title: SUB32, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: Donor4_Con_coculture

status: Public on Aug 20 2025

type: SRA

city: Cambridge

first: Fuguo

last: Liu

address: 500 Main Street

department: Koch Institute For Integrative Cancer Research at MIT

country: USA

institute: Massachusetts Institute of Technology

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the human genome with Salmon (v0.14.1) using ensembl Homo sapiens GRCh38 (release 112) transcript annotations. The resulting counts were analyzed in R (v4.3.2) using tximport (v1.30.0) and DESeq2 (v 1.42.1) for differential expression analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited files include transcripts per million (TMP) counts and read counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
RNA was isolated using verrity chemagic™ RNA isolation Kit (CMG-1212)
cDNA libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L) per the manufacturer’s instructions.

tag: tissue

value: Whole blood

tag: cell type

value: Natural killer cells


title: Donor4_#1+CAR+PDL1_resting


title: 37℃_OA (biol rep 2)

city: Shanghai

first: Yueqi

last: Zhang

address: 150 Jimo Road, Pudong New Area,Shanghai

country: China

institute: Shanghai East Hospital, School of Medicine, Tongji University

description: Library name: Sample_37_OA_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

molecule: total RNA

source_name: Cartilage (OA)

extract_protocol:
Total RNA from human non-OA and OA chondrocytes cultured at the two temperatures was extracted with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Cartilage (OA)

value: chondrocytes

tag: treatment

value: 37℃ Culture


title: SUB35, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

data_processing:
For RP, sequences of known human rRNAs, rRNA pseudogenes, tRNA pseudogenes, mitochondrial rRNAs (mtrRNAs), mitochondrial tRNAs (mt-tRNAs), mt-rRNA pseudogenes, and human tRNAs were obtained from the Ensembl database (Version 100, April 2020). In addition, known RNA sequences from GenBank (NR003285.3, NR003286.4, NR003287.4, NR023363.1) and two contaminant sequences provided by the laboratory (5’−ATGTACACGGAGTCGAGCTCAACCCGCAACGCGA−3’ and 5’ −ATGTACACGGAGTCGACCCAACGCGA−3’) were added to this sequence collection. These sequences were then used to build a Bowtie2 index of contaminant sequences. Next, 3’ and 5’ adapter sequences were trimmed from reads using Cutadapt (Version 2.10). Reads with Phred quality score of less than 20 for the majority of bases were removed using FASTQ quality filter from the FASTX Toolkit software package (Version 0.0.14). Reads that fell outside the typical length range of ribosomal footprints (25nt to 35nt) were removed. Reads were then aligned to the index of contaminant sequences using Bowtie2 (Version 2.4.1) with its local alignment option. Reads that mapped to contaminant sequences were removed, and those that did not were output to a FASTQ file for alignment to the reference genome. Reads were aligned to human reference GRCh38 using the gapped splice-aware aligner HISAT2 (Version 2.2.0). Additionally, the reads left unmapped by HISAT2 were attempted to be mapped to human reference GRCh38 in a second pass using Bowtie2 with its local alignment option. Gene expression quantification was carried out using the featureCounts function of the Subread package (Version 2.0.1). Reads that overlapped with multiple genes or mapped to multiple locations on the reference genome were excluded.
Supplementary files format and content: tab-delimited text includes raw counts of each ENSEMBL Gene ID for each Sample
Library strategy: Ribo-seq

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were removed from liquid nitrogen, placed on ice to thaw, and resuspended in 500 µl of ice-cold lysis buffer (polysome buffer (20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml CHX) plus 25 U/ml DNase I (Ambion AM2222) and 1% Triton-X-100). Lysates were kept on ice for 10 min, triturated by passing them through a 26 G needle 10 times, and then clarified by centrifugation at 20,000 g for 10 min at 4 ᵒC.
RP libraries were prepared as originally described{Ingolia, 2012 #127} with minor modifications. The main modification was a previously described re-design of the primers and adapters used for library prep so that sequencing could be done on the Ion Proton platform{Vila-Sanjurjo, 2020 #129}. We also included two rounds of rRNA-depletion and the addition of an extra rRNA-depletion oligo to the depletion pools as previously documented{Vila-Sanjurjo, 2020 #129}.
Sequencing was done on the Ion Proton (Thermo-Fisher 4474779) with Ion PIv3 200pb kits (Thermo-Fisher 4488315). Despite being bar-coded, libraries were sequenced individually using one Ion PIv2 chip (Thermo-Fisher 4482321) per sample.

value: peripheral blood mononuclear cells

tag: day


title: Donor4_#1+CAR+PDL1_coculture


title: 37℃_non_OA (biol rep 3)

description: Library name: Sample_37_CH_3

source_name: Cartilage (non-OA)

value: Cartilage (non-OA)


title: SUB11, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: Donor4_#1+CAR+SCE_coculture


title: SUB39, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: 293T_dKO-N1P2_H3K36me2

city: WASHINGTON

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th PL NW

institute: Virginia Tech

description: Library name: JY15_293T_dKO-N1P2_H3K36me2

library_source: genomic

data_processing:
Data was processed with the nf-core/chip-seq v2.1.0 pipeline, with default settings for 150bp reads.
Spike-in was performed by re-running the pipeline with dm6 genome, and dividing uniquely mapped paired hg38 reads by dm6 reads. The wild type sample’s ratio was set to 1, and mutant samples were calculated relative to the wild type. Coverage tracks were then generated using the bam_coverage function of deepTools, with the scaling factor manually set as calculated for each sample
Assembly: mm10, hg38
Supplementary files format and content: Supplementary_files_format_and_content:

molecule: genomic DNA

source_name: Kidney

growth_protocol: 37 degree and 5% CO2 in humidified incubators.

extract_protocol:
crosslinked and sheared chromatin
NEBNext Ultra II

treatment_protocol: Spiked with equal amounts Drosophila chromatin for normalization

value: Kidney

tag: cell line

value: fibroblast

tag: genotype

value: rescued with NSD1-ΔPWWP2

tag: chip antibody


title: 37℃_non_OA (biol rep 2)

description: Library name: Sample_37_CH_2


title: 37℃_non_OA (biol rep 1)

description: Library name: Sample_37_CH_1


title: 33℃_OA (biol rep 3)

description: Library name: Sample_33_OA_3

value: 33℃ Culture


title: SUB01, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: Donor4_#1+CAR_coculture


title: SUB16, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: SUB29, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: Donor4_#1+CAR_resting


title: 33℃_OA (biol rep 2)

description: Library name: Sample_33_OA_2


title: 33℃_OA (biol rep 1)

description: Library name: Sample_33_OA_1


title: SUB11, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Donor3_#1+CAR+PDL1_resting


title: 37℃_OA (biol rep 1)

description: Library name: Sample_37_OA_1


title: Donor3_Con_coculture


title: SUB05, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: 33℃_non_OA (biol rep 2)

description: Library name: Sample_33_CH_2


title: Donor3_#1+CAR+PDL1_coculture


title: SUB04, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: SUB02, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: 33℃_non_OA (biol rep 1)

description: Library name: Sample_33_CH_1


title: SUB04, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: Donor4_#1+CAR+SCE_resting


title: Donor3_#1+CAR+SCE_resting


title: SUB12, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: JPF_post_treatment_Case4

city: Beijing

first: Li

last: tao

address: 16 Dongzhimen Inner South Street, Dongcheng District, Beijin

institute: Institute of Traditional Chinese Medicine, Chinese Academy of Traditional Chinese Medicine

data_processing:
Use fastp software to clean and filter the original offline data to obtain high-quality sequences (Clean Reads)
Use Hisat2 2.1.0 software to compare Clean Reads with reference genes (the reference genome version is GRCh 38.91)
Stringtie 1.3.3b software was used to compare the results and quantify the transcriptome expression; Normalize with TMM (trimmed mean of M values) algorithm, and finally calculate count value of each gene
Differential analysis of gene expression between samples/groups using edgeR 3.30.3 software package
Assembly: GRCh 38.91
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: blood

extract_protocol:
Total RNA was extracted from human whole blood samples before and after 3 months of treatment with Jianpi Huogu Formula according to routine procedures
After the total RNA passes the quality inspection, it is further purified and reverse transcribed to obtain double stranded cDNA, which is used as a template for PCR amplification to construct a cDNA library

value: blood

tag: case


title: SUB08, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Donor3_#1+CAR+SCE_coculture


title: Donor3_#1+CAR_resting


title: SUB34, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: JPF_pre_treatment_Case4


title: JPF_post_treatment_Case3


title: Donor3_Con_resting


title: SUB33, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: SUB17, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: JPF_post_treatment_Case2


title: Donor3_#1+CAR_coculture


title: JPF_pre_treatment_Case3


title: 33℃_non_OA (biol rep 3)

description: Library name: Sample_33_CH_3


title: Donor2_Con_coculture


title: JPF_post_treatment_Case1


title: SUB26, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: JPF_pre_treatment_Case2


title: Donor2_#1+CAR+PDL1_resting


title: SUB12, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: Donor2_#1+CAR+SCE_resting


title: JPF_pre_treatment_Case1


title: Donor2_#1+CAR+SCE_coculture


title: SUB39, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: SUB08, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: NP-IL

