title: GCA1_ROI_1_well_B10

description:
DSP-1012340003501-F-B10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: rawreads

tag: sequencingsaturation


title: Hexb-CreER/CreER, oil 27_HEB63

status: Public on Aug 24 2023

type: SRA

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

country: USA

institute: University of California, Los Angeles

description:
Hexb-CreER/CreER, oil
Hexb-CreER/CreER, oil

library_source: transcriptomic

data_processing:
Aligned to mouse genome (mm10) using STAR spliced read aligner
Quantify the reads with htseq-count
Normalization and differential expression analysis using Bioconductor packages
Assembly: mm10
Supplementary files format and content: xlsx file with counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Microglia

extract_protocol:
RNA was harvested using a phenol:chloroform extraction. RNA integrity was assessed on an Agilent 2100 Bioanalyzer and samples with RIN < 7 were excluded.
Libraries were prepared from the remaining samples using SMART-Seq v4 + Nextera XT and then sequenced on NovaSeq 6000 (Illumina) with PE 100X2.

treatment_protocol:
To induce CreER activity in adults, animals were injected once daily i.p. with 100 mg/kg tamoxifen Sigma T5648) dissolved 20 mg/mL in corn oil (Sigma C8267) on postnatal days 28, 29, 30, and 31.
10,000-50,000 microglia (DAPI- CD11b+ CD45Mid) were sorted per sample on a SONY MA800 or SONY MA900 into 1.5mL tubes containing 300µL Trizol LS reagent (Invitrogen)

tag: Sex

value: Male

tag: cell type

value: Microglia

tag: genotype

value: Hexb(CreER/CreER)

tag: treatment

value: Oil

tag: age


title: Hexb-CreER/CreER, oil 30_HEB79


title: Brg1 Ab ChIP-Seq bone marrow In vitro pro-B cell Input SB(+/+)_1

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

library_source: genomic

data_processing:
After sequencing, all reads that passed the Illumina quality filtering were considered for alignment. All samples were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) (samples 111733-111741, 181421-181438, 223632-223637,227407-227408,231740-42,231896-231899), and mm9 (samples 12521-15072).
ChIP-Seq and ATAC-Seq reads were aligned with Bowtie 1.0.0 (Langmead, B. et al. ,2009). Read coverages were calculated with the BEDTool program version 2.27.1 (Quinlan, 2010), were normalized to reads per millions (RPM) using the SAMTools version 1.9 (Li, 2009) as well as the KentTools version 20190507 [Kuhn, 2013].
Assembly: mm9, mm10
Supplementary files format and content: bigwig = read coverage (reads per million) in bigWIG format; txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

molecule: genomic DNA

source_name: bone marrow

extract_protocol:
NebNext UltraII RNA Library Prep Kit
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: bone marrow

value: In vitro pro-B cell

value: Input SB(+/+)


title: Brg1 Ab ChIP-Seq bone marrow In vitro pro-B cell Pax5(+/+)_1


title: Cx3cr1-CreER (Littman), oil 26_LIT15

description:
Cx3cr1-CreER (Littman), oil
Cx3cr1-CreER (Littman), oil

value: Cx3cr1(CreER/+) Littman


title: SAM612799

type: RNA

city: South San Francisco

first: Jason

middle: A

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

hyb_protocol: Samples were hybridized to GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Inc.).  Arrays were washed and stained in the Affymetrix Fluidics station and scanned on a GeneChip® scanner 3000.

scan_protocol: GeneChip® scanner 3000

data_processing: Expression signals were obtained using the Affymetrix GeneChip® operating system and analysis software. The data was normalized using RMA and probesets that failed to meet the affymetrix A-classification were removed.

label: biotin

organism: Homo sapiens

source_name: joint tissue

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

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit.

tag: disease

value: OA


title: Cntl1_ROI_20_well_B09

city: Limoges

first: Simon

last: Parreau

state: Haute-Vienne

address: 16 rue Bernard Descottes

country: France

institute: Dupuytren hospital

description:
DSP-1012340003501-F-B09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

data_processing:
*library strategy: GeoMx Seq
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
The freshly cut sections were stained with fluorescently labeled imaging reagents and mRNA markers. Briefly, sections were labeled with the cell markers, α-smooth muscle actin, CD3, and CD68, and the nuclear stain SYTO 13
The NanoString commercial Human Whole Transcriptome Atlas (GeoMx WTA) panel (18,000 protein-coding genes) was selected. Four slides (two with GCA patients and two with controls) were scanned on a GeoMx DSP instrument (NanoString Technologies Inc., Seattle, WA, USA) and individual regions of interest (ROIs) with a maximum diameter of 400 μm were created within each of the four arterial layers in GCA and controls. Once each ROI was compartmentalized, ultraviolet-cleaved indexing oligonucleotides were collected into a 96-well plate. Libraries were prepared according to the manufacturer’s instructions (protocol 01/2019). The library quality and quantity were assessed using Bioanalyzer DNA High Sensitivity Analysis. Samples were sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) and reads were digitally quantified and normalized using GeoMx DSP Data Analysis software
The library quality and quantity were assessed using Bioanalyzer DNA High Sensitivity Analysis. Samples were sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) and reads were digitally quantified and normalized using GeoMx DSP Data Analysis software
Data obtained from the NanoString GeoMx DSP platform were analyzed using dedicated software (GeoMx Analysis Suite 2.3). The quality control analysis showed that all ROIs had raw read counts above 1 million and good alignment rate and sequencing saturation. The local outliers were negative control probes and were removed from the ROIs.
ROIs with deduplicated probe counts Q3 (upper quartile) < 2 were excluded. Furthermore, ROIs were removed if < 1% of their genes had read counts higher than the limit of quantification (LOQ). LOQ was defined as geomean(NegProbe) × geoSD(NegProbe)² for each ROI. Target filtering was applied to retain gene targets with read counts above LOQ in at least 10% of ROIs. Q3 normalization was applied on the filtered ROIs and gene targets.

source_name: Heart

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

treatment_protocol: Temporal artery specimens were cross-sectioned serially. Tissues were fixed in 10% neutral buffered formalin for 24 h, followed by transfer to 70% ethanol before paraffin embedding. For each patient and control, segments were grouped into formalin-fixed paraffin-embedded (FFPE) temporal artery blocks using the tissue microarray method. Tissue microarrays were constructed from 2-mm-diameter cores punched from each FFPE tissue block. FFPE temporal artery blocks from GCA and control patients were sectioned to a thickness of 5 μm. The sections were mounted on an adhesive or positively charged slides (cat# S21.2113.A; Bond Plus slides; Leica Biosystems, Richmond, VA, USA).

value: Heart

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: SAM612802

value: RA


title: SAM612800


title: Pax5 Ab ChIP-Seq bone marrow In vitro pro-B cell Vav-Cre Pax5(Prd/fl) _2

value: Vav-Cre Pax5(Prd/fl)


title: SAM612794


title: Cntl1_ROI_19_well_B08

description:
DSP-1012340003501-F-B08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: rawreads

tag: sequencingsaturation


title: SAM612859


title: Cx3cr1-CreER (Littman), oil 25_LIT14

tag: Sex

tag: cell type

tag: genotype

tag: treatment


title: SAM612812

tag: disease


title: Cntl1_ROI_18_well_B07

description:
DSP-1012340003501-F-B07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

tag: segment type


title: SAM612858


title: Cx3cr1-CreER (Littman), tamoxifen 24_LIT11

description:
Cx3cr1-CreER (Littman), tamoxifen
Cx3cr1-CreER (Littman), tamoxifen

value: Tamoxifen

tag: age


title: mRNA-Seq bone marrow Progenitor (alternative gating) Vav-Cre Pax5(fl/fl)_2

data_processing:
After sequencing, all reads that passed the Illumina quality filtering were considered for alignment. All samples were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) (samples 111733-111741, 181421-181438, 223632-223637,227407-227408,231740-42,231896-231899), and mm9 (samples 12521-15072).
RNA-Seq reads were aligned with STAR 2.4.2a [Dobin, 2013] in transcriptome guided alignment mode (samples 111733-111741, 181421-181438,223632-223637), and tophat 1.4.1 (samples 12521-15072). Transcripts per million (TPMs) were calculated as described previously.
Assembly: mm9, mm10
Supplementary files format and content: bigwig = read coverage (reads per million) in bigWIG format; txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

molecule: polyA RNA

tag: strain

value: Progenitor (alternative gating)

value: Vav-Cre Pax5(fl/fl)


title: mRNA-Seq bone marrow Progenitor (alternative gating) Vav-Cre Pax5(fl/fl)_1


title: Cntl1_ROI_15_well_B04

description:
DSP-1012340003501-F-B04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: alignedreads


title: Cx3cr1-CreER (Littman), tamoxifen 21_LIT8


title: Cx3cr1-CreER (Littman), oil 22_LIT9


title: Cntl1_ROI_16_well_B05

description:
DSP-1012340003501-F-B05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Cx3cr1-CreER (Littman), tamoxifen 23_LIT10

tag: Sex


title: Cntl1_ROI_14_well_B03

description:
DSP-1012340003501-F-B03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi number

tag: rawreads

tag: sequencingsaturation


title: Cntl1_ROI_17_well_B06

description:
DSP-1012340003501-F-B06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: Pax5 Ab ChIP-Seq bone marrow In vitro pro-B cell Vav-Cre Pax5(Prd/fl) _1

tag: cell type

tag: genotype


title: mRNA-Seq bone marrow Progenitor (alternative gating) Vav-Cre Pax5(Prd/fl)_1

tag: tissue


title: Cx3cr1-CreER (Littman), tamoxifen 20_LIT7

tag: treatment

tag: age


title: mRNA-Seq bone marrow Pro-B cell Vav-Cre Pax5(fl/+)_2

tag: strain

value: Pro-B cell

value: Vav-Cre Pax5(fl/+)


title: Cntl1_ROI_13_well_B02

description:
DSP-1012340003501-F-B02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: segment type

tag: area

tag: roi x coordinate


title: SAM612788

tag: disease


title: SAM612869


title: Cx3cr1-CreER (Littman), oil 19_LIT6

value: Male

value: Microglia


title: mRNA-Seq bone marrow Pro-B cell Vav-Cre Pax5(fl/+)_1


title: mRNA-Seq bone marrow Progenitor (alternative gating) Vav-Cre Pax5(Prd/fl)_2


title: SAM612891


title: Cntl1_ROI_12_well_B01

description:
DSP-1012340003501-F-B01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads


title: SAM621606

value: Control


title: Cx3cr1-CreER (Littman), tamoxifen 18_LIT5

tag: Sex


title: T+shYbx1_2_scRNA-seq

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

country: China

institute: Sun Yat-sen University

library_source: transcriptomic single cell

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to Cell Ranger pre-built mm10 genome, and counted following the Cell Ranger ARC pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R using seurat.
Assembly: Cell Ranger pre-built mm10 reference
Supplementary files format and content: Csv files contain RNA count

source_name: cardiac

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol:
Cells were harvested by trypsin and nuclei were harvested using 10x provided protocol.
Illumina libraries were prepared using Chromium Next GEM Single Cell 3’GEM Kit v3.1

treatment_protocol: For single-cell RNA-seq, cardiac fibroblasts were transduced with Tbx5 and shNT or shYbx1 viruses . After 12 days reprogramming cells were processed for library preparation following manufactural instructions from 10x Genomics.

value: heart

value: 1-3 days

tag: transduction

value: wild type


title: SAM612874


title: Cntl1_ROI_11_well_A12

description:
DSP-1012340003501-F-A12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi number

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Cntl1_ROI_10_well_A11

description:
DSP-1012340003501-F-A11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue


title: T+shYbx1_1_scRNA-seq

tag: strain

tag: age

tag: genotype


title: Cx3cr1-CreER (Jung), oil 17_JUNG15

description:
Cx3cr1-CreER (Jung), oil
Cx3cr1-CreER (Jung), oil

tag: cell type

value: Cx3cr1(CreER/+) Jung

tag: treatment

value: Oil


title: T+shNT_2_scRNA-seq

value: T+shNT


title: SAM620221

tag: disease


title: Cx3cr1-CreER (Jung), tamoxifen 16_JUNG14

description:
Cx3cr1-CreER (Jung), tamoxifen
Cx3cr1-CreER (Jung), tamoxifen


title: Cx3cr1-CreER (Jung), tamoxifen 15_JUNG13


title: T+shNT_1_scRNA-seq


title: Cntl1_ROI_9_well_A10

description:
DSP-1012340003501-F-A10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: Heart

tag: slide id

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: SAM612849

value: OA


title: Cntl1_ROI_8_well_A09

description:
DSP-1012340003501-F-A09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi number

tag: alignedreads

tag: deduplicatedreads


title: Cx3cr1-CreER (Jung), oil 14_JUNG12

tag: Sex


title: Cntl1_ROI_7_well_A08

description:
DSP-1012340003501-F-A08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Cntl1_ROI_6_well_A07

description:
DSP-1012340003501-F-A07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue


title: SAM618872

value: RA


title: ATAC-Seq bone marrow Pro-B cell Pax5(DCRD1/DCRD1)_2

data_processing:
After sequencing, all reads that passed the Illumina quality filtering were considered for alignment. All samples were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) (samples 111733-111741, 181421-181438), and mm9 (samples 12521-15072).
ChIP-Seq and ATAC-Seq reads were aligned with Bowtie 1.0.0 (Langmead, B. et al. ,2009). Read coverages were calculated with the BEDTool program version 2.27.1 (Quinlan, 2010), were normalized to reads per millions (RPM) using the SAMTools version 1.9 (Li, 2009) as well as the KentTools version 20190507 [Kuhn, 2013].
RNA-Seq reads were aligned with STAR 2.4.2a [Dobin, 2013] in transcriptome guided alignment mode (samples 111733-111741, 181421-181438), and tophat 1.4.1 (samples 12521-15072). Transcripts per million (TPMs) were calculated as described previously.
Assembly: mm9, mm10
Supplementary files format and content: bigwig = read coverage (reads per million) in bigWIG format; txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

extract_protocol:
NebNext UltraII RNA Library Prep Kit
ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: bone marrow

tag: cell type

tag: genotype

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow

tag: replicate number


title: ATAC-Seq bone marrow Pro-B cell Pax5(DCRD1,2/DCRD1,2)_2

value: Pro-B cell


title: SAM612839

tag: disease


title: Cx3cr1-CreER (Jung), tamoxifen 13_JUNG11

tag: treatment

value: Tamoxifen

tag: age


title: SAM612854


title: SAM612870


title: Cntl1_ROI_5_well_A06

description:
DSP-1012340003501-F-A06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: Cntl1_ROI_4_well_A05

description:
DSP-1012340003501-F-A05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: ATAC-Seq bone marrow Pro-B cell Pax5(DCRD1/DCRD1)_1

tag: strain

tag: tissue

tag: cell type

tag: genotype


title: Cx3cr1-CreER (Jung), tamoxifen 10_JUNG8

tag: Sex

value: Male

tag: treatment


title: ATAC-Seq bone marrow Pro-B cell Pax5(DCRD1,2/DCRD1,2)_1

tag: cell preparation

tag: replicate number


title: Cx3cr1-CreER (Jung), tamoxifen 9_JUNG7

value: Microglia

tag: age


title: Cntl1_ROI_3_well_A04

description:
DSP-1012340003501-F-A04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: sequencingsaturation


title: SAM612836

tag: disease


title: primary murine basal cell culture

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCm38 with GFP and mCherry
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCm38
Supplementary files format and content: the processed files are the standard output from the cell ranger count pipeline:

source_name: Live cultured cells (Calcein Blue+)

growth_protocol: Primary BC and iBCs are cultured as detailed in Ma et al. 2023. Briefly, cells are seeded in 3D Matrigel at 400 cells/uL and cultured in Basal Cell Media.

extract_protocol:
10X Chromium system
NextSeq 2000

value: Live cultured cells (Calcein Blue+)

value: wildtype 129X1/S1


title: Cx3cr1-CreER (Jung), oil 12_JUNG10


title: Cntl1_ROI_2_well_A03

description:
DSP-1012340003501-F-A03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: mouse ESC-derived basal cell culture

tag: cell type

tag: genotype

value: lenti-GFP+; Nkx2.1-mCherry+


title: Recipient Animal #2 donor-derived cells

source_name: trachea

extract_protocol:
10X Chromium system
NextSeq 500

tag: tissue

value: trachea

value: airway epithelium (Calcein blue+; GFP+)

tag: treatment

value: Donor-derived


title: Cntl1_ROI_1_well_A02

description:
DSP-1012340003501-F-A02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: stitchedreads


title: Cx3cr1-CreER (Jung), oil 11_JUNG9

tag: Sex

value: Cx3cr1(CreER/+) Jung

value: Oil

tag: age


title: Recipient Animal #2 endogenous cells

value: airway epithelium (Calcein blue+; GFP-)

value: Endogenous


title: SAM612855

value: OA


title: Tmem119-CreER, oil 6_TM24

description:
Tmem119-CreER, oil
Tmem119-CreER, oil


title: Tmem119-CreER, oil 7_TM25

description:
Tmem119-CreER, oil
Tmem119-CreER, oil


title: SAM612879

value: RA


title: SAM612847


title: Recipient Animal #1 donor-derived cells


title: SAM625242


title: SAM612830


title: MMA 6 days 2

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis.
Bowtie was used to map 150-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70/hg19)
Quantification of gene expression levels as RPKM and counts per transctipt was performed using MMSEQ.
DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Assembly: hg19
Supplementary files format and content: comma-separated values file with raw counts and RPKM for each sample

source_name: human peripheral blood

growth_protocol: Macrophage were differenciated from monocyte by culturing in RPMI 1640 supplemented with 10% human AB serum, 10 μg/mL gentamycin, 10mM L-glutamine, and 10mM pyruvate for 6 days.

extract_protocol:
Poly(A) selection
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

treatment_protocol: We trained macrophages with mixture of GMP/GLP-grade 0.5ng/mL Al(OH)3, 25 ng/mL PHAD and 0.25 μg/mL Mannan for 24 hours, and rested two or five days.

value: human peripheral blood

value: macrophage

value: 24hr MMA, followed by 5 day of culture using 10% human serum


title: MMA 6 days 3


title: Tmem119-CreER, oil 8_TM28

description:
Tmem119-CreER, oil
Tmem119-CreER, oil

value: Male


title: Tmem119-CreER, oil 5_TM21

description:
Tmem119-CreER, oil
Tmem119-CreER, oil

value: Microglia


title: SAM612845


title: Non-epithelial cells (transplant recipient)

description: 10x Genomics

source_name: lung

growth_protocol: all cells are collected from mouse lungs

extract_protocol: 10X Chromium system

value: lung

value: Endogenous cells from injured transplant recipient


title: Tmem119-CreER, tamoxifen 3_TM19

description:
Tmem119-CreER, tamoxifen
Tmem119-CreER, tamoxifen

value: Tamoxifen


title: Recipient Animal #1 endogenous cells

value: trachea

value: wildtype 129X1/S1


title: Tmem119-CreER, tamoxifen 2_TM18


title: Tmem119-CreER, tamoxifen 4_TM20


title: MMA 6 days 1


title: MMA 3 days 3

value: 24hr MMA, followed by 2 day of culture using 10% human serum


title: MMA 3 days 1


title: Non-epithelial cells (media only recipient)

description: 10x Genomics

value: Endogenous cells from injured mouse


title: MMA 3 days 2


title: ESC-derived cell transplant (donor-derived cells)

description: 10x Genomics

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCm38 with GFP and mCherry
Downstream analysis and QC done on Seurat
Differential expression using MAST models
GRCm38
Assembly: the processed files are the standard output from the cell ranger count pipeline:

value: Donor-derived


title: SAM612835


title: Tmem119-CreER, tamoxifen 1_TM17


title: ESC-derived cell transplant (endogenous cells)

description: 10x Genomics


title: Naive macrophage 3

value: Macrophage differenciated from PBMCs isolated monocyte cultured using 10% human serum


title: SAM612842


title: SAM612837


title: Primary cell transplant (donor-derived cells)

description: 10x Genomics

value: lenti-DsRed+ 129X1/S1


title: SAM612857

value: OA


title: Naive macrophage 2


title: SAM612844

value: RA


title: SAM612826


title: RNA-seq_MMA_21_days_mouse_3

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 150-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Assembly: hg19
Supplementary files format and content: .gene.mmseq.txt files contain counts per gene

source_name: Mouse spleen

growth_protocol: Mice were vaccinated with an adjuvant combination vaccine (MMA). Splenic macrophages were extracted from Naïve (non vaccinated) mice, and vaccinated mice at 3 days and 21 days following vaccination.

extract_protocol:
Macrophages were purified using flow and marker XYZ… X number of cells were put in Trizol/RLT? …
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

value: spleen

value: Macrophage

value: Spleen macrophages collected 21 days after MMA vaccination


title: Primary cell transplant (endogenous cells)

description: 10x Genomics

value: Endogenous


title: Naive macrophage 1

value: human peripheral blood

value: macrophage


title: RNA-seq_MMA_21_days_mouse_2


title: RNA-seq_MMA_21_days_mouse_1


title: monocyte 3

value: monocyte

value: monocytes -  immunogenetic negative selection


title: RNA-seq_MMA_3_days_mouse_3

value: Spleen macrophages collected 3 days after MMA vaccination


title: RNA-seq_MMA_3_days_mouse_2


title: monocyte 2


title: monocyte 1


title: RNA-seq_MMA_3_days_mouse_1


title: SAM612815


title: SAM612864


title: MMA_6_days_3

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis.
ChIP-seq reads were aligned to the hg19 genome assembly using bwa.
For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15. The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the genomic regions enriched for histone marks at p-value of 10-5.
DESeq2  was used to normalise count data and determine differential H3K27ac peaks between treatments.
Assembly: hg19
Supplementary files format and content: BigWig files for visualization

extract_protocol:
Monocytes and macrophages were rinsed in PBS, and resuspended in PBS containing 2% FBS and 1 mM EDTA. H3K27ac chromatin immunoprecipitation (ChIP) was performed using anti-H3K27ac polyclonal antibody (Diagenode, C15410196) and iDeal ChIP-seq kit for Histones (Diagenode, C01010051).  10^6 cells per sample.
Library preparation was performed using the Ovation Ultralow DNA-seq library preparation kit and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 30 million reads per sample.

