title: s0076_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well76


title: s0075_mouse1_MDAMB231_Tumor_1cells

status: Public on May 13 2022

type: SRA

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

description:
Fluidigm C1 platform
well75

library_source: transcriptomic single cell

data_processing:
Reads were aligned to human genom with STAR. Following observation under the microscope, wells containing more than 1 cell or debris were marked and removed from further analyses.
Following observation under the microscope, wells containing more than 1 cell or debris were marked and removed from further analyses.
Cell cycle of individual cells were inferred using sets of known cell cycle-regulated genes known to peak in transcription at given cell cycle stages obtained from (PMID: 12058064, PMID:11416145)
The cell cycle and library complexity (percentage of detected genes) were modeled as covariates and regressed out of the log-normalized counts using glm.fit (R package glm).
Differential gene expression between single cell clusters was performed using pairwise t-test implemented in FindMarkers function from R package scran.
Gene set enrichment was performed with bioconductor packages fgsea and msigdb
Assembly: hg38
Supplementary files format and content: counts_raw.csv is a matrix containing raw counts after alignment. counts_afterQC are counts for the cells passing QC. Cccorected_logcounts.csv contains logcounts  of the cells that passed QC after the cell-cycle correction. metadata.csv contains addition information on the column names of counts_raw.csv  and CCcorected_logcounts.csv.

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

growth_protocol: MDA-MB-231 and PDX models were implanted in the 4th mammary fat pad (cleared) of 4-8 week-old NSG mice. Primary tumors were resected. Lung metastasis cells were isolated out of the dissected lung at a later time (when mice reached ethical endpoints)

extract_protocol:
Primary tumors and lung metastases were mechanically and enzymatically digested with a collagenase/hyaluronidase solution (Stem Cell Technologies, 07912). Human cancer cells were recovered by FACS sorting, based CD298 or GFP expression.
Single cell isolation was performed on the Fluidigm C1 platform according to  manufacturer protocol. mRNA was isolated with the Takara SMART-Seq Ultra Low RNA kit (Takara Bio; 634833) . Libraries for Illumina sequencing were prepared with the Nextera XT DNA Library Preparation Kit (Illumina; FC-131-1096).

tag: tissue

value: Tumor

tag: cell line

tag: cell type

value: cancer cells


title: s0074_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well74


title: NF-42_RNA

city: Guangzhou

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

country: France

institute: Guangdong Provincial People's Hospital

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to hg19 using STAR. The reads mapped to gene exon regions were counted using featureCounts. Differential expression was determined using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: hic forrmat for visualization in Juicebox
Supplementary_files_format_and_content: bigwig format for visualization in IGV or washU Genome Browser

molecule: total RNA

source_name: heart tissue

growth_protocol: The left ventricular (LV) heart samples were collected from DCM patients during surgery and the LV tissues were immediately dissected and snap frozen in liquid nitrogen.

extract_protocol: RNA-seq: Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Approximately 1 µg total RNA per sample was depleted from rRNA with the Ribo-Zero™ Magnetic Kit (Epicentre). The retrieved RNA was subjected to fragmentation by adding the First Strand Master Mix (Invitrogen). First-strand cDNA was generated using random primers and reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and was 3’ adenylated. The adapters were ligated to the ends of these 3’ adenylated cDNA fragments. A total of 10 rounds of PCR with PCR Primer Cocktail and PCR Master Mix were performed to amplify the cDNA fragments. The PCR products were purified and size selected by 0.5X SPRI beads followed by 0.9X SPRI beads. The identity of the final library was verified by the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantified by the Qubit High sensitivity assay. The Qualified libraries were sequenced pair end on the Illumina HiSeq Xten (150 bp, pair-end).

value: heart

tag: method

value: RNA-Seq

tag: factor

tag: condition

value: non-failing


title: NF-41_RNA


title: OMCPmut.IL-2 expanded CD8+ T cells_4

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: JPA, 1312A Pinn Hall

department: Bioinformatics Core

country: USA

institute: University of Virginia

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome and transcriptome using STAR aligner. Count for each gene was generated using Htseq count.
Assembly: mm10
Supplementary files format and content: raw count

organism: Mus musculus

source_name: CD8+ Tcells

growth_protocol: CD8+ T cells were grwin in 24 well plate with 0.5 million cells/ well in RPMI-1640 complete media

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were expanded in respective cytokines throughout the entire length experiemnt

tag: strain

value: isolated from spleen

value: CD8+ Tcells

tag: age

value: expanded for 14 days


title: s0073_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well73


title: OMCPmut.IL-2 expanded CD8+ T cells_3


title: s0072_mouse1_MDAMB231_Tumor_2cells

description:
Fluidigm C1 platform
well72


title: s0071_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well71


title: OMCPmut.IL-2 expanded CD8+ T cells_2


title: NF-4_RNA


title: NF-39_RNA


title: s0070_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well70


title: NF-38_RNA


title: OMCPmut.IL-2 expanded CD8+ T cells_1


title: Disease,rectus femoris muscle, patient 15

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Sequence-libraries of each of the 84 remaining samples were equimolarly pooled and sequenced on two Illumina NovaSeq 6000 S1 100 flow-cells (Xp workflow, Paired Read 51-8-8-51, 1% PhiX v3) (Illumina, San Diego, CA, USA) at the VIB Nucleomics Core (www.nucleomics.be). RNA-seq was performed twice, in two runs. In the first run, data from 84 samples were analyzed (i.e. 93 samples minus 9 excluded samples because of too low RNA amount). The first run was successful with high quality (~95% of the bases >=Q30) and output according to the expectations (~2000 M Passed Filter clusters). With 25M PF reads on average per sample, the output per sample was quite variable, ranging from 9.4M to 47.4M PF reads. We also observed a high percentage of duplicates in some samples and a high percentage of adapters in the sequences, corresponding to samples with very low input material. The mapping of the reads is relatively correct (90%) but the filtering based on the mapping quality has a huge impact (~50% loss of reads for many samples), which should be due to duplicated reads as the filtering discard similar reads. Out of 84 samples, we selected the 38 best samples (<22% No Features, Number of final counts > 12M), whereas 46 samples were pooled for a second sequencing run in order to reach 20M final counts (=assigned reads) for each sample.
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using using FastX 0.0.14 and ShortRead 1.36.1 [Morgan et al, 2009]. With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina [Langmead and Salzberg, 2012].
The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38) [Dobin et al, 2013].  Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments [Li et al, 2009].
The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.5.3 [Liao et al, 2014]. Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor [Risso et al, 2011].
Raw count matrices were uploaded to the online R-based UniApp data analysis platform (Unicle Biomedical Data Science, Leuven Belgium) for analysis. We used the R packages plotly and ggplot to generate bar, pie, line and scatter plots. Genes expressed at a level of at least 1 count per million reads in at 10% of samples were filtered and normalized using the EdgeR package. Samples with less than 1 Million reads were filtered out from the final analysis.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts summarized over the sequencing runs for every gene and every sample.

source_name: rectus femoris muscle

extract_protocol:
We used the same protocol for RNA extraction from muscle tissue as the one described by Cummings et al. RNA was extracted from the 93 muscle biopsies using the Direct-zol RNA Miniprep Plus kit ZY-R2073 (Zymo Research, Irvine, CA, USA) according to the kit’s instructions. In order to avoid technical variability, all samples were extracted with the same kit on two consecutive days in the same lab by the same  lab technician. Ninety-three RNA samples were treated with DNase prior to their submission to the VIB Nucleomics Core (www.nucleomics.be). RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). RNA Integrity Number (RIN) scores mostly varied from 6.3 (partially degraded) to 8.4, except for a few samples that were highly degraded.
Per sample, an amount of 5 ng of total RNA (or 7µl RNA when 5 ng was not available) was used as input for the SMART-Seq Stranded Kit (Cat. No. 634444; protocol version “022819”; low input option; Takara Bio USA, San Jose, CA, USA). This kit can deal with degraded as well as high-integrity input RNA. Positive and negative controls were included in the experimental design using 5 ng control RNA (included in the kit) and 7µl RNase-free water, respectively.First, RNA is converted to cDNA using random priming (scN6 Primer) and SMART (Switching Mechanism At 5’ end of RNA Template) technology (Takara Bio USA, San Jose, CA, USA) and then full-length adapters for Illumina sequencing (including specific barcodes for dual-indexing libraries) are added through PCR using a limited number of cycles (5 cycles). The PCR products are purified and then ribosomal cDNA is selectively depleted by cleaving the ribosomal cDNAs by scZapR in the presence of mammalian-specific scR-Probes which target nuclear and mitochondrial rRNA sequences. This process leaves the library fragments originating from non-rRNA molecules untouched. The remaining cDNA fragments are further amplified with primers universal to all libraries (14 cycles). Lastly, the PCR products are purified once more to yield the final cDNA library. All libraries were finally quantified using Qubit dsDNA HS kit (Thermo Fisher Scientific, Waltham, MA, USA) and their size distribution was checked using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). Nine libraries were excluded from downstream sequencing as there was no yield: control C6 (VL), control C8 (SM), patient 6 (SM), patient 7 (SM), patient 8 (VL), patient 12 (RF), and patient 16 (SM, VL, RF) (Supplementary tables 1 and 2).

value: rectus femoris muscle

tag: disease state

value: Disease


title: s0069_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well69


title: IL-2 expanded CD8+ T cells_1


title: s0067_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well67


title: s0068_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well68


title: Disease,semimembranosus muscle, patient 15

source_name: semimembranosus muscle

value: semimembranosus muscle


title: NF-35_RNA


title: NF-36_RNA


title: E13_snATAC_cerebella

city: Farmington

first: Nagham

last: Khouri-Farah

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

library_source: genomic

data_processing:
The raw reads were processed to molecule counts using the Cell Ranger pipeline with default setting
The raw UMI counts from Cell Ranger was processed by the Seurat R package (version 1.4).
The count matrix without filtering was uploaded.
Genome_build: mm10
Supplementary_files_format_and_content: raw UMI counts in csv format for scRNA-seq and Fragments files for snATAC-seq samples

molecule: genomic DNA

source_name: Cerebellum

extract_protocol:
The cerebella were dissected from mouse embryos at embryonic stages (E12-E14) in ice-cold phosphate buffered saline. The dissected tissues were pooled and cut into pieces smaller than 1 mm in dimension and processed according to 10X Genomics protocaols for scRNA-seq and snATAC-seq of embryonic mouse brain
10X Genomics Chromium Kits was used to create libraries.
10X Genomics

value: Outbred (CD1)

value: Cerebellum

value: Embrhonic day 13.5

tag: genotype

value: wild type

tag: Sex

value: pooled males and females


title: Disease,rectus femoris muscle, patient 14


title: E14_snATAC_cerebella

value: Embrhonic day 14.5


title: s0066_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well66

value: Tumor


title: NF-40_RNA


title: NF-37_RNA


title: NF-34_RNA


title: Disease,vastus lateralis muscle, patient 14

source_name: vastus lateralis muscle

value: vastus lateralis muscle


title: s0065_mouse1a_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well65

value: cancer cells


title: E12_snATAC_cerebella

value: Embrhonic day 12.5


title: NF-33_RNA

value: heart

value: RNA-Seq

value: non-failing


title: Tumor_miR_222_3

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Reads were mapped and quantified with Salmon using the Ensembl 97 Mus musculus transcriptome
Genome_build: GRCm38
Supplementary_files_format_and_content: Salmon output files (.sf) with estimated read counts and TPM per transcript

source_name: 4T1 tumor

growth_protocol: Mice were kept on standard light cycles of 12 h light, 12 h dark. Food and water were provided ad libitum.

extract_protocol:
QIAGEN miRNeasy kit
Illumina TruSeq Stranded mRNA kit

treatment_protocol: 1e5 4T1 cells were subcutaneously injected into the right flank of 6-8 week old female BALB/c mice. Five days later, mice were randomly divided into 4 groups and had peritumoral injection of miR-67 (ctrl)-loaded EVs, miR-142-5p-loaded EVs, miR-183-5p-loaded EVs or miR-222-3p-loaded EVs (3µg/injection, every 2 days). On day 21, the mice were sacrificed and RNA harvested from the tumors.

tag: treatment

value: miR-222-3p loaded EVs

value: 4T1 tumor


title: Disease,semimembranosus muscle, patient 14

value: Disease


title: NF-31_RNA


title: Disease,rectus femoris muscle, patient 13

value: rectus femoris muscle


title: NF-32_RNA


title: s0063_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well63


title: Disease,vastus lateralis muscle, patient 15


title: s0062_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well62


title: Tumor_miR_222_1


title: s0064_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well64


title: Tumor_miR_222_2


title: Tumor_miR_183_3

value: miR-183-5p loaded EVs


title: NF-30_RNA


title: NF-3_RNA


title: Disease,vastus lateralis muscle, patient 13


title: Tumor_miR_183_2


title: Disease,semimembranosus muscle, patient 13

value: semimembranosus muscle


title: s0060_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well60


title: s0061_mouse1_MDAMB231_Tumor_2cells

description:
Fluidigm C1 platform
well61


title: NF-29_RNA


title: Tumor_miR_183_1


title: s0058_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well58


title: Disease,semimembranosus muscle, patient 12


title: Disease,rectus femoris muscle, patient 11


title: Disease,vastus lateralis muscle, patient 11


title: Tumor_miR_142_3

value: miR-142-5p loaded EVs


title: s0059_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well59


title: s0057_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well57


title: NF-27_RNA


title: Tumor_miR_142_2


title: NF-28_RNA


title: NF-26_RNA


title: NF-25_RNA


title: Disease,semimembranosus muscle, patient 11


title: s0056_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well56


title: Disease,rectus femoris muscle, patient 10


title: Tumor_miR_ctrl_3

value: miR-ctrl loaded EVs


title: Disease,vastus lateralis muscle, patient 12


title: Disease,vastus lateralis muscle, patient 10


title: Tumor_miR_ctrl_1


title: s0053_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well53


title: s0054_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well54


title: Disease,semimembranosus muscle, patient 10


title: NF-24_RNA


title: RAW_miR_222_3

data_processing:
Reads were mapped and quantified with Salmon using the Ensembl 97 Mus musculus transcriptome
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output files (.sf) with estimated read counts and TPM per transcript

growth_protocol: Cells were cultured in DMEM with 10% FBS. FBS was depleted of EVs by ultracentrifugation at 110,000xg for 16 h.

treatment_protocol: EVs purified from MS-1 endothelial cell cultures via ultracentrifugation were electroporated with pre-miRNA mimics: premiR control, mouse pre-miR-142-5p, mouse pre-miR-183-5p, or mouse pre-miR-222-3p. RAW macrophages were seeded in 12-well plates and treated with EVs loaded with pre-miRNA mimics (3 µg protein/ml). 48 h later, cells were washed twice with PBS, then lysed for RNA extraction.


title: s0052_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well52


title: NF-21_RNA


title: Disease,vastus lateralis muscle, patient 9


title: RAW_miR_222_2


title: NF-22_RNA


title: NF-23_RNA


title: s0050_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well50


title: Tumor_miR_142_1


title: s0051_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well51


title: RAW_miR_222_1


title: Disease,rectus femoris muscle, patient 9


title: s0055_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well55


title: Tumor_miR_ctrl_2


title: NF-2_RNA


title: Disease,semimembranosus muscle, patient 9


title: Disease,rectus femoris muscle, patient 8


title: NF-19_RNA


title: Disease,semimembranosus muscle, patient 8


title: s0048_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well48


title: RAW_miR_183_2


title: NF-18_RNA


title: s0047_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well47


title: RAW_miR_183_1


title: Disease,rectus femoris muscle, patient 7


title: NF-17_RNA


title: RAW_miR_142_3


title: NF-20_RNA


title: RAW_miR_142_2


title: s0045_mouse1a_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well45


title: Disease,rectus femoris muscle, patient 6


title: s0046_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well46


title: NF-16_RNA


title: Disease,vastus lateralis muscle, patient 6


title: RAW_miR_183_3


title: RAW_miR_ctrl_3

value: miR-ctrl


title: RAW_miR_142_1


title: NF-15_RNA


title: s0044_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well44


title: NF-13_RNA


title: s0049_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well49


title: NF-14_RNA


title: s0043_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well43


title: s0042_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well42


title: RAW_miR_ctrl_2


title: Disease,vastus lateralis muscle, patient 5


title: RAW_miR_ctrl_1


title: Disease,rectus femoris muscle, patient 5


title: NF-12_RNA


title: NF-11_RNA


title: Disease,rectus femoris muscle, patient 4


title: Disease,semimembranosus muscle, patient 5


title: Disease,vastus lateralis muscle, patient 7


title: s0041_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well41


title: S168-TXCK-4wk-WT-gp38+CD26-

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
10X GEX: Single cell libraries were processed using Cellranger (version 3.1.0). Cells were excluded from analysis if the total UMI count was <1,000 or >32,000, the number of detectable features was <562 or >7,943 or the proportion of UMIs mapping to mitochondrial genes was >10%.
RNA-seq: reads were aligned against the Ensembl transcriptome and genome (GRCh38.EBVB95-8wt.ERCC) using STAR (version 2.5.3a). The allocation of reads to protein coding gene meta-features was done using HTSeq.
Genome_build: Mus musculus: mm10
Supplementary_files_format_and_content: Processed data includes count matrices for RNA-seq/10X GEX and meta-data for 10X GEX

extract_protocol:
10X: live Ter119-CD45-EpCAM- (developmental) or Ter119-CD45- (Tbx1Crkl) thymic stromal cells were sorted for 10X Genomics 3' gene expression. For the Tbx1Crkl dataset, cells were pre-fixed with RNA Protect. RNA-seq: Live CD45- thymic stromal cells were sorted for ultra-low input RNA-seq.
10X GEX: libraries were prepared as per manufacturer's protocol for 3' gene expression libraries. RNA-seq: ultra low RNA-seq protocol (equivalent to Smarter-seq)

value: thymic stroma

value: wild-type

value: 4 weeks

value: bulk RNA-seq


title: s0040_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well40

value: Tumor

value: cancer cells


title: NF-10_RNA

value: heart

value: RNA-Seq


title: S167-TXCK-4wk-WT-gp38+CD26-


title: s0039_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well39


title: NF-1_RNA

value: non-failing


title: s0038_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well38


title: S161-DFCK-4wk-WT-gp38+CD26-


title: DCM-9_RNA

value: dilated cardiomyopathy


title: s0037_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well37


title: S163-TXCK-4wk-WT-gp38+CD26-


title: Disease,vastus lateralis muscle, patient 4

value: vastus lateralis muscle

value: Disease


title: Disease,semimembranosus muscle, patient 4


title: DCM-8_RNA


title: Disease,vastus lateralis muscle, patient 1


title: s0036_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well36


title: DCM-7_RNA


title: S156-TXCK-4wk-WT-mTEChi

source_name: mTEChi


title: S158-DFCK-4wk-WT-gp38+CD26-


title: Disease,rectus femoris muscle, patient 3

value: rectus femoris muscle


title: s0035_mouse1a_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well35


title: S160-DFCK-4wk-WT-gp38+CD26-


title: DCM-6_RNA


title: Disease,vastus lateralis muscle, patient 3


title: DCM-50_RNA


title: Disease,semimembranosus muscle, patient 3

value: semimembranosus muscle


title: S155-TXCK-4wk-WT-mTEChi


title: s0033_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well33


title: S151-TXCK-4wk-WT-mTEChi


title: s0034_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well34


title: Disease,vastus lateralis muscle, patient 2


title: DCM-49_RNA


title: Disease,semimembranosus muscle, patient 2


title: s0031_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well31


title: DCM-48_RNA


title: Disease,rectus femoris muscle, patient 2


title: S148-DFCK-4wk-WT-mTEChi


title: S149-DFCK-4wk-WT-mTEChi


title: s0030_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well30


title: S146-DFCK-4wk-WT-mTEChi


title: Healthy,rectus femoris muscle, patient C15

value: Healthy


title: s0029_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well29


title: DCM-47_RNA


title: S143-TXCK-4wk-WT-Ly51+38-


title: Healthy,vastus lateralis muscle, patient C15


title: DCM-46_RNA


title: s0028_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well28


title: DCM-45_RNA


title: Healthy,semimembranosus muscle, patient C15


title: DCM-5_RNA


title: s0032_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well32


title: S139-TXCK-4wk-WT-Ly51+38-


title: s0027_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well27


title: Healthy,rectus femoris muscle, patient C14


title: DCM-43_RNA


title: DCM-44_RNA


title: Healthy,vastus lateralis muscle, patient C14


title: DCM-42_RNA


title: Disease,rectus femoris muscle, patient 1


title: DCM-41_RNA


title: S134-DFCK-4wk-WT-Ly51+38-


title: Healthy,vastus lateralis muscle, patient C13


title: s0024_mouse1a_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well24


title: S136-DFCK-4wk-WT-Ly51+38-


title: Healthy,rectus femoris muscle, patient C13


title: S127-TXCK-4wk-WT-gp38+CD26+


title: Healthy,semimembranosus muscle, patient C14


title: s0026_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well26


title: DCM-4_RNA


title: S132-TXCK-4wk-WT-gp38+CD26+


title: s0021_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well21


title: DCM-39_RNA


title: S144-TXCK-4wk-WT-Ly51+38-


title: S137-DFCK-4wk-WT-Ly51+38-


title: Healthy,rectus femoris muscle, patient C12


title: Healthy,semimembranosus muscle, patient C13


title: Healthy,vastus lateralis muscle, patient C12


title: S124-DFCK-4wk-WT-gp38+CD26+


title: s0020_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well20


title: s0023_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well23


title: S131-TXCK-4wk-WT-gp38+CD26+


title: DCM-40_RNA


title: s0019_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well19


title: s0022_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well22


title: S125-DFCK-4wk-WT-gp38+CD26+


title: Healthy,rectus femoris muscle, patient C11


title: s0017_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well17


title: S120-TXCK-4wk-WT-mTEC-all

source_name: mTEC


title: s0018_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well18


title: s0025_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well25


title: S122-DFCK-4wk-WT-gp38+CD26+


title: DCM-35_RNA


title: s0016_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well16


title: s0015_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well15


title: S119-TXCK-4wk-WT-mTEC-all


title: DCM-38_RNA


title: Healthy,rectus femoris muscle, patient C10


title: DCM-36_RNA


title: S112-DFCK-4wk-WT-mTEC-all


title: DCM-34_RNA


title: Healthy,vastus lateralis muscle, patient C11


title: DCM-37_RNA


title: DCM-33_RNA


title: Healthy,semimembranosus muscle, patient C10


title: S115-TXCK-4wk-WT-mTEC-all


title: S113-DFCK-4wk-WT-mTEC-all


title: DCM-32_RNA


title: s0013_mouse1a_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well13


title: Healthy,semimembranosus muscle, patient C12


title: S107-TXCK-4wk-WT-cTEC

source_name: cTEC


title: DCM-31_RNA


title: Healthy,vastus lateralis muscle, patient C9


title: Healthy,vastus lateralis muscle, patient C10


title: s0009_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well9


title: S110-DFCK-4wk-WT-mTEC-all


title: s0012_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well12


title: s0014_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well14


title: DCM-30_RNA


title: S103-TXCK-4wk-WT-cTEC


title: Healthy,rectus femoris muscle, patient C9


title: s0008_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well8


title: Healthy,semimembranosus muscle, patient C11


title: DCM-3_RNA


title: s0010_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well10


title: DCM-29_RNA


title: Healthy,rectus femoris muscle, patient C8


title: S101-DFCK-4wk-WT-cTEC


title: DCM-27_RNA


title: Healthy,semimembranosus muscle, patient C9


title: Healthy,vastus lateralis muscle, patient C8


title: s0011_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well11


title: S108-TXCK-4wk-WT-cTEC


title: s0006_mouse1_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well6


title: DCM-26_RNA


title: S100-DFCK-4wk-WT-cTEC


title: S98-DFCK-4wk-WT-cTEC


title: s0007_mouse1a_MDAMB231_Tumor_0cells

description:
Fluidigm C1 platform
well7


title: s0005_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well5


title: Healthy,rectus femoris muscle, patient C7


title: DCM-28_RNA


title: DCM-25_RNA


title: S94-DFCK-D0-WT-CD31+


title: DCM-24_RNA


title: Healthy,semimembranosus muscle, patient C7


title: DCM-23_RNA


title: S93-DFCK-D0-WT-CD31+


title: S91-DFCK-D0-WT-CD31+


title: Healthy,semimembranosus muscle, patient C6


title: DCM-22_RNA


title: s0001_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well1


title: s0004_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well4


title: s0003_mouse1_MDAMB231_Tumor_1cells

description:
Fluidigm C1 platform
well3


title: s0002_mouse1_MDAMB231_Tumor_2cells

description:
Fluidigm C1 platform
well2


title: DCM-21_RNA


title: Healthy,vastus lateralis muscle, patient C7


title: S90-TXCK-D0-WT-CD31+


title: S85-TXCK-D0-WT-CD31+


title: Healthy,semimembranosus muscle, patient C5


title: S82-DFCK-D0-WT-gp38+CD26-


title: DCM-2_RNA


title: DCM-19_RNA


title: Healthy,rectus femoris muscle, patient C4


title: Healthy,rectus femoris muscle, patient C5


title: control, pair5 [22A]

city: Kraków

first: Mateusz

last: Siedliński

address: Skarbowa 1

country: Poland

institute: Jagiellonian University Medical College

data_processing:
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. Below are the statistics of mapping the reads to the reference genome.
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: GRCh38

source_name: mammary artery

growth_protocol: Vascular rings (mammary artery) from 6 female patients were incubated with 100 nM docetaxel (Cayman Chemicals) and vehicle (solvent) as a control (paired design). The vessels were incubated in a buffer containing: Hank's Balanced Salt Solution (HBSS; Gibco), 20 mM Hepes (Gibco) and gentamicin with glutamine in an incubator at 37°C in a humidified atmosphere for 24 hours. After incubation, vascular function was measured or rings were placed in RNAlater (Ambion) for gene expression and RNAseq studies.

extract_protocol: RNA was isolated using Direct-zol RNA MiniPrep kit (Zymo Research) and treated with DNase I

value: mammary artery

tag: gender

value: female

value: control 24h


title: docetaxel, pair5 [22B]

value: docetaxel 100nM 24h


title: control, pair6 [23A]


title: Healthy,vastus lateralis muscle, patient C4


title: S81-DFCK-D0-WT-gp38+CD26-

value: thymic stroma

value: wild-type


title: DCM-18_RNA


title: DCM-17_RNA


title: docetaxel, pair4 [21B]


title: docetaxel, pair6 [23B]


title: S79-DFCK-D0-WT-gp38+CD26-

value: bulk RNA-seq


title: DCM-15_RNA


title: S78-TXCK-D0-WT-gp38+CD26-


title: Healthy,rectus femoris muscle, patient C3


title: Healthy,semimembranosus muscle, patient C4


title: S74-TXCK-D0-WT-gp38+CD26-


title: control, pair4 [21A]


title: Healthy,vastus lateralis muscle, patient C3


title: DCM-16_RNA


title: Healthy,vastus lateralis muscle, patient C5


title: S73-TXCK-D0-WT-gp38+CD26-


title: docetaxel, pair3 [6B]


title: Healthy,rectus femoris muscle, patient C6


title: Healthy,semimembranosus muscle, patient C3


title: DCM-14_RNA


title: DCM-13_RNA


title: DCM-20_RNA


title: Healthy,rectus femoris muscle, patient C2


title: docetaxel, pair2 [4B]


title: Healthy,vastus lateralis muscle, patient C2


title: S86-TXCK-D0-WT-CD31+


title: DCM-12_RNA


title: control, pair2 [4A]


title: DCM-11_RNA


title: docetaxel, pair1 [2B]


title: S66-TXCK-D0-WT-Ly51+38-


title: Healthy,semimembranosus muscle, patient C2


title: S69-DFCK-D0-WT-Ly51+38-


title: control, pair1 [2A]


title: S67-DFCK-D0-WT-Ly51+38-


title: S62-TXCK-D0-WT-Ly51+38-


title: control, pair3 [6A]


title: Healthy,rectus femoris muscle, patient C1


title: DCM-10_RNA


title: S61-TXCK-D0-WT-Ly51+38-


title: Healthy,vastus lateralis muscle, patient C1


title: CD45_neg.1 [4_HD_BM_003_CD45_neg]

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCh38 genome.
Assembly: GGRCh38
Supplementary files format and content: .txt

extract_protocol:
Punch biopsie, human whole skin dissociation kit (Miltenyi), human CD45+ microBeads (Miltenyi), RLT plus lysis buffer (Qiagen)+ ßME
Total RNA was isolated using RNeasy plus micro kit (Qiagen). Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 50 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.

tag: subject status

value: healthy donor

value: CD45- cells


title: S70-DFCK-D0-WT-Ly51+38-


title: DCM-10_ATAC

data_processing:
Illumina Casava1.7 software used for basecalling.
The adapters were removed and the filtered reads were mapped to hg19 using bwa mem. The duplicated reads were removed using Picard (https://broadinstitute.github.io/picard/) and the reads with quality lower than 20 were filtered.
Genome_build: hg19
Supplementary_files_format_and_content: hic forrmat for visualization in Juicebox
Supplementary_files_format_and_content: bigwig format for visualization in IGV or washU Genome Browser

extract_protocol: ATAC-seq: A total of 20-50 mg heart tissue sample was cut on dry ice for each ATAC-seq assay. Each sample was placed into the corresponding 5 cm petri dish (labeled on bottom of dish) with PBS on ice and minced as finely as possible with a razor (the use of a clean razor was ensured for each sample). The end was cut off with a 1 ml pipette tip at an angle and the samples were transferred to the corresponding conical tubes with PBS (a fresh tip was used for each sample). Subsequently, the tubes were centrifuged at 500 x g for 5 min at 4°C. The PBS was decanted as thoroughly as possible without losing the pellet and 1 ml ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) was added to each sample. Each sample was added to a 1 ml dounce. The samples were dounced with a pestle 40-50 times slowly in order to avoid foaming. Following douncing, the samples were filtered through a 40 μM mesh strainer into a 1.5 ml tube on ice. Immediately following filtration of each sample, 10 μl aliquots were obtained for counting the nuclei. For each 10 μl of aliquot, 10 μl Trypan Blue was added, mixed, loaded onto the hemocytometer and counted. The tubes were inverted and flicked to mix. Subsequently, 100,000 cells were aliquoted from each sample into a PCR tube and stripped on ice. The ATAC lysis buffer was added to the PCR tube to ensure that the reaction volume was not less than 100 μl. The samples were spun down at 500 x g for 5 min at 4°C. The supernatant was removed very carefully, ensuring not to disturb the cell pellet. The tagmentation reaction was immediately continued. The transposition reaction master mix was prepared and the samples were mixed by pipetting gently, spun quickly and left on ice. The tagmentation master mix included the following reagents: 25 μl 2x TD Buffer (Illumina Cat #FC-121-1030), 8 μl Tn5 Transposase (Illumina Cat #FC-121-1030), 17 µl PBS, 5 µl 1% Digitonin (dissolved in 50% DMSO in dH2O) and 5 µl 10% Tween 20. A total of 50 μl tagmentation master mix was added to each sample, which was gently pipetted to resuspend the cells in the transposition reaction mix. The samples were incubated at 37°C for 30 min in a thermomixer at 800 rpm. The purification was conducted using a Qiagen MinElute Kit. The DNA was eluted with a 35 μl EB buffer (10 mM Tris buffer, pH 8.0), allowed to settle at room temperature for 1 min and centrifuged at max speed for 30 sec. Each elution was transferred to a 250 μl PCR tube and the PCR reactions were prepared by adding the components in the order shown. The PCR reaction contained the following components: 5 μl Index mix (Illumina Nextera Kit, 10 μl 5x Phusion HF reaction Buffer, 1.5 μl dNTPs (10 mM), 0.5 μl Phusion HF Polymerase (NEB) and 33 μl tagmented DNA. The reagents were pipetted to mix. The PCR was performed using the following program on a thermal cycler (with heated lid): heating at 72°C for 5 min and at 98°C for 30 sec. A total of 10 cycles were performed at 98°C for 10 sec, at 63°C for 30 sec and at 72°C for 30 sec. A final extension was performed at 72°C for 1 min. The AMpure double size selection was performed and 80 µl AMpure beads were added to the sample, vortexed briefly to mix and quickly spun. The solution was incubated at room temperature for 5 min. The samples were placed in a magnetic rack and left for 1 min. The liquid was removed with a pipette, taking care not to disrupt the pellet. The samples were washed by addition of 180 µl fresh 70% ethanol to the tube, taking care not to disrupt the pellet. The ethanol was removed with a pipette and the procedure was repeated a second time. The ethanol was removed slowly from the tube. The samples were allowed to dry for 30 sec and the pellet was resuspended with 22 µl Buffer EB (10 mM Tris, pH 8.0) and mixed by pipetting. The sample was allowed to stand for 1 min and placed in a magnetic rack on the magnetic side for 1 min. A total of 20 µl of the eluate were transferred to a new tube, taking care not to collect any magnetic beads. The aliquots of the libraries were run on an Agilent 2100 bioanalyzer and quantified with the Qubit High sensitivity assay. The libraries were sequenced by the Illumina HiSeq Xten (150 bp, pair-end).

value: heart

value: ATAC-Seq


title: CD45_neg.2 [13_CD45_neg]

value: scleroderma patients (SSc)


title: DCM-1_RNA

value: RNA-Seq

value: dilated cardiomyopathy


title: Healthy,semimembranosus muscle, patient C1


title: DCM-9_ATAC


title: S58-DFCK-D0-WT-gp38+CD26+


title: S57-DFCK-D0-WT-gp38+CD26+


title: Disease,semimembranosus muscle, patient 1

value: Disease


title: iTCE day 7

city: Lausanne

first: Omid

last: Mashinchian

state: Vaud

address: EPFL INNOVATION PARK, BUILDING H

institute: Nestlé Institute of Health Science, Nestlé Research

description: 10x Genomics

data_processing:
demultiplexing using mkfastq from cellRanger
counting using cellRanger -count
raw data were processed using cellRanger-2.0.2
The barcodes correspond to the following samples:
Barcode -1: iTCE day 13
Barcode -2: IPSC Day0
Barcode -3: iTCE day 7
Assembly: GRCh38-1.2.0
Supplementary files format and content: barcodes.tsv; genes.tsv; matrix.mtx

source_name: Induced pluripotent stem cells (hiPSCs)

growth_protocol: hiPSCs alone or in combination with support cell types were prepared for 3D-aggregation by adding a total of 5.5×106 cells per well in Corning Costar ultra-low attachment 6-well plates (CLS3471, Sigma-Aldrich) in STEMdiff APEL2 medium (05270, STEMCELL Technologies) supplemented with 10 μM ROCK inhibitor (Y-27632, 1254, Tocris Bioscience) with constant shaking (Orbi-Shaker CO2, Benchmark Scientific) at 95 rpm at 37 °C and 8% CO2 overnight.

extract_protocol: Chromium Single Cell 3’ kit from 10X Genomics

treatment_protocol: For Wnt/FGF pathway stimulation, the medium was then replaced with STEMdiff APEL2 medium (05270, STEMCELL Technologies), supplemented with 2.5 μM of GSK3-inhibitor CHIR99021 (Tocris Bioscience) for 6 days. On day 7 the embryoids were switched to essential 6 medium (A1516401, Thermo Fisher Scientific), supplemented with 20 ng/mL of bFGF (FGF-2, PHG0023, Thermo Fisher Scientific) until day 13. Culture medium was changed every other day. In conditions without Wnt/FGF pathway stimulation, DMSO was used as a vehicle-control. For iTCE scale-up culture, a total of 1×108 cells were added to Corning 850cm² polystyrene roller bottles (CLS430851, Sigma-Aldrich) in 250 mL of STEMdiff APEL2 medium (05270, STEMCELL Technologies) supplemented with 10 μM ROCK inhibitor (Y-27632, 1254, Tocris Bioscience) under constant rolling conditions (FlexiRoll, BioTool AG) at 32 rpm at 37 °C and 8% CO2 overnight. Subsequently, media composition was similar to the horizontal shaker protocol.

value: Induced pluripotent stem cells (hiPSCs)

tag: time point

value: day 7


title: iTCE day 13

description: 10x Genomics

data_processing:
demultiplexing using mkfastq from cellRanger
counting using cellRanger -count
The barcodes correspond to the following samples:
Barcode -1: iTCE day 13
Barcode -2: IPSC Day0
Barcode -3: iTCE day 7
raw data were processed using cellRanger-2.0.2
Assembly: GRCh38-1.2.0
Supplementary files format and content: barcodes.tsv; genes.tsv; matrix.mtx

value: day 14


title: S55-DFCK-D0-WT-gp38+CD26+


title: DCM-8_ATAC


title: Patient 9_B

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Bulk RNAseq for each sample (FASTQ) were aligned to corresponding genome with STAR (v2.6.0)
Count based expression profiles were quantified using Subread featureCounts (v1.5.1)
Assembly: hs37 (GRCh37.75)
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen, QIACube). 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA LT Kit following manufacturer's protocols.

value: Patients with metastatic uveal melanoma

value: tumor

tag: recist

value: PD

tag: timepoint

value: On-tx


title: iPSC day 0

description: 10x Genomics

data_processing:
demultiplexing using mkfastq from cellRanger
counting using cellRanger -count
raw data were processed using cellRanger-2.0.2
The barcodes correspond to the following samples:
Barcode -1: IPSC Day14
Barcode -2: IPSC Day0
Barcode -3: IPSC Day7
Assembly: GRCh38-1.2.0
Supplementary files format and content: barcodes.tsv; genes.tsv; matrix.mtx

value: day 0


title: Patient 8_A

tag: tissue

value: Pre-tx


title: DCM-7_ATAC


title: S54-TXCK-D0-WT-gp38+CD26+

value: thymic stroma

value: wild-type

value: bulk RNA-seq


title: Patient 9_A


title: DCM-6_ATAC

value: heart

value: ATAC-Seq


title: S50-TXCK-D0-WT-gp38+CD26+


title: DES_C

city: Shanghai

first: Qiaohong

last: Wang

address: 160 Pujian Road

department: OB & GYN

country: China

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: peripheral blood, circulating neutrophils

growth_protocol: Isolated neutrophils were planted in 48-well plates, added with 500 μL RPMI-1640 (HyClone, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, USA) and 1% penicillin/streptomycin/amphotericin B (Gibco, USA).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One replicate was treated by decidual  explant supernatant (DES) or not  for 12 hours.

tag: years

value: 26 years

value: blood

value: female

value: decidual  explant supernatant (DES)


title: Patient 7_B


title: S49-TXCK-D0-WT-gp38+CD26+


title: DES_B

value: 25 years


title: DCM-3_ATAC

value: dilated cardiomyopathy


title: DCM-5_ATAC


title: DCM-4_ATAC


title: S46-DFCK-D0-WT-mTEC-all


title: Patient 7_A

value: Patients with metastatic uveal melanoma


title: Patient 6_B

value: tumor

value: Post-PD


title: DES_A


title: CON_C

value: Control, untreated


title: DCM-2_ATAC


title: CON_A


title: S45-DFCK-D0-WT-mTEC-all


title: Patient 6_A

value: PD


title: CON_B


title: DCM-1_ATAC


title: S43-DFCK-D0-WT-mTEC-all


title: Patient 5_A

value: Pre-tx


title: NF-10_ATAC


title: NF-9_ATAC

value: non-failing


title: S38-TXCK-D0-WT-mTEC-all

value: thymic stroma

value: wild-type


title: Patient 4_A

value: SD


title: Patient 3_B

value: On-tx


title: NF-8_ATAC

value: heart

value: ATAC-Seq


title: Patient 3_A


title: NF-7_ATAC


title: S34-DFCK-D0-WT-cTEC

value: bulk RNA-seq


title: CXCL4+ORN8L-2

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

description: Sample_EC-GC-4230_Female_OOO_Mphage_CXCL4-ORN8L_OOO_Donor-2

data_processing:
Read quality was assessed and adaptors trimmed using FASTP. Reads were then mapped to the mouse genome (hg38) and reads in exons were counted against Gencode v27 with STAR2.6 Aligner. Differential gene expression analysis was performed in R using edgeR3.24.3. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. Differential expression was estimated using quasi-likelihood framework. Benhamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with an unadjusted p-value less than 0.01 were considered differentially expressed. Downstream analyses were performed in R using a visualization platform built with Shiny developed by bioinformaticians at the David Z. Rosensweig Genomics Research Center at HSS
Genome_build: hg38
Supplementary_files_format_and_content: tab limited text containing raw counts

source_name: human blood primary monocytes

growth_protocol: CD14+ human monocytes were cultured in 20 ng/ml hM-CSF

extract_protocol:
CD14+ human monocytes were harvested and total RNA were extreacted using RNeasy Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® using total RNA (polyA mRNA workflow)

treatment_protocol: CD14+ human monocytes were treated with CXCL4 and/or ORN8L for 6 h

tag: cell type

value: monocytes

tag: donor


title: ORN8L-3

description: Sample_EC-GC-4230_Female_OOO_Mphage_ORN8L_OOO_Donor-3


title: CXCL4+ORN8L-1

description: Sample_EC-GC-4230_Male_OOO_Mphage_CXCL4-ORN8L_OOO_Donor-1


title: CXCL4+ORN8L-3

description: Sample_EC-GC-4230_Female_OOO_Mphage_CXCL4-ORN8L_OOO_Donor-3


title: S31-DFCK-D0-WT-cTEC

tag: method


title: NF-5_ATAC

tag: factor

tag: condition


title: Patient 2_A


title: NF-6_ATAC


title: S42-TXCK-D0-WT-mTEC-all

tag: age


title: ORN8L-2

description: Sample_EC-GC-4230_Female_OOO_Mphage_ORN8L_OOO_Donor-2


title: Patient 4_B


title: Patient 1_B


title: CXCL4-3

description: Sample_EC-GC-4230_Female_OOO_Mphage_CXCL4_OOO_Donor-3


title: NF-4_ATAC


title: S26-TXCK-D0-WT-cTEC


title: S37-TXCK-D0-WT-mTEC-all


title: Patient 1_A


title: NF-3_ATAC


title: S33-DFCK-D0-WT-cTEC


title: CXCL4-2

description: Sample_EC-GC-4230_Female_OOO_Mphage_CXCL4_OOO_Donor-2


title: CXCL4-1

description: Sample_EC-GC-4230_Male_OOO_Mphage_CXCL4_OOO_Donor-1


title: NF-2_ATAC


title: S25-TXCK-D0-WT-cTEC


title: S30-TXCK-D0-WT-cTEC


title: S192-TXCK-4wk-WT-CD31

value: 4 weeks


title: S191-TXCK-4wk-WT-CD31


title: Resting-3

description: Sample_EC-GC-4230_Female_OOO_Mphage_UTC_OOO_Donor-3

value: Resting


title: K562 10ng 5 min heat

city: Singapore

first: Lih Feng

last: Cheow

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

data_processing:
Adapter trimming was done using Cutadapt
Alignment and determination of methylation status was done using Bismark
Deduplication was done using Picard tools
Assembly: hg38
Supplementary files format and content: Methylation extractor output file for CpG context

source_name: Bone marrow

extract_protocol:
gDNA was extracted using Qiagen Dneasy Blood and Tissue kit.
gDNA was fragmented using the LE220 Focused ultrasonicator (Covaris) and size selected for 100-200 bp fragments using BluePippin 2% agarose cassette (Sage Sciences).
End repair and A-tailing using Kapa hyper prep kit and methylated Truseq nano adapters. Bisulfite conversion was done using Zymo EZ DNA Methylation-Gold kit

value: Bone marrow

tag: cell line

value: 5 min heat


title: K562 10ng 2 min heat

value: 2 min heat


title: ORN8L-1

description: Sample_EC-GC-4230_Male_OOO_Mphage_ORN8L_OOO_Donor-1


title: K562 10ng 20 min heat

value: 20 min heat


title: Resting-2

description: Sample_EC-GC-4230_Female_OOO_Mphage_UTC_OOO_Donor-2


title: K562 10ng 10 min heat

value: 10 min heat


title: S185-DFCK-4wk-WT-CD31

tag: genotype


title: NF-2_HiC

data_processing:
Illumina Casava1.7 software used for basecalling.
In situ HiC data were processed using HiC-Pro. The raw reads were mapped using bowtie2 and all valid pairs were kept for downstream analysis. The hic files were generated using hicprotojuiebox utilities in HiC-Pro from allValidPairs file.
Genome_build: hg19
Supplementary_files_format_and_content: hic forrmat for visualization in Juicebox
Supplementary_files_format_and_content: bigwig format for visualization in IGV or washU Genome Browser

extract_protocol: In situ Hi-C: In situ HiC was performed in a similar way as HiChIP with the exception of chromatin immunoprecipitation being performed using the H3K27ac antibody and protein A beads.

value: Hi-C


title: NF-1_ATAC

value: non-failing


title: S187-TXCK-4wk-WT-CD31

value: thymic stroma


title: NF-1_HiC


title: K562 10ng heat_rep1

value: heat


title: S182-DFCK-4wk-WT-CD31

value: wild-type


title: K562 10ng heat_rep2


title: Resting-1

description: Sample_EC-GC-4230_Male_OOO_Mphage_UTC_OOO_Donor-1


title: CD14+ Monocytes-ORN8L+CXCL4-ATAC-Donor2

data_processing:
Reproducible ATAC-seq data processing pipline TaRGET II ATAC-seq pipeline (https://github.com/Zhang-lab/TaRGET-II-ATACseq-pipeline) built into a singularity image was implemented process ATAC-seq reads to the reference human genome hg38.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig and normalized signal per 10M input single ends for visualization purpose in genome browsers
Supplementary_files_format_and_content: narrowPeak and macs2 output that records peaks called by the macs2 software

source_name: CD14+ Monocytes isolated from whole blood buffy coats

growth_protocol: CD14+ human monocytes were cultured in RPMI-1640 medium supplemented with 10% FBS and 20 ng/ml hM-CSF

extract_protocol:
~0.5-1 million CD14+ human monocytes were collected and centrifuged at 500 × g for 5 min at 4 °C. Omni-ATAC protocol was implemented to obtain ATAC-seq libraries. Briefly, CD14+ monocyte cell pellets were washed once with 1x PBS followed by centrifugation at 500 g for 5 min at 4oC. Cells pellets were lysed in 50 μL of lysis buffer. Cell pellets were gently resuspended in 50 μL of resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% v/v IGEPAL CA-630, 0.1% v/v Tween-20, 0.01% Digitonin) by pipetting up and down 3x times followed by incubation on ice for 3 minutes immediately followed by the addition of l ml of RSB buffer containing only 0.1% v/v Tween-20 but without 0.1% v/v IGEPAL CA-630 and 0.01% Digitonin. The lysates were centrifuged immediately at 500 × g for 10 min at 4 °C. The supernatants (cytoplasmic contents) were discarded and the resulting nuclear pellet containing intact chromatin was subjected to TN5 mediated transposition. The nuclear pellet was resuspended in a final volume of 50 μl transposase reaction mix (25 μL 2 × TD buffer, 2.5 μL Illumina Tn5 transposase, 16.5 μL 1X PBS, 0.5 μl 10% Tween-20 (final 0.1% v/v), 0.5 μl 1% Digitonin (final 0.01% v/v), 5 μl nuclease-free H2O). The transposition reaction was carried out for 30 min at 37 °C on a thermomixer set at 1,000 rpm. Immediately following transposition, the sample was purified using a QIAGEN MinElute Purification Kit.
The transposed DNA was amplified using NEBNext 2x PCR master mix and 1.25 M of ATAC indexing PCR primers, using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min. The PCR was first performed for a maximum of 5 cycles and the optimal number of PCR cycles were determined for each sample to avoid variation among samples due to PCR bias. The libraries were purified using a QIAGEN PCR purification kit followed by a quality control check on a bioanalyzer to check the distribution of the transposed DNA fragments. Libraries were pooled and subjected to high-throughput sequencing on an Illumina Hi-Seq 4000 Sequencer.