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and GRCh38. genome.
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Exosomes

growth_protocol: 10%FBS high-glucose DMEM were used as culture medium for primary cell culture. When cells reach 80% confluent, the cell were lysed with trypsin for passage. After 2 passages, the primary cells were ready to perform exosome collection. For exosome collection, we use 1% exosome free FBS/DMEM for culture, the medium were collected at a 3-days interval for exosome collection.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
AF,NP; Proton Sequencing Protocol
AF-IL,AF-TNF,NP-IL,NP-TNF: HiSeq Sequencing Protocol

treatment_protocol: 25ng/ml IL-1β or 50ng/ml TNFα were treated to the primary AF or NP cells for AF-IL, AF-TNF, NP-IL, NP-TNF exosome collection.

tag: subject status

value: spine fracture patients who underwent discectomy

value: primary annulus fibrosis (AF)

tag: treated with

value: 25ng/ml IL-1β


title: Donor2_#1+CAR_resting


title: AF-TNF

value: primary nuclues pulposus (NP) cells

value: 50ng/ml TNFα


title: SUB05, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: AF-IL


title: Donor2_Con_resting

value: Whole blood


title: SUB07, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: RAW 264.7 cells, acoustics-on-3

city: Durham

first: Bryan

last: Pan

state: NC

address: 3 Genome Ct

institute: Duke University

description:
Library name: Sample 6
3--4_SamQuant

data_processing:
For the data analysis, the fastQ files of mouse cell RNA-seq data were trimmed and filtered using Trim Galore (v.0.6.8). Then, they were aligned to the GRCm38/mm10 mouse genome using STAR (v.2.7.11) with the following parameters: outSAMtype BAM Unsorted- quantMode TranscriptomeSAM. The transcript abundance for each sample was estimated using salmon (v.1.4.0) to quantify the transcriptome defined by Gencode vM25. Gene level counts were summed across isoforms, and genes with low counts (maximum expression < 10) were filtered out from downstream analyses. We tested genes for differential expression in DESeq2 (v.1.38.2) in R, and GO/KEGG analysis was performed using clusterProfiler (v.3.10.1) package in R. The heatmap (v.1.0.12) package produced the heatmaps of gene expressions.
Assembly: mm10
Supplementary files format and content: normalized abundance measurements

organism: Mus musculus

source_name: RAW 264.7 cells

growth_protocol: Cryopreserved RAW264.7 murine macrophage cell line was obtained from American Type Culture Collection. Cells were cultured in Dulbecco’s modified Eagle’s medium (ATCC 30-2002, for RAW264.7 cells), with 10% of fetal bovine serum (v/v) under a 5% CO2 atmosphere at 37°C. The medium was replaced on the first day and every 2 days thereafter. Cells in the third passage were used in this study.

extract_protocol:
For RNA-seq, total RNA was extracted using the RNeasy Mini Kit (Qiagen #74106) with the on-column digestion by DNase (Qiagen #79254) for 0.5 hours.
The libraries were prepared using the NEBNext rRNA Depletion Kit (NEB #E6310L) and NEB Ultra II DNA Library Prep Kit (NEB #E7103) per manufacturer's instruction.

treatment_protocol: Before cell experiments, the devices were ultrasonically cleaned with ethanol and distilled water and sterilized by UV light overnight. Next, a 250-μl droplet of suspended RAW264.7 cells (~5 × 104 cells) was added to each device. Then, the cell samples were cultured overnight in a cell incubator to allow cell attachment. After that, the devices were connected to function generators. After turning the acoustics on, each sample was treated for 48 hours. The acoustic parameters were set to a peak-to-peak voltage of 18 V and a frequency of 5 kHz. The cell samples were cultured for 48 hours without acoustics for the petri dish control and acoustics-off groups.

value: RAW 264.7 cells

value: acoustics-on


title: Donor2_#1+CAR_coculture

value: Natural killer cells


title: RAW 264.7 cells, acoustics-on-2

description:
Library name: Sample 5
3--3_SamQuant


title: SUB40, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: Donor1_#1+CAR+PDL1_resting


title: SUB13, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: Donor1_Con_coculture


title: Donor1_Con_resting


title: RAW 264.7 cells, acoustics-off-3

description:
Library name: Sample 3
1--4_SamQuant

value: acoustics-off


title: SUB28, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1

value: peripheral blood mononuclear cells


title: SUB19, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Donor1_#1+CAR+SCE_resting


title: NP-TNF


title: SUB21, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Donor2_#1+CAR+PDL1_coculture


title: SUB15, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: RAW 264.7 cells, acoustics-off-1

description:
Library name: Sample 1
1--1_SamQuant


title: SUB01, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: SUB16, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: Donor1_#1+CAR_coculture


title: Cis7d Group rep.4

city: Nanjing

first: Bingquan

last: Deng

state: Jiangsu

address: Nanjing Medical University, No.109 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

data_processing:
Using the Illumina paired-end RNA-seq approach
Paired-end clean reads were mapped to the mouse reference genome GRCm38 using Hisat (vision 2.0)
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
FastQC (Version 0.10.1) was used for evaluating the quality of sequenced data
The mRNAs at a cut-off of 10 reads were compared and considered as differentially expressed if the fold change >2 and P value <0.05
Assembly: GRCm38
Supplementary files format and content: text files included FPKM values for each Sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) from kidney samples of the 3 groups (Sham, Cis3d, Cis7d, n=3) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. cDNA libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit (NEB) following the manufacturer’s instructions, and then sequenced using the Illumina sequencing technology on an Illumina Hiseq4000 at LC Bio (Hangzhou, China) according to the recommended protocols

treatment_protocol: 3/7 days after intraperitoneal injection of 20mg/kg (body weight) cisplatin, Sham group injected with the same volume of normal saline

tag: strain

tag: Sex

value: male

tag: age

value: 8-10 weeks

value: 7 days after intraperitoneal injection of cisplatin


title: Cis7d Group rep.3

value: Kidney


title: Donor1_#1+CAR_resting


title: SUB30, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: SUB06, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: RAW 264.7 cells, acoustics-on-1

description:
Library name: Sample 4
3--2_SamQuant


title: human primary PTEC, PBS control, biol_rep6

city: Portland

first: Michael

last: Hutchens

state: OR

address: 3710 SW US Veterans Hospital Road R&D5

department: Anesthesiology, Nephrology

institute: Oregon Health & Science University

data_processing:
Libraries were sequenced on a NovaSeq 6000 (Illumina). Raw data files were converted to fastq files using bcl2fastq (Illumina).
Adapter sequences were removed using Trimmomatic (Bolger et al. 2014, Bioinformatics 30, 2114). Trimmed reads were aligned to a reference genome using STAR (Dobin et al. 2013, Bioinformatics 29, 15).
Assembly: hg38
Supplementary files format and content: tab-delimited UTF-8 txt files with 5 lines of header data. The first header line is the field list, tab delimited. The fields included are: GeneId UnstrandedCount 1stStrandCount 2ndStrandCount GeneName BioType GeneDescription

source_name: kidney

growth_protocol: Cells were prepared from research-designated donor kidneys. After FACS selection using CD10/CD13, cells were passaged once and plated in 6-well dishes.   Growth media contained  5% fetal bovine serum.

extract_protocol:
At the conclusion of 6h incubation, cells were lysed, harvested, and RNA was extracted using the Qiagen RNAEasy kit according to instructions for adherent animal cells.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA protocol (Illumina). Total RNA integrity was checked on a Bioanalyzer NanoChip (Agilent). Poly(A)+ RNA was then selected using oligo-d(T)-coated magnetic beads, followed by fragmentation using divalent cations and heat. Fragment RNA was converted to double strand cDNA using dUTP in the second strand synthesis to enforce strandedness in the final library. Indexed adapters were ligated to the cDNA and the library was then amplified by limited rounds of PCR. The final libraries were profiled on a Tapestation D1000 tape (Agilent) and quantified by real time PCR (Kapa Biosystems) on a StepOnePlus real time PCR workstation (Thermo/ABI).

treatment_protocol: After serum starvation for 24h, cells were exposed to 10nM recombinant CSRP3 (Origene #TB325217) or equivalent volume of PBS for 6h

value: kidney

value: primary culture

value: proximal tubular epithelial

value: wild type

value: PBS control for 6h


title: SUB17, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: Donor1_#1+CAR+PDL1_coculture


title: SUB35, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: human primary PTEC, PBS control, biol_rep5


title: human primary PTEC, PBS control, biol_rep4


title: RAW 264.7 cells, acoustics-off-2

description:
Library name: Sample 2
1--3_SamQuant


title: Cis7d Group rep.1


title: SUB23, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Cis3d Group rep.4

value: 3 days after intraperitoneal injection of cisplatin


title: SUB32, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: human primary PTEC, PBS control, biol_rep3


title: Cis3d Group rep.3


title: Cis3d Group rep.2


title: SUB23, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: human primary PTEC, PBS control, biol_rep1


title: human primary PTEC, PBS control, biol_rep2


title: Cis3d Group rep.1


title: Donor1_#1+CAR+SCE_coculture


title: SUB21, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: Cis7d Group rep.2


title: human primary PTEC, 10nM CSRP3, biol_rep6

value: 10nM recombinant CSRP3 for 6h


title: SUB27, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: human primary PTEC, 10nM CSRP3, biol_rep4


title: human primary PTEC, 10nM CSRP3, biol_rep3


title: Sham Group rep.2

value: Intraperitoneal injection of normal saline


title: SUB20, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: Sham Group rep.1


title: GFP negative_4

city: South San Francisco

first: Kimberle

last: Shen

state: CA

address: 1 Dna way

institute: Genentech

description:
Library name: Sample 16
Non-cH cells

data_processing:
Quality control of the sequencing data was performed using FastQC and then the QC filtered FASTQ files were obtained. Paired-end reads were mapped to the Zebrafish reference genome (GRCz11v104) using STAR based on GRCz11 annotations.
Assembly: GRCz11(v104)
Supplementary files format and content: Raw read counts

organism: Danio rerio

source_name: Brain

extract_protocol:
Transgenic lines Tg(76A:Gal4FF:UAS:GCaMP6s) and Tg(116A:Gal4FF:UAS:GFP) were used to obtain lateral and caudal hypothalamic populations respectively. Whole brains were dissected from one month old transgenic zebrafish and eight brains were pooled for each of the four biological replicates. Dissociation was carried out with a Papain Dissociation System (Worthington Biochemical Corporation) using a modified protocol described by Raj et al. (2018). GCaMP6s/GFP+ve cells were collected using FACS and total RNA was extracted from sorted cell populations using Arcturus PicoPure RNA Isolation kit (Thermo Fisher Scientific) according to the manufacturer's protocol.
cDNA libraries were prepared using 0.5 ng of total RNA using the SMARTSeq v2 protocol with the following modifications: 1. Addition of 20 µM TSO; 2. cDNA amplification of 16 cycles; 3. A total of 200 pg of cDNA was utilized with one-fifth of the standard reaction volume from the Illumina Nextera XT kit. Library fragment size distributions were assessed using the DNA High Sensitivity Reagent Kit on a Perkin Elmer Labchip system.

value: Brain


title: SUB33, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: GFP negative_1

description:
Library name: Sample 13
Non-cH cells


title: GFP negative_3

description:
Library name: Sample 15
Non-cH cells


title: human primary PTEC, 10nM CSRP3, biol_rep2


title: SUB24, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: SUB25, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: GFP negative_2

description:
Library name: Sample 14
Non-cH cells


title: SUB09, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: SUB24, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: SUB22, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: C5_1

city: Wenzhou

first: Chan

last: Chen

state: Zhejiang

address: Nanbaixiang, Ouhai District

department: Department of Geriatric Medicine

institute: The First Affiliated Hospital of Wenzhou Medical University

description: treatment(normal lung decellularized scaffold)

data_processing:
CLC Genomics Workbenchy 11.0.1
Sequence reads were trimmed for adaptor sequencellow-gualty sequence using CLC genomic benchwork (parameter- Quality imit. 0.05)
Trimmed sequence reads were mapped to GrCM38lmm10 using CLC genomic benchwork (parameters- mismath cost 2 inserion cost 3 delelion cost 3 length fraction:0.8)
Read count extraction and normalization were performed usina CLc genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung

growth_protocol: HELFs were cultured in Eagles minimum essential medium supplemented with 10% fetal calf serum (FCS), streptomycin and penicillin (both 100 U/ml) under a 5% CO2-containing humidified atmosphere at 37°C.

extract_protocol:
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol:
Prepare fibroblasts into a cell suspension with a concentration of 1×10^7 cells/ml. Add 10 ul of cell suspension onto each slice of the normal and BLM decellularized scaffold. After 30 minutes, transfer the bio-scaffold slices to individual 6-well plates, add culture medium along the walls, and culture at 37°C, 5% CO2 in a CO2 incubator for 72 hours.
The TGFβ group consists of HELFs stimulated with TGFβ1 (5 ng/ml) for 72 hours.

value: lung

value: HELFs

value: normal lung decellularized scaffold


title: GFP positive_4

description:
Library name: Sample 12
cH cells


title: SUB26, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1

value: peripheral blood mononuclear cells


title: human primary PTEC, 10nM CSRP3, biol_rep1


title: GFP positive_2

description:
Library name: Sample 10
cH cells


title: GFP positive_3

description:
Library name: Sample 11
cH cells


title: human primary PTEC, 10nM CSRP3, biol_rep5


title: C5_2


title: SUB34, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: SUB10, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: T2

description: treatment(TGFβ)

value: TGFβ


title: C2

description: control

value: untreated


title: GFP positive_1

description:
Library name: Sample 9
cH cells


title: Vaccinated, liver, replicate 4

city: Ljubljana

first: Špela

last: Malenšek

address: Hajdrihova 19

department: Department of Synthetic Biology and Immunology

country: Slovenia

institute: National Institute of Chemistry

data_processing:
RNAlysis 3.9.2: Sequence reads were trimmed for adaptor sequences using CutAdapt and aligned to mouse genome, version GRCm38/mm10, using Kallisto.
R: DESeq2 package was used for analysis of differential expression,
WebGestalt online server was used for over-representation analysis to determine non redundant gene ontology terms, describing biological processes
Assembly: GRCm38/mm10
Supplementary files format and content: normalized_counts.txt: tab-delimited file includes DESEq2 normalized counts for each sample from liver tissue.

source_name: Liver

extract_protocol:
Total RNA was extracted from the fresh murine liver using TriPure Isolation Reagent (Roche), following the manufacturer's protocol.
Azenta Life Sciences (Genewiz, Leipzig) performed sample quality control, library preparation and rRNA removal by polyA selection for mRNA species from liver tissue.

value: Liver

value: B6.129P2 Apoetm1Unc/J

value: plasmid DNA, complexed with jetPEI (pCG1-chPCSK9-tox) - intramuscular injection


title: Vaccinated, liver, replicate 3


title: F5_1

description: treatment(bleomycin-induced lung decellularized scaffold)


title: T1

description: treatment(TGFβ)


title: Sham Group rep.3

value: Kidney

value: male

value: 8-10 weeks


title: GCaMP6s negative_4

description:
Library name: Sample 8
Non-LH cells


title: SUB30, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8

data_processing:
These sequences were then used to build a Bowtie2 index of contaminant sequences. Next, 3’ and 5’ adapter sequences were trimmed from reads using Cutadapt (Version 2.10). Reads with Phred quality score of less than 20 for the majority of bases were removed using FASTQ quality filter from the FASTX Toolkit software package (Version 0.0.14). Reads were then aligned to the index of contaminant sequences using Bowtie2 (Version 2.4.1) with its local alignment option. Reads that mapped to contaminant sequences were removed, and those that did not were output to a FASTQ file for alignment to the reference genome. Reads were aligned to human reference GRCh38 using the gapped splice-aware aligner HISAT2 (Version 2.2.0). Additionally, the reads left unmapped by HISAT2 were attempted to be mapped to human reference GRCh38 in a second pass using Bowtie2 with its local alignment option. Gene expression quantification was carried out using the featureCounts function of the Subread package (Version 2.0.1). Reads that overlapped with multiple genes or mapped to multiple locations on the reference genome were excluded
Supplementary files format and content: tab-delimited text includes raw counts of each ENSEMBL Gene ID for each Sample

extract_protocol:
Total RNA was isolated using RNeasy Mini Kits (Qiagen 74104). Poly-A RNA was isolated using Oligo(dT)25 Dynabeads (Thermo, 61002) from 5µg of total RNA (assuming recoveries of 1%) previously spiked-in with ERCC Control Mixes (Thermo, 4456740).
RNA-Seq libraries were prepared from recovered mRNA using Total RNA-Seq Kits v2 (Thermo, 4479789) following the manufacturer's instructions.
Sequencing was done on the Ion Proton (Thermo-Fisher 4474779) with Ion PIv3 200pb kits (Thermo-Fisher 4488315). Despite being bar-coded, libraries were sequenced individually using one Ion PIv2 chip (Thermo-Fisher 4482321) per sample.


title: Vaccinated, liver, replicate 2


title: GCaMP6s negative_3

description:
Library name: Sample 7
Non-LH cells


title: GCaMP6s negative_2

description:
Library name: Sample 6
Non-LH cells


value: diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP)


title: A549_AFF4_1

city: Anhui

first: Xueyi

last: Feng

address: TangHe street

department: College of Life Science

institute: Anhui Medical University

description:
RNA-seq of human lung adenocarcinoma:A549 cell line AFF4 KD
DAI-006

data_processing:
Cutadapt/Tophat2/bowtie
Assembly: hg38
Supplementary files format and content: fastq

source_name: Lung

growth_protocol: A549 cells were cultured in DMEM medium (Vivocell) with 10% FBS. They were all cultured at 37 °C with 5% CO2.

extract_protocol:
Total RNA was harvested using RNA isolater Total RNA Extraction Reagent(Vazyme) . 2ug of total RNA  was used for construction of sequencing libraries.
RNA library for RNA-seq was prepared follwing manufacturer's protocols.

treatment_protocol: A549 cells are transfected with AFF4 knockdown or control virus.

value: Lung

value: Human non-small cell lung cancer cells

value: AFF4 over-expression


title: SUB27, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: F5_2

value: bleomycin-induced lung decellularized scaffold


title: GCaMP6s positive_3

description:
Library name: Sample 3
LH cells

value: Brain


title: GCaMP6s negative_1

description:
Library name: Sample 5
Non-LH cells


title: C1

description: control

value: lung

value: HELFs


title: A549_Control_1

description:
RNA-seq of human lung adenocarcinoma:A549 cell line control
DAI-001

value: WT


title: Control, liver, replicate 4

value: plasmid DNA, complexed with jetPEI (empty pCG1 vector) - intramuscular injection


title: SUB08, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8

value: peripheral blood mononuclear cells


title: Vaccinated, liver, replicate 1

value: Liver


title: Control, liver, replicate 3

value: B6.129P2 Apoetm1Unc/J


title: SUB15, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: A549_Control_rep1

description:
RNA-seq of human lung adenocarcinoma:A549 cell line control replicate
DAI-002


title: SUB39, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Control, liver, replicate 2


title: GCaMP6s positive_1

description:
Library name: Sample 1
LH cells


title: SUB19, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: E15.5 mouse metatarsal, digit 1, rep 3

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

data_processing:
concatenate reads
adapter trimming with NGmerge v0.3
Alignment to mm10 with Bowtie2 v2.3.4.1
duplicate removal with picard v2.9.0
mitochondrial read filtering with removeChrom.py
peak calling with MACS3 v3.0.3.1.1.2 -f bampe --nolambda –bdg --verbose
IDR https://github.com/nboley/idr
idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 –plot
Assembly: mm10
Supplementary files format and content: bed format; contains the coordinates of the peaks called

source_name: Metatarsal, digit I

growth_protocol: in vivo collected E15.5 mouse autopod chondrocytes

extract_protocol:
The fore- and hind limbs of three to five embryos were microdissected under a light microscope in 5% FBS/DMEM on ice. The pooled phalanges (proximal and distal for digit I, proximal, intermediate, and distal for digits III and V) and metapodials were collected separately for digits I, III, and V for both the forelimb and the hind limb. The right and left sides of each element were pooled together, resulting in a total pool of elements from 6 to 10 individual limbs. All embryos in each biological replicate were from the same litter. Samples were then sent out for 1-2 rounds of sequencing on an Illumina NovaSeq 6000 at the Harvard Bauer Core in order to obtain at least 40 million reads per sample.
ATAC-seq protocol was performed as described in Young et al., 2022.

treatment_protocol: E15.5 mouse embryos were collected from pregnant FVB/NJ females.

value: Metatarsal, digit I

value: chondrocytes

value: FVB/NJ


title: GCaMP6s positive_2

description:
Library name: Sample 2
LH cells


title: Control, liver, replicate 1


title: A549_AFF4_rep1

description:
RNA-seq of human lung adenocarcinoma:A549 cell line AFF4 KD replicate
DAI-005


title: SUB07, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: Mutant zebrafish with loss-of-function sdhb, rep3

city: Montréal

first: Martine

last: Tetreault

state: QC

address: 900 rue Saint-Denis

country: Canada

institute: CRCHUM

description: Library name: SDHB_Mut_3

data_processing:
Alignment of raw paired reads was performed using STAR in two pass mode (v2.7.11a) against the reference genome Danio rerio Ensembl version GRCz11.105.
Reads counts were obtained using featureCounts (v2.0.6)
Differential expression quantification using R version 4.3.3 and DESeq2 package (v1.42.1)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: whole fish/larvae

extract_protocol:
Total RNAs were extracted from three batches of 5 dpf sdhb-CRISPant and Cas9-control larvae (10 larvae per sample).
The NEBNext Ultra II directional RNA library prep kit for Illumina (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare mRNA sequencing libraries, according to manufacturer’s instruction.

value: whole fish/larvae

value: sdhb-CRISPant

tag: developmental stage

value: larvae


title: Mutant zebrafish with loss-of-function sdhb, rep2

description: Library name: SDHB_Mut_2


title: SUB33, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: GCaMP6s positive_4

description:
Library name: Sample 4
LH cells


title: E15.5 mouse metatarsal, digit 3, rep 3

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: PC9_AFF4

city: Hefei

first: qian

last: dai

state: Anhui

address: Tanghe Road, Yaohai District

data_processing:
*library strategy: CUT&Tag
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
10e5 A549 or PC9 cells were collected and bound to ConA beads for 10 min at 25°C before incubating with 1 μg primary antibody at 4 °C overnight. Secondary antibody was added and incubated for 1 h at 25 °C the next day.
Adding 0.04 μM pA/G–Tnp for 1 h at 25 °C to cut the genome and add a special adaptor sequence to build a library. Proteinase K, buffer LB and DNA extract beads were used to stop the reaction. After cells were combine with magnet, wash twice with 80% ethanol then eluting DNA with double-distilled water. Last, constructing the library and sequence.

value: Lung

value: Lung adenocarcinoma


title: A549_AFF4


title: E15.5 mouse foot phalanges, digit 5, rep 3

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: Mutant zebrafish with loss-of-function sdhb, rep1

description: Library name: SDHB_Mut_1


title: Liver, Resolved, Patient14-BX4, GEX

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

institute: Cincinnati Children's Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing and FASTQ generation using CellRanger version 6.0.0
Generate single-cell expression matrix using CellRanger version 6.0.0
Process BCR and TCR data using CellRanger version 6.0.0
Quality control and filtering using R 4.3.2
Create Seurat objects using Seurat version 5.0.1
Normalization using SCTransform version 0.4.1
Sample integration, clustering, and sub-clustering using Seurat version 5.0.1
Predict cell-cell interactions using CellPhoneDB and Seurat version 5.0.1
Assembly: NCBI Genome assembly GRCh38
Supplementary files format and content: Cell Ranger output files for GEX samples: tab-separated barcodes.tsv.gz, features.tsv.gz, and matrix.tsv.gz
Supplementary files format and content: Cell Ranger output files for BCR and TCR samples: comma-separated clonotypes.csv and filtered_contig_annotations.csv

extract_protocol:
Liver core biopsies were thawed, minced into 1-2mm pieces with a sharp scissors, and gently digested at 4C in RPMI+10% FBS containing 100mg/mL soy trypsin inhibitor (Roche, cat #10109886001), 250U DNase I (Roche, cat #4536282001), 5mM CaCl2, 25ug/mL collagenase A from clostridium histolyticum (Roche, cat #10103586001), and 25ug/mL collagenase type IV from clostridium histolyticum (Worthington, LS004186). Digestion was performed for 3min on ice with intermittent inversion and gentle pipetting with wide-bore pipet tips. The cell suspension was filtered via a pre-primed 30mm cell strainer, then centrifuged at 300g for 5 min at 4C. Trypan blue exclusion was used to determine cell viability and concentration. Cells were resuspended at 1,000cell/mL per the 10x Genomics Chromium protocol and immediately prepared for single-cell barcoding.
Samples were processed for single-cell sequencing following the Chromium Next GEM Single Cell V(D)J Reagent Kit, version 1.1 or 1.2 protocols. Briefly, cells were uniquely barcoded by using 10x fluidics (10x Genomics Single Cell Controller) to combine each individual cell with an individual barcoded Single Cell 5’ Gel Bead creating a Gel Beads-in-Emulsion (GEMs) solution (10x Genomics, PN-1000165 and PN-1000120). An average of 17,400 cells were loaded to achieve an estimated recovery of 10,000 cells per biopsy. GEM gel beads were dissolved and cDNA was synthesized from the resulting tagged mRNA transcripts over 14 amplification cycles; 50ng of cDNA was used for the construction of each library.

treatment_protocol: Baseline immunosuppression and rejection treatment meta data columns describe treatments the patients received prior to the biospy. No treatments were applied after sample collection. Abbreviations: ATG: anti-thymocyte globulin, MMF: mycophenolate mofetil, TAC: tacrolimus, RAPA: rapamycin.

tag: library type

value: mRNA

tag: baseline immunosuppression

tag: rejection treatment

value: TAC+steroids+RAPA


title: SUB24, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1

tag: tissue


title: Liver, Resolved, Patient14-BX4, BCR

description: 10x Genomics


title: E15.5 mouse foot phalanges, digit 3, rep 3

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III

tag: cell type


title: SUB36, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1

tag: treatment


title: SUB09, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8

tag: day


title: E15.5 mouse metatarsal, digit 5, rep 3

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: Zebrafish control, rep3

description: Library name: SDHB_Ctl_3

value: WT


title: E15.5 mouse foot phalanges, digit 1, rep 3

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: Liver, Late ACR, Patient14-BX1, BCR

description: 10x Genomics

value: Liver

value: TAC+steroids+RAPA+ATG


title: E15.5 mouse metacarpal, digit 5, rep 3

source_name: Metacarpal, digit V

value: Metacarpal, digit V

value: chondrocytes


title: SUB35, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1

source_name: peripheral blood mononuclear cells

value: peripheral blood mononuclear cells


title: Zebrafish control, rep2

description: Library name: SDHB_Ctl_2

value: whole fish/larvae


title: Liver, Resolved, Patient14-BX4, TCR

description: 10x Genomics


title: Zebrafish control, rep1

description: Library name: SDHB_Ctl_1

value: larvae


title: E15.5 mouse metacarpal, digit 3, rep 3

source_name: Metacarpal, digit III

value: Metacarpal, digit III

value: FVB/NJ


title: Liver, Late ACR, Patient14-BX1, TCR

description: 10x Genomics


title: SUB22, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: Liver, Late ACR, Patient14-BX1, GEX

description: 10x Genomics


title: E15.5 mouse metacarpal, digit 1, rep 3

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: C5_Boscalite_5

city: East Lansing

first: Karilyn

middle: E

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

data_processing:
Imported into Galaxy, FastQC used for read quality assessment. They were sequenced over two lanes, and therefore have 4 files per sample.
Cutadapt used for trimming: settings for paired-end reads, a minimum filter length of 20 and a quality cutoff of 20
Alignment and annotation using Spliced Transcripts Alignment to a Reference (STAR) software, Read counts from the featureCounts software
DEseq2 used to assess differential expression
Lrpath's RNA-Enrich function was used for pathway analysis (KEGG)
Assembly: Genome build and transcription annotation files were obtained from the Lawson Lab, Umass Medical School (v. 4.3.2) - https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/
Supplementary files format and content: Two processed data .csv files are included with the RPKM for all samples, annotated to the Lawson Lab transcript ID (publicly available at https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/)
Supplementary files format and content: Two processed data .csv files are included with the DEseq2 outputs, annotated with Lawson Lab transcript ID, gene symbol, and Entrez gene ID. Also included are log2 fold change, mean normalized reads, and p-values.

source_name: Whole eleutherolarvae

extract_protocol:
RNA was isolated using the Thermo GeneJet RNA Extraction kit, following manufacturer instructions. RNA was stored at -80°C until library preparation and sequencing.
Library preparation and sequencing were performed at the UCSD Institute for Genomic Medicine Genomics Center. Stranded libraries were prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit per manufacturer instructions.
bulk RNA-sequencing, PE100, 25M reads per sample, Illumina NovaSeq 6000 platform

treatment_protocol: RNA was isolated from 96 hpf embryos exposed to boscalid or M510F01.

value: Whole eleutherolarvae

value: AB (wild-type)

value: 96 hours post fertilization (hpf)

tag: concentration


title: SUB20, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: E15.5 mouse hand phalanges, digit 5, rep 3

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V

tag: genotype


title: Liver, Resolved, Patient13-BX2, TCR

description: 10x Genomics

value: mRNA


title: Liver, Resolved, Patient13-BX2, BCR

description: 10x Genomics


title: C4_Boscalite_4


title: C3_Boscalite_3


title: SUB10, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Liver, Resolved, Patient13-BX2, GEX

description: 10x Genomics


title: E15.5 mouse hand phalanges, digit 1, rep 3

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: C2_Boscalite_2


title: SUB04, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: E15.5 mouse hand phalanges, digit 3, rep 3

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: SUB03, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: SUB28, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: C1_Boscalite_1


title: E15.5 mouse metatarsal, digit 5, rep 2

value: Metatarsal, digit V


title: B5_Boscalid_5


title: Liver, Late ACR, Patient13-BX1, BCR

description: 10x Genomics

source_name: Liver

value: Liver

value: TAC

value: TAC+steroids


title: Liver, Late ACR, Patient13-BX1, TCR

description: 10x Genomics


title: SUB14, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1

value: peripheral blood mononuclear cells


title: E15.5 mouse metatarsal, digit 1, rep 2

value: Metatarsal, digit I

value: chondrocytes


title: Liver, Resolved, Patient12-BX5, BCR

description: 10x Genomics

value: TAC+MMF


title: Liver, Late ACR, Patient13-BX1, GEX

description: 10x Genomics


title: B4_Boscalid_4


title: B3_Boscalid_3


title: E15.5 mouse metatarsal, digit 3, rep 2

value: Metatarsal, digit III

value: FVB/NJ


title: E15.5 mouse foot phalanges, digit 5, rep 2

value: Foot phalanges, digit V


title: B2_Boscalid_2

value: Whole eleutherolarvae

value: AB (wild-type)


title: E15.5 mouse foot phalanges, digit 3, rep 2

value: Foot phalanges, digit III


title: Liver, Resolved, Patient12-BX5, GEX

description: 10x Genomics

value: mRNA


title: SUB29, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: E15.5 mouse foot phalanges, digit 1, rep 2

value: Foot phalanges, digit I


title: B1_Boscalid_1

value: 96 hours post fertilization (hpf)


title: SUB19, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: Liver, Resolved, Patient12-BX4, BCR

description: 10x Genomics


title: SUB18, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: E15.5 mouse metacarpal, digit 5, rep 2

value: Metacarpal, digit V


title: Liver, Resolved, Patient12-BX4, TCR

description: 10x Genomics

value: Liver


title: SUB23, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: E15.5 mouse metacarpal, digit 3, rep 2

value: Metacarpal, digit III


title: A2_DMSO_2

value: dimethyl sulfoxide (DMSO) (CAS#:67-68-5)

value: 0.01% v/v (vehicle control)


title: A3_DMSO_3


title: Liver, Resolved, Patient12-BX4, GEX

description: 10x Genomics


title: SUB35, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8

value: peripheral blood mononuclear cells


title: SUB11, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Liver, Resolved, Patient12-BX5, TCR

description: 10x Genomics


title: E15.5 mouse metacarpal, digit 1, rep 2

value: Metacarpal, digit I

value: chondrocytes


title: Liver, Resolved, Patient12-BX3, BCR

description: 10x Genomics

value: TAC+MMF


title: EW8 cells, TOP1 KD, 72h, RepB

city: bethesda

first: Jack

last: Shern

address: 10 Center drive

institute: NCI

description:
Library name: Sample 29
36_cl_19_72h_B

data_processing:
Illumina Casava1.7 software used for basecalling.
Use CCBR RENEE pipeline to analyze the sequenced reads
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

growth_protocol: Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

extract_protocol:
RNA was extracted using RNeasy Plus mini kit (Qiagen).
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep

treatment_protocol: Treated with 40nM GNF-7 for 0, 4, 8, 16, 24, 48, or 72 hours

tag: cell line

value: Human Ewing sarcoma


title: Liver, Resolved, Patient12-BX3, TCR

description: 10x Genomics


title: SUB37, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1

first: Johannes

last: Goll

address: 401 N Washington St


title: A1_DMSO_1


title: SUB26, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: SUB05, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: EW8 cells, TOP1 KD, 72h, RepA

description:
Library name: Sample 28
22_cl_19_72h_A


title: E15.5 mouse hand phalanges, digit 1, rep 2

city: Cambridge

value: Hand phalanges, digit I

value: FVB/NJ


title: EW8 cells, TOP1 KD, 48h, RepB

description:
Library name: Sample 27
35_cl_19_48h_B


title: Liver, Late ACR, Patient12-BX2, BCR

description: 10x Genomics

value: TAC+steroids+ATG


title: SUB34, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: E15.5 mouse hand phalanges, digit 5, rep 2

value: Hand phalanges, digit V


title: A4_DMSO_4

value: Whole eleutherolarvae

value: AB (wild-type)


title: E15.5 mouse metatarsal, digit 5, rep 1

value: Metatarsal, digit V


title: Liver, Resolved, Patient12-BX3, GEX

description: 10x Genomics

value: mRNA


title: SUB07, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: E15.5 mouse hand phalanges, digit 3, rep 2

value: Hand phalanges, digit III


title: EW8 cells, TOP1 KD, 48h, RepA

description:
Library name: Sample 26
21_cl_19_48h_A


title: Liver, Late ACR, Patient12-BX2, TCR

description: 10x Genomics

value: Liver


title: E15.5 mouse metatarsal, digit 3, rep 1

value: Metatarsal, digit III


title: SUB26, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: SUB05, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: Liver, Late ACR, Patient12-BX2, GEX

description: 10x Genomics


title: E15.5 mouse metatarsal, digit 1, rep 1

value: Metatarsal, digit I


title: EW8 cells, TOP1 KD, 24h, RepB

description:
Library name: Sample 25
34_cl_19_24h_B


title: EW8 cells, TOP1 KD, 24h, RepA

description:
Library name: Sample 24
20_cl_19_24h_A


title: Liver, Late ACR, Patient12-BX1, BCR

description: 10x Genomics

value: TAC

value: TAC+steroids


title: E15.5 mouse foot phalanges, digit 5, rep 1

value: Foot phalanges, digit V

value: chondrocytes


title: SUB32, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1

value: peripheral blood mononuclear cells


title: SUB21, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: E15.5 mouse foot phalanges, digit 3, rep 1

value: Foot phalanges, digit III


title: Liver, Late ACR, Patient12-BX1, TCR

description: 10x Genomics


title: EW8 cells, TOP1 KD, 16h, RepA

description:
Library name: Sample 22
19_cl_19_16h_A

value: Human Ewing sarcoma


title: EW8 cells, TOP1 KD, 16h, RepB

description:
Library name: Sample 23
33_cl_19_16h_B


title: Liver, Late ACR, Patient12-BX1, GEX

description: 10x Genomics


title: Liver, Late ACR, Patient11-BX3, BCR

description: 10x Genomics

value: TAC+steroids+ATG


title: SUB01, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: SUB17, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: SUB28, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: E15.5 mouse metacarpal, digit 5, rep 1

value: Metacarpal, digit V

value: FVB/NJ


title: Liver, Late ACR, Patient11-BX3, TCR

description: 10x Genomics


title: EW8 cells, TOP1 KD, 8h, RepB

description:
Library name: Sample 21
32_cl_19_8h_B


title: EW8 cells, TOP1 KD, 8h, RepA

description:
Library name: Sample 20
18_cl_19_8h_A


title: E15.5 mouse metacarpal, digit 3, rep 1

value: Metacarpal, digit III


title: Liver, Late ACR, Patient11-BX2, BCR

description: 10x Genomics


title: SUB25, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: SUB01, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: E15.5 mouse metacarpal, digit 1, rep 1

value: Metacarpal, digit I


title: E15.5 mouse hand phalanges, digit 5, rep 1

value: Hand phalanges, digit V


title: EW8 cells, TOP1 KD, 0h, RepC

description:
Library name: Sample 17
30_cl_19_0h_B


title: EW8 cells, TOP1 KD, 4h, RepA

description:
Library name: Sample 18
17_cl_19_4h_A


title: SUB24, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: E15.5 mouse foot phalanges, digit 1, rep 1

value: Foot phalanges, digit I


title: Liver, Late ACR, Patient11-BX2, TCR

description: 10x Genomics

value: Liver

value: mRNA


title: E15.5 mouse hand phalanges, digit 3, rep 1

value: Hand phalanges, digit III


title: EW8 cells, TOP1 KD, 0h, RepA

description:
Library name: Sample 15
16_cl_19_0h_A


title: EW8 cells, TOP1 KD, 0h, RepB

description:
Library name: Sample 16
21_EW8_sgTop1_6_Cl_19


title: SUB37, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: E15.5 mouse hand phalanges, digit 1, rep 1

value: Hand phalanges, digit I


title: KPC-shV, scRNAseq

city: Peking

first: Mingyang

last: Liu

address: No.17, Panjiayuan South, Chaoyang District

institute: State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

description: 10X Genomics

data_processing:
Fastq files were processed with Cell Ranger (v 7.0.1), using default parameters
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreas

extract_protocol:
Freshly harvested orthotopic allograft tumor tissues from mice (KPC-shV, n=1; KPC-shZEB1, n=1) were sectioned into 2–4 mm³ segments and temporarily stored in tissue preservation solution (MACS, 130-100-008) at 4°C to ensure simultaneous tissue dissociation and sequencing of all samples. The tissues were carefully washed twice with pre-cooled medium (DMEM supplemented with 0.04% BSA) and thoroughly minced into small pieces. Tissue fragments were then digested at 37°C and 22 rpm for approximately 30 min in an enzyme solution containing DMEM, 0.04% BSA, 0.2% collagenase II (Gibco), and 100 μg/L DNase I (Applichem). Additionally, 0.25% trypsin (Gibco) was added for further digestion for 5 min. The resulting cell suspension was filtered through a 40 μm cell strainer, followed by centrifugation at 300 × g for 7 min at 4°C. MACS Red Cell Lysis Solution (130-094-183) was applied to lyse erythrocytes. Cell pellet after washing with medium was resuspended in 200μL PBS with 1% BSA. The Luna Fluorometer (Logos Biosystems) was used to confirmed the number of viable cells, and the cell suspension concentration was then adjusted to 700-1200 cells/μL.
According to the user manual (CG00315) for the 10x Genomics Chromium Next GEM Single Cell 3ʹ Kit v3.1 (1000268), the single cell suspension was immediately loaded onto a chip to generate GEMs (Gel Bead-in-Emulsion) droplets using the 10x Chromium Controller. Reverse transcription, cDNA amplification, and DNA library construction were performed sequentially according to the protocol. The concentration and fragment size of the libraries were measured using the Invitrogen Qubit 4.0 and Agilent 4150 TapeStation. High-throughput sequencing was conducted using high-throughput paired-end 150 bp (PE-150) mode.