value: 24hr MMA, followed by 5 day of culture using 10% human serum

value: chip_antibody:Rabbit anti-H3K27ac Antibody(Diagenode #C15410196)


title: MMA_6_days_2


title: SAM612831


title: MMA_21_days_mouse_3

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15. The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the genomic regions enriched for histone marks at p-value of 10-5. H3K4me1 peaks were called using the broad setting of MACS2 while H3K27ac peaks were called using the default (narrow) setting.
Assembly: hg19
Supplementary files format and content: BigWig files for visualization

growth_protocol: Mice were vaccinated with a protein free vaccine (A + M + MA). Splenic f4/80+ macrophages were extracted from Naïve (non vaccinated) mice, and vaccinated mice at 3 days and 21 days following vaccination.

extract_protocol:
The spleens of mice were collected, mashed through a 70-µm cell strainer with a 35-mL syringe plunger, and rinsed with Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) by volume (DMEM + 10% FBS).  Splenocytes were rinsed in PBS, and resuspended in PBS containing 2% FBS and 1 mM EDTA.  Following the manufacturer’s protocol (StemCell Technologies, 100-0659), f4/80+ macrophages were isolated.  H3K27ac chromatin immunoprecipitation (ChIP) was performed using anti-H3K27ac polyclonal antibody (Diagenode, C15410196) and iDeal ChIP-seq kit for Histones (Diagenode, C01010051).  10^6 cells per sample. Isolated f4/80+ macrophages were sent to Azenta Life Sciences for RNA isolation and sequencing
Library preparation was performed using the Ovation Ultralow DNA-seq library preparation kit and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 30 million reads per sample.

tag: chip antibody

value: Rabbit anti-H3K27ac Antibody (Diagenode #C15410196)


title: RNA-seq_Naive_mouse_1

value: naive spleen macrophages. No vaccination.


title: SAM613149


title: SAM613147


title: SAM612873


title: MMA_3_days_3

value: 24hr MMA, followed by 2 day of culture using 10% human serum


title: MMA_3_days_2


title: SAM612818


title: MMA_21_days_mouse_2


title: MMA_3_days_1


title: Naive_macrophage_3

value: Macrophage differenciated from PBMCs isolated monocyte cultured using 10% human serum


title: MMA_6_days_1


title: Naive_macrophage_2


title: MMA_3_days_mouse_3


title: SAM618887


title: MMA_3_days_mouse_1


title: BU3-NGPT iBC donor-derived cells, recipient #2

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCh38 with GFP and tdTomato
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the cell ranger count pipeline:

source_name: Adult mouse trachea

treatment_protocol: Adult NSG mice were given 2% polidocanol intra-tracheally. 5 hours later, 2e6 human primary or iBC were transplanted intra-tracheally. The recipients were chased for 6 weeks post-transplantation for the scRNA-Seq analysis. To prepare for the analysis, recipient tracheas were dissected and digested in a pronase digested as described in Plasschart et al., 2018. Resulting cells were FACS sorted on a live gate, and into GFP+ (primary BC recipient) or tdTomato+ (iBC recipients) cells prior to library preparation. GFP- and tdTomato- endogenous mouse cell were also collected to make up the cell number required for the technical reasons. Mouse cells are later excluded bioinformatically.

tag: strain

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG)

tag: sort gates

value: Calcein Blue+/tdTomato+


title: RNA-seq_Naive_mouse_3

value: spleen


title: RNA-seq_Naive_mouse_2

value: Macrophage


title: SAM612871

tag: disease

value: OA


title: SAM612821


title: SAM612867


title: SAM612833


title: SAM612807


title: MMA_21_days_mouse_1

value: Spleen macrophages collected 21 days after MMA vaccination


title: BU3-NGPT iBC donor-derived cells, recipient #1


title: Naive_mouse_3

value: Naive spleen macrophages. No vaccination.


title: monocyte_3

value: human peripheral blood


title: monocyte_2

value: monocyte


title: monocyte_1

value: monocytes -  immunogenetic negative selection


title: SAM612814


title: Naive_mouse_2


title: KOLF2 iBC donor-derived cells, recipient #2


title: KOLF2 iBC donor-derived cells, recipient #1


title: MMA_3_days_mouse_2

value: Spleen macrophages collected 3 days after MMA vaccination


title: Naive_macrophage_1

value: macrophage


title: Naive_mouse_1


title: Primary BC donor-derived cells, recipient #2

value: Calcein Blue+/GFP+


title: SAM612884

value: RA


title: SAM613145


title: Primary BC donor-derived cells, recipient #1


title: CM_m6A_IP_D15

first: Xuehong

last: Liu

state: Guangdong Province

address: Haizhuqu, No.135 Xingangxi lu

institute: Sun Yat-Sen University

data_processing:
library strategy: meRIP-seq
Reads were mapped to the hg19 genome using hisat2 v2.1.0. with default parameters.
Reads with duplicate UMI were removed using UMI_tools v1.0.1
Peak calling was performed by MACS2 with the parameters “--nomodel”.
bigWig files were generated using Deeptools v3.3.0
Assembly: hg19
Supplementary files format and content: bigWig

source_name: H1 human embryonic stem cells

growth_protocol: H1 human embryonic stem cells (hESCs) were grown on Matrigel-coated 6-well plates in E8 medium at 37 ℃ with 5% CO2. Cells were passaged every 3-4 days using 0.5 mM EDTA in Dulbecco’s phosphate buffered saline (DPBS) without Ca2+ or Mg2+ at 37 ℃. 5μM Rho kinase inhibitor Y-27632 was added for the first 24 hours after passaging. The E8 medium was changed every day.

extract_protocol:
Total RNA was extracted using the NucleoZol reagent (ThermoFisher, 15596026). Then mRNA was purified from total RNA using Dynabeads™ mRNA Purification Kit (ThermoFisher, 61006).
The pooling MeRIP-seq libraries were prepared by RNA fragmention, 3' adapter ligation, sample pooling, m6A IP, 5' adapter ligation, cDNA synthesis and amplification.

treatment_protocol: Undifferentiated hESCs cultured in E8 medium were dissociated into single cell suspension by Accutase and reseeded onto Matrigel-coated 24-well plate at a density of 105 cells/well in E8 medium containing 10μM Y-27632. When cells reach ~80% confluence 2-3 days after plating, CM differentiation was initiated by switching to the differentiation medium named E8 basal+Lip (DMEM/F-12 supplemented with 50 U/ml Penicillin-Streptomycin, Chemically Defined Lipid Concentrate (1:100), 10.7μg/ml holo-Transferrin human, 71μg/ml L-Ascorbic acid, 14ng/ml Sodium selenite). 5μM CHIR99021 or 3μM IWP2 was added into the cardiac differentiation medium from days 0-1 and days 2-5, respectively. 3μg/ml heparin was added into the cardiac differentiation medium from days 1-7. 20μg/ml Insulin was added into the cardiac differentiation medium from day 7 onward and renewed every 2-3 days.

tag: cell line

value: H1 human embryonic stem cells

value: Cardiomyocytes

value: WT

tag: time

value: Day 15

value: cardiomyocytes differentiation

tag: antibody


title: CM_m6A_Input_D15


title: CP_m6A_Input_D5

value: Cardiac Progenitor

value: Day 5


title: SAM612886


title: pirmary BC recipient donor-derived cells (69 days post-transplantation)

data_processing:
The sample was processed using the standard Cell ranger STARsolo pipeline
Reads were mapped to GRCm38 with GFP and mCherry
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCm38
Supplementary files format and content: the processed files are the standard output from the STARsolo pipeline:

treatment_protocol: Adult wild type 129X1/S1 or C57BL/6 mice were given 2% polidocanol intra-tracheally. 5 hours later, 6e6 murine iBCs or primary BCs were transplanted intra-tracheally. The recipients were chased for 69 or 192 days post-transplantation for the scRNA-Seq analysis. To prepare for the analysis, recipient tracheas as well as a control trachea (without injury or transplantation) were dissected and digested in a pronase digested as described in Plasschart et al., 2018. Resulting cells were FACS sorted on a live gate into GFP+ or GFP- samples prior to library preparation.


title: SAM612882


title: CP_m6A_IP_D5


title: pirmary BC recipient endogenous cells (69 days post-transplantation)

value: Calcein Blue+/GFP-


title: Mesoderm_m6A_Input_D2

value: Mesoderm

value: Day 2


title: SAM625244


title: SAM612877


title: iBC recipient donor-derived cells (192 days post-transplantation)


title: iBC recipient endogenous cells (192 days post-transplantation)


title: T+shYbx1_scATAC

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to Cell Ranger pre-built mm10 genome, and counted following the Cell Ranger ARC pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R using seurat.
Genome_build: Cell Ranger pre-built mm10 reference
Supplementary_files_format_and_content: Two csv files for RNA count and peak counts for cells

extract_protocol:
Cells were harvested by trypsin and nuclei were harvested using 10x provided protocol.
Illumina libraries were prepared using Single Cell Multiome ATAC + Gene Expression kit.
scRNA-seq and scATAC-seq

treatment_protocol: For single-cell dual-omics, cardiac fibroblasts were transduced with Tbx5 and shYbx1 viruses. After 3 days T+shYbx1 reprogramming cells were processed for library preparation following manufactural instructions from 10x Genomics.

value: heart

value: 1-3 days

value: wild type


title: hESC_m6A_Input_D0

value: hESC

value: Day 0


title: SAM612890


title: No injury no transplantation control

data_processing:
The sample was processed using the standard Cell ranger STARsolo pipeline
Reads were mapped to GRCm38 together with GRCh38, with GFP and mCherry
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCm38 and GRCh38
Supplementary files format and content: the processed files are the standard output from the STARsolo pipeline:

treatment_protocol: Adult wild type 129X1/S1 mice were given 2% polidocanol intra-tracheally. 5 hours later, 6e6 iBCs were transplanted intra-tracheally. The recipients were chased for 40 or 56 days post-transplantation for the scRNA-Seq analysis. To prepare for the analysis, recipient tracheas as well as a control trachea (without injury or transplantation) were dissected and digested in a pronase digested as described in Plasschart et al., 2018. Resulting cells were FACS sorted on a live gate into GFP+ or GFP- samples prior to library preparation

value: Calcein Blue+


title: Donor-derived cells (56 days post-transplantation

value: Calcein Blue+/GFP+


title: T+shYbx1_scRNA


title: SAM612824

value: OA


title: SAM611254

value: Control


title: Set 2_Donor 6 LC_biol rep 2

city: Singapore

first: Shu Hui

last: Neo

address: 61 Biopolis Dr, Proteos, Singapore 138673

department: IMCB

country: Singapore

institute: A*STAR

data_processing:
Partek®Genomics Suite®
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Genomics Suite software based on quality score with end minimum quality level (Phred) at 20 and trimmed from 3-prime (right end). After trimming, reads less than 25bp are discarded.
Trimmed sequence reads were mapped to hg38 using STAR 2.7.8a index available in Partek Genomics Suite software.
Read count extraction and normalization with CPM (counts per million) was performed using Partek Genomics Software.
ANOVA was performed for differential expression gene analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Bone marrrow

growth_protocol: Human bone marrow-derived mesenchymal stromal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37˚C.

extract_protocol:
Cells were trypsinized and harvested before subjected to RNA extraction. RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq stranded mRNA library following manufacturer's protocols.

treatment_protocol: Cells were seeded at two different conditions(low density and high density), cultured for a period of 7 days, before harvesting for RNAseq analysis. There are 2 conditions for each donor: low-confluency (LC) and high-confluency (HC).

value: Bone marrrow

tag: condition

value: low confluency

value: primary cells

value: mesenchymal stromal cells

value: WT

tag: gender

value: female


title: Endogenous cells (56 days post-transplantation)

value: Calcein Blue+/GFP-


title: Day5_2_RNAseq

description: total RNA

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the mm10 reference genome using Bowtie2.
Genome_build: mm10 genome
Supplementary_files_format_and_content: two csv files containing raw count values for Ribo-seq and RNA-seq, respectively, for Day0 and Day5 samples

extract_protocol:
For each sample, around 5-10 million cells were used for both Ribo-seq and RNA-seq. The cells were first washed with cold ice-cold PBS supplemented with 100 μg/ml cycloheximide and then were lysed for 5 minutes on ice in polysome lysis buffer (5mM MgCl2, 150mM NaCl, 20mM Tris-Cl (pH=7.5), 1% Triton X-100, 1 mM dithiothreitol, 20 U/ml DNase I, 100 μg/ml cycloheximide and nuclease-free H2O). Using immediate repeated pipetting we dissociated cells to create a homogeneous lysate. Lysates were next centrifuge at 10,000g at 4°C for 5 minutes to precipitate cell debris and the supernatant was quantitated by Qubit.
To accurately dissect translational control, both Ribo-seq and RNA-seq libraries were prepared for each biological replicate from the identical lysate by Ribomaps Ltd. One aliquot of the lysate (10%) was supplemented with RNseq inhibitor and processed for RNA-seq library generation. Remaining lysate (90%) was treated with RNase. Then ribosome protected mRNA fragments were isolated and used to generate Ribo-seq library.

treatment_protocol: For direct cardiac reprogramming, mouse cardiac fibroblasts were infected with retrovirus encoding the reprogramming factors Mef2c, Gata4 and Tbx5.

value: day 5

value: Primary mouse cardiac fibroblast

value: Heart


title: Day5_1_RNAseq

description: total RNA

value: 1-3 days

value: wild type


title: Set 2_Donor 6 HC_biol rep 2

value: high confluency


title: Donor-derived cells (40 days post-transplantation


title: Set 1_Donor 6 LC_biol rep 1


title: SAM612872

data_processing: Expression signals were obtained using the Affymetrix GeneChip® operating system and analysis software. The data was normalized using RMA and probesets that failed to meet the affymetrix A-classification were removed.


title: Mesoderm_m6A_IP_D2

value: H1 human embryonic stem cells

value: Mesoderm

value: Day 2

value: cardiomyocytes differentiation


title: Day0_2_RNAseq

description: total RNA

value: day 0


title: Set 1_Donor 6 HC_biol rep 1

value: Bone marrrow


title: Endogenous cells (40 days post-transplantation)


title: Day0_1_RNAseq

description: total RNA


title: hESC_m6A_IP_D0

value: hESC

value: Day 0


title: SAM611221

value: RA


title: in vitro iBC culture

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCm38 with mCherry
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCm38
Supplementary files format and content: the processed files are the standard output from the cell ranger count pipeline:

source_name: Cultured ESC-derived cells

growth_protocol: iBCs were grown in 3D-Matrigel in BCM for 6 passages. iBCs were purified with Nkx2-1mCherry+/NGFR+ gating at P5. iBCs are derived from ESC with methods specified in Ma et al., 2022

tag: culture

value: BCM (Basal Cell Media)


title: SAM612840

value: OA


title: SAM612853


title: Primary tip-like cells

source_name: Cultured primary cells

growth_protocol: ESC-derived and primry tip-like cells were grown in lung progenitor media for 4 or 3 passages, respecitvely, and collected at 6 days since the last passage. D13 cells were specified in line with the WBRF protocol outlined in Herriges et al., 2022.

treatment_protocol: A 9 week old wild type 129X1/S1 mouse was given 1.5U/kg bleomycin intratracheally. 10 days later 5e5 ESC-derived tip-like cells were transplanted intratracheally into the same mouse. At 15 weeks post-transplantation the lungs of this mouse were digested and sorted using FACS. We collected both endogenous and donor-derived epithelial cells from the same lung. To analyze pre-transplantation donor populations, we collected passage 4 ESC-derived and passage 3 primary tip-like cells grown in Lung progenitor media for 6 days since passaging. Finally, we collected D13 ESC-derived epithelial cells from the WBRF lung specification protocol as outlined in Herriges et al., 2022.

value: LPM (lung progenitor media)


title: SAM612813


title: SAM612806


title: SAM612862


title: Day5_1_Riboseq

description: Ribosome protected mRNA fragments

value: day 5

tag: cell type

value: Primary mouse cardiac fibroblast


title: ESC-derived tip-like cells


title: SAM613146


title: Set 1_Donor 5 LC_biol rep 1

value: low confluency

value: primary cells

value: mesenchymal stromal cells

tag: genotype

value: WT

value: female


title: Day0_2_Riboseq

description: Ribosome protected mRNA fragments

tag: tissue

value: Heart

value: 1-3 days

value: wild type


title: Set 1_Donor 5 HC_biol rep 1

value: Bone marrrow

value: high confluency

tag: treatment


title: Day0_1_Riboseq

description: Ribosome protected mRNA fragments

value: day 0


title: Day 13 EpCAM+ cells

value: WBRF differentiation media


title: Endogenous cells (15 week)

source_name: Adult mouse lung

value: Fresh primary collection


title: Donor-derived cells (15 week)

value: DRAQ7-/(GFP+ or mCherry+)


title: SAM612828

value: OA


title: Set 2_Donor 4 HC_biol rep 2

value: male


title: Day5_2_Riboseq

description: Ribosome protected mRNA fragments

value: day 5

value: Primary mouse cardiac fibroblast


title: Donor-derived cells (6 week)

growth_protocol: N/A all cells are collected from mouse lungs

treatment_protocol: A 9 week old wild type 129X1/S1 mouse was given 1.5U/kg bleomycin intratracheally. 10 days later 6e5 ESC-derived tip-like cells were transplanted intratracheally into the same mouse. At 6 weeks post transplantation the lungs of this mouse were digested and sorted using FACS. We collected both endogenous and donor-derived epithelial cells from the same lung. In parallel an 11 week old uninjured control 129X1/S1 mouse was similarly dissected and lung epithelial cells were collected.


title: Set 2_Donor 5 LC_biol rep 2

value: low confluency

value: primary cells


title: Set 1_Donor 4 LC_biol rep 1

value: mesenchymal stromal cells

value: WT


title: Set 2_Donor 5 HC_biol rep 2

value: female


title: SAM612866


title: Set 2_Donor 4 LC_biol rep 2


title: SAM612793


title: Set 1_Donor 4 HC_biol rep 1


title: SAM612888

value: RA


title: Degs2_KO1

city: Dallas

first: Jin Huk

last: Choi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
S72475
genes.count_tracking
genes.fpkm_tracking
gene_exp.diff

data_processing:
Adapters were trimmed from fastq.gz files using cutadapt v1.9.dev4
Trimmed fastq.gz were aligned to the mm10 reference genome using tophat-2.0.10
BAM files resulting from alignments were run through cuffdiff (cufflinks v2.1.1) for differential expression
Assembly: mm10

source_name: colon

extract_protocol: Distal colons were isolated from mice and stool removed from the lumen. Colons were then cut to 5-10 mm pieces and incubated at room temperature for 30 minutes in PBS containing 5 mM EDTA with rotation on a platform shaker. The epithelial cells were collected by passing through a 100-μm cell strainer. RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.

value: colon

value: colonic epithelial cells

value: Degs2 homozygous mutant

tag: strain background


title: Degs2_KO3

description:
S73425
genes.count_tracking
genes.fpkm_tracking
gene_exp.diff


title: Degs2_KO2

description:
S73066
genes.count_tracking
genes.fpkm_tracking
gene_exp.diff


title: Control


title: Degs2_KO4

description:
S74173
genes.count_tracking
genes.fpkm_tracking
gene_exp.diff


title: SAM612801


title: Set 3_Donor 3 LC_biol rep 3

value: Bone marrrow


title: Endogenous cells (6 week)


title: Set 3_Donor 3 HC_biol rep 3

value: high confluency


title: Huang Protocol Epithelial Cells

growth_protocol: N/A all cells were taken directly from mouse lungs

treatment_protocol: Lungs ere digested using distinct digestion buffers as outlined in the digestion section.


title: WT4

description:
S75925
genes.count_tracking
genes.fpkm_tracking
gene_exp.diff

value: wild type


title: WT3

description:
S74172
genes.count_tracking
genes.fpkm_tracking
gene_exp.diff


title: Huang Protocol Non-Epithelial Cells

value: DRAQ7-/(EpCAM-,CD45+, or CD31+)


title: WT2

description:
S73422
genes.count_tracking
genes.fpkm_tracking
gene_exp.diff


title: Morrisey Protocol Epithelial Cells


title: SAM613141

value: OA


title: Set 2_Donor 3 HC_biol rep 2

value: male


title: SAM625126


title: WT1

description:
S72476
genes.count_tracking
genes.fpkm_tracking
gene_exp.diff


title: Morrisey Protocol Non-Epithelial Cells


title: SAM612791


title: Set 1_Donor 3 LC_biol rep 1


title: SAM612878


title: SAM613150


title: HH24g, rep 2

city: Sheffield

first: Sofia

last: Sedas Perez

address: Western Bank

country: United Kingdom

institute: The University of Sheffield

data_processing:
Raw sequencing reads were cleaned by removing reads containing adapter, reads containing poly-N and low quality reads.
Reads were mapped to the reference genome using Hisat2 v2.0.2 with default parameters.
Salmon output was used to quantify the data (number of reads).
Count data for the samples were normalised using trimmed mean of m-value normalisation and transformed with Voom, resulting in log2-counts per million with associated precision weights.
A statistical analysis using an adjusted p-value of <0.05 and fold-chage >2 identified differentially expressed genes.
Gene clusters were identified from the set of differential expressed genes cIValud R package.
Assembly: UCSC Gallus_gallus galGal4
Supplementary files format and content: samplequant.csv are tab-separated files that include name, length, effective length, Transcripts per million (TPM) and estimated number of reads mapping to each transcript (NumReads)  of each sample per gene.

organism: Gallus gallus

source_name: Graft distal limb bud

growth_protocol: Eggs were incubated at 37C until the desired stage according to Hamburger Hamilton (HH).

extract_protocol:
Total RNA was extracted from samples using Trizol-chloroform extractions.
TrueSeq Stranded Total RNA and Ribo-Zero.
Enzymatic fragmentation by Illumina Elute, Fragment, Prime mix.

treatment_protocol:
For tissue grafting 150 um strip of distal mesoderm was dissected from HH20 wing buds of  GFP transgenic chicken. The epithelim was removed and the mesoderm cut into cubes.
The HH20 mesoderm was then placed in slits between the AER and the underlying mesoderm in the mid-distal region of WT HH24 wing buds and allowed to develop for 24 hours before collection.

value: Graft distal limb bud

value: Mesenchyme

value: CMV-GFP

value: Tissue graft


title: SAM612860

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit.


title: TKO-2 RNA-seq

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw data were trimmed by Trim Galore (v0.5.0) with default settings. Then, the clean data were mapped to mouse reference genome mm9 using Hisat2 (v2.1.0) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Gene count matrices were calculated by featureCounts (v1.6.4) with the parameters -p -M -O.
Assembly: mm9
Supplementary files format and content: comma-separated values file, raw counts for gene expression.

source_name: GV oocytes

extract_protocol:
Ten GV oocytes in each biological replicate were pooled, lysed and subjected to first-strand cDNA synthesis.
cDNA was purified once by using the Ampure XP beads. Next, purified cDNA products were fragmented by using the Covaris M220, and an RNA-seq library was prepared by following the instruction manual of the NEBNext UltraII DNA Library Prep Kit for Illumina (New England Biolabs). Finally, the libraries were checked, pooled and sequenced with 150-bp paired-end reads on the Illumina HiSeq X-Ten platform (Novogene).  Batch1: WT-1, WT-2, WT-3, KO-1, KO-2, KO-3; Batch2: WT-4, KO-4, KO-5, HD-1, HD-2, HD-3; Batch3: WT-5, WT-6, Tet3KO-1, Tet3KO-2, D3aKO-1, D3aKO-2, DKO-1, DKO-2, KO-6, KO-7.

value: GV oocytes

value: Tet1, 2, 3f/f; Zp3-Cre


title: Set 3_Donor 2 LC_biol rep 3

value: low confluency

value: primary cells

value: mesenchymal stromal cells

value: WT


title: TKO-1 RNA-seq


title: HH24g, rep 1


title: Set 1_Donor 3 HC_biol rep 1


title: Tet3KO-1 RNA-seq

value: Tet3f/f; Zp3-Cre


title: Set 3_Donor 2 HC_biol rep 3

value: Bone marrrow


title: HH27, rep 2

source_name: HH27 distal wing bud

value: HH27 distal wing bud


title: Tet3KO-2 RNA-seq


title: Set 2_Donor 3 LC_biol rep 2


title: HH27, rep 3


title: Set 2_Donor 2 LC_biol rep 2


title: SAM613144

source_name: joint tissue


title: HH27, rep 1


title: SAM612797


title: Set 2_Donor 2 HC_biol rep 2

value: high confluency


title: HD-5 RNA-seq

value: Tet3 LCD HD Mutf/f; Zp3-Cre


title: SAM612856

value: OA


title: SAM612795


title: HD-4 RNA-seq


title: Set 1_Donor 2 LC_biol rep 1

value: male


title: HH24, rep 2

source_name: HH24 distal wing bud

value: HH24 distal wing bud


title: Set 1_Donor 2 HC_biol rep 1


title: HH24, rep 1

value: Mesenchyme


title: HD-2 RNA-seq


title: Set 4_Donor 1 LC_biol rep 4


title: WT unstimulated_3

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the raw counts for each sample.

source_name: Primary brain endothelial cell

growth_protocol: Brain endothelial cells were isolated from the cortices of 8-12 week mice, and cultured on plates coated with 100 mg/ml collagen IV (Sigma) and 100 mg/ml Fibronectin (Sigma). Cultures were maintained in DMEM (Gibco) supplemented with Penicillin-Streptomycin (Gibco), 20% heat inactivated heat-inactivated fetal bovine serum (FBS, Sigma) and 1 ng/ml basic fibroblast growth factor (bFGF, Invitrogen). The medium was supplemented with 3 mg/ml puromycin (Sigma) for the first 3 days to selectively propagate puromycin-resistant endothelial cells.

extract_protocol:
RNA was harvested from cultured endothelial cells using the NucleoSpin RNA kit from Macherey-Nagel
Libraries were prepared with 500 ng total RNA using the TruSeq stranded mRNA Sample Preparation Kit (Illumina)
RNA-seq libraries were multiplexed, normalized, and pooled for sequencing. The libraries were sequenced on the HiSeq 2500 system (Illumina) at single read 50bp

treatment_protocol: Confluent monolayers of brain endothelial cells were stimulated with 300nM UNC2025, or PBS alone, in full growth medium for 20h

value: Primary brain endothelial cell

value: unstimulated (PBS)


title: SAM612876

value: RA


title: SAM612798


title: SAM613142


title: Set 4_Donor 1 HC_biol rep 4


title: SAM612892


title: DKO-2 RNA-seq

value: GV oocytes

value: Dnmt3af/f, Tet3 LCDf/f; Zp3-Cre


title: Set 3_Donor 1 LC_biol rep 3

value: low confluency

value: primary cells


title: WT unstimulated_2

value: WT


title: SAM612829


title: HH24, rep 3


title: DKO-1 RNA-seq


title: WT unstimulated_1


title: Set 3_Donor 1 HC_biol rep 3

value: mesenchymal stromal cells


title: WT UNC2025_2


title: D3aKO-1 RNA-seq

value: Dnmt3af/f; Zp3-Cre


title: WT UNC2025_3


title: Set 2_Donor 1 LC_biol rep 2

value: Bone marrrow


title: HD-3 RNA-seq


title: SAM612850


title: D3aKO-2 RNA-seq


title: Set 2_Donor 1 HC_biol rep 2

value: high confluency


title: HD-1 RNA-seq

value: Tet3 LCD HD Mutf/f; Zp3-Cre


title: SAM612803


title: Set 1_Donor 1 LC_biol rep 1


title: WT UNC2025_1


title: KO-7 RNA-seq

value: Tet3 LCDf/f; Zp3-Cre


title: SAM612834

value: OA


title: Mertk-/- unstimulated_3

value: Mertk-/-


title: SAM612832


title: SAM612789


title: Mertk-/- unstimulated_2


title: Set 1_Donor 1 HC_biol rep 1

value: male


title: PPAC1C-12wT

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
the Cell Ranger pipeline v3 was used to process the fastq files and generate the count matrix
Assembly: hg19

source_name: in vitro derived cartilage chrondrocytes, TGFb-treated, 12-weeks

growth_protocol: A detailed description of the protocol for generating chondrogenic cells and tissues from human pluripotent stem cells has been published (PMID: 25961409).

extract_protocol: RNA libraries were prepared using the 10x Chromium v2 3' kit following the manufacturer's protocols

tag: Sex

value: F

value: 12 weeks


title: PPAC1-12wT


title: Mertk-/- unstimulated_1

value: Primary brain endothelial cell

value: unstimulated (PBS)


title: KO-4 RNA-seq

value: GV oocytes


title: KO-3 RNA-seq


title: Mertk-/- UNC2025_2


title: Mertk-/- UNC2025_3


title: Differentiating norepinephrine cells at day11

city: Nanjing

first: Yunlong

last: Tao

state: Jiangsu

address: 163 Xianlin Road

department: School of life sciences

institute: Nanjing University

data_processing:
Alignment of raw sequencing reads and generation of feature barcode matrices were done by Cellranger (7.1.0)
Seurat (4.1.3) was used to process the feature barcode matrices and analyze the snRNA-Seq data
Single cells with more than 600 unique genes (nFeature) and less than 5% mitochondrial gene reads (percent.mt) were selected for follow-up analysis.
For day 6 sample, nCount_RNA is set >4500 and the total unique gene number is set <6000. For day 14 sample, nCount_RNA is set >2200 and the unique gene number is set between 1500 and 5500.
snRNA-Seq data were normalized using the SCTransform function in Seurat with the mitochondria genes regressed out.
Assembly: hg38
Supplementary files format and content: feature barcode matrices

source_name: cell culture in vitro

extract_protocol:
500 µl of chilled 0.1x Lysis Buffer (Lysis Buffer: 10 mM Tris-HCl (pH 7.4; Sigma #T2194), 10 mM NaCl (Sigma #59222C), 3mM MgCl2 (Sigma #M1028), 0.1% Tween-20 (Bio-Rad 1662404), 0.1% Nonidet P40 Substitute (Sigma #74385), 0.01% Digitonin (Thermo Fisher Scientific #BN2006), 1% BSA (Miltenyi Biotec #130-091-376), 1 mM DTT (Sigma #646563), 1U/µl RNase inhibitor (Sigma #3335402001), Nuclease-free water (AmericanBio #AB02123-0500); Lysis Dilution Buffer: 10 mM Tris-HCl (pH 7.4; Sigma #T2194), 10 mM NaCl (Sigma #5922C), 3mM MgCl2 (Sigma #M1028),  1% BSA (Miltenyi Biotec #130-091-376), 1mM DTT (Sigma #646563), 1U/µl RNase inhibitor (Sigma #3335402001), Nuclease-free water (AmericanBio #AB02123-0500)) was added to a tube containing the cell pellet. After resuspending the cells in 0.1x Lysis Buffer, the suspension was transferred to an autoclaved ice-cold 1 ml dounce tissue grinder (DWK Life Sciences #357538) and homogenized 30 times with a loose pestle, and 30 times with a tight pestle; applying constant pressure and ensuring no contamination from air. After a 5-minute incubation on ice, the sample was gently pipette mixed 15 times, a 10-minute incubation on ice followed. 500 µl of Wash Buffer (10 mM Tris-HCl (pH 7.4; Sigma #T2194), 10 mM NaCl (Sigma #59222C), 3 mM MgCl2 (Sigma #M1028), 1% BSA (Miltenyi Biotec #130-091-376), 0.1% Tween-20 (Bio-Rad #1662404), 1 mM DTT (Sigma #646563), 1U/µl RNase inhibitor (Sigma #33335402001), Nuclease-free water (AmericanBio #AB02123-0500)). The solution was filtered through a 70 µm tube top cell strainer (Corning #352350) pre-wetted with 250 µl of wash buffer. The filtered homogenate was then filtered through a 40 µm tube top cell strainer (Corning #352340) pre-wetted with 250 µl of wash buffer. The filtered homogenate was then transferred to a 15 ml tube and centrifuged at 500 rcf for 5 minutes at 4 ºC in an ultracentrifuge using a swing-out rotor (eppendorf, #5943000343). After centrifugation, the supernatant was removed and the pellet was resuspended in 1 ml of wash buffer. After gently pipette mixing 5 times, the solution was centrifuged at 500 rcf for 5 minutes at 4 ºC. After centrifugation, the supernatant was removed and the pellet was resuspended in 1 ml of wash buffer. 10 µl of sample was loaded onto a hemocytometer, with the concentration found used in a calculation to determine the final resuspension volume. The solution was centrifuged at 500 rcf for 5 minutes at 4 ºC. After removing the supernatant completely without disturbing the pellet, it was resuspended in the volume calculated in the previous step using Diluted Nuclei Buffer (1X; 10x Genomics #2000153), 1mM DTT (Sigma #646563), RNase inhibitor 1U/µL (Sigma #3335402001), Nuclease-free water (AmericanBio #AB02123-0500). After final resuspension, 10 µl of sample was loaded onto a hemocytometer and counted to determine the final concentration.
only samples that had a minimum concentration of 3.23 million nuclei/ml were used for generation of snRNA-seq libraries using Chromium Next GEM Single Cell Multiome Reagent Kit A (PN-1000282) following the instruction of “Chromium Next GEM Single Cell Multiome Reagent Kits User Guide”. For snRNA-seq libraries, after pre-amplification cDNA was constructed and sample-indexed libraries were generated using Library Construction Kit (10x Genomics, PN-1000190) and Dual Index Kit TT Set A (10x Genomics, PN-1000215) following the manufacturer’s protocol.

value: cell culture in vitro

value: H9 ESC

value: Neural cells

value: wildtype

value: untreated


title: KO-1 RNA-seq


title: Mertk-/- UNC2025_1


title: Differentiating norepinephrine cells at day14


title: KO-2 RNA-seq


title: SAM612848


title: WT-6 RNA-seq

value: Tet3 LCDf/f


title: Differentiating norepinephrine cells at day6


title: KO-6 RNA-seq


title: SAM620732

value: Control


title: PPAC4_T_rep3

description: WISP3 KO

data_processing:
alignment to hg19: Star align version 2.7.3, default parameters for hg19 alignment
RNA-seq read mapping: Salmon version 1.2.1, salmon -l A --numBootstraps 100 --gcBias –validateMappings
Read abundance normalization: DESeq2 version 1.36.0
Assembly: hg19
Supplementary files format and content: Batch1-4_normalized_counts.xlsx : Normalized abundance counts across primary RNA-seq datasets generated

source_name: PPAC iPSC line

extract_protocol: TruSeq RNA Library Prep Kit v2 (Illumina)

value: human iPSC-derived articular cartilage treated with TGFB3 for 12 weeks

value: treated with TGFB3 for 12 weeks


title: KO-5 RNA-seq

value: Tet3 LCDf/f; Zp3-Cre


title: DAneuron, PFF and SARS-CoV-2, rep2

city: Seoul

first: Yong Jun

last: Kim

address: 26 Kyungheedaero

department: Department of Pathology

country: South Korea

institute: Kyung Hee University

data_processing:
Illumina Real-Time Analysis 3 (RTA3) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie 2 v2.2.5 with following parameters: Seed lenth 22, Seed mismatches 0, Seed extension attempts 15, Max re-seed attempts 2, Interval between seeds S,1.0,1.25, Ambiguous character function L,0.0,0.15, Gaps per read 15, Gap end buffer 4, Ambiguous character penalty 1, Alignment score cutoff L,-0.6,-0.6, Mismatch penalty range Max6 Min2, Rad gap penalties Open5 and extend 3penalties, Reference gap penalties Open5 and extend 3 penalties.
Normalized by criteria Transcripts Per Million (TPM) using a protocol from Abrams et al., BMC Bioinformatics, 2019. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38 (RefSeq Transcripts 83, 2017-11-01)
Supplementary files format and content: Matrix table with raw gene counts for every gene

source_name: WA09 hESC

growth_protocol: Human embryonic stem cell–derived dopaminergic neurons were routinely generated by neuroepithelial cell differentiation cultures (typically 2–3 × 106 cells into a 24 well plate) on Geltrex coated plastic in Neurobasal medium (Thermo Fisher) supplemented with N2, B27,3uM 100nM LDN193189, 10uM SB431549, followed by addition of 20ng/ml NGF, 20ng/ml BDNF, 20ng/ml GDNF, 100uM dbcAMP.

extract_protocol:
Total RNA samples from hESC-derived dopaminergic neurons were harvested using Trizol reagent.
The libraries were prepared for 150 bp paired-end sequencing using TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero H/M/R (Illumina, CA, USA).

treatment_protocol: SARS-CoV-2 (10^3.0 TICD 50/ml, strain NCCP43326) was incubated with PFF-treated or PFF-non treated dopaminergic neurons for initial 24 hours, and neurons were incubated for additional 72 hours after wash out of uninfected virus.

value: WA09 hESC

value: hESC-derived dopaminergic neuron

value: WT

value: Dopaminergic neuron differentiation, α-synuclein preformed fibril, SARS-CoV-2 infection


title: SAM612841

value: OA


title: PPAC4_T_rep2

description: WISP3 KO

value: male


title: SAM612885

value: RA


title: WT-5 RNA-seq

value: GV oocytes


title: SAM612808


title: DAneuron, PFF and SARS-CoV-2, rep1


title: SAM613720


title: WT-4 RNA-seq


title: SAM613148


title: PPAC4_T_rep1

description: WISP3 KO


title: SAM612843


title: DAneuron, PFF, rep2

value: Dopaminergic neuron differentiation, α-synuclein preformed fibril


title: SAM612804


title: PPAC1_T_rep3

description: WISP3 KO

value: female


title: WT-3 RNA-seq


title: PPAC1_T_rep1

description: WISP3 KO


title: PPAC1_T_rep2

description: WISP3 KO


title: DAneuron, PFF, rep1


title: WT-2 RNA-seq


title: PPAC1C_T_rep3

description: WISP3 WT


title: WT-1 RNA-seq


title: DAneuron, SARS-CoV-2, rep2

value: Dopaminergic neuron differentiation, SARS-CoV-2 infection


title: DAneuron, SARS-CoV-2, rep1


title: DAneuron, non-treated, rep2

value: Dopaminergic neuron differentiation


title: SAM612820


title: PPAC1C_T_rep2

description: WISP3 WT


title: KO-2 BiSulfite-seq

data_processing:
Raw sequencing data were processed using Trim Galore (v0.6.6) to remove adaptor sequences, random primers and low-quality bases. The trimmed reads with the length less than 50 bp were excluded. The clean reads were aligned to the mouse genome (mm9) using Bismark (v0.23.0) in paired-end mode. The unmapped reads were further aligned in the single-end mode. PCR deduplicates were removed using SAMtools (v0.1.18). The methylation levels of CpG sites were quantified using MethylDackel (v0.5.0).
Assembly: mm9
Supplementary files format and content: compressed bedGraph file, DNA methylation level for each CpGs.

extract_protocol:
30 full-grown GV oocytes in each biological replicate were pooled and subjected to bisulfite conversion and purification by following the instruction manual (Zymo Research).
WGBS libraries were constructed via TAILS method. The final quality-ensured libraries were pooled and sequenced on the Illumina HiSeq X-Ten sequencer (Novogene) for 150 bp paired-end sequencing.


title: DAneuron, non-treated, rep1


title: KO-3 BiSulfite-seq


title: KO-1 BiSulfite-seq


title: DSE_BG_PacBio

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

institute: Yunnan Agricultural University

data_processing:
smrtlink (version 9.0, parameters) was used to perform primer removal, polyA tail removal, chimeric reads removal, and reads clustering on the long reads (LRs).
The clustered LRs were aligned to the susScr11 reference genome using GMAP (version 2018-07-04, parameters -t 10 -B 5 -A --nofails -f samse -n1). The aligned LRs with clipping region longer than 100-nt at either end were filtered out.
The SRs were aligned to the susScr11 reference genome using STAR (version 2.7.10a, parameters --alignEndsType EndToEnd --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All -- outSAMtype BAM).
Illumina paired-end short reads were quantified using Salmon (v1.9.0), and TPM values were summaized in the processed data table.
Illumina single-end small RNA reads were predicted potential miRNA using miRDeep2 (v0.1.3). Small RNA reads were mapped to mature miRNA and precursor miRNA from the prediction and miRbase (Release 22.1) using bowtie (v1.3.1).
Assembly: susScr11
Supplementary files format and content: Long reads numbers mapped to each transcript have been summarized into Summary_PacBio.txt. Transcript TPM values were summarized into RNAseq_expression.tpm.txt. MiRNA RPM values were summarized into miRNAseq_expression.rpm.txt
Supplementary files format and content: PacBio's assembly file was tab-delimited.

organism: Sus scrofa

source_name: bulbourethral gland

growth_protocol: All samples were acquired from 12-month adult male pigs. Pigs were housed in a temperature (64-79°F) and humidity (30-70%) controlled room.

extract_protocol:
Total RNAs were extracted using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
PacBio SMRTseq uses PacBio library construction protocol. Illumina paired-end sequencing uses standard RNAseq library construction protocol. Illumina single-end sequencing library was constructed using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA)

value: bulbourethral gland


title: SAM612863


title: SAM612825


title: SAM612846


title: PPAC1C_T_rep1

description: WISP3 WT


title: SAM612880


title: In-vitro TGF-beta treated sample [H9_T_30_rep1]

source_name: HESC-derived chondrocytes

treatment_protocol: Collagenase digestion

value: chondrocytes

value: In-vitro TGF-beta treated sample


title: BMI_BG_PacBio


title: SAM612792


title: WT-2 BiSulfite-seq

value: Tet3 LCDf/f


title: WT-1 BiSulfite-seq


title: DSE_VG_PacBio

source_name: vesicular gland

value: vesicular gland


title: In-vitro TGF-beta treated sample [H9_T_28_rep1]


title: DSE_PG_PacBio

source_name: prostate gland

value: prostate gland


title: WT-3 BiSulfite-seq


title: SAM612883


title: In-vitro TGF-beta treated sample [H9_T_44_rep3]


title: KO-3 ACE-seq

data_processing:
Raw sequencing FASTQ files were processed using Trim Galore (v0.6.6) to remove sequencing adapters and low-quality reads, followed by aligning to the mouse genome (mm9) using Bismark (v0.23.0) in the paired-end mode. The unmapped reads were further aligned in single-end mode. PCR deduplicates were removed with sambamba markdup (v0.6.6). All replicates were merged for the downstream analysis. To eliminate reads from strands not deaminated by A3A, reads with more than three consecutive non-converted cytosines in the CH context were removed by the filter_non_conversion.pl script of Bismark. 5hmC signals were called using Bismark.
Assembly: mm9
Supplementary files format and content: compressed bedGraph file, DNA hydroxymethylation level for each CpGs.
Library strategy: ACE-seq

extract_protocol:
The ACE-seq libraries were constructed following the published protocol (Yan, et al., Nature Genetics, 2022), and 200 full-grown GV oocytes were pooled as one biological replicate.
In brief, gDNA was first fragmented by using the Covaris M220. Then, UDP-glucose and T4 Phage β-glucosyltransferase (New England Biolabs) were used to modify 5hmC to 5ghmC at 37°C for 1 h. After that, 0.1 N NaOH was added to the modified fragments for denaturation at 55°C for 10 mins. Then, the APOBEC enzyme (New England Biolabs) was used to deaminate C/5mC to U at 37°C for 3 hrs. After deamination, DNA fragments were purified and subjected to the library construction. Finally, the ACE-seq libraries were checked and sequenced on an Illumina Hiseq X-Ten platform (Novogene) by 150 bp paired-end sequencing.

value: Tet3 LCDf/f; Zp3-Cre


title: In-vitro TGF-beta treated sample [H9_T_44_rep2]


title: In-vitro TGF-beta treated sample [H9_T_25_rep1]


title: KO-1 ACE-seq


title: BMI_PG_PacBio


title: BMI_VG_PacBio


title: In-vitro TGF-beta treated sample [H9_T_44_rep1]


title: BMI_Epi_PacBio

source_name: epididymis

value: epididymis


title: KO-2 ACE-seq


title: WT-3 ACE-seq


title: SAM612861


title: WT-2 ACE-seq


title: SAM612811


title: SAM620718

value: Control


title: SAM612817

value: OA


title: SAM612868


title: SAM612887


title: DSE_Tes_PacBio

source_name: testis

value: testis


title: SAM611357


title: DSE_Epi_PacBio


title: C5

status: Public on Aug 23 2023

city: Tianjin

first: Xue

last: Liang

address: Pingjiang Road

institute: Tianjin Institute of Cardiology, the Second Hospital of Tianjin Medical University

data_processing:
Briefly, paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
circRNA: The reads were aligned to the reference genome/transcriptome with bowtie2 software and circRNAs were detected and identified with find_circ software. Raw junction reads for all samples were normalized by total mapped reads and log2 transformed. Differentially expressed circRNAs were identified by ttest between two groups, and fold change between two samples. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
LncRNA & mRNA: The high quality reads were aligned to the dog reference genome (UCSC canFam3) with hisat2 software. Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Canis lupus familiaris

source_name: atrial

extract_protocol:
Total RNA was separated using Trizol Reagent (Invitrogen, USA) and resuspended in sterile water for RNA quality control. When the OD260/OD280 value ranges from 1.8 to 2.1, it indicates that RNA purity is suitable for sequencing samples. rRNAs removal using Ribo-Zero rRNA Removal Kits (Illumina, USA).
 Briefly, total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

value: atrial

value: rapid right atrial pacing model


title: C1miRNA

value: control group


title: C6


title: C5miRNA


title: C2miRNA


title: WGBS of ISKNV sample 3

city: Zhuhai

first: Mincong

address: No. 2 Daxue Road

department: School of Marine Sciences

description: Mandarin fish fry (MFF-1) cells were infected with ISKNV for 7 days.

data_processing:
The raw data were trimmed and filtered by Trimmomatic v0.39 (“ILLUMINACLIP:TruSeq3-PE-2:2:30:10:8:true SLIDINGWINDOW:5:20 LEADING:5 TRAILING:5 MINLEN:36”).
Clean data were mapped to the ISKNV genome, deduplicated and methylation extracted (--ignore_r2 2) using Bismark v0.24.1, Bowtie2 v2.5.2 and SAMtools v1.17.
Assembly: OP896201.1
Supplementary files format and content: Tab-delimited text file includes number of methylations and unmethylations counts for cytosines in ISKNV genome for each sample.

organism: Infectious spleen and kidney necrosis virus

source_name: Virion

extract_protocol:
The total DNA of virion was extracted following to the manufacturer's protocol (Vazyme).
Libraries were prepared using kit following to the manufacturer's protocol.

value: Virion


title: WGBS of ISKNV sample 1


title: WGBS of ISKNV sample 2


title: C4


title: low daughter fertilty A7

city: quebec

first: ying

last: zhang

address: 735 Ave.Neree tremblay

country: Canada

institute: UNIVERSITY LAVAL

description: low daughter fertilty

data_processing:
Adapter-removal and quality trimming of the libraries were performed with TRIMMOMATIC. BISMARK was then used to align the bisulfite-converted libraries to a synthetic converted bovine genome (ARS-UCD1.2)
The MethylKit package was also used for cytosine methylation analysis and searching of hypermethylated and hypomethylated regions with an adjusted p value.
Assembly: ARS-UCD1.2
Supplementary files format and content: CSV file including the CG  that correlated with daughter fertility
Supplementary files format and content: CSV file including the  DMR that correlated with daughter fertility
Library strategy: EM-Seq

organism: Bos taurus

source_name: sperm

extract_protocol:
Genomic DNA was extracted with the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA).
EM-seq (Enzymatic methylation seq) workflow was adopted to perform the whole genome methylation sequencing, which reduced the DNA fragmentation and damage compared to the traditional bisulfite sequencing

value: sperm

value: male

value: low daughter fertilty


title: C4miRNA


title: C6miRNA


title: C3miRNA


title: BMI_Tes_PacBio


title: C3


title: SAM625318

first: Jason

last: Hackney

address: 1 DNA Way

institute: Genentech, Inc.


title: C1


title: C2


title: low daughter fertilty A8

description: low daughter fertilty


title: WT-1 ACE-seq

source_name: GV oocytes

value: GV oocytes


title: SAM612822

source_name: joint tissue


title: high daughter fertility A12

description: high daughter fertility

value: high daughter fertility


title: high daughter fertility A21

description: high daughter fertility


title: high daughter fertility A20

description: high daughter fertility


title: high daughter fertility A19

description: high daughter fertility


title: high daughter fertility A17

description: high daughter fertility


title: low daughter fertility A16

description: low daughter fertility

value: low daughter fertility


title: high daughter fertility A18

description: high daughter fertility


title: low daughter fertility A15

description: low daughter fertility


title: low daughter fertility A14

description: low daughter fertility


title: low daughter fertility A13

description: low daughter fertility


title: immunoMPRA CRS-BC association

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

data_processing:
75xbp paired-end reads were trimmed using cutadapt with the following parameters: -m 12 -a GAATTCATCTGGTA -G GACCGGATCAACT -u 1 --discard-untrimmed. In case of 2x150bp PE, reads were first filtered using cutadapt (-m 12 -a GAATTCATCTGGTACCTCGGTTCACGCAATG -G ^CCAGGACCGGATCAACT -u 1 --discard-untrimmed --action=none --interleaved | cutadapt -g GAATTCATCTGGTACCTCGGTTCACGCAATG -G ^CCAGGACCGGATCAACT --discard-untrimmed --action=none –interleaved) and subsequently forward as well as reverse read were trimmed individually using -l 12 for the barcode, -g ^CCAGGACCGGATCAACT --discard-untrimmed (forward CRE reads) or -g GAATTCATCTGGTACCTCGGTTCACGCAATG --discard-untrimmed -l 105 (reverse CRE read). Trimmed fastq reads for both, 75xbp PE and 150xbp PE were separated based on a 5’-four-basepair identifier (GTCA or TCAG) and CRE-Barcode-association was performed separately on wildtype, mutant sequences using the MPRAflow association pipeline. The resulting pickle libraries were merged to increase the number of recovered CREs and filtered for promiscuous barcodes.
Supplementary files and format and content:  Compressed files contain sequences of selecred CREs (design.fa.gz), their annotation (labels.tsv.gz) and a pickle library with filtered CRE - Barcode associations (CRE_BC_association.pickle.gz)
Library strategy: Targeted barcode amplification from RNA/DNA

organism: Escherichia coli

source_name: Plasmid DNA

extract_protocol:
Plasmid DNA was purified using QIAprep Spin Miniprep Kit (Qiagen; Cat. N: 27106) according to the manufacturer instructions.
5 ng of the plasmid pool was used to attach P5 and P7 sequencing adapters in two separated PCRs. Bother PCRs were performed using the NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs; Cat. N: M0544) with RV_univ_MPRA (CGACGCTCTTCCGATCT) + FWD_CRS_Tn7 (0.5µM each; GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCAGGACCGGATCAACT; PCR conditions: (98°C 30s; {98°C 10s, 65°C 30s, 72°C 3min} x3; 72°C 3min; Hold at 4°C) and P5NEXT_SXXX primers (0.1 µM each; AATGATACGGCGACCACCGAGATCTACAC NNNNNNNN ACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T ) + indexed Ad2.X (0.1 µM each; CAAGCAGAAGACGGCATACGAGAT XXXXXXXX GTCTCGTGGGCTCGGAGATGT; PCR conditions: 98°C 30s; {98°C 10s, 65°C 90s} x10; 72°C 5min; Hold at 4°C), respectively.

tag: technique

value: immunoMPRA

tag: genome build


title: ∆mce3R, cholesterol, pH 5.7, replicate 1

first: Shumin

last: Tan

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

data_processing:
Illumina bcl2fastq was used for demultiplexing and conversion of reads to FASTQ file format.
RNAseq data were analyzed using the Geneious program (version 2023.0.4). Specifically, raw data were trimmed using BBDuk with the following parameters: trim adapters (All Truseq), Kmer length 27, trim low quality on both ends with minimum quality 30, discard short reads with minimum length 36 bp, minimum entropy 0.1, entropy window size 4 and entropy Kmer size 5. Trimmed sequences were assembled onto the CDC1551 genome (GenBank AE000516.2) using the Bowtie2 mapper with end-to-end alignment. Gene expression levels were then calculated and excluded ambiguously mapped reads from calculation, with comparison of expression levels performed via DEseq2.
Assembly: M. tuberculosis CDC1551 genome (NCBI accession AE000516).
Supplementary files format and content: The file is presented in the .csv file format. It contains gene expression analysis from 2 biological replicates for each condition.

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: Mtb strain CDC1551 (streptomycin resistant) and ∆mce3R were grown in 20 ml of 7H9, pH 7 media, in standing, filter-capped T-75 flasks.

extract_protocol:
RNA was extracted as previously described by Rohde, Abramovitch, and Russell (Cell Host and Microbe 2:352-364, 2007). In brief, RNA was stabilized with guanidine-thiocyanate lysis buffer prior to a freeze-thaw step. Once thawed, bacteria were lysed with 5 µg/ml lysozyme, followed by hot Trizol and physical disruption through silica bead agitation in a Beadbeater.  A chloroform extraction was used to further isolate the RNA before purification with an RNAeasy kit (Qiagen). DNA was degraded with Turbo DNAfree DNAse (Ambion). RNA quality was assessed with an Aligent Bioanalyzer before removal of rRNA with a Ribo-Zero Plus kit (Ilumina).
The cDNA library was constructed with the Illumina stranded total RNA with Ribo-Zero Plus kit. The polyA enrichment procedure was skipped.

treatment_protocol: Log-phase Mtb strain CDC1551 (streptomycin-resistant) or ∆mce3R (OD600 ~0.6) were used to inoculate standing T-25 flasks with filter caps at an OD600 = 0.3, containing 10 ml of the following media: (i) 7H9, pH 7.0, (ii) 7H9, pH 5.7, (iii) cholesterol, pH 7.0, or (iv) cholesterol, pH 5.7. After four hours of exposure to the specific environmental conditions in a humidified, 37°C, 5% CO2 incubator, Mtb samples were collected and RNA isolated.

tag: strain

value: Bacterial cell

value: cholesterol, pH 5.7


title: ∆mce3R, cholesterol, pH 7, replicate 2

value: cholesterol, pH 7


title: ∆mce3R, cholesterol, pH 5.7, replicate 2


title: WT, cholesterol, pH 7, replicate 1

value: WT


title: ∆mce3R, 7H9, pH 5.7, replicate 2


title: ∆mce3R, 7H9, pH 5.7, replicate 1


title: WT, 7H9, pH 5.7, replicate 2


title: ∆mce3R, 7H9, pH 7, replicate 2

description:
Deltamce3R_pH57_vs_pH7.csv
Deltamce3R_cholpH7_vs_pH7.csv
Deltamce3R_cholpH57_vs_pH7.csv


title: ∆mce3R, 7H9, pH 7, replicate 1


title: WT, cholesterol, pH 5.7, replicate 2


title: Negative Control group, NC_3

city: Kunming

first: Nianqiu

state: China/Yunnan

address: 519 Kunzhou Road, Xishan

department: Breast Surgery

institute: The Third Affiliated Hospital of Kunming Medical University: Yunnan Cancer Center, Kunming, 650000, Yunnan

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchw ork (parameter-Qualitu limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchw ork (parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity fration:0.8)
Read count extraction and normalization were performed using CLC genomic benchw ork
Supplementary files format and content: tab-delimited text file include FPKM for each sample

organism: Oryctolagus cuniculus

source_name: Primary cells

extract_protocol:
RNA was harvested using RNA Quick Purification kit (ESscience). 1.1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruePrep RNA Library Prep Kit for Illumina (Vazyme)

value: Parathyroid cell


title: Model group, M_2

value: IRI


title: Model group, M_3


title: WT, cholesterol, pH 5.7, replicate 1


title: Negative Control group, NC_1


title: Negative Control group, NC_2


title: WT, cholesterol, pH 7, replicate 2


title: WT, 7H9, pH 5.7, replicate 1


title: Model group, M_1


title: Treatment group, T_3

value: IRI with GA

value: GA

value: GA pretreatment for 24h


title: Treatment group, T_2


title: WT, 7H9, pH 7, replicate 2

description:
WT_pH57_vs_pH7.csv
WT_cholpH7_vs_pH7.csv
WT_cholpH57_vs_pH7.csv


title: Kcr_Nitrogen-deprivation_N2_replicat2

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

institute: Hainan normal university

data_processing:
In brief, reads were trimmed using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), then aligned against the N. oceanica reference genome using BWA (Li, Durbin, 2009). The mapped reads were with duplication marked using Picard and analyzed by DeepTools (Ramirez, Dundar, Diehl, Gruning, Manke, 2014) and MACS2 (Liu, 2014; Zhang, Liu, Meyer, Eeckhoute, Johnson, Bernstein, Nusbaum, Myers, Brown, Li, Liu, 2008). The “--broad” flag was on for peak calling, with reads from the input samples used as controls. Besides, differential analysis was performed using diffReps (Shen, Shao, Liu, Maze, Feng, Nestler, 2013), the resulting differential peaks were annotated using ChIPpeakAnno package (Zhu, Gazin, Lawson, Pages, Lin, Lapointe, Green, 2010).
Assembly: Nannochloropsis oceanica IMET1 genome
Supplementary files format and content: bedgraph were generated.
Supplementary files format and content: differential peak text files

organism: Nannochloropsis oceanica

source_name: cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into the modified f/2 liquid medium, which was prepared with 35 g L-1 sea salt (Realocean, USA), 1 g L-1 NaNO3, 67 mg L-1 NaH2PO4*H2O, 3.65 mg L-1 FeCl3*6H2O, 4.37 mg l-1 Na2EDTA*2H2O, trace metal mix (0.0196 mg L-1 CuSO4*5H2O, 0.0126 mg L-1 NaMoO4*2H2O, 0.044 mg L-1 ZnSO4*7H2O, 0.01mg L-1 CoCl2, and 0.36 mg L-1 MnCl2*4H2O), and vitamin mix (2.5 µg L-1 VB12, 2.5 µg L-1 biotin, and 0.5 µg L-1 thiamine HCl).The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm).

extract_protocol:
N. oceanica cells (1-2 million cells · mL−1) from 400 mL culture were fixed under vacuum for 30 min with 1% formaldehyde (Sigma)at room temperature. After fixation, cells were incubated at room temperature for ten min under vacuum with 0.15 M glycine. Nuclei were isolated as described (Wei, Xu, 2018).
All subsequent end repairing, A-tailing, adaptor ligation, and library amplification steps were done following a standard protocol (Illumina). The final library was sequenced on an Illumina HiSeq 2500 instrument with 1×150-bp reads.

treatment_protocol: The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm). The seed cultures were bubbled with air-level CO2. At the logarithmic phase (OD750=2.5), cells were harvested by centrifugation, one was sampled for RNA extraction as control (C0) with three replicates and the other was washed with fresh medium (nitrogen-free) for three times before being used for the following experiments. Cell pellets were inoculated into Nitrogen-free (for sampling of mRNA-seq, ChIP-seq and HiC-seq) and Nitrogen-repletion f/2 medium (for physiological measurement). Cultures started with the same initial cell concentration of OD750 = 2.5 and were exposed to continuous illumination of 50±5 μmol m−2 s−1. Cell aliquots were collected  for sampling of mRNA-seq, ChIP-seq and HiC-seq after being transferred to the designated conditions for one and two days  as nitrogen-deprivation samples (N1 and N2) with three replicates

tag: chip antibody

value: Kcr (PTM-501)

value: Nitrogen-deprivation


title: Kcr_Nitrogen-deprivation_N2_replicat1


title: H3K36me2_Nitrogen-deprivation_N2_replicat2

value: H3K36me2 (Millipore, 07-360)


title: Treatment group, T_1


title: ∆mce3R, cholesterol, pH 7, replicate 1


title: H3K36me2_Nitrogen-deprivation_N2_replicat1


title: H3K27ac_Nitrogen-deprivation_N2_replicat2

value: H3K27ac (Millipore, 07-360)


title: Kcr_Nitrogen-deprivation_N1_replicat1


title: Kcr_Nitrogen-deprivation_N1_replicat2


title: H3K36me2_Nitrogen-deprivation_N1_replicat2


title: H3K27ac_Nitrogen-deprivation_N1_replicat1


title: H3K36me2_Nitrogen-deprivation_N1_replicat1


title: H3K36me2_Nitrogen-repletion_C0_replicat2

value: Nitrogen-repletion


title: Kcr_Nitrogen-repletion_C0_replicat1


title: WT, 7H9, pH 7, replicate 1


title: H3K36me2_Nitrogen-repletion_C0_replicat1


title: H3K27ac_Nitrogen-repletion_C0_replicat2


title: H3K27ac_Nitrogen-deprivation_N1_replicat2


title: H3K27ac_Nitrogen-repletion_C0_replicat1


title: ∆rpoS, high osmolarity, 180min, rep C

city: Claremont

first: Daniel

last: Stoebel

address: 301 Platt Blvd

department: Biology

institute: Harvey Mudd College

data_processing:
Sequencing reads from each sample in a pool were demultiplexed based on their associated barcode sequence using custom scripts.  Up to 1 mismatch in the barcode was allowed provided it did not make assignment of the read to a different barcode possible. Barcode sequences were removed from the first read as were terminal G’s from the second read that may have been added by SMARTScribe during template switching.
Reads were aligned to the NCBI E. coli K-12 MG1655 genome (RefSeq assembly GCF_000005855.2) using BWA v0.7.17 (Li, 2013).
Reads were counted with htseq-count v2.0.1 (Anders et al., 2015).
Assembly: RefSeq assembly GCF_000005855.2
Supplementary files format and content: Processed data are the output of htseq-count

source_name: Strain K-12, substrain BW27786

extract_protocol:
200 μL of culture was pelleted and resuspended in 500 μL of Trizol heated to 65°C and then stored at -80°C until use. Samples were purified on a column using the Zymo Direct-Zol RNA Miniprep kit. They then went through two DNase I treatments using Turbo DNA-free (Invitrogen) for 30 minutes each at 37˚C to ensure that all DNA was degraded. The samples were further purified on a column using the Zymo RNA Clean and Concentrator Kit and again stored at -80˚C until they were ready to be sent to get sequenced.
Illumina cDNA libraries were generated using a modified version of the RNAtag-seq protocol (Shishkin et al., 2015). Briefly, 500 ng to 1 μg of total RNA was fragmented, depleted of genomic DNA, dephosphorylated, and ligated to DNA adapters carrying 5’-AN8-3’ barcodes of known sequence with a 5’ phosphate and a 3’ blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (Epicentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcoded adaptor with addition of an adapter to the 3’ end of the cDNA by template switching using SMARTScribe (Clontech) as described (Zhu et al., 2001); (ii) PCR amplification using primers whose 5’ ends target the constant regions of the 3’ or 5’ adaptors and whose 3’ ends contain the full Illumina P5 or P7 sequences. cDNA libraries were sequenced on the Illumina [NextSeq 500] platform to generate paired end reads.

treatment_protocol: For RNA isolation, strains were inoculated from -80°C frozen cultures and grown aerobically overnight in 5 mL of Luria-bertani (LB) broth (1% tryptone, 0.5% yeast extract, 1% NaCl) at 37˚C with shaking at 225 rpm. The next morning, 250μL of each culture was diluted in 25mL of LB and continued to grow at 37˚C with shaking at 225 rpm until the OD600 of the culture reached approximately  0.3. At this point, samples were taken for RNA and protein isolation and then the culture was exposed to the stressor of interest: for low temperature, they were moved to a 15°C shaking water bath; for high osmolarity, 3mL of 5M NaCl was added to the cultures; or they were left to continue growing to reach stationary phase.

value: Strain K-12, substrain BW27786

value: delta-rpoS

value: low tempearture


title: ∆rpoS, high osmolarity, 60min, rep C


title: ∆rpoS, high osmolarity, 180min, rep D


title: Kcr_Nitrogen-repletion_C0_replicat2


title: ∆rpoS, high osmolarity, 90min, rep D


title: ∆rpoS, high osmolarity, 30min, rep D


title: ∆rpoS, high osmolarity, 30min, rep C


title: ∆rpoS, high osmolarity, 0min, rep C


title: ∆rpoS, high osmolarity, 120min, rep C


title: ∆rpoS, high osmolarity, 0min, rep D


title: ∆rpoS, high osmolarity, 180min, rep A


title: H3K27ac_Nitrogen-deprivation_N2_replicat1


title: ∆rpoS, high osmolarity, 90min, rep A


title: ∆rpoS, high osmolarity, 60min, rep A


title: ∆rpoS, high osmolarity, 120min, rep A


title: ∆rpoS, high osmolarity, 60min, rep D