each gene region after alignment, and then the TMM (trimmed mean of M values) algorithm is used for normalization. Therefore, to comprehensively measure gene expression, the concept of FPKM is used to represent the expression levels of different genes. The resulting FPKM values can be regarded as the expression levels of each gene. Based on this, the software edgeR is used to calculate differentially expressed genes between two groups according to the experimental grouping information.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested by RNeasy Mini Kit (Qiagen). 1.2μg of total RNA was used for the construction of slicing libraries.
RNA libraries for RNA-seq were prepared using TIANSeq Fast RNA Library Prep Kit following manufacture's protocols.


title: shPRRG1-3_2


title: cardiomyocyte,KLH_only, replicate1-52, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-53, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx