title: CML 339 NDC

description: 10X Genomics

data_processing:
Single cell RNA-seq data were pre-processed using the 10X Genomics Cell Ranger (6.1.1) suite of analysis pipelines.  Demultiplexing of raw base call (BCL) files produced by the Illumina Hiseq4000 platform and conversion to FASTQ file formats was performed using the cellranger mkfastq pipeline. Alignment of sequencing reads (FASTQ) to the GRCh38 (GENCODE v32/Ensembl 98) human genome assembly was performed using the cellranger count pipeline.
Assembly: human GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: blood

growth_protocol: CML CD34+CD38- cells were cultured at 37oC in serum free media (20% BIT, 100 μM β-mercaptoethanol, 0.04 mg/mL low density lipoprotein, 2 mM L-glutamine and 1% penicillin-streptomycin in IMDM) containing physiological levels of growth factors (SCF 0.2ng/mL, G-CSF 1ng/mL, GM-CSF 0.2ng/mL, IL-6 1ng/mL, LIF 0.05ng/mL, MIP-α 0.2ng/mL, StemCell Technologies) for 48 hrs in vitro.

extract_protocol:
For isolation of stem cells (CD34+CD38-), CD34+ cell samples were stained with anti-human (hu) CD34-APC, CD38-V450 or CD38-Pe-Cy7 antibodies (BD Biosciences), before being subjected to fluorescence activated cell sorting (FACS) to obtain the stem cell populations using a FACSAriaTM Fusion cell sorter (BD Biosciences).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells 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 retrotranscribed 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 appropriate 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. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

treatment_protocol: Fluphenazine alone and/or nilotinib were added to cells at a final concentration of 5 µM for each drug.

value: blood

value: CD34+CD38- cells

tag: tumour stage

value: chronic phase

value: F

value: vehicle (no drug) control


title: humanDLPFC_Schizophrenia_1

status: Public on Dec 01 2025

type: SRA

city: Madison

first: anthony

middle: shawn

last: abrantes

state: WI

address: 402 Paunack st apt 1

department: genetic medicine

country: USA

institute: unc-chapel hill

library_source: transcriptomic

data_processing:
SMRTLink (v8.0.0)
removed primers using Lima (v2.0.0).
clustered using IsoSeq3
aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
SQANTI3 QC filtering
Assembly: GRCh38.p13
Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts

molecule: total RNA

organism: Homo sapiens

source_name: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)

extract_protocol:
The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.

tag: tissue

tag: disease state

value: Schizophrenia

tag: batch


title: H19,Time2

city: Santa Cruz

first: Aidan

middle: Christian

last: Manning

state: CA

address: 2125 Delaware Ave. Suite B

institute: RealSeq Biosciences

description: Library name: H19_2

data_processing:
First, sequencing reads were trimmed of the adapter sequence using cutadapt (Martin, 2011). Trimming statistics revealed excluded dimers in a range of 5.41% – 21.76%, nevertheless, their average proportions were comparable in individual sampling times: 13.40%, 12.55%, 11.79% for T1-T3 respectively. The final average reads passing the filters were 8,133,803 per sample. Next, the per-base sequence quality was checked. This test indicated high-quality scores (above 30) for all positions in reads up to 91 bases. An additional part of the data quality control (FastQC) focused on the distribution of the read length. The data showed a comparable trend in distribution among the individual samples, with the majority of read lengths being around 21 nucleotides. Reads were then sequentially aligned using either bowtie or bowtie2 (Langmead and Salzberg, 2012) to vector the contaminants (UniVec), rRNAs, tRNAs (with the addition of the -CCA tail) identified using tRNAScan-SE (Chan et al., 2021), miRNAs from miRbase (Kozomara et al., 2019), snRNAs/snoRNAs from Ensembl (Dyer et al., 2025), piRNAs from piRbase (Wang et al., 2022), processed mRNA transcripts (mRNA/protein coding) from Ensembl (Dyer et al., 2025), and lastly to the genome. The counts associated with these features were then quantified using a custom Python script, choosing the feature annotation with the largest degree of overlap. Multimapping ncRNA reads with more than one highest-scoring alignment were randomly selected, while multimapping protein-coding reads were not included in the downstream analysis. For tRNA mapping reads, a read was assigned as either a ‘5p’, ‘3p’, or as an ‘internal’ feature based on where it mapped in the parent transcript. For ‘5p’ features, it must map within 10 bp of the 5’ end, ‘3p’ features must map within 10 bp of the 3’ end, and an ‘internal’ feature does not map within 10 bp of either the 5’ or 3’ end of the parent transcript. Furthermore, the Median Absolute Deviation Analysis (MAD) method was used for the identification of samples with extreme deviations in count distributions for individual experimental groups. The MAD method computed a modified Z-score for each sample, resulting in eleven samples with normal values and one T1 sample as a potential outlier (|Z| > 3). Additional analysis included mapping statistics: (i) the percentage of mapped reads were in the range 89.04% - 97.68% among individual samples, with an average of 3,747,657 reads; (ii) for the distribution of RNA biotypes and the number of detected transcripts, see section 3.2. In general, the data presented in this study were mostly analyzed and/or visualized by Principal Component Analyses (PCA), Differential Expression Analyses using DESeq2 (Love et al., 2014) with the following settings: log2FC (Fold Change) cutoff = 1; adjusted p-value cutoff = 0.05, and boxplots showing the normalized count values across different experimental conditions for selected transcripts (see Results section).
Assembly: GRCh38/hg38
Supplementary files format and content: readcounts.csv contains raw counts for annotated RNA transcripts.

source_name: Blood

growth_protocol: The personal and exposure characteristics obtained from the questionnaires are summarized in Table 1. Participants of this pilot study were firefighters (mean age 45) with long-time occupational exposure history (14-30 years, starting at the age of 19-22 years). At the time of sampling, all subjects were active firefighters, with mostly 5 – 10 fire interventions during the last year. Additional inhalation exposure from smoking at the time of the study was reported by one of these participants.

extract_protocol:
The total RNA was extracted from 2.5 ml of whole blood samples by using a PAXgene Blood miRNA Kit (PreAnalytiX, Qiagen, Switzerland). The RNA quantity and concentration were measured with a Qubit 4.0 Fluorometer using a High-Sensitivity RNA kit, the Qubit® RNA HS (High Sensitivity) Assay Kit (both ThermoFisher Scientific, Wilmington, DE, USA). The RNA quality and fragmentation were assessed with a Fragment Analyzer using an SS RNA kit (both Agilent Technologies, Santa Clara, CA, USA). The mean RNA integrity number (RIN) for all samples was 7.6 (range: 4-9.6), with individual RINs of 8.6, 7.1, and 7 for sampling times T1 to T3, respectively. The following analysis steps were performed to identify a broad spectrum of individual RNAs, including mRNA, rRNA, tRNA, miRNA, snRNA, snoRNA, lncRNA, piRNA, other sRNAs, and unannotated and unmapped RNAs.
RiboMarker® RNA Fragmentomics Library Preparation Kit #400-00012 (RealSeq Biosciences, Santa Cruz, USA) was used for preparing all individual libraries from 50 ng of the total RNA according to the manufacturer’s protocol. Briefly, the two-day workflow involved: (i) RNA pretreatment [with RNA Clean & Concentrator-5 #R1015 (Zymo Research, Irvine, CA, USA)], adapter ligation, and blocking on the first day, followed by (ii) circularization, dimer removal, reverse transcription, PCR amplification, and size selection with SPRI beads on the second day. The RNA libraries concentration was measured with the 1× dsDNA HS kit (ThermoFisher Scientific) on the Qubit 4.0 fluorometer, and the quality was checked using the Fragment Analyzer with the HS NGS Fragment Kit (Agilent Technologies). The libraries had estimated profiles with the main peak of fragment length between 147-162bp.

value: Blood

tag: time


title: TX BX_1124245_03

type: RNA

city: La Jolla

first: SUNIL

last: KURIAN

address: 10666 N Torrey Pines Rd

institute: Scripps Health

description:
TX
_

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained in the Affymetrix Gene Titan MC.

scan_protocol: GeneChips were scanned in the Affymetrix Gene Titan MC.

data_processing: All samples were processed using the Affymetrix Gene Titan MC instrument following the standard procedure outlined in the user guide for the HT HG-U133 Plus PM Array Plate. https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fgenetitan_mc_user_guide.pdf

label: Biotin

source_name: Renal Biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: PAXgene extraction of total RNA was performed using the PAXgene RNA extraction kit according to the manufacturer's instructions.

tag: tag

value: Well Functioning Transplant


title: subAR BX_1123765_03

description:
subAR
_

value: Subclinical acute rejection


title: liver, BRMKO, ZT10, Input

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: genomic

data_processing:
Reads were aligned using BWA (v0.7.17).
Duplicates were flagged by MarkDuplicates (Picard tools). Filtering steps were applied to exclude reads with low mapping quality (MAPQ<30), reads/mates that were unmapped, reads failing platform and those not classified as primary alignments and duplicates (samtools view -q 30 -F 1804 -f 2).
Peaks were called using MACS2 (BAMPE format), with broad settings and a q-value cutoff of 0.05. Input samples (IPs) were used as a control in peak calling and all IPs in one experiment were pooled. Reads in peaks were quantified and normalized via DiffBind (v3.0.15) with default settings except filter=0. Overlapping TF binding sites was performed using Intervene software.
DeepTools was used for generation of bigwig tracks with RPGC normalization. Bigwig files from replicates were merged using WiggleTools for heatmaps. SparK was used for visualization of bigwig tracks.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak (consensus peak of WT samples)

molecule: genomic DNA

organism: Mus musculus

source_name: liver

growth_protocol: Wild type mice: C57BL/6N. Smarca2-/- and Smarca4fl/fl mice on 129/Sv background and backcrossed with C57BL/6N mice and subsequently intercrossed. 8-10 weeks old mice were used for experiments.

extract_protocol:
For all ChIPs 2-3 biological replicates for each condition were pooled by weighing a total of ~220-250mg of snap-frozen liver tissue. Which was homogenized in 10mL PBS containing 2mM DSG (ProteoChem, 79642-50-5) using IKA T10 standard ULTRA TURRAX on level 4 for 15 sec followed by dounce homogenization in a 15mL douncer for 20 strokes with a tight pestle. The samples were incubated for 40 min at RT under rotation and centrifuged for 5 min at 900g. Supernatant was discarded, and the pellet was resuspended in 10mL PBS, centrifuged for 5 min at 900g, and supernatant was discarded. The pellet was resuspended in 10mL PBS containing 1% formaldehyde (Thermo Scientific, 28908) and incubated at RT for 5 min under rotation. 1mL 1.25M glycine was added, and samples were incubated for 5 min at RT under rotation to stop the crosslinking. The samples were dounce homogenized in a douncer for 20 strokes with a tight pestle and filtered through a 70µM pluriStrainer (pluriSelect, 43-50070). The samples were centrifuged at 900g for 5min at 4 °C and supernatant was discarded. Pellet was resuspended in 10mL PBS with 1mM phenylmethylsulfonyl fluoride (PMSF) (Sigma, 11359061001). The samples were centrifuged at 900g for 5min at 4 °C and supernatant was removed. The pellet was resuspended in 10mL cell wash buffer 1 (10mM Tris-HCl pH 8, 10mM EDTA, 0.5mM egtazic acid (EGTA), 0.25% Triton X-100) containing 1mM PMSF, centrifuged, and supernatant was discarded. Hereafter the pellet was resuspended in 10mL cell wash buffer 2 (10mM Tris-HCl pH 8, 1mM EDTA, 0.5mM EGTA, 200mM NaCl) containing 1mM PMSF. The samples were centrifuged, and supernatant was discarded. The pellet was resuspended in 1mL of ChIP buffer (50mM Trish-HCl pH 8, 1mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% deoxycholic Na, 0.1% SDS) with 1:200 PIC.
25µL Pierce ChIP-grade Protein A/G Magnetic Beads (Thermo Scientific, 26162) were prepared for each sample. The total volume of beads needed was aliquoted to a new tube and placed in a magnetic rack for 5 min. Supernatant was removed. Beads were washed twice by resuspending in 600µL ChIP buffer, placing the tube in a magnetic rack, turning 20x180°, leaving it for 2 min, and discarding supernatant. After the second wash the beads were resuspended in the initial volume of ChIP buffer (25µL per sample). 25µL of the prepared beads were added to each sample and they were incubated under rotation for 30 min at 4 °C. This preclearing gets rid of chromatin fragments that bind unspecifically to the beads, meaning that they bind to the beads without the presence of antibody. After incubation, the samples were placed in a magnetic rack, incubated for 5 min, and the supernatant was transferred to a new tube. 1% of the volume was transferred to a new tube and saved as an input. 5µL drosophila spike-in chromatin (active motif, 53083) and 2µL spike-in antibody (active motif, 61686) was added. The spike-in can be used to normalize for efficiency of immunoprecipitation after sequencing. However, this normalization method was not used in this report. 10µL of BRG1 antibody (Abcam, ab110641) was added to the samples, followed by ON incubation under rotation at 4 °C.
50µL of beads, prepared as described above, was added to each sample, and the samples were incubated for 1 hour under rotation at 4 °C. The samples were placed in a magnetic rack for 2 min and supernatant was discarded. Beads were subsequently washed by resuspending in different wash buffers, listed below, by placing the tube in a magnetic rack, turning 20x180°, incubating for 2 min, and discarding the supernatant. The washing buffers are: ChIP wash 1 (20mM Tris pH 8, 150mM NaCl, 2mM EDTA, 0.1% deoxycholic Na, 1% Triton X-100), ChIP wash 2 (20mM Tris pH 8, 500mM NaCl, 2mM EDTA, 0.1% deoxycholic Na, 1% Triton X-100), ChIP wash 3 (10mM Tris pH 8, 250mM LiCl, 1mM EDTA, 0.7% deoxycholic Na, 1% Igepal CA-630), and twice with TE buffer (10mM Tris-HCl pH 8, 1mM EDTA). After the final wash in TE buffer the supernatant was discarded and 150µL of elution buffer (1% SDS, 100mM NaHCO3) was added to the beads. The samples were incubated in a thermomixer at 65 °C at 1000 rpm for 30 min. The tubes were placed in a magnetic rack and incubated for 5 min. The supernatant was transferred to a new tube and the beads was resuspended with 150µL elution buffer and incubated in the thermomixer again. The tubes were transferred to a magnetic rack and the supernatant was pooled with supernatant from first elution and the beads were discarded. Elution buffer was added to the input samples for a final volume of 300µL. 12µL 5M NaCl was added to all samples, including inputs, and the samples were incubated at 65 °C ON to reverse DNA-protein crosslinking. 6µL 0.5M EDTA, 12µL 1M Tris-HCl pH 6.5, and 1µL 10mg/mL RNase A (Thermo Scientific, EN0531) was added to the samples. The samples were incubated at 37 °C for 30 min. 5µL 20 g/L proteinase K (Invitrogen, 25530049) was added and the samples was incubated at 56 °C for one hour.
The DNA was purified using MinElute PCR purification kit. 7 volumes of buffer PB was added to the samples. 700µL of the sample was loaded onto the column, centrifuged at 16000g, and flowthrough was discarded. This process was repeated until the entire sample was passed through the column. The column was washed twice with buffer PE. Flowthrough was discarded and the column was centrifuged an additional time to get rid of excess ethanol, possible leftover ethanol around the O-ring was removed with a pipette. The column was transferred to a clean DNA LoBind tube (Eppendorf). 12µL of buffer EB was loaded to the center of the membrane, the samples were incubated for 1 min and centrifuged for 1 min. DNA concentrations of the samples was determined using Qubit.
ChIP samples were generated using NEBNext® reagents and kits for Illumina® Sequencing following manufacturer’s instrcutions. Samples were sequenced on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Smarca2-/- mice, Smarca4fl/fl mice, and Smarca2-/-;smarca4fl/fl mice were tail vein injected AAV-TBG-GFP or AAV-TBG-CRE. Ten days after injection the mice were trained to night restricted feeding for another 4 days. Mice were sacrificed by cervical dislocation at different timepoints during the day (ZT 2, 6, 10, 14, 18, and 22).

tag: strain

tag: Sex

value: male

tag: genotype

value: Smarca2 -/- Smarca4 fl/fl

tag: treatment

value: AAV-TBG-GFP

tag: chip antibody

value: BRG1 antibody (Abcam, ab110641)

value: liver

tag: zeitgeber time_(zt)


title: TX BX_1123660_03

description:
TX
_


title: H17,Time2

description: Library name: H17_2


title: CML 339 FLU + NIL

city: Glasgow

first: David

last: Vetrie

address: Wolfson Wohl Cancer Research Centre

department: Institute of Cancer Sciences

country: United Kingdom

institute: Glasgow University

description: 10X Genomics

library_source: transcriptomic single cell

tag: cell type

value: CML

tag: age

value: fluphenazine (5 uM) plus nilotinib (5 uM)


title: liver, BRMKO, ZT10, BRG1, ChIP


title: TX BX_1123658_03

description:
TX
_


title: H10,Time2

description: Library name: H10_2


title: TX BX_1123657_03

description:
TX
_


title: liver, WT, Input, rep2

value: WT


title: CML 339 FLU

description: 10X Genomics

value: blood

value: fluphenazine (5 uM)


title: C3 T1 S1

data_processing:
Raw sequencing data was pre-processed using the University of Glasgow high performance computing clusters for which quality control was performed by FastQC (0.11.9) and the reads were trimmed by fastp (0.23.2). Trimmed reads were aligned to human reference genome hg38 using STAR (2.7.10a) and assigned by the feature counting tool featureCount (2.0.1). Differentially expressed genes between experimental conditions were obtained by DESeq2 (1.36.0) in R.
Assembly: human reference genome GRCh38/hg38
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

source_name: JURL-MK1 (C3) nilotinib resistant

growth_protocol: The nilotinib resistant JURL-MK1 (C3) cell line and the parental JURL-MK1 (WT) cell line were grown in RPMI 1640 (Sigma) supplemented with 10% fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine and 1% (v/v) penicillin-streptomycin.

extract_protocol:
The cells were pelleted by centrifugation in culture media, washed and then pelleted again in phosphate buffered saline pH 7.4, and total cellular RNA extracted from a minimum of 1 x106 cells in TRIzoLTM Reagent (ThermoFisher). The concentration of the RNA was measured using the Nanodrop 2000, and the quality and RIN value was determined using the Agilent Bioanalyser RNA Nano kit (Agilent).
RNA-seq libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) with single indexing following the manufacturers’ instructions. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

treatment_protocol: The nilotinib resistant JURL-MK1 cell line (C3) was cultured as above with the addition of 1µM NIL to maintain resistance prior to its use in experiments. Prior to RNA extraction for this study, nilotinib resistant JURL-MK1 cells were grown in the absence of nilotinib for 72 hrs.

tag: cell line

value: JURL-MK1 (C3) nilotinib resistant

value: leukaemia

value: M


title: liver, WT, Input, rep1


title: TKI_plus_sh53 Day_3  Biol rep 3

growth_protocol: JURL-MK1 cell line (mycoplasma-negative; obtained from DSMZ; authenticated by Northgene Ltd, Newcastle in 2020), was grown in RPMI 1640 (Sigma) supplemented with 10-20% fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine and 1% (v/v) penicillin-streptomycin.

treatment_protocol: 14.2 µg of each shRNA were transfected into 293T human embryonic kidney (HEK) cells along with 12.45 μg Pax2 and 4.5 μg VSV-G constructs. After 6, 24 and 48 hr, the media was collected and replaced with 10 mL DMEM containing 20% serum. Virus was concentrated by ultracentrifugation and stored at -80ºC until needed. JURL-MK1 cells (5 x 106) were incubated with virus particles (MOI = 1) for 48 hr, with the media replaced after 24 hr. Transduction efficiency (% GFP+ cells; nominally >90% for each experiment) was measured by flow cytometry (FACSVerse) and time course experiments +/- TKI (niltotinib; 2 nM) were carried out.

value: leukaemia cell line

value: CML myeloid blast crisis

value: DRD4 KD sh53 + nilotinib

value: day 3

value: 73 yrs


title: H9,Time2

description: Library name: H9_2

value: Blood


title: TX BX_1123655_03

description:
TX
_

value: Well Functioning Transplant


title: liver, WT, ZT22, BRG1, ChIP, rep2

value: male

value: BRG1 antibody (Abcam, ab110641)


title: TKI_plus_sh53 Day_3  Biol rep 2


title: liver, WT, ZT22, BRG1, ChIP, rep1

value: liver


title: TKI_plus_sh53 Day_2  Biol rep 3

value: day 2


title: cAR BX_1123535_03

description:
cAR
_

value: Clinical acute rejection


title: TX BX_1123654_03

description:
TX
_


title: H19,Time1

description: Library name: H19_1


title: TX BX_1123534_03

description:
TX
_


title: H10,Time1

description: Library name: H10_1


title: liver, WT, ZT18, BRG1, ChIP, rep2

value: WT


title: TKI_plus_sh53 Day_2  Biol rep 2


title: H9,Time1

description: Library name: H9_1


title: CML 339 NIL

description: 10X Genomics

value: blood

value: CD34+CD38- cells

value: CML

value: chronic phase

value: F

value: nilotinib (5 uM)


title: liver, WT, ZT18, BRG1, ChIP, rep1


title: ADNR BX_1123528_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: TKI Day_3  Biol rep 4

value: leukaemia cell line

value: CML myeloid blast crisis

value: nilotinib treatment

value: day 3


title: liver, WT, ZT14, BRG1, ChIP, rep2

value: male


title: subAR BX_1123271_03

description:
subAR
_

value: Subclinical acute rejection


title: Huh7 YBX1 KO1 cells 3

city: Galveston

first: Tania

middle: I

last: Strilets

state: Texas

address: 301 University Blvd

department: BMB

institute: University of Texas Medical Branch

description:
Library name: TS-8
Huh7 YBX1 KO1 3

data_processing:
The pooled library was sequenced on Illumina NextSeq 550 for paired end 75bp reads.  The reads are aligned to human reference genome GRCh38 and quantified for gene level expression using STAR version 2.7.10a.  The counts were normalized and differential expression detected using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Excel file contains Log2 normalized counts for all samples

growth_protocol: All Huh7 cells were maintained in Dulbecco’s Modified Eagle medium (DMEM, Genesee Scientific) supplemented with 10 % heat-inactivated fetal bovine serum (FBS) (Genessee Scientific) and 100 U/mL penicillin and 100 mg/ mL streptomycin (P/S, Gibco, Waltham, MA) at 37°C with 5% CO2.

extract_protocol:
RNA was extracted using Trizol (Thermo Fisher Scientific) according to the manufacturer's protocol. Ribosomal RNA was removed from the RNA sample using NEBNext ribosomal RNA depletion kit (NEB).
Stranded RNA-Seq library prepared using NEBNext ultra II stranded RNA library preparation kit (NEB) following the manufacturer’s recommended procedure.

treatment_protocol: Cells were seeded into 10cm dishes and grown for two days, to 80% confluency (approximately).


title: liver, WT, ZT14, BRG1, ChIP, rep1

value: BRG1 antibody (Abcam, ab110641)

value: liver


title: H17,Time1

description: Library name: H17_1

value: Blood


title: TKI Day_3  Biol rep 2

value: 73 yrs


title: Huh7 YBX1 KO1 cells 1

description:
Library name: TS-6
Huh7 YBX1 KO1 1


title: cAR BX_1123264_03

description:
cAR
_

value: Clinical acute rejection


title: TX BX_1123263_03

description:
TX
_

value: Well Functioning Transplant


title: TKI Day_2  Biol rep 4

value: day 2


title: liver, WT, ZT10, BRG1, ChIP, rep2

value: WT


title: Huh7 YBX1 KO3 cells 3

description:
Library name: TS-5
Huh7 YBX1 KO3 3


title: liver, WT, ZT10, BRG1, ChIP, rep1


title: TKI Day_2  Biol rep 3


title: cAR BX_1123261_03

description:
cAR
_


title: Huh7 YBX1 KO3 cells 2

description:
Library name: TS-4
Huh7 YBX1 KO3 2


title: TKI Day_2  Biol rep 2


title: liver, WT, ZT6, BRG1, ChIP, rep1


title: sh55 Day_3  Biol rep 3

value: DRD4 KD sh55


title: Huh7 WT cels  2

description:
Library name: TS-2
Huh7 WT 2


title: TKI Day_3  Biol rep 3


title: liver, WT, ZT6, BRG1, ChIP, rep2


title: TX BX_1123022_03

description:
TX
_


title: sh55 Day_3  Biol rep 2


title: Huh7 YBX1 KO1 cells 2

description:
Library name: TS-7
Huh7 YBX1 KO1 2


title: liver, WT, ZT2, BRG1, ChIP, rep2


title: Huh7 WT cells 1

description:
Library name: TS-1
Huh7 WT 1


title: TX BX_1123067_03

description:
TX
_


title: subAR BX_1123023_03

description:
subAR
_


title: TX BX_1122532_03

description:
TX
_


title: liver, WT, ZT2, BRG1, ChIP, rep1


title: sh55 Day_2  Biol rep 2


title: liver, dKO, rep4

data_processing:
Reads were trimmed with Trim Galore using the specified Nextera adaptors. Reads were aligned to mm10 using STAR (v2.7.5c). Mitochondrial and unmapped contig reads were removed.  Duplicate reads were removed. Only fragments with a size < 100 was used for ATAC-seq, to assess chromatin accessibility. For ATAC-seq, peaks were called using MACS2  with paired-end format and a q-value threshold of 0.05. DiffBind was used to quantify reads in peaks and subsequent normalization with default settings.
Duplicates were flagged by MarkDuplicates (Picard tools). Filtering steps were applied to exclude reads with low mapping quality (MAPQ<30), reads/mates that were unmapped, reads failing platform and those not classified as primary alignments and duplicates (samtools view -q 30 -F 1804 -f 2).
Peaks were called using MACS2 (BAMPE format), with broad settings and a q-value cutoff of 0.05. Input samples (IPs) were used as a control in peak calling and all IPs in one experiment were pooled. Reads in peaks were quantified and normalized via DiffBind (v3.0.15) with default settings except filter=0. Overlapping TF binding sites was performed using Intervene software.
DeepTools was used for generation of bigwig tracks with RPGC normalization. Bigwig files from replicates were merged using WiggleTools for heatmaps. SparK was used for visualization of bigwig tracks.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
For the wild type mice biological replicates was merged in the circadian setup, and the tagmentation was performed in three replicates. In the SWI/SNF perturbation models tagmentation was performed on four biological replicates. A 2mL douncer was used to homogenize 15mg of tissue. 2.5 µL of TDE1 enzyme (Illumina 20034197) and 50000 nuclei were used for transposition reactions .  DNA was size selected using AMPure beads (Beckman Coulter A63881) before sequencing.
The Illumina Nextera DNA Flex Library Prep Kit was used to prepare libraries for Illumina sequencing (Illumina, 20018705).

value: Smarca2 -/- Smarca4 fl/fl

value: AAV-TBG-CRE


title: Sample 20, skeletal muscle, control

city: Stockholm

first: Alen

last: Lovric

address: Nobels väg 5

country: Sweden

institute: Karolinska Institutet

data_processing:
Raw sequencing reads were submitted to FASTQCR (v0.1.2) for quality control, and aligned to reference genome (GRCh38.92) using STAR (v2.7.9a). Gene counts were summarised using featureCount (v1.5.1). After trimmed mean M normalization, expression matrices were converted to log2CPM values using edgeR.
Assembly: GRCh38
Supplementary files format and content: Text file with raw counts for all samples

source_name: Vastus lateralis

extract_protocol:
RNA was isolated from muscle tissue using Trizol (Thermofisher) and subsequently purified using RNAEasy columns (Qiagen).
Trueseq Poly-A enriched libraries (Illumina) were prepared from 200 ng of total RNA and libraries were pair-end sequenced using Illumina Nextseq 550.

value: Vastus lateralis

value: Male

value: Control


title: Sample 19, skeletal muscle, control


title: sh55 Day_2  Biol rep 3

value: leukaemia cell line

value: CML myeloid blast crisis


title: liver, dKO, rep3

value: male


title: Sample 18, skeletal muscle, control

value: Female


title: TX BX_1122219_03

description:
TX
_


title: liver, dKO, rep2

value: liver


title: Huh7 YBX1 KO3 cells 1

description:
Library name: TS-3
Huh7 YBX1 KO3 1


title: sh55 Day_1  Biol rep 3

value: day 1


title: TX BX_1121663_03

description:
TX
_


title: sh55 Day_1  Biol rep 2

value: 73 yrs


title: Sample 17, skeletal muscle, control


title: sh53 Day_3  Biol rep 3

value: DRD4 KD sh53

value: day 3


title: TX BX_1122218_03

description:
TX
_

value: Well Functioning Transplant


title: subAR BX_1122530_03

description:
subAR
_

value: Subclinical acute rejection


title: Sample 16, skeletal muscle, control


title: cAR BX_1121662_03

description:
cAR
_

value: Clinical acute rejection


title: liver, L-BRG1KO, rep4

value: Smarca2 +/+ Smarca4 fl/fl


title: sh53 Day_3  Biol rep 2


title: liver, dKO, rep1

value: Smarca2 -/- Smarca4 fl/fl

value: AAV-TBG-CRE


title: Sample 15, skeletal muscle, control

value: Vastus lateralis


title: TX BX_1121658_03

description:
TX
_


title: liver, L-BRG1KO, rep2


title: TX BX_1121525_03

description:
TX
_


title: Sample 13, skeletal muscle, control

value: Control


title: liver, L-BRG1KO, rep3


title: liver, L-BRG1KO, rep1


title: Sample 14, skeletal muscle, control


title: sh53 Day_2  Biol rep 2

value: leukaemia cell line

value: day 2


title: sh53 Day_1  Biol rep 3

value: CML myeloid blast crisis

value: male


title: Sample 12, skeletal muscle, control

value: Female


title: TX BX_1121521_03

description:
TX
_


title: sh53 Day_1  Biol rep 2

value: day 1


title: Sample 11, skeletal muscle, control

value: Male


title: liver, BRMKO, rep3

value: AAV-TBG-GFP

value: liver


title: sh47 Day_3  Biol rep 3

value: DRD3 KD sh47

value: day 3

value: 73 yrs


title: liver, BRMKO, rep2


title: sh47 Day_3  Biol rep 2


title: Sample 10, skeletal muscle, control


title: sh53 Day_2  Biol rep 3

value: DRD4 KD sh53


title: Sample 9, skeletal muscle, control


title: liver, BRMKO, rep1

value: Smarca2 -/- Smarca4 fl/fl


title: sh47 Day_2  Biol rep 3


title: TX BX_1121271_03

description:
TX
_

value: Well Functioning Transplant


title: Sample 8, skeletal muscle, control

value: Vastus lateralis


title: liver, BRG1/BRM, rep4

value: Smarca2 +/+ Smarca4 fl/fl


title: sh47 Day_2  Biol rep 2

value: leukaemia cell line


title: liver, BRG1/BRM, rep3


title: TX BX_1121112_03

description:
TX
_


title: Sample 7, skeletal muscle, control

value: Control


title: sh47 Day_1  Biol rep 3

value: CML myeloid blast crisis


title: liver, BRMKO, rep4

value: male


title: liver, BRG1/BRM, rep2


title: cAR BX_1121131_03

description:
cAR
_

value: Clinical acute rejection


title: Sample 5, skeletal muscle, control

value: Female


title: sh47 Day_1  Biol rep 2

value: day 1


title: liver, BRG1/BRM, rep1

value: AAV-TBG-GFP


title: sh46 Day_3  Biol rep 3

value: DRD3 KD sh46


title: Sample 4, skeletal muscle, control


title: sh46 Day_3  Biol rep 2


title: Sample 3, skeletal muscle, control


title: liver, WT, ZT22, rep3

value: WT

value: liver


title: subAR BX_1121519_03

description:
subAR
_

value: Subclinical acute rejection


title: liver, WT, ZT22, rep2


title: Sample 6, skeletal muscle, control

value: Male


title: sh46 Day_2  Biol rep 3

value: day 2

value: 73 yrs


title: ADNR BX_1120920_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: TX BX_1121518_03

description:
TX
_

value: Well Functioning Transplant


title: Sample 2, skeletal muscle, control

value: Vastus lateralis


title: liver, WT, ZT22, rep1


title: TX BX_1121661_03

description:
TX
_


title: Sample 1, skeletal muscle, control

value: Control


title: sh46 Day_2  Biol rep 2

value: leukaemia cell line

value: CML myeloid blast crisis


title: subAR BX_1120921_03

description:
subAR
_


title: TX BX_1120663_03

description:
TX
_


title: sh46 Day_1  Biol rep 3

value: male


title: liver, WT, ZT18, rep3


title: liver, WT, ZT18, rep2


title: Sample 57, skeletal muscle, heart failure

value: Female

value: Heart Failure


title: TX BX_1120649_03

description:
TX
_


title: sh46 Day_1  Biol rep 2

value: day 1


title: subAR BX_1120289_03

description:
subAR
_


title: liver, WT, ZT18, rep1


title: SCRAMBLED Day_3  Biol rep 4

value: SCR control

value: day 3


title: TX BX_1119869_03

description:
TX
_


title: ADNR BX_1120015_03

description:
ADNR
_


title: Sample 56, skeletal muscle, heart failure


title: SCRAMBLED Day_3 Biol rep 3


title: cAR BX_1119878_03

description:
cAR
_

value: Clinical acute rejection


title: liver, WT, ZT14, rep3

value: WT

value: liver


title: TX BX_1119861_03

description:
TX
_


title: TX BX_1119860_03

description:
TX
_


title: liver, WT, ZT14, rep2


title: Sample 54, skeletal muscle, heart failure

value: Male


title: SCRAMBLED Day_2  Biol rep 4

value: day 2

value: 73 yrs


title: liver, WT, ZT14, rep1


title: Sample 55, skeletal muscle, heart failure


title: SCRAMBLED Day_3  Biol rep 2


title: SCRAMBLED Day_2 Biol rep 3


title: Sample 53, skeletal muscle, heart failure


title: liver, WT, ZT10, rep3


title: ADNR BX_1119791_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: Sample 52, skeletal muscle, heart failure

value: Vastus lateralis


title: liver, WT, ZT10, rep2


title: SCRAMBLED Day_1 Biol rep 4


title: TX BX_1119742_03

description:
TX
_

value: Well Functioning Transplant


title: ADNR BX_1119738_03

description:
ADNR
_


title: liver, WT, ZT6, rep3


title: Sample 50, skeletal muscle, heart failure


title: SCRAMBLED Day_1 Biol rep 3

value: leukaemia cell line


title: TX BX_1119072_03

description:
TX
_


title: Sample 49, skeletal muscle, heart failure


title: TX BX_1120019_03

description:
TX
_


title: SCRAMBLED Day_1 Biol rep 2

value: CML myeloid blast crisis


title: Sample 48, skeletal muscle, heart failure


title: liver, WT, ZT6, rep2

value: male


title: TX BX_1119052_03

description:
TX
_


title: subAR BX_1119051_03

description:
subAR
_

value: Subclinical acute rejection


title: liver, WT, ZT2, rep3


title: Sample 47, skeletal muscle, heart failure

value: Heart Failure


title: Sample 51, skeletal muscle, heart failure

value: Female


title: liver, WT, ZT6, rep1


title: LK_ZF_Rett

city: Rotterdam

first: Naomi

last: Kakiailatu

address: Naomi

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

description: 10x Genomics

data_processing:
Cellranger count (v 4.0.0) was employed for barcode processing, gene counting and aggregation of the samples
Downstream analysis was performed in Seurat (v 4.1.1)
Assembly: GRCz10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Whole gut

growth_protocol: Zebrafish were kept on a 14/10h light/dark cycle. Embryos and larvae were kept in an incubator at 28.5°C in HEPES-buffered E3 medium.

extract_protocol:
At 4 dpf, rethu2846/hu2846 mutant tg(phox2bb:GFP) zebrafish with a total colonic HSCR phenotype were selected. In total 266 intestines of 5 days post-fertilization (dpf) larvae were isolated, cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single-cell RNA sequencing.
Libraries were made according to the manufacter’s instructions (Single Cell 3' v3 chemistry, 10x Genomics)

value: Whole gut

value: rethu2846/hu2846 mutant tg(phox2bb:GFP)

value: 5 days post fertilization


title: ADNR BX_1118900_03

description:
ADNR
_


title: liver, WT, ZT2, rep2

value: WT


title: 20_Ndufs2-homorec_7-dpf_clutch-12

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3401 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: Sample 20

data_processing:
RNA-seq data were preprocessed using the nf-core/RNAseq pipeline version 3.9 with reads aligned to GRCz11 using STAR and quantified using RSEM based on the Lawson Lab Transcriptome Annotation v4.3.2.
Assembly: GRCz11
Supplementary files format and content: tab-separated values file includes raw counts for each sample

source_name: whole organism

growth_protocol: Zebrafish larvae were maintained in E3 media at 28C. On 5 dpf, larvae were maintained in 10 mM Tris E3 media.

extract_protocol:
RNA was harvested using the Qiagen RNeasy Plus Micro kit.
Libraries were generated using PerkinElmer Sciclone® NGSx Workstation.

value: whole organism

tag: days post_fertilization

tag: clutch


title: TX BX_1118189_03

description:
TX
_


title: Sample 46, skeletal muscle, heart failure

value: Male


title: TX BX_1118600_03

description:
TX
_


title: Sample 45, skeletal muscle, heart failure


title: liver, WT, ZT2, rep1

value: liver


title: 19_Ndufs2-homorec_7-dpf_clutch-11

description: Sample 19


title: BMMs, Treatment rep4, 5 days

city: Shanghai

first: Zhuoxuan

last: Jia

state: Shanghai

country: China

institute: Shanghai 9th People’s  Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Bone marrow

value: BMMs

value: M-CSF(30 ng/ml) + RANKL(50 ng/ml) + Annexin A5(2 ug/ml)


title: Sample 43, skeletal muscle, heart failure

value: Vastus lateralis


title: 18_Ndufs2-homorec_7-dpf_clutch-9

description: Sample 18


title: TX BX_1118086_03

description:
TX
_

value: Well Functioning Transplant


title: TX BX_1118089_03

description:
TX
_


title: 21_Ndufs2-homorec_7-dpf_clutch-11

description: Sample 21


title: Sample 58, skeletal muscle, heart failure


title: Sample 42, skeletal muscle, heart failure


title: 16_Ndufs2-homorec_6-dpf_clutch-11

description: Sample 16


title: BMMs, Treatment rep2, 5 days


title: Sample 41, skeletal muscle, heart failure


title: Sample 40, skeletal muscle, heart failure


title: TX BX_1117854_03

description:
TX
_


title: 14_Ndufs2-mix_7-dpf_clutch-12

description: Sample 14


title: BMMs, Model rep4, 5 days

value: M-CSF(30 ng/ml) + RANKL(50 ng/ml)


title: Sample 39, skeletal muscle, heart failure


title: BMMs, Model rep3, 5 days


title: BMMs, Treatment rep1, 5 days


title: Sample 44, skeletal muscle, heart failure


title: 15_Ndufs2-homorec_6-dpf_clutch-9

description: Sample 15


title: 13_Ndufs2-mix_7-dpf_clutch-11

description: Sample 13


title: ADNR BX_1117583_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: BMMs, Treatment rep3, 5 days


title: Sample 38, skeletal muscle, heart failure


title: TX BX_1117182_03

description:
TX
_


title: BMMs, Model rep2, 5 days


title: 17_Ndufs2-homorec_6-dpf_clutch-12

description: Sample 17


title: 12_Ndufs2-mix_7-dpf_clutch-9

description: Sample 12


title: TX BX_1117179_03

description:
TX
_


title: Sample 37, skeletal muscle, heart failure


title: TX BX_1117855_03

description:
TX
_


title: BMMs, Model rep1, 5 days


title: TX BX_1117852_03

description:
TX
_


title: 11_Ndufs2-mix_6-dpf_clutch-12

description: Sample 11


title: Sample 36, skeletal muscle, heart failure


title: TX BX_1117176_03

description:
TX
_


title: 10_Ndufs2-mix_6-dpf_clutch-11

description: Sample 10


title: Sample 35, skeletal muscle, heart failure


title: BMMs, Control rep3, 5 days

value: M-CSF(30 ng/ml)


title: 8_AB_7-dpf_clutch-2

description: Sample 8

value: AB


title: Sample 34, skeletal muscle, heart failure

value: Heart Failure


title: Sample 33, skeletal muscle, heart failure


title: subAR BX_1117054_03

description:
subAR
_

value: Subclinical acute rejection


title: BMMs, Control rep1, 5 days


title: BMMs, Control rep2, 5 days


title: 7_AB_7-dpf_clutch-11

description: Sample 7


title: Sample 32, skeletal muscle, heart failure


title: 6_AB_7-dpf_clutch-9

description: Sample 6


title: Cx3cr1 Cre tomato Pos Day 2

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

data_processing:
Alignment: Cell Ranger V3, aligned to mm10 transcriptome
QC and Filtering: Seurat V4
Unsupervised Clustering: Seurat V4
Assembly: mm10
Supplementary files format and content: Clustered and annotated data in R objects (.rds)

source_name: Heart

extract_protocol:
Hearts were collected, perfused, and enzymatically digested to a single cell supsension. Monocytes and macrophages were sorted via FACS. In the case of the Cx3cr1:CreERT2,Rosa26:tdTomato mice, additional gate was used to separate tdtomato positive and negative cells into separate libraries.
Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics

value: Heart

value: Ischemia reperfusion, tamoxifen pulse chase


title: TX BX_1117046_03

description:
TX
_


title: subAR BX_1117048_03

description:
subAR
_


title: BMMs, Control rep4, 5 days

value: WT


title: Sample 31, skeletal muscle, heart failure


title: Sample 30, skeletal muscle, heart failure

value: Female


title: 5_AB_6-dpf_clutch-11

description: Sample 5

value: whole organism


title: Cx3cr1 Cre tomato Neg Day 2


title: 9_Ndufs2-mix_6-dpf_clutch-9

description: Sample 9


title: 4_AB_6-dpf_clutch-9

description: Sample 4


title: Ccr2 Cre tdTomato Day 28

value: Ischemia reperfusion, single dose tamoxifen


title: Sample 29, skeletal muscle, heart failure

value: Male


title: TX BX_1117040_03

description:
TX
_


title: TX BX_1117174_03

description:
TX
_


title: 3_AB_6-dpf_clutch-2

description: Sample 3


title: Ccr2 Cre tdTomato Day 7


title: 2_AB_6-dpf_clutch-2

description: Sample 2


title: TX BX_1117038_03

description:
TX
_


title: Sample 28, skeletal muscle, heart failure


title: Sample 27, skeletal muscle, heart failure


title: TX BX_1117043_03

description:
TX
_


title: TX BX_1116931_03

description:
TX
_


title: Ccr2 Cre tdTomato Day 3


title: Sample 26, skeletal muscle, heart failure


title: 1_AB_6-dpf_clutch-2

description: Sample 1


title: Embryonic day 12.5 primary mouse orofacial prominences, replicate #3 [snATAC-seq]

city: Farmington

first: Emma

middle: Wentworth

last: Winchester

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

description: sn-Multiome-seq fastq raw reads and aligned matrices

library_source: genomic single cell

data_processing:
Cellranger multiome alignment to mm10 standard build (ATAC and RNA)
Assembly: mm10
Supplementary files format and content: cell x gene matrix (filtered_feature_bc_matrix.h5)
Supplementary files format and content: cell x fragment matrix (atac_fragments.tsv.gz)

source_name: mouse embryonic craniofacial region

extract_protocol:
single nuclei were generated using standard protocols from 10X genomics for generating cryo-protected nuclei.
snMultiome-seq; Chromium Single Cell Multi-ome 3′ Library and Gel Bead kit following the manufacturer’s instructions (10x Genomics)

treatment_protocol: Mouse orofacial regions from multiple mixed sex C57BL/6J Mus Musculus embryos (Jackson Laboratories) were pooled and crosslinked using 1% formaldehyde

value: mouse embryonic craniofacial region


title: Sample 25, skeletal muscle, heart failure


title: TX BX_1116617_03

description:
TX
_


title: Embryonic day 12.5 primary mouse orofacial prominences, replicate #3 [snRNA-seq GEX]


title: cAR BX_1116621_03

description:
cAR
_

value: Clinical acute rejection


title: subAR BX_1116616_03

description:
subAR
_


title: Ccr2 Cre tdTomato Day 13


title: Sample 24, skeletal muscle, heart failure

value: Vastus lateralis


title: Embryonic day 12.5 primary mouse orofacial prominences, replicate #2 [snATAC-seq]


title: Sample 23, skeletal muscle, heart failure


title: Embryonic day 12.5 primary mouse orofacial prominences, replicate #1 [snATAC-seq]


title: Embryonic day 12.5 primary mouse orofacial prominences, replicate #1 [snRNA-seq GEX]


title: Sample 21, skeletal muscle, heart failure


title: subAR BX_1116615_03

description:
subAR
_


title: TX BX_1116372_03

description:
TX
_

value: Well Functioning Transplant


title: subAR BX_1116367_03

description:
subAR
_


title: RAF-D1_R3

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

hyb_protocol: 0,8 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After fragmentation 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K v2  Microarrays (Agilent-026655) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried briefly in acetonitrile.

scan_protocol: Whole Human Genome Microarrays 8x60K v3 (Agilent Technologies)  were scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).Fluorescent signals were extracted and normalized with the Feature Extraction software version 10.5.1.1 (Agilent Technologies),

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MRC5 fibroblast with RAF-ER 1 days after treatment with 10 nM of Tamoxifen (4-OHT). Replicate 3

label_protocol: cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommandations, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MRC5 normal human fibroblasts (ATCC) were cultured in Dulbecco′s modified Eagle′s medium (DMEM, Life Technologies) with GlutaMax and supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin/streptomycin (ThermoFisher Scientific). Cells were maintained at 37°C under a 5% CO2 atmosphere. All experiments were carried out on cells at early passages (between 22 and 28).

extract_protocol: Total RNA was extracted from MRC5 cells using NucleoSpin® RNA (Macherey Nalgen) following the manufacturer's recommendations

treatment_protocol: MRC5 RAFER cells were cultured with vehicle or 4-OHT (10nM) during 1 day

value: MRC5 human fibroblasts


title: Sample 20, skeletal muscle, heart failure


title: RSC 96 cells,(C3, Control)

city: Chengdu

first: Guihua

last: Wei

address: No.111, North 1st Section, 2nd Ring Rd

institute: Southwest Jiaotong University

description:
Library name: C2
Control

data_processing:
Differential gene expression analysis was performed using DESeq2 (v1.4.5), with a Q value threshold of ≤ 0.05.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPkM walues for each sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted from RSC96 Schwann cells using the RNeasy Mini Kit (Qiagen, Catalog ). On-column DNase I digestion (RNase-Free DNase Set, Qiagen, Catalog ) was performed to remove genomic DNA contamination, following the manufacturer's instructions.
All libraries passed standard quality control metrics (average Q-scores >35, mapping percentage > 80).

value: Schwann cell

value: wild type

value: Control

value: batch 3


title: Embryonic day 11.5 primary mouse orofacial prominences, replicate #3 [snRNA-seq GEX]


title: RSC 96 cells, (C1, Control)

description:
Library name: C1
Control

value: batch 1


title: RAF-D1_R1

source_name: MRC5 fibroblast with RAF-ER 1 days after treatment with 10 nM of Tamoxifen (4-OHT). Replicate 1


title: Sample 18, skeletal muscle, heart failure

value: Heart Failure


title: Embryonic day 12.5 primary mouse orofacial prominences, replicate #2 [snRNA-seq GEX]


title: Embryonic day 11.5 primary mouse orofacial prominences, replicate #2 [snATAC-seq]


title: Sample 22, skeletal muscle, heart failure


title: RAF-D1_R2

source_name: MRC5 fibroblast with RAF-ER 1 days after treatment with 10 nM of Tamoxifen (4-OHT). Replicate 2


title: RSC 96 cells,(B3,H+PCL@PDA)

description:
Library name: B2
This sample represents RSC96 Schwann cells treated with macrophage-conditioned medium and the no piezoelectric material PVDF@PDA under hypoxic conditions.

value: Hypoxia + PCL@PDA


title: TX BX_1116094_03

description:
TX
_


title: TX BX_1116093_03

description:
TX
_


title: Sample 17, skeletal muscle, heart failure


title: CTRL-D1_R2

source_name: MRC5 fibroblast with RAF-ER 1 days after treatment with control vehicule. Replicate 2


title: Embryonic day 11.5 primary mouse orofacial prominences, replicate #2 [snRNA-seq GEX]

value: WT


title: ADNR BX_1116099_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: TX BX_1116095_03

description:
TX
_


title: subAR BX_1116366_03

description:
subAR
_

value: Subclinical acute rejection


title: CTRL-D1_R3

source_name: MRC5 fibroblast with RAF-ER 1 days after treatment with control vehicule. Replicate 3


title: Embryonic day 11.5 primary mouse orofacial prominences, replicate #3 [snATAC-seq]


title: Sample 19, skeletal muscle, heart failure


title: RSC 96 cells,(B1,H+PCL@PDA)

description:
Library name: B1
This sample represents RSC96 Schwann cells treated with macrophage-conditioned medium and the no piezoelectric material PVDF@PDA under hypoxic conditions.


title: Sample 16, skeletal muscle, heart failure


title: CTRL-D1_R1

source_name: MRC5 fibroblast with RAF-ER 1 days after treatment with control vehicule. Replicate 1


title: RSC 96 cells, (A3, H+PVDF@PDA)

description:
Library name: A2
This sample represents RSC96 Schwann cells treated with macrophage-conditioned medium and the piezoelectric material PVDF@PDA under hypoxic conditions.

value: Hypoxia + PVDF@PDA


title: Sample 15, skeletal muscle, heart failure

value: Male


title: Embryonic day 11.5 primary mouse orofacial prominences, replicate #1 [snRNA-seq GEX]

value: mouse embryonic craniofacial region


title: subAR BX_1116087_03

description:
subAR
_


title: RSC 96 cells, (A1, H+PVDF@PDA)

description:
Library name: A1
This sample represents RSC96 Schwann cells treated with macrophage-conditioned medium and the piezoelectric material PVDF@PDA under hypoxic conditions.


title: TX BX_1116089_03

description:
TX
_


title: Sample 14, skeletal muscle, heart failure

value: Female


title: Embryonic day 10.5 primary mouse orofacial prominences, replicate #3 [snATAC-seq]


title: ADNR BX_1116091_03

description:
ADNR
_


title: ADNR BX_1116083_03

description:
ADNR
_


title: SSLS2pm6

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

description: Library name: OK71

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: reference genome was built using Hisat2 v2.0.5 a
Supplementary files format and content: excel file with FPKM

source_name: Kidney cortex

extract_protocol:
RNA was extracted using the Trizol reagent according to the manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification). The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Kidney cortex

value: SS WT

value: 0.4% NaCl diet


title: Embryonic day 10.5 primary mouse orofacial prominences, replicate #3 [snRNA-seq GEX]


title: Sample 13, skeletal muscle, heart failure

value: Vastus lateralis


title: Sample 12, skeletal muscle, heart failure


title: Embryonic day 10.5 primary mouse orofacial prominences, replicate #2 [snATAC-seq]


title: SSLS2pm4

description: Library name: OK63


title: Embryonic day 11.5 primary mouse orofacial prominences, replicate #1 [snATAC-seq]


title: TX BX_1115735_03

description:
TX
_

value: Well Functioning Transplant


title: Sample 11, skeletal muscle, heart failure


title: Embryonic day 10.5 primary mouse orofacial prominences, replicate #2 [snRNA-seq GEX]


title: SSLS2pm3

description: Library name: OK62


title: Sample 10, skeletal muscle, heart failure


title: SSLS2pm2

description: Library name: OK61


title: Sample 9, skeletal muscle, heart failure


title: Embryonic day 9.5 primary mouse orofacial prominences, replicate #3 [snATAC-seq]


title: Embryonic day 10.5 primary mouse orofacial prominences, replicate #1 [snRNA-seq GEX]


title: subAR BX_1115734_03

description:
subAR
_


title: Sample 8, skeletal muscle, heart failure


title: Per1LS2am5

description: Library name: AZ283


title: ADNR BX_1115395_03

description:
ADNR
_


title: TX BX_1115731_03

description:
TX
_


title: SSLS2pm5

description: Library name: OK64


title: ADNR BX_1115394_03

description:
ADNR
_


title: Sample 7, skeletal muscle, heart failure


title: Per1LS2am4

description: Library name: AZ282


title: Sample 6, skeletal muscle, heart failure


title: Embryonic day 9.5 primary mouse orofacial prominences, replicate #2 [snATAC-seq]


title: Per1LS2am2

description: Library name: AZ280


title: Per1LS2am3

description: Library name: AZ281


title: Embryonic day 10.5 primary mouse orofacial prominences, replicate #1 [snATAC-seq]


title: Embryonic day 9.5 primary mouse orofacial prominences, replicate #3 [snRNA-seq GEX]


title: TX BX_1115282_03

description:
TX
_


title: SSLS2pm1

description: Library name: OK60


title: Sample 5, skeletal muscle, heart failure


title: Embryonic day 9.5 primary mouse orofacial prominences, replicate #2 [snRNA-seq GEX]


title: TX BX_1115733_03

description:
TX
_


title: Sample 4, skeletal muscle, heart failure


title: Embryonic day 9.5 primary mouse orofacial prominences, replicate #1 [snATAC-seq]


title: TX BX_1115281_03

description:
TX
_


title: Per1LS2am1

description: Library name: AZ279


title: ADNR BX_1115120_03_2

description:
ADNR
_


title: Embryonic day 9.5 primary mouse orofacial prominences, replicate #1 [snRNA-seq GEX]


title: SSLS2am6

description: Library name: AZ256


title: Sample 3, skeletal muscle, heart failure


title: TX BX_1115005_03

description:
TX
_


title: Sample 2, skeletal muscle, heart failure


title: SSLS2am5

description: Library name: AZ255


title: KO3

city: Beijing

first: Zheng

last: LV

address: State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China

institute: China Agricultural University

description: Tmc7 knockout

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: testis

extract_protocol:
Trizol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: testis

value: knockout


title: KO2

description: Tmc7 knockout


title: SSLS2am4

description: Library name: AZ254


title: KO1

description: Tmc7 knockout


title: SSLS2am3

description: Library name: AZ253


title: Nuclei from P3 pooled from mouse kidneys

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

description:
Library name: mouse_p3d_kidney
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were performed  using the Cell Ranger software v5.0.1 (P3) and v7.0.0 (E18.5) (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-delimited value files and matrix files.

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
Kidneys were dissected in cold PBS without calcium or magnesium, snap-frozen for genotyping, and then thawed on ice for pooling. We minced the kidneys using razorblades and homogenized them with a Dounce homogenizer in Nuclei EZ Lysis buffer (Sigma) supplemented with protease inhibitor (Roche), RNase inhibitor (Promega and Life Technologies). The homogenate was filtered through a 40μm cell strainer (pluriSelect) and centrifuged at 500 x g for 5 min at 4°C. The pellet was resuspended, washed, and filtered again through a 5μm cell strainer (pluriSelect).
The resulting nuclei suspensions were submitted to UTSW Next Gen Sequencing Core for library preparation and sequencing using the Chromium Single Cell 3' Prime Gene Expression kit (10x Genomics) on an Illumina NextSeq 2000.

value: Kidney

value: Wild type

value: pooled male and female

tag: strain background


title: TX BX_1115016_03

description:
TX
_

source_name: Renal Biopsy


title: Ctrl3

description: Control

tag: tissue

value: heterozygote


title: ADNR BX_1114724_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: Ctrl2

description: Control


title: Sample 6 R403Q-EMPA

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

description:
Library name: Sample 6
10x Genomics

data_processing:
BaseCalls performed using Illumina
Demultiplexing performed using Cell Ranger v8.0.1 with default settings
Reads aligned to GRCm39 reference genome using Cell Ranger v8.0.1 with --expect-cells=3000
Assembly: GRCm39
Supplementary files format and content: Tab delimited text files containing the counts values for each sample

source_name: left ventricle

growth_protocol: Mice were housed under standard laboratory conditions with controlled temperature, humidity, and light.

extract_protocol:
Nuclei were isolated from 50 mg fresh frozen cardiac samples (n=2) using the 10x Genomics Chromium Nuclei isolation kit (PN-1000494, with RNAse inhibitor; 10X Genomics, Pleasanton, CA, USA), conforming to the manufacturer protocol.
scRNA-seq libraries were generated in BU DOM Single Cell sequencing core facility and sequenced by BU Microarray and Sequencing Resource Core Facility according to 10x Genomics protocol

treatment_protocol: Hypertrophic cardiomyopathy (HCM) is a hereditary cardiac disorder caused by mutations in several sarcomere genes, integral to the heart's contractile machinery. Mice harboring R403Q mutation in cardiac myosin heavy chain (a mouse model of HCM) were used in this study. Mice were randomized by body weight and divided into 3 groups: i) WT-CD; ii) R403Q-CD; and iii) R403Q-EMPA. Nine-to-ten-week-old male mice harboring R403Q mutation in cardiac myosin heavy chain or wild-type littermates (WT) were fed ad libitum a control diet (CD; 10 % kcal lard, 0 % sucrose; product No. D09071703; Research Diets, New Brunswick, NJ, USA) or the same diet enriched with empagliflozin (EMPA, 0.15 mg/g of diet; Boehringer Ingelheim, Ingelheim am Rhein, Germany) for 16 weeks. This dose of empagliflozin is equivalent to approximately 15 mg/kg body weight. Single-nucleus RNA sequencing was performed in hearts from 12-week-old mice.

value: left ventricle

value: cardiomyocytes, endocardial, epicardial fat, endothelial, lymphoid, myeoloid, smooth muscle, stromal cells

value: Empagliflozin diet (EMPA)


title: TX BX_1114721_03

description:
TX
_

data_processing: All samples were processed using the Affymetrix Gene Titan MC instrument following the standard procedure outlined in the user guide for the HT HG-U133 Plus PM Array Plate. https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fgenetitan_mc_user_guide.pdf

extract_protocol: PAXgene extraction of total RNA was performed using the PAXgene RNA extraction kit according to the manufacturer's instructions.


title: cAR BX_1114723_03

description:
cAR
_

value: Clinical acute rejection


title: SSLS2am1

description: Library name: AZ251


title: Per1LS2pm6

description: Library name: AZ043


title: SSLS2am2

description: Library name: AZ252


title: Sample 5 R403Q-CD

description:
Library name: Sample 5
10x Genomics

value: Control Diet (CD)


title: Ctrl1

description: Control


title: Sample 4 WT-CD

description:
Library name: Sample 4
10x Genomics

value: wild-type (WT)


title: Per1LS2pm5

description: Library name: AZ042

value: Kidney cortex


title: Sample 1, skeletal muscle, heart failure

source_name: Vastus lateralis

value: Male

tag: disease state

value: Heart Failure


title: TX BX_1114715_03

description:
TX
_

value: Well Functioning Transplant


title: TX BX_1114718_03

description:
TX
_


title: ADNR BX_1114713_03

description:
ADNR
_


title: Nuclei pooled from from E18.5 mouse kidneys

description:
Library name: mouse_e18.5d_kidney
10x Genomics

value: Mycf/f;Mycnf/f (no Cre)

value: mixed


title: TX BX_1114714_03

description:
TX
_


title: ADNR BX_1114361_03

description:
ADNR
_


title: Old injured 2

city: San Francisco

first: Javier

last: Gomez Ortega

address: 513 Parnassus Ave.

institute: UCSF

description:
The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform
O_I_2

data_processing:
The demultiplexed FASTQ files were aligned to the mouse genome (mm10) using PIPseeker 1.0.0 (Fluent Biosciences), indicating that a v4 chemistry kit was used. After sequence alignment, we observed around 50% of input cells being called when PIPseeker sensitivity level was set to 3, which was near the inflection point of the barcode rank plot.
Assembly: mm10

source_name: Lung

extract_protocol:
For lung injury, mice anesthetized with isoflurane were instilled with bleomycin (Fresenius, 3U/Kg) by oropharyngeal aspiration, and lungs were isolated after 7 days after injury. After mincing with scissors, the tissue was resuspended in RPMI with 0.2% Collagenase (10103586001, Roche), 2000 U/ml DNase I (4716728001, Roche) and 0.1 mg/ml Dispase II (4942078001, Sigma). The suspension was incubated for 1 hour at 37oC and passed through a 70 mm filter (130-110-916, MACS SmartStrainers) to obtain single cells. The cells were washed twice with 1X PBS pH 7.4 (10010023, Gibco). Immune cells were obtained by positive selection by binding to CD45 microbeads and passing through MACS columns (130-049-601, Miltenyi Biotech). Primary mouse lung fibroblasts were freshly isolated after magnetic bead-based negative selection of epithelial cells (118204, Biotin anti-mouse CD326 Epcam, Clone: G8.8, BioLegend), endothelial cells (102404, Biotin anti-mouse CD31, clone: 390), immune cells (103104, Biotin anti-mouse CD45, clone: 30-F11, BioLegend), pericytes and smooth muscle cells (134716, Biotin anti-mouse CD146, clone: ME-9F1, BioLegend), and red blood cells (116204, Biotin anti-mouse Ter119, clone: TER-119, BioLegend) with biotinylated antibodies and Dynabeads (MyOne Streptavidin T1, 65601, Thermo Fisher Scientific)
PIPseq T2 3ʹ Single Cell RNA Kit (v4.0 – directly sequenced cells) was used for pre-templated instant partitioning (PIP) to capture single-cell mRNA transcripts with PIP beads according to manufacturer’s protocol (Fluent Biosciences). In the case of directly sequenced cells, 7 days after bleomycin injury, cells were isolated by the isolation procedure described above for scRNAseq workflow. Cells were washed in ice-cold PIPseq Cell Suspension Buffer. Cells were counted and stained with Trypan blue to confirm >90% viability. Cell concentration was adjusted to around 1,000 cells/mL with Cell Suspension Buffer. Five mL of ice-cold cell suspension from each co-culture group were loaded (around 5,000 cells) into individual PIPseq tubes. PIP beads and cells were vortexed droplet encapsulation. Emulsified lysis reagents were mixed and incubated with PIP droplets to lyse cells and release mRNA at 37° C. PIP droplets were cooled down to 4C for mRNA annealing to the PIP beads. After emulsion breakage and bead washing, the captured transcripts on PIP beads were converted into cDNAs with reverse transcription and template-switching reagents. The beads were washed again and then mixed with whole transcriptome amplification (WTA) reagents, which amplified the library from cDNAs on the PIP beads. The WTA library was purified with Solid Phase Reversible Immobilization (SPRI) beads before library fragmentation, end-repair, and A-tailing reactions. The fragmented library was then ligated with indexing adapters. Finally, sequencing adapters and dual-indices were attached to the library through indexing PCR. The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform, with a target yield of 100 million reads per sample, or 20,000 reads per input cell.

value: Lung

value: CD45+ cells and fibroblasts

value: WT

value: Bleomycin


title: Old injured 1

description:
The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform
O_I_1


title: Per1LS2pm4

description: Library name: AZ041

value: 0.4% NaCl diet


title: Sample 2 R403Q-CD

description:
Library name: Sample 2
10x Genomics

value: left ventricle


title: Per1LS2pm3

description: Library name: AZ040


title: Old uninjured 2

description:
The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform
O_UI_2

value: Control


title: Sample 3 R403Q-EMPA

description:
Library name: Sample 3
10x Genomics

value: cardiomyocytes, endocardial, epicardial fat, endothelial, lymphoid, myeoloid, smooth muscle, stromal cells

value: Empagliflozin diet (EMPA)


title: TX BX_1114354_03

city: La Jolla

first: SUNIL

last: KURIAN

institute: Scripps Health

description:
TX
_


title: Per1LS2pm2

description: Library name: AZ039


title: Per1LS2pm1

description: Library name: AZ038


title: Epididymitis, Cauda, E6-4

city: GLEN IRIS

first: Claire

last: Sun

state: VIC

address: 27-31 wright street

country: Australia

institute: hudson institute of medical research

data_processing:
Base calling was performed using Dragen BCLConvert (3.7.4).
Assembly: MM10
Supplementary files format and content: CSV file includes counts.