value: pancreas

tag: tissue type

value: orthotopic allograft tumor tissue

value: orthotopic mouse model

value: injected with KPC-shV cells


title: EW8 cells, TOP1 KD, 4h, RepB

description:
Library name: Sample 19
31_cl_19_4h_B


title: Liver, Late ACR, Patient11-BX1, BCR

description: 10x Genomics

value: TAC

value: TAC+steroids


title: EW8 cells, WT, 72h, RepA

description:
Library name: Sample 13
15_EW8_72h_A

value: Human Ewing sarcoma


title: Liver, Late ACR, Patient11-BX3, GEX

description: 10x Genomics

value: TAC+steroids+ATG


title: Liver, Late ACR, Patient11-BX1, TCR

description: 10x Genomics


title: KPC-shZEB1, scRNAseq

description: 10X Genomics

value: injected with KPC-shZEB1 cells


title: EW8 cells, WT, 72h, RepB

description:
Library name: Sample 14
29_EW8_72h_B


title: Liver, Late ACR, Patient10-BX1, BCR

description: 10x Genomics


title: SUB29, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2

city: Rockville

institute: The Emmes Company

value: peripheral blood mononuclear cells


title: KPC-shV, spatial transcriptomics

description: 10X Genomics

data_processing:
library strategy: spatial transcriptomic
Fastq files were processed with Space Ranger software (version 2.0.1), using default parameters
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Freshly harvested mouse tumor tissues (KPC-shV, n=2; KPC-shZEB1, n=2) were sectioned into appropriately sized fragments, embedded in OCT, and rapidly frozen in liquid nitrogen. Tissue blocks were then subjected to methanol fixation, followed by Hematoxylin & Eosin (H & E) staining, imaging, and destaining, according to the experimental protocol recommended by 10x Genomics (Pleasanton, CA, USA). Subsequently, tissue sections were mounted onto a 10x Visium CytAssist Spatial Gene Expression Slide. This slide contains two capture areas, each measuring 6.5 x 6.5 mm, with approximately 5,000 barcoded spots per area, designed for mRNA capture via oligonucleotides. Following the guidelines from 10x Genomics, probe hybridization and release were performed, and then the probes were transferred to the Visium CytAssist slide.
Library construction was subsequently carried out using the Visium CytAssist Spatial Gene Expression for FFPE kit (PN-1000521). The DNA libraries were sequenced using the PE-150 mode.


title: EW8 cells, WT, 48h, RepB

description:
Library name: Sample 12
28_EW8_48h_B


title: SUB20, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: Liver, Late ACR, Patient10-BX1, TCR

description: 10x Genomics


title: SUB03, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: SUB12, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: KPC-shZEB1, spatial transcriptomics

description: 10X Genomics


title: MPP3-4_KO_RNA-seq_rep4

city: St. Louis

first: Jeffrey

middle: J

last: Bednarski

state: Missouri

address: 660 S. Euclid Ave.

department: Pediatrics

institute: Washington University School of Medicine

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
Alignment with STAR version 2.5.1a to Ensembl release 76 primary assembly
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: GRCm38.76/mm10
Supplementary files format and content: tsv file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM and CPM values for each sample

source_name: E17.5 fetal liver

extract_protocol:
1000-2000 HSCs and MPP3/4s were sorted directly into RLT+ buffer (Qiagen RNeasy kit). RNA was extracted using RNeasy Micro kit (Qiagen #74004).
cDNA amplification and library prep were conducted by Washington University Genome Technology Access Center using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. Briefly, Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: E17.5 fetal liver

value: KO


title: EW8 cells, WT, 48h, RepA

description:
Library name: Sample 11
14_EW8_48h_A


title: EW8 cells, WT, 24h, RepA

description:
Library name: Sample 9
13_EW8_24h_A


title: Liver, Late ACR, Patient11-BX1, GEX

description: 10x Genomics


title: MPP3-4_KO_RNA-seq_rep2


title: Liver, Late ACR, Patient10-BX1, GEX

description: 10x Genomics


title: SUB27, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: SUB30, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: SUB06, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: EW8 cells, WT, 16h, RepA

description:
Library name: Sample 7
12_EW8_16h_A


title: SUB02, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: EW8 cells, WT, 16h, RepB

description:
Library name: Sample 8
26_EW8_16h_B


title: Liver, Late ACR, Patient9-BX1, BCR

description: 10x Genomics


title: SUB14, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: Liver, Late ACR, Patient8-BX2, BCR

description: 10x Genomics

value: TAC+MMF


title: EW8 cells, WT, 24h, RepB

description:
Library name: Sample 10
27_EW8_24h_B


title: MPP3-4_KO_RNA-seq_rep1


title: Liver, Late ACR, Patient9-BX1, GEX

description: 10x Genomics

value: Liver


title: SUB12, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: EW8 cells, WT, 8h, RepB

description:
Library name: Sample 6
25_EW8_8h_B


title: EW8 cells, WT, 8h, RepA

description:
Library name: Sample 5
11_EW8_8h_A


title: Liver, Late ACR, Patient8-BX2, TCR

description: 10x Genomics

value: mRNA


title: MPP3-4_WT_RNA-seq_rep2

value: WT


title: MPP3-4_KO_RNA-seq_rep3


title: Liver, Late ACR, Patient8-BX2, GEX

description: 10x Genomics


title: SUB23, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: Liver, Late ACR, Patient9-BX1, TCR

description: 10x Genomics


title: EW8 cells, WT, 4h RepB

description:
Library name: Sample 4
24_EW8_4h_B


title: MPP3-4_WT_RNA-seq_rep1


title: SUB15, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: Liver, Late ACR, Patient7-BX4, BCR

description: 10x Genomics


title: HSC_KO_RNA-seq_rep3

value: HSC


title: SUB39, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: MPP3-4_WT_RNA-seq_rep4


title: Liver, Late ACR, Patient7-BX4, TCR

description: 10x Genomics


title: SUB36, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: Liver, Late ACR, Patient7-BX4, GEX

description: 10x Genomics


title: EW8 cells, WT, 0h, RepB

description:
Library name: Sample 2
23_EW8_0h_B


title: MPP3-4_WT_RNA-seq_rep3


title: EW8 cells, WT, 0h, RepA

description:
Library name: Sample 1
20_EW8


title: HSC_KO_RNA-seq_rep1


title: SUB34, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: HSC_KO_RNA-seq_rep2


title: NP31 Rep2

city: Cleveland

first: Katreya

last: Lovrenert

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

description: Library name: AH762 NP31 replica 2 ATAC-Seq

data_processing:
Libraries were processed using the ENCODE‐DCC/atac‐seq‐pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline)
Assembly: Oviari4 for all sheep gall bladder epithelial cell libraries, hg19 for all other libraries
Supplementary files format and content: bigWig

growth_protocol: Cell lines were grown by standard protocols as per ATCC. Cholangiocyte organoids were grown as per https://pubmed.ncbi.nlm.nih.gov/34764255/ ; Sweat gland duct cells were grown as per https://pubmed.ncbi.nlm.nih.gov/38969603/