treatment_protocol: human CD14+ monocytes exposed for 6 h to CXCL4 ( 10 ug/ml) or ORN8L( 20 ug/ml) or both CXCL4 and ORN8L

value: CD14+ Monocytes

value: CXCL4 + ORN8L


title: DCM-2_HiC

source_name: heart tissue

value: heart

value: dilated cardiomyopathy


title: CD14+ Monocytes-ORN8L+CXCL4-ATAC-Donor3


title: NPC_TM439

city: Foshan

first: Guoyi

last: Zhang

address: Tumor Center, First People's  Hospital of Foshan, Foshan, Guangdong

institute: Tumor Center, Foshan First People's Hospital

data_processing:
Raw files obtained by sequencing with Illumina high-throughput sequencers
The original file is an image file, and after base calling and Bcl2Fastq transformation, the original sequenced sequence (sequenced reads) in FASTQ (fq for short) format can be obtained
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
Cells were collected from peripheral blood samples of nasopharyngeal carcinoma patients and single cell whole transcriptome sequencing libraries were constructed using the BD platform R hapsody Reverse Transcription Kit and BD R hapsody Whole Transcriptome Amplification Kit
RNA libraries were prepared for sequencing using standard BD RhapsodyTM Single cell 3’ whole transcriptome amplification (WTA) with sample multiplexing kit (SMK) protocol

tag: tissue/cell type

value: MCs isolated from RAB and PVB (cubital vein blood)

value: patient with newly diagnosed (untreated) nonmetastatic NPC


title: DCM-9_HiChIP

data_processing:
Library strategy: HiChIP
Illumina Casava1.7 software used for basecalling.
HiChIP data were processed using HiC-Pro with default parameters with the exception of the LIGATION_SITE being set to GATCGATC, GANTGATC, GANTANTC, GATCANTC and the GENOME_FRAGMENT that was generated using digest_genome.py in HiC-Pro utilities. The following parameters were used: -r ^GATC G ^ANTC -o hg19_restriction sites.bed hg19.fasta. The raw reads were mapped to the hg19 reference genome and were assigned to restriction fragments. The raw reads were filtered for valid pairs (VI). 1D coverage files for the visualization in bigwig format were converted from bam format using deepTools and RPKM (Reads Per Kilobase per Million reads to normalize the number of reads per bin) normalization was used. The HiC files were generated using hicprotojuiebox.py utilities in HiC-Pro.
Genome_build: hg19
Supplementary_files_format_and_content: hic forrmat for visualization in Juicebox
Supplementary_files_format_and_content: bigwig format for visualization in IGV or washU Genome Browser

extract_protocol: H3K27ac HiChIP: biotin-labeled proximally-ligated chromatin was prepared using the Arima-HiC kit (Arima Genomics Cat # A510008). Briefly, the crosslinked chromatin was initially digested using a restriction enzyme (RE) cocktail. The 5’-overhangs were subsequently filled in and labeled with a biotinylated nucleotide. Subsequently, the spatially proximal digested ends of DNA were ligated. The resulting proximally-ligated chromatin was fragmented using the Diagenode Bioruptor Pico instrument, bound to an H3K27ac antibody (Abcam Cat # ab4729) overnight and immunoprecipitated on Protein A magnetic beads (Thermo Cat # 10002D). The immunoprecipitated chromatin was reverse crosslinked and purified using the Arima-HiC kit. Subsequently, the Illumina-compatible sequencing libraries were prepared by initial enrichment for biotin using C1 streptavidin beads (Thermo Cat # 65001). The samples were tagmented on-bead utilizing Tagment DNA Enzyme and Buffer (Illumina Cat # 20034197). Subsequently, DNA was PCR amplified utilizing NPM and the indexing primers from the Nextera XT DNA Library Prep kit (Illumina Cat # FC-131-1024). The PCR products were purified and size selected by 0.5X SPRI beads followed by 0.7X SPRI beads.

value: HiChIP


title: NPC_TM440


title: DCM-10_HiChIP


title: CD14+ Monocytes-ORN8L+CXCL4-ATAC-Donor1

tag: treatment


title: S180-TXCK-4wk-WT-mTEClo

source_name: mTEClo

value: 4 weeks

value: bulk RNA-seq


title: DCM-1_HiC


title: S175-TXCK-4wk-WT-mTEClo


title: DCM-7_HiChIP


title: S179-TXCK-4wk-WT-mTEClo


title: CD14+ Monocytes-ORN8L-ATAC-Donor3


title: CD14+ Monocytes-ORN8L-ATAC-Donor2


title: DCM-8_HiChIP


title: NPC_TM437


title: CD14+ Monocytes-ORN8L-ATAC-Donor1


title: DCM-6_HiChIP


title: NPC_TM421


title: CD14+ Monocytes-CXCL4ATAC-Donor3


title: S172-DFCK-4wk-WT-mTEClo


title: NPC_TM438


title: S184-DFCK-4wk-WT-CD31


title: NPC_TM420


title: S173-DFCK-4wk-WT-mTEClo


title: DCM-5_HiChIP


title: CD14+ Monocytes-CXCL4-ATAC-Donor2


title: S170-DFCK-4wk-WT-mTEClo


title: NPC_TM419


title: DCM-4_HiChIP


title: NPC_TM418


title: CD14+ Monocytes-CXCL4-ATAC-Donor1


title: Tbx1CrklWtR03

description:
TbxCrklStroma.counts.gz
TbxCrklStroma_metadata.txt.gz

source_name: CD45- thymic stroma

value: 10X gene expression


title: DCM-3_HiChIP


title: CD14+ Monocytes-Resting-ATAC-Donor3

value: Resting


title: Tbx1CrklWtR02


title: Tabula Sapiens

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316.
Reads were aligned using to the GRCh38 genome using STAR version 2.5.2b with parameters TK.
Gene counts were produced using HTSEQ version 0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Sequences from the microfluidic droplet platform were de-multiplexed and aligned using CellRanger version 2.0.1, available from 10x Genomics with default parameters.
Assembly: GRCh38
Supplementary files format and content: Processed data is available as h5ad

source_name: 24 human tissues and organs

extract_protocol:
For FACS data, single cells sorting in 384 well plates followed by cDNA preparation using modified SmartSeq2. For droplet data, capture and processing in microfluidics droplets via 10x Genomics.
For FACS data, SmartSeq2 for preparation of cDNA followed by library preparation using either Nextera XT or a homebrew adapted version. For droplet cDNA, library preparation using TruSeq.
For FACS data, Tn5 tagmentation according the standard protocol for single cell RNA-seq following SmartSeq2. For droplet data, fragmentation, end repair,  ligation according to the standard protocol for 10x Chromium Single Cell 3’ Kit (v2).

value: Various tissues

value: mixed sample (non-demultiplexed)


title: DCM-2_HiChIP


title: Tbx1CrklWtR01


title: CD14+ Monocytes-Resting-ATAC-Donor2


title: DCM-1_HiChIP


title: Sample0114PCWThymicStroma RNA

data_processing:
Fastq files were trimmed prior to analysis: ATAC R1 50bp 5prime, ATAC R2 16bp 3prime, ATAC R3 49bp 5prime, cDNA R1 28bp 5prime, cDNA R3 90bp 5prime. Sequencing data were processed using Cell Ranger ARC (version 1.0.1). Counts and ATAC data were analysed using Seurat (version 4.0.3) and Signac (version 1.2.1). Barcodes were filtered to high quality cells (ATAC library size 1,000-100,000, RNA library size 1,000-31,622, ATAC peaks 1,000-31,622, RNA features 1,000-10,000 and proportion of mitochondrial RNA reads ≤0.15). ATAC peaks were recalled across each sample for all cells.
Genome_build: Homo sapiens: GRCh38
Supplementary_files_format_and_content: Processed data includes count matrices for the GEX and ATAC component of 10x Genomics multiomics and meta-data for cells that passed QC.

molecule: nuclear RNA

source_name: thymic stroma

extract_protocol:
10x Genomics multiomics: Human thymi were dissociated and sorted for live CD45- MHC intermediate-high cells. Nuclei were isolated using the NP40 lysis buffer for 6 minutes and processed using the 10x Genomics Multiomics ATAC (Assay for Transposase-Accessible Chromatin using sequencing) + Gene Expression kit, following the manufacturer’s instructions. Nuclei were captured into droplets on the 10x Genomics Chromium platform.
10x Genomics multiomics: libraries were constructed as per manufacturer's protocol for multiomics (gene expression [GEX] and Assay for Transposase-Accessible Chromatin [ATAC]) analysis from single nuclei
10x Genomics multiomics: libraries were prepared as per manufacturer's protocol for multiomics (gene expression [GEX] and Assay for Transposase-Accessible Chromatin [ATAC]) analysis and sequenced on an Illumina NovaSeq platform.

value: 14 post-conceptional weeks

value: 10x multiomics - GEX


title: Tbx1CrklHetR03

data_processing:
10X GEX: Single cell libraries were processed using Cellranger (version 3.1.0). Cells were excluded from analysis if the total UMI count was <1,000 or >32,000, the number of detectable features was <562 or >7,943 or the proportion of UMIs mapping to mitochondrial genes was >10%.
RNA-seq: reads were aligned against the Ensembl transcriptome and genome (GRCh38.EBVB95-8wt.ERCC) using STAR (version 2.5.3a). The allocation of reads to protein coding gene meta-features was done using HTSeq.
Genome_build: Mus musculus: mm10
Supplementary_files_format_and_content: Processed data includes count matrices for RNA-seq/10X GEX and meta-data for 10X GEX

value: thymic stroma

value: Tbx1+/- Crkl+/-


title: CD14+ Monocytes-Resting-ATAC-Donor1

value: CD14+ Monocytes


title: Sample0517PCWThymicStroma RNA

value: 17 post-conceptional weeks


title: Tbx1CrklHetR02


title: H9-HSCs

city: West Lafayette

first: Xiaoping

last: Bao

state: Indiana

address: 480 Stadium Mall Drive

department: Chemical Engineering

institute: Purdue University

data_processing:
Casava1.8 software used for basecalling
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2
the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: hPSC-derived Hematopoietic Cells

growth_protocol: Day 18 hPSC-derived hematopoietic cells were generated by treating hPSCs with CHIR99021 to induce SOX17+ hemogenic endothelium, followed by TGFβ inhibitor SB431542 treatment from day 4 to day 6.

extract_protocol:
RNA of hPSC-derived hematopoietic cells was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

tag: developmental stage

value: day 18 from hPSC

value: hPSC-derived Hematopoietic Cells


title: Sample0517PCWThymicStroma ATAC

value: 10x multiomics - ATAC


title: NF-10_HiChIP

value: heart

value: HiChIP

value: dilated cardiomyopathy


title: Sample0114PCWThymicStroma ATAC


title: NF-8_HiChIP

value: non-failing


title: NF-9_HiChIP


title: Day 18: H9 AGM-HC scRNA-seq

first: Shihuan

last: Kuang

state: IN

address: 270 S. Russell Street

data_processing:
all data was processed using the default parameters for 10X genomics CellRanger software to align the reads to the mouse genome and create count matrices of genes for each cell
data was log-normalized and analyzed using Seurat v3 in R
Genome_build: hg19-1.2.0
Supplementary_files_format_and_content: all data is in a .rds file that contains @ metadata slot which references the cell barcode number and sample, cell type, and contains the normalized count matricies

source_name: day 18 from hPSCs

growth_protocol: hPSC-derived day 8 AGM-like cells were generated from hPSCs by treatment of CHIR99021 from day 0-1 and SB431542 or Heparin from day 4 to 6, followed by SCF and FLT3L treatment every 3 days until day 18

extract_protocol:
Floating live cells were sorted in FACS and applied to 10X Genomics Chromimum Controller
libraries were prepared following 10X Genomics protocol for v3 3' single-cell sequencing and samples were prepared for high throughput sequencing following Illumina's specifications. Prior to sequencing all samples were evaluated using an Agilent Bioanalyzer high sensitivity chip

treatment_protocol: Day 0-1, CHIR99021; Day 4 to 6, SB431542 or Heparin; Day 7-18, SCF and FLT3L

value: aorta-gonad-mesonephros

value: hPSC-derived AGM-like hematopoietic cells


title: H9-HSC-eGFP


title: Tbx1CrklHetR01

extract_protocol:
10X: live Ter119-CD45-EpCAM- (developmental) or Ter119-CD45- (Tbx1Crkl) thymic stromal cells were sorted for 10X Genomics 3' gene expression. For the Tbx1Crkl dataset, cells were pre-fixed with RNA Protect. RNA-seq: Live CD45- thymic stromal cells were sorted for ultra-low input RNA-seq.
10X GEX: libraries were prepared as per manufacturer's protocol for 3' gene expression libraries. RNA-seq: ultra low RNA-seq protocol (equivalent to Smarter-seq)

value: 10X gene expression


title: 6-9-9-HSCs


title: NF-7_HiChIP

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road


title: ThymicStromaWtW4R01

description:
ThymicStroma.counts.gz
ThymicStroma_metadata.txt.gz

source_name: CD45- Epcam- thymic stroma

value: wild-type

value: 4 weeks


title: Day 8: H9 AGM-EC scRNA-seq

source_name: day 8 from hPSCs

value: hPSC-derived AGM-like endothelial/hematopoietic cells


title: PMDK002F_S6: Crh1KO_Rep3

city: Reno

first: Pedro

last: Miura

state: Nevada

address: 1664 N VIRGINIA ST MS 0314

department: Biology

institute: University of Nevada, Reno

data_processing:
Illumina’s bcl2fastq_v2.19 software
Sequenced reads were trimmed for adaptor sequence, then mapped to WBcel235 whole genome using HISAT2 v2.1.0 (options: --no-mixed --no-discordant --dta)
read counts for each gene per exon were obtained using featurecounts v1.5.0 (options: -t exon -g gene_id)
normalized abundance measurements and differential expression analysis were obtained using DESeq2 v1.26.0 with default parameters
Genome_build: WBcel235
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were age-synchronized by hypochlorite treatment and collected eggs were hatched overnight at 20°C in 1x M9 buffer. L1 larvae were then plated onto NGM plates seeded with 10x concentrated E. coli OP50 bacteria and allowed to develop to the L4 larval stage at 20°C. L4 larvae were then collected, washed, and re-plated onto 25 µM 5-fluorodeoxyuridine (FUdR) (Milipore Sigma, Cat #50-91-9) containing NGM plates unless indicated otherwise seeded with 10x E. coli OP50 bacteria in order to prevent progeny formation. Day-1 adult worms were collected by filtering through a 30 µM nylon mesh to remove bacteria

extract_protocol:
1-day adult worms were collected using Trizol LS reagent. Total RNA was extracted via isopropanol precipitation and treated with Turbo DNase (AM2238) according to manufacturer instructions. RNA quality was assessed by Bioanalyzer (Agilent) prior to library construction.
Illumina TruSeq Stranded Total RNA Library Prep Gold kit (Cat #20020598) was used with 1ug of total RNA to construct sequencing libraries

tag: strain

value: whole worm

value: day-1 adult


title: NF-6_HiChIP

institute: Guangdong Provincial People's Hospital


title: ThymicStromaWtP0R02

value: thymic stroma


title: NF-5_HiChIP


title: PMDK002E_S5: Crh1KO_Rep2


title: ThymicStromaWtP0R01


title: PMDK002D_S4: Crh1KO_Rep1


title: NF-3_HiChIP


title: PMDK002C_S3: WT_Rep3

value: wild type


title: PMDK002B_S2: WT_Rep2


title: NF-2_HiChIP


title: ThymicStromaWtE165R01


title: ThymicStromaWtE135R01


title: NF-4_HiChIP


title: NF-1_HiChIP


title: ThymicStromaWtE125R01


title: ThymicStromaWtW4R02


title: PMDK002A_S1: WT_Rep1


title: ThymicStromaWtE165R02


title: Lineage_wATAC-p9H9

status: Public on May 12 2022

city: Seattle

first: Anna

last: Minkina

state: WA

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

department: Genome Sciences

institute: University of Washington

description:
lineage_profiles_wATAC.txt
H9-TARGp9_GATTGCAGAC_S93

data_processing:
demultiplex using bcl2fastq
adaptor trimming using trim_galore
align to reference genome using STAR
reads deduplicated by UMIs
(All code available at: https://github.com/minkinaa/TheLorax)
sciRNA_lib:
Sequencing was performed as previously described (Cao et al. 2017). Reads were adapter-trimmed using trim_galore and aligned to the reference genome (hg38) using STAR. Non-unique mappers were removed. Reads were then deduplicated using a custom script (190223_sciRNA_remove_duplicates.cpp), taking into account both UMIs and cell indices to call a duplicated read. Only cells with at least 2048 deduplicated non-mitochondrial UMIs were used for subsequent analyses.
A custom script (190704_process_sciRNA_mapped_file.cpp) was used to map reads to genes. Reads which overlapped multiple genes but only fell in an exon in one gene were counted towards that gene.
RNA processing to generate the cell by gene raw counts file is implemented in script 190807_sciRNA_wrapper_ALL.txt, with user-defined UMI cutoff of 2^11.
sciATAC_lib:
For processing sci-ATAC-seq sequencing reads, we first compare observed and expected lists of single cell indices, correcting any indices with a likely off-by-one error. All reads are then adaptor trimmed using trimmomatic (parameters: TRAILING:3 SLIDINGWINDOW:4:10 MINLEN:20), and all reads associated with a single cell are then aligned to the genome using bowtie2 (hg38 genome build). Reads are then deduplicated by UMIs using a custom script (191226_CROPt_process_atac_bedfile.cpp). Both cell by gene and cell by interval counts were generated using a custom script (191226_CROPt_make_cell_by_interval_count_file.cpp).
Lineage_wRNA & Lineage_wATAC:
Processing of raw data to generate the categorical processed data file is described in associated manuscript ("Computational processing and edit calling from lineage target sequencing data") with all associated code at https://github.com/minkinaa/TheLorax.
Cell IDs found in the processed data file are related to raw fastq files as follows:
sciRNA_lib: Each fastq pair file contains information from 25 cells (or less). The cell IDs are a combination of the plate/batch, PCR well index (index #2) during combinatorial indexing (in fastq file name), and index #1, the last 10 bases of the read1 sequence. E.g. the raw data for the cell called "p1A10_ACTAATTGAG", can be found in the raw data file "p1A10-RNA_CCAGGTCTAC_S10", with those sequences with "ACTAATTGAG" as the last 10 bases in the R1 file corresponding to this cell. The first 8 bases of R1 are the UMI.
sciATAC_lib: Cell IDs corresponding to those found in the processed file can be found in the sequence name in the fastq (e.g. "@p2H1_TGAGCTACTT-R1.1" --> cell ID = "p2H1_TGAGCTACTT")
Lineage_wRNA & Lineage_wATAC: Cell IDs are related to fastq file names as described for "sciRNA_lib" except index #1 is located in positions 9-18 in the R1 fastq file. The first 8 bases of R1 are the UMI. Read structure is further describe in manuscript Materials & Methods, and at https://github.com/minkinaa/TheLorax.
A list of index #1's can be found in supplementary file "Index_1_List.txt".
Assembly: hg38
Supplementary files format and content: Tab-separated values, raw cell by gene/tss counts matrices

extract_protocol:
sci-RNA-seq: whole cells, methanol fixes; sci-ATAC-seq: nuclei
sci-RNA-seq-2level, sci-ATAC-seq2level, targeted lineage mRNA capture as described

tag: data type

value: Targeted lineage amplicon captured alongside sci-ATAC-seq


title: Lineage_wATAC-p9H6

description:
lineage_profiles_wATAC.txt
H6-TARGp9_TCATCTAATC_S90


title: sciATAC_lib-atac_R2_plate1thru5_run2

description:
AllPlates_upstr5000_plusWholeGeneBody_cell_by_tss.txt.gz
atac_plate1thru5_run2

value: sci-ATAC-seq


title: Lineage_wATAC-p9H7

description:
lineage_profiles_wATAC.txt
H7-TARGp9_AGATCCTATA_S91


title: sciATAC_lib-atac_R2_plate6thru11_run2

description:
AllPlates_upstr5000_plusWholeGeneBody_cell_by_tss.txt.gz
atac_plate6thru11_run2


title: Lineage_wATAC-p9H4

description:
lineage_profiles_wATAC.txt
H4-TARGp9_TGCCAGATGG_S88


title: Lineage_wATAC-p9H2

description:
lineage_profiles_wATAC.txt
H2-TARGp9_TGGCCGCAAT_S86


title: Lineage_wATAC-p9H5

description:
lineage_profiles_wATAC.txt
H5-TARGp9_AACTTATAAG_S89


title: Lineage_wATAC-p9H3

description:
lineage_profiles_wATAC.txt
H3-TARGp9_CCAAGCTGAA_S87


title: Lineage_wATAC-p9H1

description:
lineage_profiles_wATAC.txt
H1-TARGp9_TTCTACGCCA_S85


title: Lineage_wATAC-p9H11

description:
lineage_profiles_wATAC.txt
H11-TARGp9_AAGATCCAAC_S95


title: AD_leukocytes_rep3

type: RNA

city: Urumqi

first: juan

last: Bu

address: 29 Tianchi Road

institute: People's Hospital of Xinjiang Uygur Autonomous Region

description: CircrRNAs expression in Alzheimer's disease peripheral blood leukocytes

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Alzheimer's disease peripheral blood leukocytes , replicate 3

label_protocol: rRNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Alzheimer's disease and normal human peripheral blood leukocyte

extract_protocol: RNA was prepared using the mirVana miRNA Isolation Kit (Ambion Inc., Austin) following the manufacturer's recommendations.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Totally 3-5 mL peripheral blood was collected and lysed with the red blood cell lysate to separate the leukocytes. The total RNA was extracted from the leukocytes, which was quantified using NanoDrop one spectrophotometer.

tag: disease state

value: Alzheimer's disease

value: peripheral blood leukocytes

tag: gender

value: male


title: Normal_leukocytes_rep1

description: CircrRNAs expression in normal human peripheral blood leukocytes

source_name: Normal peripheral blood leukocytes , replicate 1

value: Healthy control

tag: tissue

value: female


title: Normal_leukocytes_rep4

source_name: Normal peripheral blood leukocytes , replicate 4


title: Normal_leukocytes_rep3

source_name: Normal peripheral blood leukocytes , replicate 3


title: AD_leukocytes_rep2

source_name: Alzheimer's disease peripheral blood leukocytes , replicate 2


title: AD_leukocytes_rep1

source_name: Alzheimer's disease peripheral blood leukocytes , replicate 1


title: Normal_leukocytes_rep2

source_name: Normal peripheral blood leukocytes , replicate 2


title: Lineage_wATAC-p9H10

description:
lineage_profiles_wATAC.txt
H10-TARGp9_ATAAGAGGCG_S94


title: Lineage_wATAC-p9H12

description:
lineage_profiles_wATAC.txt
H12-TARGp9_CTGCAATCGC_S96


title: HCC1954

first: Marcin

last: Imielinski

address: 413 E 69th Street

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

data_processing:
Library strategy: Pore-C
Basecalling was done using Guppy base caller version 3.4.0rc3 run in hac mode
Pore-C reads were aligned using bwa bwasw with parameters -b 5 -q 2 -r 1 -T 15 -z 10. Further processing done by custom Pore-C pipeline found here https://github.com/nanoporetech/pore-c
CpG methylation was called using f5c (https://github.com/hasindu2008/f5c), an optimized and gpu-compatible re-implementation of the call-methylation module in Nanopolish (https://github.com/jts/nanopolish}. Per-read calls were aggregated into per-locus calls using f5c meth-freq -s with the default log-likelihood ratio threshold.
Pair wise contacts using pore_c to-matrix in the pore-c pipelines with default settings
mcool files were made using cooler zoomify with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: .csv Pore-C multi-way contacts files where each row is a Pore-C monomer and metadata related to them including the concatemer they blong to.
Supplementary_files_format_and_content: .csv Pore-C pair-wise contacts files where each row is a pair-wise contact
Supplementary_files_format_and_content: .mcool Pore-C pair-wise cooler contacts files
Supplementary_files_format_and_content: .csv Pore-C phased methylation file, phased in two haplotypes with aggregated methylation

source_name: Breast

growth_protocol: Human B lymphocytes (GM12878) [Coriell Institute] and HG002 cells [Coriell Institute] were each maintained in suspension at a concentration greater than 200,000 cells/mL in RPMI-1640 [ATCC 30-2001] supplemented with 15% fetal bovine serum (FBS) and 1% penicillin/streptomycin. HCC1954 [ATCC CRL-2388] human breast cancer cells were maintained using a subculture ratio of 1:4 every three days in RPMI-1640 (ATCC 30-2001) supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
To reverse cross-link, samples were treated with 100 μL 20 mg/mL Proteinase K [Thermo Fisher Scientific cat no. 25530049], 100 μL 10% SDS [Thermo Fisher Scientific cat no. 15553027] and 500 μL 20% v/v Tween-20 [Sigma Aldrich cat no. P9416] in a total volume of 2000 μL with nuclease-free water. Samples were incubated in a thermomixer at 56°C for 18 hours with < 1000 rpm rotation (< 30 sec every 15 min) to prevent condensation inside the lid. In order to purify DNA, the sample was transferred to a 5 mL centrifuge tube. The original tube was rinsed with a further 200 μL of nuclease-free H2O to collect any residual sample, bringing the total sample volume to 2.2 mL. DNA was then purified from the sample using a standard phenol chloroform extraction and ethanol precipitation.
Purified DNA was SPRI size selected for fragments >1.5 kb, then prepared for sequencing using Oxford Nanopore Technologies SQK-LSK109, and sequenced on ONT's MinION, GridIONor PromethION platforms.

treatment_protocol: Cross Linking: 10 million cells were washed three times in chilled 1X phosphate buffered saline (PBS) in a 50 mL centrifuge tube, and pelleted by centrifugation at 500 xg for 5 min. at 4°C between each wash. Cells were re-suspended in 10 mL room temperature 1X PBS 1% formaladehyde [EMD Millipore cat no. 818708] by gently pipetting with a wide-bore tip, then incubated at room temperature for 10 min. To quench the cross-linking reaction, 527 μL of 2.5 M glycine was added to achieve a final concentration of 1% w/v or 125 mM in 10.5 mL. Cells were incubated for 5 min. at room temperature followed by 10 min. on ice. The cross-linked cells were pelleted by centrifugation at 500 xg for 5 min. at 4°C. Restriction enzyme digest: Each cell pellet was resuspended in a mixture of 50 μL of protease inhibitor cocktail [Sigma Aldrich cat no. P8340] in 500 μL of cold permeabilization buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630) and placed on ice for 15 min. Cells were centrifuged at 500 xg for 10 min. at 4°C after which the supernatant was aspirated and replaced with 200 μL of chilled 1.5X digestion reaction buffer [NEB ] compatible with the restriction enzyme used. Cells were centrifuged again at 500 xg for 10 min. at 4°C, then aspirated and re-suspended in 300 μL of chilled 1.5X digestion reaction buffer. To denature the chromatin, 33.5 μL of 1% w/v SDS [Thermo Fisher Scientific cat no. 15553027] was added to each cell suspension and incubated for exactly 10 min. at 65°C with gentle agitation, and then placed on ice immediately afterwards. To quench the SDS, 37.5 μL of 10% v/v Triton X-100 [Sigma Aldrich cat no. 93443] was added for a final concentration of 1%, followed by incubation for 10 min. on ice. Permeablized cells were then digested with a final concentration of 1 U/μL of either DpnII, NlaIII or HindIII [NEB] brought to volume with nuclease-free water to achieve a final 1X digestion reaction buffer in 450 μL. Cells were then mixed by gentle inversion. Cell suspensions were incubated in a thermomixer at 37°C for 18 hours with periodic < 1000 rpm rotation (< 30 sec every 15 min.) to prevent condensation inside the lid. Proximity ligation and reverse cross-linking: DpnII and NlaIII restriction digests were heat inactivated at 65°C for 20 min. with 300 rpm rotation. HindIII digests were chemically inactivated with a final concentration of 0.1% w/v SDS at 65°C for 20 min. with 300 rpm rotation, then quenched with a final concentration of 1% v/v Triton X-100 [Sigma Aldrich cat no. 93443].Proximity ligation was set up at room temperature with the addition of the following reagents: 100 μL of 10X T4 DNA ligase buffer [NEB], 10 μL of 10 mg/mL BSA and 50 μL of T4 Ligase [NEB M0202L] in a total volume of 1000 μL with nuclease-free water. The ligation was cooled to 16°C and incubated for 6 hours with gentle rotation.

value: Breast cancer cell line


title: sciATAC_lib-atac_R2_plate1thru5_run1

description:
AllPlates_upstr5000_plusWholeGeneBody_cell_by_tss.txt.gz
atac_plate1thru5_run1


title: sciATAC_lib-atac_R2_plate6thru11_run1

description:
AllPlates_upstr5000_plusWholeGeneBody_cell_by_tss.txt.gz
atac_plate6thru11_run1