source_name: Epididymis - cauda region

extract_protocol:
Total cellular RNA was extracted from C57bl6 adult mouse epididymal cauda using the RNeasy mini kit (QIAGEN GmBH, Hilden, Germany), and on-column DNase treatment was performed. Total RNA concentration was quantified by Qubit (Invitrogen) and quality checked by Bioanalyzer (Agilent).
Briefly index is added during initial pA priming and pooled samples amplified using template switching oligo. P5 is added by tagmentation by Nextera transposase and PCR. Shared NextSeq2000 run using P3 100cycle kit. (cDNA reads generated 100nt).

value: Epididymis - cauda region


title: Young injured 2

description:
The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform
Y_I_2


title: Epididymitis, Cauda, E7-2


title: Young injured 1

description:
The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform
Y_I_1


title: TX BX_1114350_03

address: 10666 N Torrey Pines Rd

description:
TX
_


title: SSHS2am5

description: Library name: AZ249

value: SS WT

value: 4% NaCl diet


title: ADNR BX_1114207_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: Young uninjured 2

description:
The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform
Y_UI_2


title: SSHS2am4

description: Library name: AZ247

value: Kidney cortex


title: Young uninjured 1

description:
The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform
Y_UI_1


title: Epididymitis, Cauda, E12-2ev

value: Male


title: SSHS2am3

description: Library name: AZ246


title: TX BX_1114204_03

description:
TX
_

value: Well Functioning Transplant


title: Sample 1 WT-CD

description:
Library name: Sample 1
10x Genomics

value: wild-type (WT)

value: Control Diet (CD)


title: Old uninjured 1

description:
The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform
O_UI_1

value: Lung

value: CD45+ cells and fibroblasts


title: Prrc2bf/f; Olig2-Cre OPC Rep3

city: beijing

first: Zhihong

last: Song

address: Taiping Road 27

institute: Beijing Institute of Basic Medical Sciences

data_processing:
Firstly, clean reads were aligned to mouse genome (version mm10) using HISAT2 (version 2.2.1). Then the number of reads were mapped to each gene and counted using HTSeq (version 0.12.4), with -stranded = no. Differentially expressed genes (DEGs) were defined by absolute value of log2(fold change) higher than 0.26 and P<0.05 using DESeq2 (version 1.26.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include reads count  values for each Sample

source_name: oligodendrocyte progenitor cell

growth_protocol: OPCs were cultured in medium for proliferation (DMEM/ F12 plus 1 mM sodium pyruvate, 10 ng/ml PDGF-AA, 10 nM D-biotin, 100 units/ml penicillin, and 100 μg/ml streptomycin, 5 μg/ml Insulin, Glutamax, N2, B27, 10 ng/ml bFGF, 10 ng/ml CNTF, 5 μg/ml NAC, 2 μM Forskolin, 1 ng/ml NT3)

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. The RNA integrity was assessed by Bioanalyzer 2100 with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China).

treatment_protocol: OPC could  be obtained from the cortex of C57BL/6J mouse pups at postnatal days 4 (P4). The isolated tissues were cut into pieces and digested into a single-cell suspension with the papain buffer at 37℃ for 20 min. Cells were resuspended with the panning buffer (DPBS with 0.2% BSA) and incubated in dishes successively pre-coated with the second (IgG) and primary antibodies (GalC) for 1h. Subsequently, the cell suspension was transferred into the O4-coated dishes for 2h. After rinsed twice, cells absorbed on dishes were digested with 0.125% trypsin and be purified OPCs. OPCs were plated in poly-D-lysine-coated plates and cultured in medium.

value: oligodendrocyte progenitor cell

value: Prrc2bf/f; Olig2-Cre


title: SSHS2am2

description: Library name: AZ234


title: Prrc2bf/f; Olig2-Cre OPC Rep2


title: TX BX_1114351_03

description:
TX
_


title: Control, Cauda, C17-2ev

value: WT


title: subAR BX_1114001_03

description:
subAR
_

value: Subclinical acute rejection


title: SSHS2am1

description: Library name: AZ233


title: cAR BX_1114018_03

description:
cAR
_

value: Clinical acute rejection


title: subAR BX_1114017_03

description:
subAR
_


title: Prrc2bf/f; Olig2-Cre OPC Rep1


title: Control, Cauda, C11-2

value: Control


title: SSHS2pm5

description: Library name: AZ61


title: Epididymitis, Cauda, E27-2ev

value: Epididymis - cauda region


title: TX BX_1114000_03

description:
TX
_


title: Control, Cauda, C10-1


title: Prrc2bf/f  OPC Rep3


title: SSHS2pm4

description: Library name: AZ60

value: SS WT


title: TX BX_1113998_03

description:
TX
_


title: Adjuvant, Cauda, A25-3ev

value: Adjuvant


title: Prrc2bf/f  OPC Rep2


title: Prrc2bf/f  OPC Rep1


title: Adjuvant, Cauda, A24-2ev


title: SSHS2pm3

description: Library name: AZ59

value: 4% NaCl diet


title: SSHS2pm2

description: Library name: AZ008

value: Kidney cortex


title: Adjuvant, Cauda, A1-2

value: Male


title: Prrc2bf/f; Nestin-Cre NSC Rep2

data_processing:
Firstly, clean reads were aligned to mouse genome (version mm10) using HISAT2 (version 2.2.1). Then the number of reads were mapped to each gene and counted using HTSeq (version 0.12.4), with -stranded = no. Differentially expressed genes (DEGs) were defined by absolute value of log2(fold change) higher than 0.26 and P<0.05 using DESeq2 (version 1.26.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include reads count values for each Sample

source_name: brain

growth_protocol: Neural stem cells were purified and cultured in a proliferation medium (Neurobasal A medium/DMEM/F12 plus 2% B27 supplement, 100 units/mL penicillin, 100 μg/mL streptomycin, 10 ng/mL bFGF, and 10 ng/mL EGF).

treatment_protocol: The cerebral cortex was isolated from embryos of E17 mice, mechanically blown with a pipetting gun and filtered through a filter to single cell suspension. Neural stem cells were grown in proliferation medium for 1 days.

value: brain

value: Neural stem cells

value: Prrc2bf/f; Nestin-Cre


title: Prrc2bf/f; Nestin-Cre NSC Rep1


title: Adjuvant, Cauda, A13-1ev


title: Epididymitis, Cauda, E12-3ev


title: SSHS2pm1

description: Library name: AZ007


title: Per1HS2am5

description: Library name: AZ289


title: TX BX_1113997_03

description:
TX
_

value: Well Functioning Transplant


title: MC903, HTO_derived_cDNA

city: ILLKIRCH

first: Mei

last: Li

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
BFPRFP_barcodes.tsv.gz
BFPRFP_features.tsv.gz
BFPRFP_matrix.mtx.gz

library_source: other

data_processing:
After sequencing (with a mean depth of 59451 reads/cell), reads were processed with Cell Ranger count (10X Genomics) version 7.0.0 on a hybrid reference composed of the Mus mus-culus genome assembly GRCm39 (mm39) with BFP and RFP sequences.
Assembly: genome assembly GRCm39 (mm39) with BFP and tdRFP sequences
Supplementary files format and content: barcodes, features, and matrix files. Matrix contain counts for each barcodes and genes.
Library strategy: CITE-seq

molecule: protein

source_name: Ear-draining lymph node

extract_protocol:
At D5, EDLN were proceeded for cell sorting. Migratory non-LC-non-cDC1 (nLCncDC1, gated as B220-MHCIIhiCD11clowtointXCR1-CD326-) were FACS-sorted in 4 populations accord-ing to the expression of reporters: BFP+RFP+ (B+R+), BFP-RFP+ (B-R+), BFP+RFP- (B+R-) or BFP-RFP- (B-R-). These cells were then labelled with A0301 Hashtag1 (H1) (Biolegend, #155801), A0302 Hashtag2 (H2) (Biolegend, #155803), A0303 Hashtag3 (H3) (Biolegend, #155805) and A0304 Hashtag4 (H4) (Biolegend, #155807), respectively. Meanwhile, cells were also labelled with for Antibody Derived Tags (ADT): TotalSeq™ A0014 anti-CD11b (Biolegend, #101265),  A0002 anti-CD8a (Biolegend, #100773), TotalSeq™ C0422 anti-CD172a(Biolegend, #144033) and TotalSeq™ B0566 anti-CD301b (Biolegend, #146817)
The 4 labelled migDC populations were pooled at the ratio 1:1:2:1 (5200 B+R+ cells, 5200 B-R+ cells, 10400 B+R- cells and 5200 B-R- cells), and submitted for 3’mRNAseq library preparation using the Single Cell 3' Reagent Kit v3.1 chemistry (dual index) following the guidelines of the 10X Genomics user manual: CG000317 Rev D, and the Biolegend protocol TotalSeq™-A An-tibodies and Cell Hashing. Single cell suspensions were processed on the 10X Genomics Chromium iX. cDNA amplification was carried out using 11 cycles of PCR. Dual index library construction was performed with 13 (HTO), 14 cycles (ADT), or 12 cycles (3’ gene expression library) during sample index PCR. Final library quantification and quality control were complet-ed using Bioanalyzer 2100 (Agilent Technologies, Les Ulis, France). Libraries were sequenced in one lane on an Illumina NextSeq 2000 sequencer as paired-end 28 + 85 base reads.

treatment_protocol: SiglechiCreTg/0 ROSA26LoxP-STOP-LoxP-RFP Tnfsf4KI/+ mice were treated with MC903 at D0, D2 and D4.

