title: run_29_P1-11A_S81

description: sci-RNA-seq3 library


title: run_29_P1-10H_S80

status: Public on Apr 07 2023

type: SRA

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

description: sci-RNA-seq3 library

library_source: transcriptomic single cell

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

molecule: polyA RNA

organism: Mus musculus

source_name: sci-RNA-seq3 of mouse organogenesis and fetal development

growth_protocol: For the newly generated mouse embryo data (ranging from E8 to P0), we employed a combination of staging methodologies depending on gestational age of harvest. To maximize temporal coherence, resolution, and accuracy, we sought to stage individual embryos based on well-defined morphological criteria, rather than by gestational day alone. Embryos harvested between E8.0 - E10.0 were staged based upon the number of somites counted at the time of harvest and further characterized by morphological features. Based upon an estimated 1.5 to 2 hour periodicity for somite formation, E8.0 - E10.0 embryos were grouped into 4 somite bins. For E10.25-E14.75 embryos, developmental age was determined using the embryonic Mouse Ontogenetic Staging System (eMOSS, https://limbstaging.embl.es/), which leverages dynamic changes in hindlimb bud morphology and landmark-free based morphometry to estimate the absolute developmental stage of a sample. A modified staging tool, implemented in python, with increased performance on E14.0-E15.0 samples was used to confirm staging of samples within this window (documentation and python scripts available at: https://github.com/marcomusy/welsh_embryo_stager). To distinguish samples staged via eMOSS, these samples are designated with “mE” for morphometric embryonic day (e.g. mE13.5). Due to the increased complexity of limb morphology at later stages automated staging beyond ~E15.0 is not possible. As a consequence, harvests for all remaining embryonic samples (E15.0-E18.75) were performed precisely at 00:00, 06:00, 12:00, and 18:00 on the targeted day. From close inspection of limbs in this sample set we defined additional dynamics related to digit morphogenesis that allowed further binning of samples collected on Days 15 and 16. Therefore, amongst samples profiled in this study only the E17.0-E18.75 samples were staged solely by gestational age. Lastly, P0 samples were harvested from litters at noon of the day of birth (parturition for C57BL/6NJ occurs between E18.75 and E19.0).

extract_protocol: To generate the dataset, we used the optimized sci-RNA-seq3 protocol, adjusting the volume and type of lysis buffer to the size of the embryos. Briefly, frozen embryos were pulverized on dry ice and cells were lysed with a phosphate-based, hypotonic lysis buffer containing magnesium chloride, Igepal, diethyl pyrocarbonate (DEPC) as an RNase inhibitor, and either sucrose or bovine serum albumin (BSA). Lysate is passed over a 20um filter, and the nuclei-containing flow-through is fixed with a mixture of methanol and dithiobis (succinimidyl propionate) (DSP). Nuclei are rehydrated and washed in a sucrose/PBS/triton/magnesium chloride buffer (SPBSTM), then counted and distributed into 96-well plates for reverse transcription with indexed oligo-dT primers.

tag: developmental stage

value: somitogenesis validation (ranging from 8 to 21 somites)

tag: strain


title: DSP-1001660008747-A-C05

city: New Haven

first: Niki

last: Gavrielatou

address: 310 Cedar Street

institute: Yale University School of Medicine

library_source: transcriptomic

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx®-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered/counted as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Supplementary files format and content: CD45_10%_norm.xlsx  contains read counts from the leukocyte (CD45) compartment over the 10% LoD threshold, after Q3 normalization
Supplementary files format and content: CD68_10%_norm.xlsx  contains read counts from the macrophage (CD68) compartment over the 10% LoD threshold, after Q3 normalization
Supplementary files format and content: CK_10%_norm.xlsx  contains read counts from the tumor (CK) compartment over the 10% LoD threshold, after Q3 normalization

molecule: total RNA

organism: Homo sapiens

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx®-DSP protocol (MAN-10150-01).Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5/666 nm, excitation 645/19 nm, emission 683/30 nm), CD45 for lymphocyte compartment (Texas Red/615 nm, excitation 588/19 nm, emission 623/30 nm), S100B (Cy3/568 nm, excitation 538/19 nm, emission 564/15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx®-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx®-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

tag: tissue

tag: cell type

value: leukocyte

tag: disease state

value: HNSCC

tag: patient

tag: treatment

value: ICI


title: run_13_seq_1_PA-12D_S92

description: sci-RNA-seq3 library

value: mouse embryos spanning late gastrulation (E8) to birth (P0)


title: DSP-1001660008747-A-E06


title: run_29_P1-10C_S75

description: sci-RNA-seq3 library


title: run_29_P1-10E_S77

description: sci-RNA-seq3 library


title: run_29_P1-10D_S76

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-E01


title: run_13_seq_1_PA-12C_S91

description: sci-RNA-seq3 library


title: run_13_seq_1_PC-01A_S97

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-D08


title: run_13_seq_1_PA-12H_S96

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-12B_S90

description: sci-RNA-seq3 library


title: run_29_P1-10A_S73

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-B12


title: run_29_P1-09H_S72

description: sci-RNA-seq3 library


title: run_29_P1-10G_S79

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-B10


title: run_29_P1-09G_S71

description: sci-RNA-seq3 library


title: run_29_P1-09F_S70

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-12A_S89

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-B07


title: run_29_P1-09E_S69

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-11H_S88

description: sci-RNA-seq3 library


title: run_29_P1-09D_S68

description: sci-RNA-seq3 library


title: run_29_P1-09B_S66

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-B01


title: run_29_P1-09C_S67

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-11G_S87

description: sci-RNA-seq3 library


title: run_29_P1-09A_S65

description: sci-RNA-seq3 library


title: run_29_P1-08G_S63

description: sci-RNA-seq3 library


title: run_29_P1-10B_S74

description: sci-RNA-seq3 library


title: run_29_P1-08H_S64

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-11F_S86

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-11E_S85

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-A10


title: run_29_P1-08F_S62

description: sci-RNA-seq3 library


title: run_29_P1-08E_S61

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-A07


title: run_29_P1-08C_S59

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-11D_S84

description: sci-RNA-seq3 library


title: run_29_P1-08D_S60

description: sci-RNA-seq3 library


title: DSP-1001660008747-A-A05


title: run_29_P1-08B_S58

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-11C_S83

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-B10


title: DSP-1001660008747-A-B04


title: run_13_seq_1_PA-11B_S82

description: sci-RNA-seq3 library


title: run_29_P1-07G_S55

description: sci-RNA-seq3 library


title: run_29_P1-07F_S54

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-B07


title: DSP-1001660008746-B-B04


title: run_29_P1-07H_S56

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-11A_S81

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-10H_S80

description: sci-RNA-seq3 library


title: run_29_P1-07C_S51

description: sci-RNA-seq3 library


title: run_29_P1-07E_S53

description: sci-RNA-seq3 library


title: run_29_P1-07B_S50

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-10G_S79

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-10F_S78

description: sci-RNA-seq3 library


title: run_29_P1-07A_S49

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-A10


title: run_29_P1-06H_S48

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-10E_S77

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H09


title: run_13_seq_1_PA-10D_S76

description: sci-RNA-seq3 library


title: run_29_P1-06G_S47

description: sci-RNA-seq3 library


title: run_29_P1-06F_S46

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H06


title: run_29_P1-08A_S57

description: sci-RNA-seq3 library


title: run_29_P1-06E_S45

description: sci-RNA-seq3 library


title: run_29_P1-06C_S43

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-10C_S75

description: sci-RNA-seq3 library


title: run_29_P1-06B_S42

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-10B_S74

description: sci-RNA-seq3 library


title: DSP-1001660008746-B-B01


title: DSP-1001660008745-C-G10


title: run_29_P1-07D_S52

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H01


title: run_29_P1-05G_S39

description: sci-RNA-seq3 library


title: run_29_P1-06A_S41

description: sci-RNA-seq3 library


title: run_29_P1-05H_S40

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-G07


title: run_13_seq_1_PA-10A_S73

description: sci-RNA-seq3 library


title: run_29_P1-05F_S38

description: sci-RNA-seq3 library


title: run_29_P1-05E_S37

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-09H_S72

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-G02


title: run_29_P1-05D_S36

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-09G_S71

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-F11


title: run_29_P1-06D_S44

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-09F_S70

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-H04


title: run_29_P1-05C_S35

description: sci-RNA-seq3 library


title: run_29_P1-05A_S33

description: sci-RNA-seq3 library


title: run_29_P1-05B_S34

description: sci-RNA-seq3 library


title: run_29_P1-04H_S32

description: sci-RNA-seq3 library


title: run_29_P1-04G_S31

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-F08


title: run_13_seq_1_PA-09E_S69

description: sci-RNA-seq3 library


title: run_29_P1-04F_S30

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-F03


title: run_13_seq_1_PA-09D_S68

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-E10


title: run_29_P1-04D_S28

description: sci-RNA-seq3 library


title: run_29_P1-04E_S29

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-09C_S67

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-E05


title: run_29_P1-04C_S27

description: sci-RNA-seq3 library


title: run_29_P1-04B_S26

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-09B_S66

description: sci-RNA-seq3 library


title: run_29_P1-04A_S25

description: sci-RNA-seq3 library


title: run_29_P1-03H_S24

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-E02


title: run_13_seq_1_PA-08H_S64

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-09A_S65

description: sci-RNA-seq3 library


title: run_29_P1-03G_S23

description: sci-RNA-seq3 library


title: run_29_P1-03C_S19

description: sci-RNA-seq3 library


title: run_29_P1-03E_S21

description: sci-RNA-seq3 library


title: run_29_P1-03F_S22

description: sci-RNA-seq3 library


title: run_29_P1-03D_S20

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-D08


title: DSP-1001660008745-C-D05


title: run_13_seq_1_PA-08G_S63

description: sci-RNA-seq3 library


title: run_29_P1-03B_S18

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-08F_S62

description: sci-RNA-seq3 library


title: run_29_P1-02H_S16

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-D02


title: run_13_seq_1_PA-08D_S60

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-08E_S61

description: sci-RNA-seq3 library


title: run_29_P1-02G_S15

description: sci-RNA-seq3 library


title: run_29_P1-02F_S14

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-C11


title: run_29_P1-02E_S13

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-C08


title: DSP-1001660008745-C-D11


title: run_13_seq_1_PA-08C_S59

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-08B_S58

description: sci-RNA-seq3 library


title: run_29_P1-02B_S10

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-C02


title: run_29_P1-01H_S8

description: sci-RNA-seq3 library


title: run_29_P1-01F_S6

description: sci-RNA-seq3 library


title: run_29_P1-01G_S7

description: sci-RNA-seq3 library


title: run_29_P1-01E_S5

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-07H_S56

description: sci-RNA-seq3 library


title: run_29_P1-01D_S4

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-B08


title: run_13_seq_1_PA-07G_S55

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-B05


title: run_29_P1-01B_S2

description: sci-RNA-seq3 library


title: run_29_P1-01A_S1

description: sci-RNA-seq3 library


title: run_29_P1-02D_S12

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-07F_S54

description: sci-RNA-seq3 library


title: run_29_P1-03A_S17

description: sci-RNA-seq3 library


title: run_29_P1-02C_S11

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-C05


title: T.adornatum_RedC_rep2

city: Moscow

first: Grigory

last: Evko

address: Vavilova str., 34/5

country: Russia

institute: Institute of Gene Biology of the Russian Academy of Sciences

library_source: other

data_processing:
For raw data processing RedClib pipeline was used (github: https://github.com/agalitsyna/RedClib)
Supplementary files format and content: Processed RedC data files are available as TSV files with individual mapped RNA-DNA contacts. Each row corresponds to an individual RNA-DNA contact that passed filtering steps. Columns represent information about 3' RNA, 5' RNA and DNA mapping position (chromosome, start, end, strand), CIGAR string and mapped sequence length.
Library strategy: RedC

molecule: other

organism: Thermofilum adornatum

growth_protocol:
E. coli DH5α and B. subtilis 168 strains were grown overnight in Luria-Bertani broth at 37 °C and 180 rpm to a final OD600 ~ 1.7.
T. adornatum 1910bT strain was grown on strictly anaerobic modified Pfennig medium supplemented with 0.1 g/L of yeast extract, 1/100 (v/v) of sterile culture broth filtrate of Desulfurococcus sp. 1910a and 1.0 g/L of glucose as the substrate under N2 in the gas phase at 80°C and pH 5.75 to a final growth yield of 3×10^7 cells/mL.

extract_protocol: RedC uses custom oligos and adapters resulting in libraries ready for sequencing on the Illumina platform.


title: run_29_P1-02A_S9

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-07E_S53

description: sci-RNA-seq3 library


title: Decitabine induced HLAG+ regulatory T cells - scRNAseq

city: Patras

first: Alexandros

last: Spyridonidis

state: Achaia

address: University Campus, Rio

department: Institute of Cell Therapy

country: Greece

institute: University of Patras

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Primary human T lymphocytes

growth_protocol: T cells were stimulated with anti CD3/CD28 magnetic beads at a bead:cell ratio 1:1 for 3 days in RPMI1640 supplemented with 10% FBS, 2mM L-Glutamine and 1% Pen/Strep

extract_protocol:
HLAG+ regulatory T cells were FACS sorted based on their surface expression of HLAG
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

treatment_protocol: Post activation cells were treated with 5uM decitabine in the presence of 50U/ml IL2 for an additional 3 days

value: Primary human T lymphocytes

tag: cell population

value: HLAG+


title: T.adornatum_RedC_rep1


title: DSP-1001660008745-C-B11


title: run_13_seq_1_PA-07D_S52

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-A11


title: run_13_seq_1_PA-07C_S51

description: sci-RNA-seq3 library


title: run_29_P1-01C_S3

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-A08


title: SP4

city: Boston

first: Feng

last: Feng

state: United States

address: 650 Albany Street X248

institute: Boston University

data_processing:
Trimmomatic with a sliding window of 4 nucleotides and a minimum quality score of 20 for the QC step.
Bowtie2 for comparing the sequences to an Ig heavy-chain database to filter out non-IG genes
An in-house developed C++ program for isotype classification (IgG vs IgM) with flexibility for mismatches and offset isotype sequences.
An in-house algorithm for deduplicating UMIs in python to generate consensus sequences.
Cloanalyst to estimate recombination parameters and clonal partitioning.
Assembly: A customized IGH gene-segment library derived from the IMGT.
Supplementary files format and content: Recombination summary: tab-delimited text files include  IG recombination events and stats for each sample (IGHV, D,  J gene segments, mutation, CDR3, etc)
Supplementary files format and content: Clone and clone assignment: tab-delimited text files include clone information for each sequence and each sample.
Supplementary files format and content: Mutation: tab-delimited text files include individual detailed mutations for ech sequence.
Library strategy: Immunoglobulin RNA Sequencing

source_name: Spleen OVA alone

growth_protocol: Age-matched C57BL/6J mice (three mice each group) were immunized with ovalbumin with or without adjuvants (PBS control, Ova alone, Ova+CpG and Ova+Alum).

extract_protocol:
Total RNA was isolated using RNAZol RT from tissue cell suspension.
We adopted a 5’ rapid amplification of cDNA ends (5’RACE) approach for library prep. cDNA synthesis was done with forward template switching oligos (TSO) with unique molecular identifiers (UMI).

treatment_protocol: BMs and spleens were harvested. Single cell suspension was prepared, and total RNA was isolated.

value: Spleen

tag: genotype

value: WT

value: OVA


title: SP3

source_name: Spleen PBS control

value: PBS


title: SP6


title: SP2


title: SP15

source_name: Spleen OVA+Alum

value: OVA+Alum


title: DSP-1001660008744-D-C02


title: run_13_seq_1_PA-08A_S57

description: sci-RNA-seq3 library


title: DSP-1001660008745-C-A05


title: run_13_seq_1_PA-07A_S49

description: sci-RNA-seq3 library


title: SP12

source_name: Spleen OVA+CpG

value: OVA+CpG


title: SP11


title: SP10


title: run_13_seq_1_PA-06G_S47

description: sci-RNA-seq3 library


title: SP1


title: DSP-1001660008745-C-B02


title: SP13


title: SP14


title: DSP-1001660008744-D-B06


title: DSP-1001660008744-D-B03


title: run_13_seq_1_PA-06H_S48

description: sci-RNA-seq3 library


title: MB6

source_name: Bone marrow OVA alone

value: Bone Marrow


title: MB5


title: run_13_seq_1_PA-06F_S46

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-B11


title: run_13_seq_1_PA-07B_S50

description: sci-RNA-seq3 library


title: DSP-1001660008744-D-A12


title: MB4


title: run_13_seq_1_PA-06E_S45

description: sci-RNA-seq3 library


title: MB3

source_name: Bone marrow PBS control


title: MB11

source_name: Bone marrow OVA+CpG


title: DSP-1001660008744-D-A03


title: run_13_seq_1_PA-06C_S43

description: sci-RNA-seq3 library


title: Human Pancreatic Islet Graft Mouse In-vivo snRNA 4

city: Duarte

first: Randy

middle: B

last: Kang

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Endocrinology

institute: City of Hope Beckman Research Center

description: integrated matrix

data_processing:
Latest version of Cell Ranger with GRCh38 or GRCh38/mm10 build for corresponding sample preparation
snRNA seq was processed with intron-inclusive option
Assembly: GRCh38
Supplementary files format and content: CSV file with count matrix

source_name: Pancreatic Islet

growth_protocol: serum free culture medium in non-adhesive culture plate in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
scRNA was filtered with Miltenyi Biotec’s dead cell removal kit
snRNA and graft snRNA extraction was done by Minute single nucleus isolation kit (cat#SN-047)

value: Pancreatic Islet

tag: condition

value: Non-diabetic Normal


title: MB15

source_name: Bone marrow OVA+Alum


title: MB14


title: MB13


title: Human Pancreatic Islet Graft Mouse In-vivo snRNA 3

description: integrated matrix


title: run_13_seq_1_PA-06B_S42

description: sci-RNA-seq3 library


title: MB12


title: Human Pancreatic Islet Graft Mouse In-vivo snRNA 2

description: integrated matrix


title: MB10


title: run_13_seq_1_PA-06A_S41

description: sci-RNA-seq3 library


title: MB1


title: Human Pancreatic Islet Graft Mouse In-vivo snRNA 1

description: integrated matrix


title: run_13_seq_1_PA-05H_S40

description: sci-RNA-seq3 library


title: Human Pancreatic Islet snRNA 3

description: integrated matrix


title: PAN-CB-E10B

city: Memphis

first: John

last: Easton

state: TN

address: 1383 Island Town Dr

department: Computational Biology

institute: St.Jude Children's Research Hospital

description: Single cell were isolated from the cerebellum using Papain dissociation method,resuspended in PBS with 0.4% BSA (https://doi.org/10.1016/j.cub.2018.07.062)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 1.1.0  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/1.0/using/demultiplex)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebellum

extract_protocol:
The cerebellum was dissociate following papin enzyme protocol. More details of method refer Carter et.al. Current Biology 28, 2910–2920
The single cells were captured in the droplet in the Chromium droplet generator.The cDNA and Library was generated following Single cell gene expression Kit  V1  from 10X Genomics.
Single cell Gene expression Kit from V1 from 10X Genomics.

value: Cerebellum

tag: biological replicates


title: E12.5 Cardiomyocytes, SMV_Rep4

city: Chapel Hill

first: Whitney

last: Edwards

state: NC

address: 133 North Medical Drive

department: Biology

institute: University of North Carolina Chapel Hill

data_processing:
Libraries were run on a HiSeq2500 (Illumina) with 2×150 bp paired end reads.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_ID feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Assembly: mm10
Supplementary files format and content: text files include raw hit counts for each value

source_name: E12.5 Cardiomyocytes

extract_protocol:
Embryonic hearts were dissected from embryos, cardiac RNA was harvested using RNAqueous™-Micro Total RNA Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

tag: age

tag: Sex

value: pooled Male and Female

value: 10 micromolar simvastatin


title: run_13_seq_1_PA-05G_S39

description: sci-RNA-seq3 library


title: E12.5 Cardiomyocytes, SMV_Rep3


title: PAN-CB-E10A


title: run_13_seq_1_PA-05F_S38

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-06D_S44

description: sci-RNA-seq3 library


title: Human Pancreatic Islet snRNA 2

description: integrated matrix


title: MB2


title: E12.5 Cardiomyocytes, SMV_Rep2


title: E12.5 Cardiomyocytes, Ctrl_Rep4

value: Control


title: E12.5 Cardiomyocytes, SMV_Rep1


title: run_13_seq_1_PA-05E_S37

description: sci-RNA-seq3 library

value: mouse embryos spanning late gastrulation (E8) to birth (P0)


title: human Pancreatic Islet snRNA 1

description: integrated matrix


title: Human Pancreatic Islet scRNA 3

description: integrated matrix


title: run_13_seq_1_PA-05D_S36

description: sci-RNA-seq3 library


title: E12.5 Cardiomyocytes, Ctrl_Rep1


title: E12.5 Cardiomyocytes, Ctrl_Rep2


title: E12.5 Cardiomyocytes, Ctrl_Rep3


title: Human Pancreatic Islet scRNA 2

description: integrated matrix


title: heart, E16_Rep4

value: wild-type


title: Human Pancreatic Islet scRNA 1

description: integrated matrix


title: heart, E16_Rep3


title: run_13_seq_1_PA-05C_S35

description: sci-RNA-seq3 library


title: T2D-HAEC 2Gy rep1

city: Cheonan

first: Keunsoo

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

data_processing:
The raw RNA-seq reads acquired from the sequencing platform were processed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to eliminate adapter and low-quality sequences. The trimmed reads underwent quality assessment using FastQC (version 0.11.9) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The trimmed reads were aligned to the reference human genome (hg38 assembly; GRCh38.p13) using STAR (version 2.7.9a) (Dobin et al. Curr Protoc Bioinforma 2015) and GENCODE gene annotation (https://www.gencodegenes.org/). The RNA-seq data quality was further evaluated by calculating the transcript integrity number (TIN) score using RSeQC (tin.py; version 4.0.0) (Wang et al. Bioinforma Oxf Engl 2012). With a median TIN value exceeding 0.7 for all RNA-seq data, high data quality was confirmed.
The expression levels of known genes were estimated using the transcript per million (TPM) method with StringTie (version 2.1.7b) (Pertea et al. Nat. Biotechnol 2015). Differential expression analysis was performed using DESeq2 (version 1.36.0) (Love et al. Genome Biol 2014) with an adjusted p-value cutoff of 0.05. All software and algorithms were used with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

growth_protocol: Type 2 diabetic human aortic endothelial cells (T2D-HAECs, #CC-2920) were obtained from Lonza Group Ltd. (Walkersville, MD, USA). The cells were cultured in endothelial growth medium-2 microvascular medium (EGM-2MV, Lonza) and maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using the TRIsure solution (Bioline, London, UK) according to the manufacturer's instructions. RNA quality was assessed with an Agilent 2100 bioanalyzer and an RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, Netherlands), obtaining the RNA integrity number. Total RNA quantification was performed using a NanoDrop 2000 spectrophotometer (ND-2000; Thermo Fisher Scientific, Inc.).
RNA-seq was conducted on high-quality RNA samples (RNA integrity number > 7) from T2D-HAEC cells exposed to 0Gy (no radiation), 0.1Gy, 0.5Gy, or 2.0Gy. Samples were multiplexed into lanes and sequenced using a HiSeq 4000 system (Illumina, San Diego, CA, USA).

treatment_protocol: Cells were exposed to γ-rays using a 137Cs laboratory γ-irradiator (LDI-KCCH 137, Seoul, Korea) at a dose of 0.1 Gy (4.8 mGy/min) or a 137Cs γ-ray source (Atomic Energy of Canada, Mississauga, Ontario, Canada) at doses of 0.5 Gy or 2 Gy (2.26 Gy/min), following a procedure described previously (Kaushik et al. Sci Rep 2017).

tag: cell line

value: diabetic human aortic endothelial cells


title: T2D-HAEC 0.5Gy rep2


title: T2D-HAEC 2Gy rep2


title: run_13_seq_1_PA-05B_S34

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-05A_S33

description: sci-RNA-seq3 library


title: T2D-HAEC 0.5Gy rep1


title: heart, E16_Rep2


title: ACT5 unsort OC

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

library_source: genomic single cell

data_processing:
scATAC-seq fastq files were processed using cellranger atac pipeline
Assembly: hg19
Supplementary files format and content: fragments file containing trimmed, deduplicated, high quality atac-seq fragments and cell barcodes

molecule: genomic DNA

source_name: human brain

extract_protocol:
Nuclei were isolated from frozen postmortem brain samples
scATAC-seq libraries were constructed using 10X genomics reagents and protocols
10X genomics single cell ATAC-seq

tag: sorted

value: no

tag: brain region

value: Occipital Cortex


title: run_13_seq_1_PA-04H_S32

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-04G_S31

description: sci-RNA-seq3 library


title: T2D-HAEC 0.1Gy rep2


title: ACT3 unsort OC


title: ACT6 unsort OC


title: T2D-HAEC 0.1Gy rep1


title: heart, E14_Rep2


title: ACT12 unsort OC


title: T2D-HAEC 0Gy rep2

value: no radiation


title: run_13_seq_1_PA-04E_S29

description: sci-RNA-seq3 library


title: heart, E12_Rep4


title: T2D-HAEC 0Gy rep1


title: ACT11 unsort OC


title: run_13_seq_1_PA-04D_S28

description: sci-RNA-seq3 library


title: ACT10 unsort OC


title: heart, E12_Rep3


title: WI-38 BAFFsi + IR-2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
BAFF siRNA transfected cells were treated with 10 Gy IR and cultured for 10 days - replicate 2
mRNA

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program.
FASTQ files were aligned to human genome hg19 Ensembl v82 using STAR software.
featureCounts was used to create gene counts.
Differential expression analysis of gene counts was performed using the DESeq2.
Assembly: hg19
Supplementary files format and content: *.txt: Tab-delimited text files containing counts.

growth_protocol: THP-1 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics. WI-38 cells were grown in DMEM supplemented with 10% FBS, 1% antibiotics and 1% non essential amino acids (NEAA). Both cells were maintained in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted with RNeasy mini KIT (Qiagen).
Sequencing libraries were prepared with TruSeq Stranded mRNA kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Senescence in THP-1 cells was induced by treating the cells with 5Gy Ionizing radiation for 3 to 5 days. Senescence in WI-38 cells was induced by treating the cells with 10Gy Ionizing radiation or 10 days. Cells were transfected before the irradiation with Ctrlsi or BAFFsi.

value: human fetal lung fibroblasts

value: WT

value: BAFF siRNA transfection, IR-induced senescence

tag: time

value: 10 days


title: heart, E16_Rep1


title: run_13_seq_1_PA-04C_S27

description: sci-RNA-seq3 library

tag: developmental stage


title: heart, E12_Rep2

tag: strain


title: FOP + Activin-A 6

city: Amsterdam

first: Ton

last: Schoenmaker

state: SELECT

address: GUSTAV MAHLERLAAN 3004, Room 11N-07

department: Periodontology

country: Netherlands

institute: ACTA

data_processing:
Samples were sequenced on an Illumina HiSeq4000 with single 50bp reads at 100x106 reads per sample.
Data went through quality control using FastQC.
Reads were aligned to the human reference genome (NCBI38) using STAR v2.7.1, and annotated with Ensemble v103.
Assembly: GRCh38
Supplementary files format and content: count files were converted into DESeq2_rlog values using DESeq2 in R.

source_name: CD14+ cells from blood

growth_protocol: CD14+ monocytes were cultured for 14 days with M-CSF and RANKL

extract_protocol:
RNA was isolated using the QIAgen RNeEasy kit
Library preparation was performed using the Kapa mRNA HyperPrep kit from Roche

treatment_protocol: Samples were cultured without or with Activin-A

tag: donor

value: FOP patient

tag: activin-a presence

value: + Activin-A


title: heart, E14_Rep3

tag: tissue


title: run_13_seq_1_PA-04B_S26

description: sci-RNA-seq3 library


title: WI-38 BAFFsi + IR-1

description:
BAFF siRNA transfected cells were treated with 10 Gy IR and cultured for 10 days - replicate 1
mRNA

tag: cell type


title: FOP - Activin-A 5

value: - Activin-A


title: WI-38 Controlsi + IR-2

description:
Control siRNA transfected cells were treated with 10 Gy IR and cultured for 10 days - replicate 2
mRNA

tag: treatment

value: Control siRNA transfection, IR-induced senescence


title: heart, E14_Rep1

value: heart

value: pooled Male and Female


title: heart, E10_Rep4


title: heart, E10_Rep3


title: WI-38 Controlsi + IR-1

description:
Control siRNA transfected cells were treated with 10 Gy IR and cultured for 10 days - replicate 1
mRNA


title: run_13_seq_1_PA-04F_S30

description: sci-RNA-seq3 library


title: FOP + Activin-A 5


title: run_13_seq_1_PA-04A_S25

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-03H_S24

description: sci-RNA-seq3 library


title: WI-38 Controlsi-2

description:
Control siRNA transfected cells were cultured for 10 days - replicate 2
mRNA

value: Control siRNA transfection


title: FOP - Activin-A 4


title: run_13_seq_1_PA-03G_S23

description: sci-RNA-seq3 library

value: mouse embryos spanning late gastrulation (E8) to birth (P0)


title: heart, E10_Rep2

value: wild-type


title: FOP + Activin-A 4


title: WI-38 Controlsi-1

description:
Control siRNA transfected cells were cultured for 10 days - replicate 1
mRNA


title: run_13_seq_1_PA-03F_S22

description: sci-RNA-seq3 library


title: heart, E10_Rep1


title: FOP - Activin-A 6


title: THP1 BAFFsi + IR-2

description:
BAFF siRNA transfected cells were treated with 5 Gy IR and cultured for 72 hours - replicate 2
mRNA

value: leukemia monocytic cell line

value: 72 hours


title: FOP - Activin-A 3


title: heart, E9_Rep3


title: FOP + Activin-A 3


title: heart, E12_Rep1


title: run_13_seq_1_PA-03E_S21

description: sci-RNA-seq3 library


title: THP1 BAFFsi + IR-1

description:
BAFF siRNA transfected cells were treated with 5 Gy IR and cultured for 72 hours - replicate 1
mRNA


title: FOP - Activin-A 2


title: heart, E9_Rep2


title: THP1 Controlsi + IR-2

description:
Control siRNA transfected cells were treated with 5 Gy IR and cultured for 72 hours - replicate 2
mRNA


title: run_13_seq_1_PA-03D_S20

description: sci-RNA-seq3 library


title: heart, E9_Rep1


title: run_13_seq_1_PA-03C_S19

description: sci-RNA-seq3 library


title: FOP + Activin-A 2


title: run_13_seq_1_PA-03B_S18

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-03A_S17

description: sci-RNA-seq3 library


title: THP1 Controlsi + IR-1

description:
Control siRNA transfected cells were treated with 5 Gy IR and cultured for 72 hours - replicate 1
mRNA


title: THP1 Controlsi-2

description:
Control siRNA transfected cells were cultured for 72 hours - replicate 2
mRNA


title: Contorl with radiation exposure

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: bladder urothelial carcinoma

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt.
Quantified reads were aligned to the mouse genome (GRCh38) by STAR (v2.6.1a) and then gene-level read counts were generated based on the annotations of Gencode (v28).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level read counts.

source_name: bladder urothelial carcinoma

growth_protocol: A specific lentiviral vector carrying shRNA whose sequence targeted human HDAC6 and a control pLKO.1 vector in T24 cells were subjected to lentivirus infection. After 72 hours, the cells were selected with 2 mg/mL puromycin.

extract_protocol:
Total RNA was extracted from frozen snaps using an AllPrep DNA/RNA mini kit (Qiagen,  Hilden, Germany).
Libraries were constructed using Illumina TruSeq Stranded mRNA kit according to the manufacturers

treatment_protocol: Cells were exposed to ionizing radiation at 10 Gray using a 137Cs γ-irradiator.

value: RT


title: HDAC6 knockdown with radiation exposure

description: bladder urothelial carcinoma

value: HDAC6 KD + RT


title: FOP - Activin-A 1


title: Control

description: bladder urothelial carcinoma

value: Empty


title: Control - Activin-A 6

value: Healthy control


title: run_13_seq_1_PA-02H_S16

description: sci-RNA-seq3 library


title: THP1 Controlsi-1

description:
Control siRNA transfected cells were cultured for 72 hours - replicate 1
mRNA

value: WT


title: Control + Activin-A 6


title: S8_R1

city: Dalian

first: Jinsong

last: Yan

state: Liaoning

address: 467 Zhongshan Road, Dalian 116027, Liaoning, P. R. China

department: Department of Hematology

country: China

institute: the Second Hospital of Dalian Medical University

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: hg38
Supplementary files format and content: Excel file includes RPKM values for each Sample

source_name: Bone marrow

extract_protocol:
Mononuclear cell layer from BM sample was separated by Ficoll Hypaque (1114547, Axis-Shield) density gradient separation. Total RNA of the mononuclear cells were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

tag: individual

value: Patient S8

value: Bone marrow

value: Mononuclear cells

tag: disease state

value: AML

tag: disease stage

value: 1st Relapse


title: run_13_seq_1_PA-02F_S14

description: sci-RNA-seq3 library

source_name: sci-RNA-seq3 of mouse organogenesis and fetal development


title: S8_P

value: Primary


title: Control - Activin-A 5

value: - Activin-A


title: run_13_seq_1_PA-02E_S13

description: sci-RNA-seq3 library


title: sorted HLAG- T cells, 5

data_processing:
Trimmomatic-038 for removing adapters
HISAT2 for alignment against whole human genome: hg19 GRCh38
featureCounts tool to calculate read counts
DESEQ2 to calculate RPKM values, logarithmize data and perform differential expression analysis correcting p-values for multiple testing using Benjamini-Hockberg FDR adjustment method.
Assembly: hg19 GRCh38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: Primary human cells

extract_protocol:
RNA was extracted using Rneasy micro  kit (Qiagen).
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: Primary human cells

value: T lymphocytes

tag: genotype

tag: cell population

value: HLAG- T cells


title: sorted HLAG- T cells, 3


title: sorted HLAG- T cells, 4


title: S7_R

value: Patient S7

value: Relapse


title: Control + Activin-A 5

value: + Activin-A


title: Control - Activin-A 4


title: sorted HLAG- T cells, 1


title: run_13_seq_1_PA-02B_S10

description: sci-RNA-seq3 library

value: mouse embryos spanning late gastrulation (E8) to birth (P0)


title: S6_P

value: Patient S6


title: Control + Activin-A 4

value: Healthy control


title: run_13_seq_1_PA-02C_S11

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-02G_S15

description: sci-RNA-seq3 library


title: FOP + Activin-A 1

value: FOP patient


title: S6_R


title: S8_R2

value: Patient S8

value: 2nd Relapse


title: Control - Activin-A 3


title: sorted HLAG+ T cells, 5

value: WT

value: HLAG+ T cells


title: sorted HLAG+ T cells, 4


title: S5_R

value: Patient S5

value: Bone marrow

value: Mononuclear cells

value: AML


title: Control + Activin-A 3


title: run_13_seq_1_PA-01H_S8

description: sci-RNA-seq3 library


title: S5_P

value: Primary


title: Control - Activin-A 2

value: - Activin-A


title: sorted HLAG+ T cells, 3

value: Primary human cells

value: T lymphocytes


title: sorted HLAG+ T cells, 2


title: run_13_seq_1_PA-01G_S7

description: sci-RNA-seq3 library


title: Control + Activin-A 2

value: + Activin-A


title: run_13_seq_1_PA-02D_S12

description: sci-RNA-seq3 library

value: mouse embryos spanning late gastrulation (E8) to birth (P0)


title: sorted HLAG- T cells, 2

value: HLAG- T cells


title: S4_R2

value: Patient S4


title: S7_P

value: Patient S7


title: S4_R1

value: 1st Relapse


title: run_13_seq_1_PA-01F_S6

description: sci-RNA-seq3 library


title: Control - Activin-A 1

value: Healthy control


title: S4_P


title: S3_R2

value: Patient S3

value: 2nd Relapse


title: Control + Activin-A 1


title: run_13_seq_1_PA-02A_S9

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-01D_S4

description: sci-RNA-seq3 library


title: run_13_seq_1_PA-01E_S5

description: sci-RNA-seq3 library


title: S3_R1


title: shNT_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep3

city: Dublin

first: Eoin

middle: P

last: Cummins

state: Dublin

address: UCD Conway Institute of Biomolecular and Biomedical Research, UCD Belfield

department: Conway Institute/School of Medicine

country: Ireland

institute: University College Dublin

data_processing:
Raw data quality was evaluated with Fast QC, and per base quality score distribution plotted
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: raw counts

growth_protocol: The appropriate number of shNT THP-1 cells were counted, centrifuged at 1,200rpm (290xg) and the supernatant was removed. Cells were transferred to an environmental gas chamber (37℃, 5% CO2 or 10% CO2)  and resuspended in buffered DMEM media supplemented with 10% FBS, 1% P/S. at a concentration of 750,000 cells/ml (3 million cells/ 4 mls media on 60mm plastic cell culture dishes). Cells were incubated for 2 hours. LPS-stimulated cells were treated with 2.5ug/ml LPS  for a further 2 hours before lysis.

extract_protocol:
Cells were collected and total mRNA was extracted using the Omega EZNA Total RNA Kit I, as per the manufacturer’s instructions.
cDNA library preparation was performed with polyA selection using Illumina HiSeq, 2x150bp configuration, single index, per lane. ~350M raw paired-end reads per lane. Library preparation and sequencing were performed by Genewiz (Germany).

treatment_protocol: Cells were treated +/- LPS for 2hrs in their respective CO2 chamber

value: Human monocytic leukaemia_ THP1

tag: lentiviral particle transduction

value: non-target shRNA

value: 10percent CO2 + LPS


title: WT_NPC_3

city: Shanghai

first: Ke

last: Zhang

address: No.320 Yueyang Road

institute: SIBCB

data_processing:
For RNA-Seq, gene expression levels were calculated by HISAT2 (version 2.1.0) and FeatureCounts (version 1.5.3) (Sahraeian et al., 2017) with the reference hg19. The differentially expressed genes (DEGs) were identified by DESeq2 (version 1.16.1) (Love et al., 2014) (padj<0.05, foldchange>2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each sample in RNA-Seq

source_name: Human neuron progenitors

growth_protocol: The protocol for human ES cell differentiation was described previously. Briefly, human ES cell colonies were digested by collagenase IV (2 mg/ml, Gibco) and floated in the hESC growth medium without basic FGF. Embryonic bodies (EBs) were formed after 4 days' suspension and subsequently floated for 2 days in the neural induction medium consisting of DMEM/F12, 1% N2 supplement (Gibco), GlutaMAX, NEAA, and β-ME. The EBs then were adhered to a dish coated by Matrigel and cultured in the neuron differentiation medium consisting of 50% DMEM/F12 medium, 50% Neurobasal medium, 1% N2 supplement, 2% B27 without vitamin A (Gibco), GlutaMAX, NEAA and β-ME for additional 10 days. Then the attached EBs were dissociated into small patches by collagenase IV and cultured in neuron differentiation medium as suspended neural spheres for 4 days. Finally, these neural spheres were digested with Accutase (Gibco) into single cells and plated on Matrigel-coated dishes in the neuron differentiation medium.

extract_protocol:
For RNA-Seq, total RNA was extracted by TRIzol and subjected to quality control and quantification;
For RNA-Seq, cDNA libraries were generated using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370S, NEB).  High-throughput sequencing was performed on a Illumina HiSeq instrument at the Berry Genomics Co, Ltd.

treatment_protocol: For RNA-Seq, no treatment was done;

value: hESC-derived neuron progenitors

tag: passages

tag: chip-antibody


title: Mut_NPC_3


title: run_13_seq_1_PA-01C_S3

description: sci-RNA-seq3 library

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

extract_protocol: To generate the dataset, we used the optimized sci-RNA-seq3 protocol, adjusting the volume and type of lysis buffer to the size of the embryos. Briefly, frozen embryos were pulverized on dry ice and cells were lysed with a phosphate-based, hypotonic lysis buffer containing magnesium chloride, Igepal, diethyl pyrocarbonate (DEPC) as an RNase inhibitor, and either sucrose or bovine serum albumin (BSA). Lysate is passed over a 20um filter, and the nuclei-containing flow-through is fixed with a mixture of methanol and dithiobis (succinimidyl propionate) (DSP). Nuclei are rehydrated and washed in a sucrose/PBS/triton/magnesium chloride buffer (SPBSTM), then counted and distributed into 96-well plates for reverse transcription with indexed oligo-dT primers.


title: shNT_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep2

tag: cell line


title: S3_P

value: Bone marrow

value: Mononuclear cells

value: AML

value: Primary


title: shNT_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep1


title: S2_R

value: Patient S2

value: Relapse


title: S2_P


title: sorted HLAG+ T cells, 1

value: Primary human cells

value: T lymphocytes

value: WT

value: HLAG+ T cells


title: shNT_THP1 10% CO2_rep2

value: 10percent CO2


title: shNT_THP1 10% CO2_rep3


title: Glp1r, replicate 2, scRNA-seq

city: London

first: Alice

last: Adriaenssens

address: Room 420, Rockefeller Building, 21 University Street

country: United Kingdom

institute: University College London

description:
SIGAG10
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: Sequencing reads were aligned to an amended annotation of the mouse genome (GRCm39). The 3’ untranslated regions (UTRs) of Glp1r, Ghsr, Prokr2 and Prlhr  were compared against PolyA_DB v3 (Wang et al., 2018), and extended where necessary to include the furthermost 3’ UTRs in keeping with previous studies (10-12)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hindbrain

extract_protocol:
Single cell suspensions were prepared from coronal sections of hindbrain tissue pooled from four to six GiprEYFP or Glp1rEYFP male mice that were four to six weeks old as described previously (1). Tissue from the brain stem located between -6.00 to -8.12 mm relative to Bregma was dissected into Hibernate-A medium without calcium (BrainBits). The tissue was digested with 20 U/ml Papain (Worthington) for 30 min at 37°C, followed by trituration in Hibernate-A medium (Thermo Fisher Scientific) containing 0.005% (w/v) DNase 1 (Worthington). The cell suspension was filtered through a 40 μm cell strainer into a fresh tube.   Fluorescence-activated cell sorting was performed using a BD Influx Cell Sorter (BD Biosciences, Franklin Lakes, NJ, USA) to isolate GiprEYFP+ and Glp1rEYFP+ cells prepared from GiprEYFP or Glp1rEYFP mice, respectively. Cells were gated according to cell size (FSC), cell granularity (SSC), FSC pulse-width for singlets, fluorescence at 488 nm/532 nm for EYFP and 647/670 nm for nuclear stain with DraQ5 (Biostatus).
Single cell cDNA libraries from purified GiprEYFP+ or Glp1rEYFP+ cells were generated using the 10× Genomics Chromium Instrument and single-cell 3’ Reagent kit (V3; 10X Genomics). Pooled libraries were sequenced on an Illumina NovaSeq 6000 instrument.

value: hindbrain


title: Glp1r, replicate 1, scRNA-seq

description:
SIGAE10
10X Genomics


title: S1_R

value: Patient S1


title: uvrA_untreated_rep3

city: Paris

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description: cutadapt -a ATACCACGACCAGATCGGAA -g GACTTATCAGCCAACCTGT -n 5 -O 4 -m 10 -o Culture1_S2_L001_R1_001_cutTnseq.fastq Culture1_S2_L001_R1_001.fastq

library_source: genomic

data_processing:
Data were processed with Tn-seq explorer
FastQ files were processed with Tn-Seq explorer (Solaimanpour et al, 2015) with the Bowtie2 parameters local and very sensitive.
The number of insertions per gene was normalized according to the number of TA dinucleotides per gene and then normalized by the total number of insertions in the sample to get the Normalized Number of Insertions (NIN).
Genes collecting more than 5000 insertions were considered as Mariner host spot and excluded from the analysis
Assembly: NC_000913.3
Supplementary files format and content: xlsx contain average NIN for each genes annd conditions and their associated Pvalue, Paired t test with Individual variance for each group and a 1% False Discovery Rate (FDR) Two-stage step-up (Benjamini, Krieger, and Yekutieli)

organism: Escherichia coli

growth_protocol: LB

extract_protocol: Construction of the sequencing library was performed as described  (Yamaichi and Dorr 2017).

treatment_protocol: Library production. Tn-Seq was performed as described (Yamaichi and Dorr 2017) by conjugation from E. coli SM10 MFDpir carrying pSC189, with in E. coli MG1655 isogenic strain. About 1 million independent clones, were plated on LBA supplemented with Kanamycin and DAP when required, overnight at 30°C to get isolated colonies. The day after, all colonies from the dishes were recovered and mixed in 30ml LB. OD was adjusted to OD600nm: 0.03 in 45ml LB at 30°C 150rpm and grown to OD600nm: 0.15. The genotoxic agent (MMC 5 µg/ml or BLM 1µg/ml) was added for 20 min. To remove it, two washes were performed. Once the washes were completed, survival cells were spread to target 500k and 1000k colonies with isolated colonies plated ON 30°C LBA.

value: F- lambda- ilvG- rfb-50 rph-1 uvrA


title: uvrA_MMC_rep3


title: uvrA_BLM_rep3


title: A594-stretch

type: RNA

city: Taoyuan City

first: Yi-Chiung

address: No. 300, Zhongda Rd., Zhongli District,

department: Department of Biomedical Sciences and Engineering

institute: National Central University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Array. The hybridized arrays were washed and stained in the Affymetrix Fluidics Station for GeneChip450.

scan_protocol: GeneChips were scanned with the Scanner GCS3000 (Affymetrix).

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: A549, stretch, 4hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A549 cell line were cultured in static and stretch for 4 hours.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's instruction.

treatment_protocol: Pellet the appropriate number of cells by centrifuging for 5 min at 300 x g in a centrifuge tube. Carefully remove all cell-culture medium by aspiration. Pellet were washed with PBS two times and then placed on ice.

value: Human Lung Adenocarcinoma


title: shNT_THP1 10% CO2_rep1

value: Human monocytic leukaemia_ THP1

value: non-target shRNA


title: recN_BLM_rep3

value: F- lambda- ilvG- rfb-50 rph-1 recN


title: S1_P

value: Bone marrow

value: Mononuclear cells


title: shNT_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep3

value: 5percent CO2 + LPS


title: A549-static

source_name: A549, static, 4hr


title: Gipr, replicate 1, scRNA-seq

description:
SIGAD9
10X Genomics

value: GiprEYFP


title: run_13_seq_1_PA-01B_S2

city: Seattle

first: Chengxiang

last: Qiu

address: William H. Foege Hall, 3720 15th Ave NE

institute: University of Washington

description: sci-RNA-seq3 library

value: mouse embryos spanning late gastrulation (E8) to birth (P0)


title: ALK10_6_E775_Mesp1KO_rep2

city: San Francisco

first: Alexis

middle: Leigh

last: Krup

address: 1650 Owens Street

department: Gladstone Institutes of Cardiovascular Disease

institute: Gladstone Institutes

description: 10X Genomics

data_processing:
Libraries pooled and sequenced on Illumina NovaSeq.
Reads were demultiplexed, aligned, read normalized, and quantified using 10X Genomics cellranger-atac-1.2.0 software suite.
Assembly: mm10
Supplementary files format and content: aligned fragments tab-separated values files

source_name: whole embryo

extract_protocol:
Dissociate whole mouse embryos in 0.25% TrypLE and quench with PBS+1%FBS to single cell suspension, perform nuclear lysis. Treat 10000 singularized nuclei with transposition enzyme. Load nuclei in 10X Chromium chip.
10X Genomics Chromium scATAC Library & Gel Bead Kit v1 used for library preparation according to manufacturer's protocol.
single cell ATAC-seq

value: whole embryo

value: Late (lateE7.5-E7.75)

value: Mesp1 KO


title: shNT_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep2


title: ALK09_1_E775_Mesp1KO_rep1

description: 10X Genomics


title: KYSE510 shLHX2-2

city: Beijing

first: Xukun

last: Li

address: No.17 Panjiayuan Nanli, Chaoyang District

department: Department of Radiation Oncology

institute: NCC

data_processing:
Clean reads were obtained after the removal of reads containing adapter and ploy-N and having low quality.
Differential expression was assessed using DESeq by using read counts as input.
Assembly: hg38
Supplementary files format and content: DESeq output

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were constructed using an Illumina TruSeq RNA Sample Preparation kit.

value: esophageal cell squamous carcinoma cells

value: LHX2 knockdown

value: shRNA


title: KYSE510 shLHX2-1


title: run_13_seq_1_PA-01A_S1

description: sci-RNA-seq3 library


title: recN_MMC_rep3


title: recN_untreated_rep3


title: ALK10_2_E75_Mesp1KO_rep2

description: 10X Genomics

value: Middle (lateE6.5-earlyE7.5)


title: shNT_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep1


title: KYSE510 shNC-2

value: WT


title: shNT_THP1 5% CO2_rep3

value: 5percent CO2


title: ALK10_7_E75_Mesp1KO_rep1

description: 10X Genomics


title: shNT_THP1 5% CO2_rep2

value: Human monocytic leukaemia_ THP1


title: KYSE510 shNC-1


title: ALK09_2_E775_con_rep2

description: 10X Genomics

value: Control


title: KYSE30 shLHX2-2


title: uvrA_BLM_rep2

value: F- lambda- ilvG- rfb-50 rph-1 uvrA


title: uvrA_MMC_rep2


title: shNT_THP1 5% CO2_rep1

value: non-target shRNA


title: ALK09_3_E775_con_rep1

description: 10X Genomics


title: ALK10_1_lateE75_con_rep1

description: 10X Genomics


title: ALK10_3_E75_con_rep2

description: 10X Genomics


title: Sample 12_IL-33 Act EOS +ILC2s 3

city: Scottsdale

first: Elizabeth

middle: A.

last: Jacobsen

state: AZ

address: 13400 E. Shea Blvd.

institute: Mayo Clinic

data_processing:
Samples were sequenced using a 2x150bp Paired End (PE) configuration with Illumina HiSeq instrument (4000)
Image analysis and base calling were conducted by the HiSeq Control Software (HCS)
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequence read was trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts  were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions were counted.
Assembly: mm10

source_name: Eosinophil

growth_protocol: ILC2s were isolated from lungs of B6 mice by negative selection with Lineage antibody magnetic bead columns followed by flow cytomtery sorting, then expanded with IL-33, IL-25, IL-2, IL-7 for days. This was then cultured in IL-2 and IL-7 alone for 48 hours, followed by removal of cytokines by washes prior to culture in cytokine-free media alone or with eosinophils for 24 hours.  Eosinophils were isolated from peripheral blood of B6 mice and purified as negative fraction of B220 and CD90 antibody magentic bead columns prior to culture with IL-33 cytokine for 24 hours. These were washed and cultured in cytokine-free media alone or with ILC2s.  After twenty four hours of culture, ILC2s and eosinophils were separated by flow cytometry and placed in trizol for next steps of RNAseq.

extract_protocol:
Trizol Extraction
NEBNext Ultra II RNA Library Prep Kit

value: Eosinophil

value: EOS with IL-33 and ILC2s


title: uvrA_untreated_rep2


title: KYSE30 shNC-2


title: Sample 11_IL-33 Act EOS +ILC2s 2


title: ALK10_5_E75_con_rep1

description: 10X Genomics


title: Sample 9_IL-33 Act EOS 3

value: EOS with IL-33


title: WT_BLM_rep3

value: F- lambda- ilvG- rfb-50 rph-1


title: Sample 10_IL-33 Act EOS +ILC2s 1


title: ALK07_8_E775_con_rep2

description: 10X Genomics

data_processing:
Libraries pooled and sequenced on Illumina NovaSeq.
Raw sequencing reads converted to fastq using cellranger-3.0.2 mkfastq.
Reads aligned to mm10 reference with addition of eGFP and Ai14 sequences using cellranger-3.0.2 count to produce raw .bam files and processed feature counts, barcodes, and matrix outputs.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Dissociate whole mouse embryos in 0.25% TrypLE to single cell suspension prior to loading 10000 cells on a 10X Chromium chip.
10X Genomics Chromium 5' GEM, Library, & Gel Bead Kit v1 used for library preparation according to manufacturer's protocol for GEX library construction without target enrichment.

value: whole embryo


title: recN_BLM_rep2

value: F- lambda- ilvG- rfb-50 rph-1 recN


title: Sample 8_IL-33 Act EOS 2


title: WT_MMC_rep3


title: Sample 7_IL-33 Act EOS 1


title: recN_MMC_rep2


title: KYSE30 shNC-1


title: Cal27 cells, soft LPA to soft, rep 1

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

data_processing:
Data was processed by ROSALIND (https://rosalind.onramp.bio/)
Reads were trimmed using cutadapt.
Quality scores were assessed using FastQC.
Reads were aligned to the human genome build hg19 using STAR.
Individual sample reads were quantified using HTseq, and normalized via Relative Log Expression (RLE) using DESeq2 R library.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files with raw/normalized gene counts for each samples.

growth_protocol: Cal27 cells were cultured on either 0.48 kPa or 20 kPa polyacrylamide gel coated with collagen, and maintained in high glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 5% antibiotics at 5% CO2 at 37C

extract_protocol:
RNA was extracted by Rneasy Mini Kit (Qiagen, 74104), following the manufacturer's protocol.
Library was built using the Illumina TruSeq Stranded RNA and High Throughput Library Prep Kit.

value: epithelial cell

value: LPA


title: ALK05_7_E775_con_rep1

description: 10X Genomics

value: Late (lateE7.5-E7.75)


title: Cal27 cells, soft LPA to soft, rep 3


title: Cal27 cells, stiff to soft, rep 3


title: WT_BLM_rep2


title: recN_untreated_rep2


title: Sample 6_ILC2 + IL-33 Act EOS 3

value: cultured with IL-33 Activated EOS


title: ALK07_6_lateE75_con_rep1

description: 10X Genomics


title: Cal27 cells, soft LPA to soft, rep 2


title: Cal27 cellls, stiff to soft, rep 2


title: WT_MMC_rep2


title: WT_untreated_rep2


title: Sample 4_ILC2 + IL-33 Act EOS 1


title: ALK05_2_lateE75_Mesp1KO_rep1

description: 10X Genomics

value: Mesp1 KO


title: Sample 5_ILC2 + IL-33 Act EOS 2


title: WT_untreated_rep3


title: Cal27 cells, soft LPA to soft FAKi, rep 3

value: WT

value: LPA, FAK inhibitor


title: Cal27 cells, stiff to soft, rep 1


title: ALK07_7_earlyE75_con_rep1

description: 10X Genomics

value: Middle (lateE6.5-earlyE7.5)


title: Sample 3_ILC2 3


title: ALK07_14_E70_con_rep1

description: 10X Genomics

value: Control


title: uvrA_MMC_rep1

value: F- lambda- ilvG- rfb-50 rph-1 uvrA


title: Sample 2_ILC2 2


title: Cal27 cells, soft LPA to soft FAKi, rep 1


title: ALK07_3_lateE65_con_rep1

description: 10X Genomics


title: KYSE30 shLHX2-1

value: esophageal cell squamous carcinoma cells

value: LHX2 knockdown

value: shRNA


title: uvrA_untreated_rep1


title: ALK08_11_E70_Mesp1KO_rep1

description: 10X Genomics


title: Sample 1_ILC2 1


title: ALK04_3_lateE75_con_rep2

description: 10X Genomics


title: Cal27 cells, soft to soft, rep 3


title: recN_BLM_rep1


title: recN_MMC_rep1


title: recN_untreated_rep1


title: D5, IL6KO, 3

city: Birmingham

first: Dave

middle: Durell

last: Hill

state: AL

address: 1720 Second Avenue South

institute: University of Alabama at Birmingham

data_processing:
Quality Control: fastQC, multiQC
Adapter Trimming: TrimGalore 0.4.4, phred 33, paired, nextera adapters
Alignment: STAR 2.5.2a, default settings
Read Count: HTseq-count 0.6.1p1, unstranded, GCF_000001635.27_GRCm39_genomic.gtf
Downstream Analysis: edgeR to find differentially expressed genes among pairs of sample groups
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files of counts per gene for each sample
Supplementary files format and content: tab-delimited text file of counts per million for all samples

source_name: Blood

extract_protocol:
RNA was isolated using the Single Cell RNA Purification kit (Norgen)
RNA libraries were prepared for sequencing using standard Illumina protocols. All libraries were prepared at Genewiz.
Ultra-Low Input RNA-Seq

value: Blood

value: OTII

value: OTII TCR-transgenic CD4+ T cells

value: sensitized with HDM extract and LPS-free EndoFit ovalbumin

tag: time

value: day 5


title: Cal27 cells, soft to soft, rep 1

value: epithelial cell


title: D5, IL6KO, 2


title: Cal27 cells, soft to soft, rep 2


title: ALK08_14_lateE60_con_rep1

description: 10X Genomics

value: whole embryo

tag: developmental stage


title: ACT4 unsort OC

data_processing:
scATAC-seq fastq files were processed using cellranger atac pipeline
Genome_build: hg19
Supplementary_files_format_and_content: fragments file containing trimmed, deduplicated, high quality atac-seq fragments and cell barcodes

extract_protocol:
Nuclei were isolated from frozen postmortem brain samples
scATAC-seq libraries were constructed using 10X genomics reagents and protocols

tag: sorted

value: no

tag: patient

tag: brain region

value: Occipital Cortex


title: uvrA_BLM_rep1

tag: strain


title: D5, IL6KO, 1

tag: tissue

tag: cell type


title: ALK08_6_E65_Mesp1KO_rep1

description: 10X Genomics

value: Mesp1 KO


title: ALK07_15_E65_con_rep1

description: 10X Genomics


title: ALK08_20_E60_con_rep3

description: 10X Genomics


title: D3, IL6KO, 3

tag: treatment

value: day 3


title: ACT7 unsort OC


title: Cal27 cells, soft LPA to soft FAKi, rep 2

value: WT

value: LPA, FAK inhibitor


title: WT_BLM_rep1

value: F- lambda- ilvG- rfb-50 rph-1


title: D3, IL6KO, 2


title: WT_untreated_rep1


title: ALK06_4_E60_con_rep2

description: 10X Genomics

value: Control


title: ALK06_2_E60_con_rep1

description: 10X Genomics


title: Degrading Pygostyle IVD 4 [P8]

city: Clemson

first: Joseph

middle: Robert

last: Sheheen

state: SC

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

data_processing:
Illumina nextseq RTA for basecalling
STAR alingment to GRCg6a genome
FeatureCounts to compile count tables
DESeq2 for differential expression analysis
Genome_build: GRCg6a
Supplementary_files_format_and_content: TSV text file containing differential expression analysis results

organism: Gallus gallus

source_name: Degrading Pygostyle intervertebrak disk

extract_protocol:
IVD tissues were removed, placed in Trizol, and frozen at -80C until use. IVDs were homogonized in trizol with bashing beads and extra proteoglycan rich debris were removed with an initial centrifugation step before standard Trizol RNA isolation.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

tag: breed

value: white leghorn

tag: age

value: 10 weeks

value: Degrading Pygostyle intervertebrak disk


title: ACT2 sort OC

city: Stanford

first: Julia

address: 450 Serra Mall

institute: Stanford University

value: yes


title: WT_TLE3 CUTnTag

first: Xiaoyu

address: Tsinghua University, Haidian District

department: School of Medicine

institute: Tsinghua University

data_processing:
FASTQ format read sequences were pre-processed through Trimmomatic software which can be summarized as below: (1) Remove low-quality reads: The reads that mean quality value less than 15 were removed. (2) Remove the reads that contain more than 6 N bases. (3) Remove adapters. Remove the reads that alignment with the adapter sequence. (4) Drop reads blow the 50 bases long after trimming. The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 (Burrows Wheeler Aligner) and clean reads were aligned to the reference genome using BWA mem v0.7.12.
All peak calling was performed with MACS2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
The position of peak summit around transcript start sites of genes can predict the interaction sites of protein and gene. PeakAnnotator was used to identify the nearest TSS of every peak and the distance distribution between peaks and TSS was shown. Besides, the distribution of peak summits on different function regions, such as 5’ UTR, CDS, 3’UTR, was performed.
Assembly: mm10
Supplementary files format and content: peak text files
Library strategy: CUT&Tag-Seq

source_name: colonic macrophages

extract_protocol:
Siglec-F(-)Ly6C(lo)CD64(+) colonic macrophages were sorted from male WT (ten mice) and pooled together.
Cells were divided into two aliquots, washed once with Wash Buffer, and incubated with ConA-coated magnetic beads for 10 minutes at room temperature (RT). After magnetic separation, ConA bead-bound cells were resuspended in Antibody Buffer containing anti-IgG (CST 66362) or anti-TLE3 (Proteintech 11372-1-AP) primary antibody and incubated overnight at 4°C.
The solution was removed by magnetic separation, and an anti-rabbit secondary antibody (Vazyme, Nanjing, China) in Dig-Wash Buffer were added to each reaction, which was followed by 1-hour incubation at RT. Unbound antibodies were removed by washing with Dig-Wash Buffer, and cells were then incubated with pA-Tn5 for 1 hour at RT. The tagmentation reaction was activated by MgCl2 and terminated by the addition of EDTA, SDS, and Proteinase K.
DNA fragments were purified by phenol-chloroform method and amplified by PCR (Vazyme) using the following PCR conditions: 72°C for 3 min; 98°C for 30 s; thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 30 s (20 cycles); and 72°C 5 min. Finally, the libraries were purified using DNA clean beads (Vazyme).

value: colon

tag: genotype

value: wild type (WT)

value: colonic macrophages


title: Degrading Pygostyle IVD 3 [P10]


title: ACT6 unsort P

value: Putamen


title: Degrading Pygostyle IVD 2 [P11]


title: ACT6 sort P


title: D5, WT, 2

value: Blood

value: OTII

value: OTII TCR-transgenic CD4+ T cells

value: sensitized with HDM extract and LPS-free EndoFit ovalbumin

value: day 5


title: WT_H3K27ac CUTnTag

data_processing:
Adapter sequences were trimmed from the ends of CUT&Tag-Seq reads by Cutadapt (v1.14), and the reads that failed to pass the quality control (Q > 10) were discarded. Then, pair-end reads were aligned to mouse genome (UCSC mm10) using Bowtie2 (v2.2.5) with no more than one mismatch for each alignment seed to generate alignment files of uniquely mapped pair-end fragments with maximum length in 1000 bp.
Assembly: mm10
Supplementary files format and content: peak text files
Library strategy: CUT&Tag-Seq

extract_protocol:
Siglec-F(-)Ly6C(lo)CD64(+) colonic macrophages were sorted from male WT (four mice) and Tle4cKO (four mice) mice at the same time. Cells from mice of same genotype were pooled together.
Cells were washed once with Wash Buffer and incubated with ConA-coated magnetic beads for 10 minutes at room temperature (RT). After magnetic separation, ConA bead-bound cells were resuspended in Antibody Buffer containing anti-H3K27Ac (Abcam ab4729) primary antibody and incubated overnight at 4°C.
The solution was removed by magnetic separation, and an anti-rabbit secondary antibody (Vazyme, Nanjing, China) in Dig-Wash Buffer were added to each reaction, which was followed by 1-hour incubation at RT. Unbound antibodies were removed by washing with Dig-Wash Buffer, and cells were then incubated with pA-Tn5 for 1 hour at RT. The tagmentation reaction was activated by MgCl2 and terminated by the addition of EDTA, SDS, and Proteinase K.
DNA fragments were purified by phenol-chloroform method and amplified by PCR (Vazyme) using the following PCR conditions: 72°C for 3 min; 98°C for 30 s; thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 30 s (15 cycles); and 72°C 5 min. Finally, the libraries were purified using DNA clean beads (Vazyme).


title: D3, WT, 3

value: WT

value: day 3


title: Tle4cKO_H3K27ac CUTnTag

value: Tle4f/f Lyz2-Cre


title: Degrading Pygostyle IVD 1 [P12]


title: Permanent IVD 4 [F8]

source_name: Permanent intervertebrak disk

value: Permanent intervertebrak disk


title: D3, WT, 2


title: D3, WT, 1


title: ACT9 unsort OC

value: no

value: Occipital Cortex


title: WT colonic macrophages [ATA-Seq]

data_processing:
Adapter sequences were trimmed from the ends of ATAC-Seq reads by Cutadapt (v1.14), and the reads that failed to pass the quality control (Q > 10) were discarded. Then, ATAC-Seq pair-end reads were aligned to mouse genome (UCSC mm10) using Bowtie2 (v2.2.5) with no more than one mismatch for each alignment seed to generate alignment files of uniquely mapped pair-end fragments with maximum length in 1000 bp. The ATAC-Seq alignment files were used to call peaks for significantly opened chromatin regions using MACS2 (v2.1.1) (FDR < 0.05).
The peaks of both WT and Tle4-deficient colonic macrophages were merged as total OCRs. To identify the differentially opened chromatin regions between WT and Tle4-deficient colonic macrophages, the ATAC-Seq fragments were counted in each OCR for each sample by FeatureCounts (v1.5.0). Subsequently, the fragments count was normalized to count per 1kb per million mapped fragments (FPKM) for each sample. The normalized fragments count was used to identify differentially opened chromatin regions by edgeR (v3.28.1). Values of (fragments count+1) fold change (Tle4 KO/WT) were log2 transformed, and differentially opened chromatin regions were identified by log2 transformed fold changes (Tle4 KO/WT) ≥ 1 or ≤ -1 for upregulated or downregulated OCRs in Tle4-deficient colonic macrophages with cutoff of p-value < 0.05.
To visualize ATAC-Seq signals around genome regions of interest, we firstly counted ATAC-Seq fragments every 10 bp from the center of OCRs to ± 2.5 kb regions for each OCR by using annotatePeaks.pl program in HOMER (v4.7.2). The output counting matrices were visualized by Cluster TreeView (v1.2.0) and were further used to generate average signals around OCRs by calculating the average fragments/reads count per bin (10 bp) per OCR.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

extract_protocol:
Siglec-F(-)Ly6C(lo)CD64(+) colonic macrophages were sorted from male WT (two mice) and Tle4cKO (two mice) mice at the same time. Cells from mice of same genotype were pooled together. Nuclei were extracted as previously described (Buenrostro et al. 2013).
DNA libraries were prepared as previously described (Buenrostro et al. 2013) by using a commercial kit (Vazyme, Nanjing, China). Nuclei were pelleted by centrifugation (4 ℃, 500 g, 30 min) and resuspended in 50 μL reaction mix (5 μL Tn5 transposase (Vazyme), 10 μL 5X TTBL buffer (Vazyme), and 35 μL nuclease-free water). The transposition reaction was incubated at 37 ℃ for 30 min. DNA fragments were purified using the Purification Kit (QIAGEN). Then, the libraries of DNA fragments were amplified by PCR (Vazyme) using the following PCR conditions: 72 ℃ for 3min; 98 ℃ for 30 s; thermocycling at 98 ℃ for 15 s, 60 ℃ for 30 s and 72 ℃ for 3 min (11 cycles); and 72 ℃ 5 min. Finally, the libraries were purified using 0.5X/1.2X DNA clean beads (Vazyme).


title: D3, IL6KO, 1


title: Permanent IVD 3 [F9]

value: white leghorn

value: 10 weeks


title: ACT2 unsort OC


title: Tle4cKO colonic macrophages

data_processing:
RNA-Seq data were collected and pair-end reads were aligned to mouse genome mm10 using TopHat (v2.1.0) and only uniquely mapped reads were preserved.
For coverage of mapped RNA-seq reads in transcripts, the expression level of each gene transcript was calculated as normalized reads count per kilobase of transcript per million mapped reads (FPKM) using Cufflinks (v2.2.1).
Differential gene expression between WT and Tle3- or Tle4-deficient colonic macrophages was identified using Cufflinks (v2.2.1). Genes with p value < 0.05 and (FPKM+1) fold changes (Tle3 or Tle4 KO/WT) ≥ 2 or ≤ 0.5 were defined as upregulated or downregulated genes in Tle3- or Tle4-deficient colonic macrophages, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Siglec-F(-)Ly6C(lo)CD64(+) colonic macrophages were sorted from 9-week-old male WT (four mice), Tle3cKO (three mice), and Tle4cKO (four mice) mice at the same time. Cells from mice of same genotype were pooled together. RNA was extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene (Tianjin, China).

value: colon


title: D5, WT, 1


title: ACT9 sort OC

value: yes


title: D5, WT, 3


title: WT_MMC_rep1

value: F- lambda- ilvG- rfb-50 rph-1


title: Tle3cKO colonic macrophages

value: Tle3f/f Lyz2-Cre


title: ACT6 unsort Ce

value: Cerebellum


title: Permanent IVD 1 [F12]


title: WT colonic macrophages


title: JA-2H

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

description:
AGO002
10x Genomics

data_processing:
BCL files were demultiplexed using Cell Ranger mkfastq
FastQ files were processed using the Cell Ranger 3.1.0 count pipeline
Assembly: TAIR10.40
Supplementary files format and content: h5 files containing the count matrix (output from Cell Ranger)

organism: Arabidopsis thaliana

source_name: Root tips

extract_protocol:
6-day-old seedlings were transferred to 10 μM BAP-supplemented medium or an equal volume of DMSO as mock treatment and allowed to grow for 2 h. The root tips were then cut and incubated in protoplasting Solution B (1.5% (wt/vol) cellulysin and 0.1% (wt/vol) pectolyase in Solution A (600 mM mannitol, 2 mM MgCl2, 0.1% (wt/vol) bovine serum albumin, 2 mM CaCl2, 2 mM MES, 10 mM KCl, pH 5.5)) for approximately 1 h at room temperature. Cells were filtered through a 70 μm cell strainer and spun down at 200 g for 6 min, resuspended in Solution A, filtered through a 40 μm cell strainer and stained for live/dead using 4′,6-diamidino-2-phenylindole (DAPI) at 14 μM final concentration. Cells were sorted on a BD Aria II and protoplasts without the DAPI signal were selected for further analysis.
Sorted cells were centrifuged at 400 g at 4 °C and resuspended in Solution A to yield an estimated concentration of 1,000 cells per μl. Cellular suspensions were loaded on a Chromium Single Cell 3′ GEM, Library & Gel Bead Kit (V3 chemistry, 10X Genomics) according to the manufacturer’s instructions. Sequencing libraries were loaded on an Illumina HiSeq4000 and sequenced following recommendations of 10X genomics

value: Root tips

value: 2H 50µM Jasmonate


title: ACT6 sort Ce

last: Belk

source_name: human brain


title: B.subtilis_RedC_rep1

city: Moscow

first: Grigory

last: Evko

address: Vavilova str., 34/5

institute: Institute of Gene Biology of the Russian Academy of Sciences

data_processing:
For raw data processing RedClib pipeline was used (github: https://github.com/agalitsyna/RedClib)
Supplementary files format and content: Processed RedC data files are available as TSV files with individual mapped RNA-DNA contacts. Each row corresponds to an individual RNA-DNA contact that passed filtering steps. Columns represent information about 3' RNA, 5' RNA and DNA mapping position (chromosome, start, end, strand), CIGAR string and mapped sequence length.
Library strategy: RedC

organism: Bacillus subtilis

extract_protocol: RedC uses custom oligos and adapters resulting in libraries ready for sequencing on the Illumina platform.


title: Tle4cKO colonic macrophages [ATA-Seq]


title: Lin-neg 2

status: Public on Apr 06 2023

city: Washington

first: Marcel

middle: O

last: Schmidt

state: DC

address: 3970 Reservoir Road, N.W.,  NRB #E311

department: Oncology

institute: Georgetown University

data_processing:
demultiplexing samples
Full-length analysis with PacBio software: CSS, Lima, cDNA Cupcake, Isoseq3, minimap2
Isoform analysis with SQANTI3
Genome_build: hg38
Supplementary_files_format_and_content: sqanti_report

source_name: bone marrow

extract_protocol:
ficoll gradient, negative magnetic selection for progenitor cells (Stemcell technologies)
scRNA libraries were prepared  using 10x droplet based single cell technology

treatment_protocol: cells collected from discarded bone marrow filter bags

value: lineage negative cells


title: S2_Cerv_131 biol rep 2

first: Jacob

last: Blum

address: 279 Campus Dr

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Subsequent analyses were performed in R using the Seurat package (v4.0.4) to produce the .RDS files.  created using the filtered count matrix. Mitochondrial reads were removed and then feature  counts for each putative nucleus were normalized (normalization.method = “LogNormalize” in  Seurat NormalizeData function). Principal component analysis (PCA) was performed on scaled  data with 33,000 variable features, and the top 20 components were used for clustering and  uniform manifold approximation and projection (UMAP) visualization. For clustering, the  resolution parameter was set to 0.5.  The clusters were manually annotated using the average expression of known marker  genes, number of UMIs, and proportion of sequencing reads containing introns per cluster  (Figure S1A-S1B). To calculate the proportion of sequencing reads that contain introns, the Cell  Ranger count pipeline was run with and without the “include-introns” flag. The proportion of  intronic reads was calculated per putative nucleus by first subtracting the number of UMIs  (nCount_RNA) excluding intronic reads from nCount_RNA including intronic reads and then  dividing by nCount_RNA including intronic reads. The proportion of intronic reads was added to  the meta data of the Seurat object for each putative nucleus.
Assembly: GRCh38
Supplementary files format and content: h5 files

source_name: Cervical spinal cord

extract_protocol:
Spinal cord tissue was obtained with a postmortem inteval of 2.5 hours and cervical sections were flash frozen in 2-Methylbutane, and stored at -80 deg C until nuclear isolation. Nuclei were isolated from tissue blocks via dounce homogenization and density centrifugation through OptiPrep, and then were stained with antibody. Nuclei were then sorted by FANS and libraries were generated using 10x.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, sorted nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Spinal cord neurons and glia

value: Cervical spinal cord

tag: subject status

value: neurologically healthy control patient

value: 56 years old


title: total BM 2

value: bone marrow


title: B.subtilis_RedC_rep2


title: TKO_EpiLC_CBX7_v2

first: Cheng

last: Wang

address: College Green

department: Genetics

institute: Smurfit Institute of Genetics, Trinity College Dublin

description: 10% human NT2 cells was used for spike-in chromatin.

data_processing:
ChIP-seq reads quality was confirmed by fastqc, then high-quality reads aligned to reference mouse genome (mm10) by bowtie2. PCR duplicate reads were removed by Picard.
The duplicates-removed spike-in bam files mapped reads number was counted and used for generating the normalization factor (a). Generally, normalization factor (a) was calculated by a fix number N divide the spike-in genome bam file reads count. (Orlando, et al 2014)
For UCSC genome browser visualization, bigwigs were generated by BamCoverage with extending to 200 bp and RPGC normalization. ChIP-Rx bigwig files  were generated by BamCoverage with  Rx normalization factor.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Epiblast-like cells (EpiLC)

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatinized culture dishes in GMEM (Sigma) supplemented with 20% FBS (Gibco), 100U/mL Penicillin-Streptomycin (Gibco), 50 μM β-mercaptoethanol (Sigma), 1:100 GlutaMax, 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 1:500 homemade leukaemia inhibitory factor (LIF), and 2i components; 3 μM GSK inhibitor CHIRON99021 (Cayman) and 1 μM MEK inhibitor PD0325901 (Cayman).The ESCs were spited and changed medium every 2 days.For EpiLC differentiation experiments, the dishes were coated with 16 μl/ml fibronectin for 2~3 hours. 2 million ESCs were washed three times with PBS and seeded on the fibronectin coated dished in NDiff227 medium (Takara) supplemented with 20 ng/ml Activin A (Peprotech), 12 ng/ml bFGF (Gibco) and 1% Knockout Serum Replacement (KSR, Thermo) for 2 days. The EpiLC culture medium were changed daily.

extract_protocol: ChIP-seq library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol.

treatment_protocol: No treatment/stimulations for this project.

value: PCL1-3 TKO ESC-derived epiblast-like cells (EpiLC)

tag: chip antibody

value: CBX7 (Millipore,07-981)


title: QKO_EpiLC_CBX7_v2

value: PCL1-3  and JARID2 QKO ESC-derived epiblast-like cells (EpiLC)


title: J2KO_EpiLC_CBX7_v2

value: JARID2 KO ESC-derived epiblast-like cells (EpiLC)


title: WT_EpiLC_CBX7_v2

value: ESC-derived epiblast-like cells (EpiLC)


title: Pcgf24KO_EpiLC_H3K27ac

extract_protocol:
ChIP-seq library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol.
Illumina NextSeq 500, 75-bp single end

value: Pcgf2/4 KO ESC-derived epiblast-like cells (EpiLC)

tag: antibody

value: H3K27ac (Abcam, Ab4729)


title: WT_ESC_TAZ_MTF2

source_name: Mouse Embryonic stem cells

value: Tazemetostat Mouse Embryonic stem cells (ESC)

value: MTF2 (Peprotech, 16208-1-AP)


title: WT_ESC_TAZ_H2AK119ub1

value: H2AK119ub (Cell Signaling, D27C4)


title: TKO_ESC_CBX7

value: PCL1-3 TKO Mouse Embryonic stem cells (ESC)

value: CBX7 (Abcam, Ab21873)


title: J2KO_EpiLC_PHC1

value: PHC1 (Cell Signaling, 13768S)


title: QKO_EpiLC_PHC1


title: WT_ESC_TAZ_SUZ12

value: SUZ12 (Cell Signaling,D39F6)


title: QKO_ESC_CBX7

value: PCL1-3  and JARID2 QKO Mouse Embryonic stem cells (ESC)


title: TKO_EpiLC_PHC1


title: WT_EpiLC_PHC1


title: WT_ESC_DMSO_SUZ12

value: DMSO treated Mouse Embryonic stem cells (ESC)


title: WT_ESC_DMSO_H2AK119ub1


title: WT_ESC_DMSO_MTF2


title: WT_ESC_TAZ_H3K27me3

value: H3K27me3 (Cell Signaling, C36B11)


title: WT_ESC_TAZ_JARID2

value: JARID2 (Cell Signaling, D6M9X)


title: WT_ESC_DMSO_JARID2


title: WT_ESC_DMSO_H3K27me3


title: S1_Cerv_131 biol rep 1

description: 10x Genomics

value: Spinal cord neurons and glia

value: Cervical spinal cord

value: neurologically healthy control patient

value: 56 years old


title: WT_ESC_TAZ_CBX7


title: ResMTF2_ESC_PHC1

description: no spike in

value: QKO  plus FLAG-MTF2 ESC


title: WT_ESC_PHC1

description: no spike in

value: Mouse Embryonic stem cells (ESC)


title: QKO_ESC_PHC1

description: no spike in


title: ResJ2_ESC_PHC1

description: no spike in

value: QKO  plus FLAG-JARID2 ESC


title: ResMTF2_ESC_CBX4

description: no spike in

value: CBX4 (Cell Signaling, 30559)


title: ResJ2_ESC_CBX4

description: no spike in


title: Permanent IVD 2 [F10]

value: white leghorn

value: 10 weeks

value: Permanent intervertebrak disk


title: QKO_ESC_CBX4

description: no spike in


title: Advanced atherosclerosis, Peritoneum macrophage, replicate 4

city: Freiburg

first: Ingo

last: Hilgendorf

address: Hugstetter Straße 55

department: Department of Cardiology and Angiology

country: Germany

institute: UNIVERSITY HOSPITAL FREIBURG University Heart Center Freiburg-Bad Krozingen

description: primary cell

data_processing:
Reads were trimmed to remove adaptors and low quality ends.
Trimmed reads were aligned as pairs to the mouse genome (mm10) using STAR
Primary aligned reads were annotated and quantified as counts of features (exon) using FeatureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including feature counts of each sample

source_name: Peritoneum lavage

extract_protocol:
Cells of interest were directly sorted in RLT lysis buffer with 1% beta-mercaptoethanol. After being further homogenized with QIAshredder (Qiagen), RNA were extracted using Rneasy micro kit (Qiagen).
RNA library were constructed with Ovation SoLo RNA-seq systems (Nugen) and paired-end sequenced using Illumina NextSeq500

treatment_protocol: Aortic macrophages were extracted from collagenase-digested whole aorta. Monocytes were extracted from red blood cell-lysed blood and spleen. Peritoneal macrophages were directly isolated from peritoneal lavage. Pre-processed tissue were subjected to fluorescence-activated cell sorting of monocytes or macrophages.

value: Peritoneum lavage

value: macrophage

value: Apoe ko

value: high cholesterol diet for 6 month


title: WT_ESC_DMSO_CBX7

city: Dublin

value: DMSO treated Mouse Embryonic stem cells (ESC)

value: CBX7 (Abcam, Ab21873)


title: ResJ2_ESC_JARID2_v2

value: JARID2 (Cell Signaling, D6M9X)


title: WT_ESC_JARID2_v2


title: QKO_EpiLC_CBX2

description: no spike in

value: PCL1-3  and JARID2 QKO ESC-derived epiblast-like cells (EpiLC)

value: CBX2 (Cell Signaling,18687)


title: QKO_ESC_JARID2_v2

value: PCL1-3  and JARID2 QKO Mouse Embryonic stem cells (ESC)


title: Advanced atherosclerosis, Peritoneum macrophage, replicate 3

description: primary cell


title: TKO_EpiLC_CBX2

description: no spike in

value: PCL1-3 TKO ESC-derived epiblast-like cells (EpiLC)


title: ResJ2_ESC_CBX7_v2


title: QKO_ESC_CBX7_v2


title: ResMTF2_ESC_CBX7_v2

value: QKO  plus FLAG-MTF2 ESC


title: Early atherosclerosis, Peritoneum macrophage, replicate 4

description: primary cell

value: high cholesterol diet for 1 month


title: Advanced atherosclerosis, Peritoneum macrophage, replicate 2

description: primary cell


title: WT_ESC_CBX7_v2

value: Mouse Embryonic stem cells (ESC)


title: J2KO_EpiLC_CBX2

description: no spike in

value: JARID2 KO ESC-derived epiblast-like cells (EpiLC)


title: Early atherosclerosis, Peritoneum macrophage, replicate 2

description: primary cell


title: Baseline, Peritoneum macrophage, replicate 4

description: primary cell

value: chow diet


title: WT_ESC_CBX4

description: no spike in

value: CBX4 (Cell Signaling, 30559)


title: ResMTF2_ESC_JARID2_v2


title: Advanced atherosclerosis, Peritoneum macrophage, replicate 1

description: primary cell

value: Peritoneum lavage


title: Early atherosclerosis, Peritoneum macrophage, replicate 3

description: primary cell

value: macrophage


title: Early atherosclerosis, Peritoneum macrophage, replicate 1

description: primary cell

value: Apoe ko


title: Baseline, Peritoneum macrophage, replicate 3

description: primary cell


title: Baseline, Peritoneum macrophage, replicate 1

description: primary cell