title: Lineage_wATAC-p9G7

description:
lineage_profiles_wATAC.txt
G7-TARGp9_TCTATAAGGA_S79


title: Lineage_wATAC-p9G3

description:
lineage_profiles_wATAC.txt
G3-TARGp9_CAAGATTAAG_S75


title: Lineage_wATAC-p9G6

description:
lineage_profiles_wATAC.txt
G6-TARGp9_CATTATTACC_S78


title: Lineage_wATAC-p9G1

description:
lineage_profiles_wATAC.txt
G1-TARGp9_GACCGTAGCA_S73


title: Lineage_wATAC-p9G9

description:
lineage_profiles_wATAC.txt
G9-TARGp9_CAAGCTTGGC_S81


title: Lineage_wATAC-p9G12

description:
lineage_profiles_wATAC.txt
G12-TARGp9_ACTGAATTCC_S84


title: Lineage_wATAC-p9G5

description:
lineage_profiles_wATAC.txt
G5-TARGp9_TGATACGAGT_S77


title: Lineage_wATAC-p9G4

description:
lineage_profiles_wATAC.txt
G4-TARGp9_ACGCAACTCC_S76


title: GM12878

source_name: Blood

value: EBV transformed lymphoblastoid cell line


title: Lineage_wATAC-p9G8

description:
lineage_profiles_wATAC.txt
G8-TARGp9_TTGGAGTCGG_S80


title: Lineage_wATAC-p9F7

description:
lineage_profiles_wATAC.txt
F7-TARGp9_TATAACTTCC_S67


title: Lineage_wATAC-p9F5

description:
lineage_profiles_wATAC.txt
F5-TARGp9_ACGTTCAACC_S65


title: Lineage_wATAC-p9F8

description:
lineage_profiles_wATAC.txt
F8-TARGp9_AGGATTACCA_S68


title: Lineage_wATAC-p9F4

description:
lineage_profiles_wATAC.txt
F4-TARGp9_AACGAGGCTA_S64


title: Lineage_wATAC-p9F6

description:
lineage_profiles_wATAC.txt
F6-TARGp9_ACGAGGACCT_S66


title: Lineage_wATAC-p9F12

description:
lineage_profiles_wATAC.txt
F12-TARGp9_CGAGCTGCCA_S72


title: Lineage_wATAC-p9F11

description:
lineage_profiles_wATAC.txt
F11-TARGp9_ACTATCCGCA_S71


title: Lineage_wATAC-p9E8

description:
lineage_profiles_wATAC.txt
E8-TARGp9_ACCGTTACGA_S56


title: Lineage_wATAC-p9E6

description:
lineage_profiles_wATAC.txt
E6-TARGp9_CATGCATCTC_S54


title: Lineage_wATAC-p9E9

description:
lineage_profiles_wATAC.txt
E9-TARGp9_TCCGTCGCCA_S57


title: Lineage_wATAC-p9E7

description:
lineage_profiles_wATAC.txt
E7-TARGp9_TCCGGTAATC_S55


title: Lineage_wATAC-p9F10

description:
lineage_profiles_wATAC.txt
F10-TARGp9_AGTCCGCGGA_S70


title: Lineage_wATAC-p9G2

description:
lineage_profiles_wATAC.txt
G2-TARGp9_GTCATTGCGC_S74


title: Lineage_wATAC-p9E5

description:
lineage_profiles_wATAC.txt
E5-TARGp9_CTCCGGTTCT_S53


title: Lineage_wATAC-p9E2

description:
lineage_profiles_wATAC.txt
E2-TARGp9_ACTATCTTGA_S50


title: Lineage_wATAC-p9E3

description:
lineage_profiles_wATAC.txt
E3-TARGp9_AGGTCAATTA_S51


title: Lineage_wATAC-p9E12

description:
lineage_profiles_wATAC.txt
E12-TARGp9_ACTTCCGAAT_S60


title: Lineage_wATAC-p9E4

description:
lineage_profiles_wATAC.txt
E4-TARGp9_AAGCCGGCTG_S52


title: Lineage_wATAC-p9E10

description:
lineage_profiles_wATAC.txt
E10-TARGp9_GGCTATGACT_S58


title: Lineage_wATAC-p9E11

description:
lineage_profiles_wATAC.txt
E11-TARGp9_TGGACTTGAC_S59


title: Lineage_wATAC-p9G10

description:
lineage_profiles_wATAC.txt
G10-TARGp9_ATAGGATATG_S82


title: Lineage_wATAC-p9E1

description:
lineage_profiles_wATAC.txt
E1-TARGp9_GCTCTCGCCT_S49


title: Lineage_wATAC-p9G11

description:
lineage_profiles_wATAC.txt
G11-TARGp9_TGGCGTAGGT_S83


title: Lineage_wATAC-p9D9

description:
lineage_profiles_wATAC.txt
D9-TARGp9_GACCTCTCTG_S45


title: Lineage_wATAC-p9D8

description:
lineage_profiles_wATAC.txt
D8-TARGp9_CGATCATTAC_S44


title: Lineage_wATAC-p9F1

description:
lineage_profiles_wATAC.txt
F1-TARGp9_AACTACCGAC_S61


title: Lineage_wATAC-p9D4

description:
lineage_profiles_wATAC.txt
D4-TARGp9_GACCTCCGCC_S40


title: Lineage_wATAC-p9F2

description:
lineage_profiles_wATAC.txt
F2-TARGp9_CGTCCGTCCT_S62


title: Lineage_wATAC-p9D5

description:
lineage_profiles_wATAC.txt
D5-TARGp9_TCTAGAACTA_S41


title: Lineage_wATAC-p9F3

description:
lineage_profiles_wATAC.txt
F3-TARGp9_GGTCCAGGAG_S63


title: Lineage_wATAC-p9F9

description:
lineage_profiles_wATAC.txt
F9-TARGp9_AACCTAGCTT_S69


title: Lineage_wATAC-p9D2

description:
lineage_profiles_wATAC.txt
D2-TARGp9_CAAGTACTGG_S38


title: Lineage_wATAC-p9C9

description:
lineage_profiles_wATAC.txt
C9-TARGp9_GCAACTGGCA_S33


title: Lineage_wATAC-p9C8

description:
lineage_profiles_wATAC.txt
C8-TARGp9_AATTGCCTAC_S32


title: Lineage_wATAC-p9D3

description:
lineage_profiles_wATAC.txt
D3-TARGp9_CGGCGAGACC_S39


title: Lineage_wATAC-p9D11

description:
lineage_profiles_wATAC.txt
D11-TARGp9_CGAGTTAGAG_S47


title: Lineage_wATAC-p9D12

description:
lineage_profiles_wATAC.txt
D12-TARGp9_GATGATCGTA_S48


title: Lineage_wATAC-p9D1

description:
lineage_profiles_wATAC.txt
D1-TARGp9_CGCCGCCTCC_S37


title: Lineage_wATAC-p9D10

description:
lineage_profiles_wATAC.txt
D10-TARGp9_GGCTAATTAA_S46


title: Lineage_wATAC-p9C7

description:
lineage_profiles_wATAC.txt
C7-TARGp9_TCGTAGGCTT_S31


title: Lineage_wATAC-p9C5

description:
lineage_profiles_wATAC.txt
C5-TARGp9_CCTAGCGCCT_S29


title: Lineage_wATAC-p9C1

description:
lineage_profiles_wATAC.txt
C1-TARGp9_GTTCCGACGA_S25


title: Lineage_wATAC-p9C3

description:
lineage_profiles_wATAC.txt
C3-TARGp9_GACTAGTCTA_S27


title: Lineage_wATAC-p9C12

description:
lineage_profiles_wATAC.txt
C12-TARGp9_CTCGGTCAAT_S36


title: Lineage_wATAC-p9C6

description:
lineage_profiles_wATAC.txt
C6-TARGp9_AGTTGCATCT_S30


title: Lineage_wATAC-p9H8

description:
lineage_profiles_wATAC.txt
H8-TARGp9_CCTATAAGCT_S92


title: Lineage_wATAC-p9D7

description:
lineage_profiles_wATAC.txt
D7-TARGp9_ACCAAGATCT_S43


title: Lineage_wATAC-p9D6

description:
lineage_profiles_wATAC.txt
D6-TARGp9_CTAACTCCAA_S42


title: Lineage_wATAC-p9B9

description:
lineage_profiles_wATAC.txt
B9-TARGp9_AGCGTCAATG_S21


title: Lineage_wATAC-p9C11

description:
lineage_profiles_wATAC.txt
C11-TARGp9_GGTAGGTCTC_S35


title: Lineage_wATAC-p9B8

description:
lineage_profiles_wATAC.txt
B8-TARGp9_CCGTCGGAGG_S20


title: Lineage_wATAC-p9B6

description:
lineage_profiles_wATAC.txt
B6-TARGp9_GTCGCTCAGT_S18


title: Lineage_wATAC-p9B7

description:
lineage_profiles_wATAC.txt
B7-TARGp9_TGATTCCTCA_S19


title: Lineage_wATAC-p9B3

description:
lineage_profiles_wATAC.txt
B3-TARGp9_GAACTGCATC_S15


title: Lineage_wATAC-p9B4

description:
lineage_profiles_wATAC.txt
B4-TARGp9_GGAACGATGG_S16


title: Lineage_wATAC-p9B5

description:
lineage_profiles_wATAC.txt
B5-TARGp9_ACTCTCTCAA_S17


title: Lineage_wATAC-p9B1

description:
lineage_profiles_wATAC.txt
B1-TARGp9_TTAACGTACC_S13


title: Lineage_wATAC-p9B2

description:
lineage_profiles_wATAC.txt
B2-TARGp9_GGACTCATTG_S14


title: Lineage_wATAC-p9B12

description:
lineage_profiles_wATAC.txt
B12-TARGp9_TGAGGTAGAA_S24


title: Lineage_wATAC-p9C4

description:
lineage_profiles_wATAC.txt
C4-TARGp9_CTGCTTCGAC_S28


title: Lineage_wATAC-p9B11

description:
lineage_profiles_wATAC.txt
B11-TARGp9_TTGAGTATCA_S23


title: Lineage_wATAC-p9C2

description:
lineage_profiles_wATAC.txt
C2-TARGp9_TCATCTCGAT_S26


title: Lineage_wATAC-p9B10

description:
lineage_profiles_wATAC.txt
B10-TARGp9_CGAAGGACGA_S22


title: Lineage_wATAC-p9A5

description:
lineage_profiles_wATAC.txt
A5-TARGp9_GCTCTAACGA_S5


title: Lineage_wATAC-p9A6

description:
lineage_profiles_wATAC.txt
A6-TARGp9_TGATAGAACG_S6


title: Lineage_wATAC-p9A8

description:
lineage_profiles_wATAC.txt
A8-TARGp9_GATCAGTCAT_S8


title: Lineage_wATAC-p9A7

description:
lineage_profiles_wATAC.txt
A7-TARGp9_TTAGATTCCG_S7


title: Lineage_wATAC-p9A3

description:
lineage_profiles_wATAC.txt
A3-TARGp9_GTTGACGGCC_S3


title: Lineage_wATAC-p9C10

description:
lineage_profiles_wATAC.txt
C10-TARGp9_GATACCTAAG_S34


title: Lineage_wATAC-p9A9

description:
lineage_profiles_wATAC.txt
A9-TARGp9_TCGATATTGA_S9


title: Lineage_wATAC-p9A2

description:
lineage_profiles_wATAC.txt
A2-TARGp9_CGACTACCAA_S2


title: Lineage_wATAC-p9A12

description:
lineage_profiles_wATAC.txt
A12-TARGp9_AACGGACCAA_S12


title: Lineage_wATAC-p9A10

description:
lineage_profiles_wATAC.txt
A10-TARGp9_CCAGGTCTAC_S10


title: Lineage_wATAC-p9A1

description:
lineage_profiles_wATAC.txt
A1-TARGp9_CTCGATGGAG_S1


title: Lineage_wATAC-p9A4

description:
lineage_profiles_wATAC.txt
A4-TARGp9_CTCGTCTAGG_S4


title: Lineage_wATAC-p9A11

description:
lineage_profiles_wATAC.txt
A11-TARGp9_TTGGTCATAA_S11


title: Lineage_wATAC-p7H9

description:
lineage_profiles_wATAC.txt
H9-TARGp7_GATTGCAGAC_S477


title: Lineage_wATAC-p7H8

description:
lineage_profiles_wATAC.txt
H8-TARGp7_CCTATAAGCT_S476


title: Lineage_wATAC-p7H7

description:
lineage_profiles_wATAC.txt
H7-TARGp7_AGATCCTATA_S475


title: Lineage_wATAC-p7H6

description:
lineage_profiles_wATAC.txt
H6-TARGp7_TCATCTAATC_S474


title: Lineage_wATAC-p7H4

description:
lineage_profiles_wATAC.txt
H4-TARGp7_TGCCAGATGG_S472


title: Lineage_wATAC-p7H5

description:
lineage_profiles_wATAC.txt
H5-TARGp7_AACTTATAAG_S473


title: Lineage_wATAC-p7H2

description:
lineage_profiles_wATAC.txt
H2-TARGp7_TGGCCGCAAT_S470


title: Lineage_wATAC-p7H3

description:
lineage_profiles_wATAC.txt
H3-TARGp7_CCAAGCTGAA_S471


title: Lineage_wATAC-p7H11

description:
lineage_profiles_wATAC.txt
H11-TARGp7_AAGATCCAAC_S479


title: Lineage_wATAC-p7H12

description:
lineage_profiles_wATAC.txt
H12-TARGp7_CTGCAATCGC_S480


title: Lineage_wATAC-p7H10

description:
lineage_profiles_wATAC.txt
H10-TARGp7_ATAAGAGGCG_S478


title: Lineage_wATAC-p7G8

description:
lineage_profiles_wATAC.txt
G8-TARGp7_TTGGAGTCGG_S464


title: Lineage_wATAC-p7G9

description:
lineage_profiles_wATAC.txt
G9-TARGp7_CAAGCTTGGC_S465


title: Lineage_wATAC-p7H1

description:
lineage_profiles_wATAC.txt
H1-TARGp7_TTCTACGCCA_S469


title: Lineage_wATAC-p7G4

description:
lineage_profiles_wATAC.txt
G4-TARGp7_ACGCAACTCC_S460


title: Lineage_wATAC-p7G2

description:
lineage_profiles_wATAC.txt
G2-TARGp7_GTCATTGCGC_S458


title: Lineage_wATAC-p7G6

description:
lineage_profiles_wATAC.txt
G6-TARGp7_CATTATTACC_S462


title: Lineage_wATAC-p7G7

description:
lineage_profiles_wATAC.txt
G7-TARGp7_TCTATAAGGA_S463


title: Lineage_wATAC-p7G11

description:
lineage_profiles_wATAC.txt
G11-TARGp7_TGGCGTAGGT_S467


title: Lineage_wATAC-p7G1

description:
lineage_profiles_wATAC.txt
G1-TARGp7_GACCGTAGCA_S457


title: Lineage_wATAC-p7F9

description:
lineage_profiles_wATAC.txt
F9-TARGp7_AACCTAGCTT_S453


title: Lineage_wATAC-p7G5

description:
lineage_profiles_wATAC.txt
G5-TARGp7_TGATACGAGT_S461


title: Lineage_wATAC-p7G12

description:
lineage_profiles_wATAC.txt
G12-TARGp7_ACTGAATTCC_S468


title: Lineage_wATAC-p7F7

description:
lineage_profiles_wATAC.txt
F7-TARGp7_TATAACTTCC_S451


title: Lineage_wATAC-p7F6

description:
lineage_profiles_wATAC.txt
F6-TARGp7_ACGAGGACCT_S450


title: Lineage_wATAC-p7F8

description:
lineage_profiles_wATAC.txt
F8-TARGp7_AGGATTACCA_S452


title: Lineage_wATAC-p7F5

description:
lineage_profiles_wATAC.txt
F5-TARGp7_ACGTTCAACC_S449


title: Lineage_wATAC-p7F2

description:
lineage_profiles_wATAC.txt
F2-TARGp7_CGTCCGTCCT_S446


title: Lineage_wATAC-p7F4

description:
lineage_profiles_wATAC.txt
F4-TARGp7_AACGAGGCTA_S448


title: Lineage_wATAC-p7F3

description:
lineage_profiles_wATAC.txt
F3-TARGp7_GGTCCAGGAG_S447


title: Lineage_wATAC-p7E9

description:
lineage_profiles_wATAC.txt
E9-TARGp7_TCCGTCGCCA_S441


title: Lineage_wATAC-p7F1

description:
lineage_profiles_wATAC.txt
F1-TARGp7_AACTACCGAC_S445


title: Lineage_wATAC-p7F12

description:
lineage_profiles_wATAC.txt
F12-TARGp7_CGAGCTGCCA_S456


title: Lineage_wATAC-p7F10

description:
lineage_profiles_wATAC.txt
F10-TARGp7_AGTCCGCGGA_S454


title: Lineage_wATAC-p7E8

description:
lineage_profiles_wATAC.txt
E8-TARGp7_ACCGTTACGA_S440


title: Lineage_wATAC-p7G3

description:
lineage_profiles_wATAC.txt
G3-TARGp7_CAAGATTAAG_S459


title: Lineage_wATAC-p7F11

description:
lineage_profiles_wATAC.txt
F11-TARGp7_ACTATCCGCA_S455


title: Lineage_wATAC-p7E7

description:
lineage_profiles_wATAC.txt
E7-TARGp7_TCCGGTAATC_S439


title: Lineage_wATAC-p7E5

description:
lineage_profiles_wATAC.txt
E5-TARGp7_CTCCGGTTCT_S437


title: Lineage_wATAC-p7E4

description:
lineage_profiles_wATAC.txt
E4-TARGp7_AAGCCGGCTG_S436


title: Lineage_wATAC-p7G10

description:
lineage_profiles_wATAC.txt
G10-TARGp7_ATAGGATATG_S466


title: Lineage_wATAC-p7E3

description:
lineage_profiles_wATAC.txt
E3-TARGp7_AGGTCAATTA_S435


title: Lineage_wATAC-p7E2

description:
lineage_profiles_wATAC.txt
E2-TARGp7_ACTATCTTGA_S434


title: Lineage_wATAC-p7E1

description:
lineage_profiles_wATAC.txt
E1-TARGp7_GCTCTCGCCT_S433


title: Lineage_wATAC-p7E12

description:
lineage_profiles_wATAC.txt
E12-TARGp7_ACTTCCGAAT_S444


title: Lineage_wATAC-p7D4

description:
lineage_profiles_wATAC.txt
D4-TARGp7_GACCTCCGCC_S424


title: Lineage_wATAC-p7D6

description:
lineage_profiles_wATAC.txt
D6-TARGp7_CTAACTCCAA_S426


title: Lineage_wATAC-p7E10

description:
lineage_profiles_wATAC.txt
E10-TARGp7_GGCTATGACT_S442


title: Lineage_wATAC-p7D7

description:
lineage_profiles_wATAC.txt
D7-TARGp7_ACCAAGATCT_S427


title: Lineage_wATAC-p7D9

description:
lineage_profiles_wATAC.txt
D9-TARGp7_GACCTCTCTG_S429


title: Lineage_wATAC-p7D2

description:
lineage_profiles_wATAC.txt
D2-TARGp7_CAAGTACTGG_S422


title: Lineage_wATAC-p7D3

description:
lineage_profiles_wATAC.txt
D3-TARGp7_CGGCGAGACC_S423


title: Lineage_wATAC-p7D8

description:
lineage_profiles_wATAC.txt
D8-TARGp7_CGATCATTAC_S428


title: Lineage_wATAC-p7D11

description:
lineage_profiles_wATAC.txt
D11-TARGp7_CGAGTTAGAG_S431


title: Lineage_wATAC-p7D10

description:
lineage_profiles_wATAC.txt
D10-TARGp7_GGCTAATTAA_S430


title: Lineage_wATAC-p7E11

description:
lineage_profiles_wATAC.txt
E11-TARGp7_TGGACTTGAC_S443


title: Lineage_wATAC-p7E6

description:
lineage_profiles_wATAC.txt
E6-TARGp7_CATGCATCTC_S438


title: Lineage_wATAC-p7D5

description:
lineage_profiles_wATAC.txt
D5-TARGp7_TCTAGAACTA_S425


title: Lineage_wATAC-p7C9

description:
lineage_profiles_wATAC.txt
C9-TARGp7_GCAACTGGCA_S417


title: Lineage_wATAC-p7D1

description:
lineage_profiles_wATAC.txt
D1-TARGp7_CGCCGCCTCC_S421


title: Lineage_wATAC-p7D12

description:
lineage_profiles_wATAC.txt
D12-TARGp7_GATGATCGTA_S432