value: Ear-draining lymph node

value: non-LC-non-cDC1 migDC


title: Prrc2bf/f  NSC Rep2


title: Per1HS2am4

description: Library name: AZ288


title: Prrc2bf/f  NSC Rep1


title: MC903, ADT_derived_cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
BFPRFP_barcodes.tsv.gz
BFPRFP_features.tsv.gz
BFPRFP_matrix.mtx.gz


title: MC903, mRNA_derived_cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
BFPRFP_barcodes.tsv.gz
BFPRFP_features.tsv.gz
BFPRFP_matrix.mtx.gz

molecule: polyA RNA


title: TSC-CTL Sample 3

city: Columbia

first: Pallav

last: Singh

address: CE720 Clinical Support and Education

department: Institute for Data Science and Informatics

institute: University of Missouri

data_processing:
Trimgalore 0.6.7 was used for removing Illumina adapters, ambiguous nucleotides (N’s), any sequence reads with total read length < 20 bp and the quality Phred score < 20
Hisat2 version 2.2.1 was used for alinging the sequences with the assembely
Cufflinks version 2.2.1 was used for obtaining the FPKM values as well as cuffdiff method within the package was used for finding out the differentially expressed genes
Assembly: GRCm39
Supplementary files format and content: annotated output with FPKM values in csv file format

source_name: mTSC

growth_protocol: mTSCs grown for and were maintained in an undifferentiated state to Day 4 with FGF4 and heparin; pTGCs were differentiated to Day 6 using retinoic acid

extract_protocol:
RNA extracted using the Qiagen Allprep DNA/RNA/miRNA Universal Kit; RNA was stored at -80C
Libraries were constructed per the manufacturer’s protocol with reagents supplied in Illumina’s mRNA Stranded Library Preparation Kit

treatment_protocol: Cells were treated with either 10 ug/mL oxycodone or 0.9% saline solution in 2 mL medium each time their medium was changed

value: mTSC

value: SALINE (CTL)


title: D. rerio, RNA002 chemistry

city: Aurora

first: Laura

last: White

state: CO

address: 12801 E 17th Avenue RC1S

department: Biochemistry & Molecular Genetics

institute: University of Colorado

description: tRNA sequencing (RNA002)

data_processing:
All libraries were rebasecalled with Dorado 0.7.0 using multiple basecalling models as described in the accompanying manuscript; fastqs have been provided from the highest accuracy basecalling model for each library along with the original POD5 file.
Alignments to tRNA references were performed using BWA-MEM version 0.7.16 with the parameters bwa mem -C -W 13 -k 6 -T 20 -x ont2d.
Further description of alignment, modification analysis, custom scripts and tRNA reference files can be found at  github.com/rnabioco/tRNA004
Assembly: custom tRNA references available at github.com/rnabioco/tRNA004
Supplementary files format and content: bedgraphs of full length filtered reads aligned to tRNA references

molecule: other

source_name: 3dpf embryo

extract_protocol:
Total RNA extraction protocols for each sample type are detailed in the accompanying manuscript; library inputs were size selected for RNA 17-200 nt in length.
complete protocol for tRNA sequencing available at github.com/rnabioco/tRNA004

value: 3dpf embryo


title: TSC-OXY Sample 3

value: OXY


title: TSC-CTL Sample 2


title: Per1HS2am3

description: Library name: AZ286


title: 4-day differentiated macrophages from healthy donor 16 (D16_ArMas_SIS17)

city: Atlanta

first: Rabindra

last: Tirouvanziam

state: GA

address: 2015 Uppergate Dr

institute: Emory University

description: Library name: E17D16_ArMas_SIS17_S9

data_processing:
Hisat2 was used to align next-generation sequencing reads to the reference genome
SAMtools was used to sort BAM files.
FeatureCounts from the  Subread package was used to generate read counts expressed per gene
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: macrophage

growth_protocol: We used Alvetex (Reprocell) 200 μm-thick inert 3D scaffolds with >90% porosity (pore sizes of 36–40 μm, with interconnects of 12–14 μm). In brief, inserts were activated with 70% ethanol, coated overnight at 37ºC with rat-tail collagen I (3 mg/mL, Sigma) and seeded with H441 cells at 2.5×105 cells per 12-well insert. Cells were first grown in submerged cultures with DMEM/F12 supplemented with 10% heat-inactivated serum, penicillin, and streptomycin. After 2 days, cells were supplemented basally with serum-free DMEM/F12 with 10% Ultroser G (Pall Life Sciences) to establish air liquid interface (ALI).  Cultures were grown for 2 weeks at ALI and supplemented basally with fresh medium every 48 hours. For transmigration experiments, the ALI cultures were placed with the apical compartment exposed to RPMI, CCL2 (0.25 ng/mL), airway supernatant (ASN) from CF patiens sputum, and CFASN with EVs removed.  Then 1e6 blood monocoytes were loaded onto the 200 µm-think basal compartment of the Alvetex scaffold, and allowed to migrate at 37ºC at 5% CO2 through the collagen and epithelial layers into the apcial compartment.  The monocytes were collected 18 hours after transmigration.  Other isolated monocytes were culutred in the transmigration media without transmigrating.  Transmigrated cells were then differentiated with M-CSF for 4 days uninterrupted in either complete media (CCL2) or complete media with CFASN (CF).  Some samples were treated with SIS17 or MSA-2 for 24 hours after differentiation and other samples were used as control.

extract_protocol:
RNA was extracted from the cells using TriPure Isolation Reagent mixed with chloroform 4:1.  After spinning, the aqueous phase is mixed 1:1 with 200 proof EtOH.  The mixture is then processed following the protocol of RNA Clean and Concentrator -5 (ZYMO Research).  RNA quality and concentration was quantified using a Bioanalyzer (Agilent technologies, Inc.) and only samples with RIN >5.0 were used for sequencing.
cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) and the final sequencing library is made using the Nextera XT kit (Illumina) with an aim of ~32 million reads per sample.

treatment_protocol: In this model, circulating monocytes are migrated through a small airway epithelium grown at air-liquid interface toward CF airway supernatant (CFASN, sputum from paitents with CF sequentially centrifuged to remove cells and bacteria), CFASN without extracellular vesicles (EVs), or CCL2, placed apically.  Specifically, we transmigrated monocytes in the model for 18 hours into CFASN, CFASN without EVs, and CCL2 followed by differentiation with M-CSF.  Some samples were cultured with immunomoldulatory drugs for 24 hours after differentiation.

tag: source

value: blood

value: macrophage

tag: media condition

value: M-CSF differentiated in complete media

tag: drug treatment

value: Treated with drug:SIS17


title: Per1HS2am1

description: Library name: AZ284

value: 4% NaCl diet


title: 4-day differentiated macrophages from healthy donor 485 (D485_ArMas_SIS17)

description: Library name: E17_2D485_ArMas_SIS17_S34


title: Per1HS2pm5

description: Library name: AZ45

value: Kidney cortex


title: Per1HS2pm4

description: Library name: AZ44


title: TSC-CTL Sample 1


title: 18-hour culture of circulating monocytes from healthy donor 14 (D14_CiMos_CCL2)

description: Library name: E16_2D14_CiMos_CCL2_S12

source_name: monocyte

value: monocyte

value: 18-hour culture no transmigration

value: No Drug


title: Per1HS2am2

description: Library name: AZ285


title: TSC-OXY Sample 1


title: TSC-OXY Sample 2


title: TX BX_1113516_03

description:
TX
_

tag: tag


title: Per1HS2pm3

description: Library name: AZ006


title: Per1HS2pm1

description: Library name: AZ004


title: 18-hour transmigrated monocytes from healthy donor 8 (D8_ArMos_CCL2)

description: Library name: E16D8_ArMos_CCL2_S2

value: 18-hour transmigration toward CCL2


title: Per1HS2pm2

description: Library name: AZ005


title: pTGC-CTL Sample 2

source_name: Trophoblast Giant Cell

value: Trophoblast Giant Cell


title: Rat heart_Sac/Val_rep5

city: Nagoya-shi

first: Yuka

last: Kono

state: Aichi

address: 2-1723, Omori, Moriyama-ku

country: Japan

institute: Kinjo Gakuin University

description: Library name: Sample20-4-5

data_processing:
RNA sequencing was  performed using a NovaSeq6000 (Illumina, Inc, San Diego, USA) sequencer at 20 million paired-end reads per sample. All reads were checked, and low-quality reads were removed using fastp (ver0.23.2).
Assembly: mRatBN7.2
Supplementary files format and content: one excel file include CPM values for each Sample

source_name: Heart

extract_protocol:
RNA was extracted from the heart tissues using ISOGEN II (Nippon Gene Co., Ltd., Tokyo, Japan). Total RNA concentration was quantified using Dw-K2800 Nucleic Acid Analyzer (Shanghai Drawell Scientific Instrument Co., Ltd., Shanghai, China).
Total RNA (800 ng) from each heart sample was converted to Illumina compatible libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.

value: Heart

value: No treatment


title: Circulating monocytes from healthy donor 5 (CiMos_5)

description: Library name: E9_CiMos_5_S35

value: untreated

value: baseline no transmigration


title: pTGC-CTL Sample 3

value: SALINE (CTL)


title: ADNR BX_1113028_03

description:
ADNR
_

value: Acute dysfunction no rejection


title: Circulating monocytes from  donor with CF 485 (D485_CiMos)

description: Library name: E17_2D485_CiMos_S32

value: blood


title: ADNR BX_1113325_03

description:
ADNR
_


title: TX BX_1113332_03

description:
TX
_

value: Well Functioning Transplant


title: 4-day differentiated macrophages from donor with CF 317 (D317_ArMas_SIS17)

description: Library name: E17_2D317_ArMas_SIS17_S31

value: macrophage

value: M-CSF differentiated in complete media


title: subAR BX_1113513_03

description:
subAR
_

value: Subclinical acute rejection


title: Rat heart_Sac/Val_rep3

description: Library name: Sample18-4-3


title: pTGC-OXY Sample3

value: OXY


title: pTGC-CTL Sample1


title: Rat heart_Sac/Val_rep4

description: Library name: Sample19-4-4


title: ADNR BX_1112641_03

description:
ADNR
_


title: 18-hour transmigrated monocytes from donor with CF 485 (D485_ArMos_CF)

description: Library name: E17_2D485_ArMos_S33

value: monocyte


title: pTGC-OXY Sample2


title: Rat heart_Sac/Val_rep2

description: Library name: Sample17-4-2


title: 18-hour transmigrated monocytes from healthy donor 16 (D14_ArMos_CF)

description: Library name: E17D16_ArMos_Null_S30

value: Control for drug treatment


title: TX BX_1113512_03

description:
TX
_


title: TX BX_1112545_03

description:
TX
_


title: subAR BX_1113026_03

description:
subAR
_


title: TX BX_1112643_03

description:
TX
_


title: TX BX_1112642_03

description:
TX
_


title: pTGC-OXY Sample1


title: subAR BX_1112548_03

description:
subAR
_


title: subAR BX_1112550_03

description:
subAR
_


title: TX BX_1112553_03

description:
TX
_


title: 4-day differentiated macrophages from healthy donor 16 (D16_ArMas_null)

description: Library name: E17D16_ArMas_null_S7


title: TX BX_1112542_03

description:
TX
_


title: TX BX_1112544_03

description:
TX
_


title: Circulating monocytes from healthy donor 16 (D16_CiMos)

description: Library name: E17D16_CiMos_S10

value: No Drug


title: subAR BX_1112456_03

description:
subAR
_


title: 4-day differentiated macrophages from healthy donor 16 (D16_ArMas_MSA-2)

description: Library name: E17D16_ArMas_MSA-2_S8

value: Treated with drug:MSA-2


title: Rat heart_Cap_rep4

description: Library name: Sample14-3-4


title: E16.5 lens, scRNAseq

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Eye lens

extract_protocol:
Mouse lenses were micro-dissected at embryonic day (E) 16.5 and postnatal day (P) 0 followed by dissociation with Collagenase/Dispase and TrypLE to obtain a single-cell suspension
Single cell libraries prepared using the 10X Chromium Controller

value: Eye lens

tag: strain

value: Embryonic day E16.5