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were constructed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exceptions: Final libraries were purified with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transpostion.

value: Human pancreatic cell line


title: SUB38, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: HSC_WT_RNA-seq_rep4


title: Liver, Late ACR, Patient7-BX3, TCR

description: 10x Genomics

value: TAC+steroids+RAPA


title: HSC_WT_RNA-seq_rep3


title: NP31 Rep1

description: Library name: AH753 NP31 replica 1 ATAC-Seq


title: Liver, Late ACR, Patient7-BX3, BCR

description: 10x Genomics


title: Capan1 Rep2

description: Library name: AH773 Capan1 replica 2 ATAC-Seq


title: Liver, Late ACR, Patient7-BX3, GEX

description: 10x Genomics


title: EW8 cells, WT, 4h, RepA

description:
Library name: Sample 3
10_EW8_4h_A


title: SUB38, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Capan1 Rep1

description: Library name: AH772 Capan1 replica 1 ATAC-Seq


title: HSC_WT_RNA-seq_rep1


title: SUB32, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: E17-5_LSK_KO_ADT

description:
17KO_ADT
17K_barcodes.tsv.gz
17K_features.tsv.gz
17K_matrix.mtx.gz

library_source: other

data_processing:
The Cell Ranger v4.0.6 pipeline (10x Genomics) was used to process data and align the sequencing reads to mm10 reference genome.
Expression of antibody directed tags was calculated for each cell in Seurat.
Cells were clustered and cell types were assigned using ICGS2.
Differential expression analyses were performed by combining cells from pseudoreplicates (n = 4 per sample) to generate pseudobulk samples for each cluster using Presto.
Pseudobulk samples were compared using DESeq and GSEA.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output file: feature_reference.csv.
Library strategy: CITE-seq

molecule: protein

extract_protocol:
E17.5 fetal livers were harvested and genotyped before 10 embryos/genotype were pooled. Cells were bead enriched for c-Kit+ cells before surface staining. 1-2 million cells/50µl were stained with fluorophore-conjugated and barcoded Totalseq-B (Biolegend) for 30 minutes at 4°C. 20,000 LSK cells were double sorted (yield, then purity setting) on a BD FACSAriaII into PBS with 0.04% BSA. Cells were counted and resuspended in PBS with 0.04% BSA at a concentration of 1,200 cells/µl. 10,000 cells were loaded into a 10x Chromium Controller. 10x Genomics Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) Kit with Feature Barcoding (PN-1000269), Dual Index NT Set A, and Dual Index TT Set A were used to further process samples according to manufacturer’s instructions.
10x Genomics Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) Kit with Feature Barcoding (PN-1000269), Dual Index NT Set A, and Dual Index TT Set A were used to further process samples according to manufacturer’s instructions.

value: LSK (Lineage- Sca1+ c-Kit+)

value: ADT


title: Liver, No ACR, Patient7-BX2, TCR

description: 10x Genomics

value: TAC


title: BxPC3 Rep1

description: Library name: AH788 BxPC3 replica 1 ATAC-Seq


title: Liver, No ACR, Patient7-BX2, GEX

description: 10x Genomics


title: E17-5_LSK_KO_GEX

description:
17KO_mRNA
17K_barcodes.tsv.gz
17K_features.tsv.gz
17K_matrix.mtx.gz


title: SUB25, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: SUB09, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Liver, Late ACR, Patient6-BX5, BCR

description: 10x Genomics

value: TAC+steroids+MMF


title: SUB33, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: D28_1_D1

city: Leiden

first: Valeria

last: Orlova

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

description:
hiPSC_derived_PMEC_day6_batch6
RPKM_normalized_CMEC_PMEC_bulk.csv

data_processing:
For scRNA-seq: Single-cell expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
For bulk RNA seq: LUMC BIOPET Gentrap pipeline was used to process raw data (https://github.com/biopet/biopet). Trimming of low-quality read ends was done with Sickle (v1.2). Cutadapt (v1.1) was used for adapters clipping. Using GSNAP (gmap-2014-12-23) reads were aligned to the human reference genome GRCh38. Gene read quantification was done with with htseq-count (v0.6.1p1) against the Ensembl v87 annotation. The R package cqn (v1.24.0) was used to normalize gene length and GC content bias.
Genome_build: GRch38
Supplementary_files_format_and_content: Cell Ranger-generated files for scRNA-seq samples:  barcodes.tsv, genes.tsv, matrix.mtx.  RPKM_normalized_CMEC_PMEC_bulk.csv for bulkRNA-seq samples: RPKM normalized based on gene length and GC content.

source_name: hiPSCs

growth_protocol: CMEC differentiation was performed as follow: Briefly, 25 × 10e3 cells per cm2 were seeded on plates coated with 75 µg/ml matrigel growth factor reduced (Corning) the day before differentiation (day -1). At day 0, cardiac mesoderm was induced by changing E8 to BPEL medium (Bovine Serum Albumin [BSA] Polyvinyl alcohol Essential Lipids; 5, supplemented with a mixture of cytokines (20 ng/ml BMP4, R&D Systems; 20 ng/ml ACTIVIN A, Miltenyi Biotec; 1.5 μM GSK3 inhibitor CHIR99021, Axon Medchem). After 3 days, cytokines were removed and a Wnt inhibitor (5 μM XAV939, Tocris) and VEGF (50 ng/ml, R&D Systems) was added for 3 days. BPEL medium was refreshed every 3 days. PMEC differentiation was performed as follow: hiPSCs were split with a 1:12 ratio and seeded on 6-well plates coated with 75 µg/mL (growth factor reduced) Matrigel (Corning) on day -1. At day 0, paraxial mesoderm was induced by changing TeSR-E8 to BPEL medium, supplemented with 8 µM CHIR99021 (Axon Medchem). At day 2, cells were refreshed with BPEL supplemented 5 µM XAV939 (Tocris Bioscience). At day 3, cells were refreshed with BPEL supplemented 8 µM CHIR99021. From day 5 onwards, cells were refreshed every 3 days with BPEL medium supplemented with 50 ng/ml VEGF.

extract_protocol:
MTs were incubated in 290 U/mg of pre-warmed collagenase type II (Worthington) in HBSS solution (Sigma Aldrich). Single cells were used for single-cell RNAseq. Total RNA for bulk samples was purified using the NucleoSpin RNA Kit  (Bioke’) according to the manufacturer’s protocol.
10X library: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 2 Chemistry (10x Genomics) according to the manufacturer's protocol. For bulk RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Prior to microtissue (MT) formation, hiPSC-ECs and hiPSC-CFs were prepared as follow: briefly, 2-3 days before MT formation, a vial of cryopreserved hiPSC-ECs and a vial of cryopreserved hiPSC-CFs were thawed and cultured either in BPEL medium supplemented with VEGF on plates coated with fibronectin (hiPSC-ECs), or in FGM3 medium on uncoated plates (hiPSC-CFs). The day of MT formation (day 0), hiPSC-ECs, hiPSC-CFs, SFs, ACFs, Cx43-sh-RNA CFs, SFs Empty LV and SFs CX43 LV were detached using TrypLE 1X for 5 min at 37 oC, 5% CO2, centrifuged for 3 min at 1100 rpm, resuspended in BPEL medium and counted. hiPSC-CMs at day 14-21 that showed > 80% purity, measured as the percentage of troponin positive cells by FACS analysis, were dissociated using the Multi Tissue Dissociation Kit 3 (Miltenyi Biotec) following the manufacturer’s instructions, resuspended in BPEL medium and counted. For MT, cell suspensions were combined together to 5000 cells (70% cardiomyocytes, 15% endothelial cells and 15% cardiac fibroblasts) per 50μl BPEL medium supplemented with VEGF (50 ng/ml) and FGF2 (5 ng/ml).  For all microtissues, cell suspensions were seeded on V-bottom 96 well microplates (Greiner bio-one) and centrifuged for 10 min at 1100 rpm. MTs were incubated at 37 oC, 5% CO2 for 21 days with media refreshed every 3-4 days. Dibutyryl cAMP (dbcAMP) treatment was performed on CMECFs in BPEL medium supplemented with 0.5 mM dbcAMP for 7 days (from day 14 to day 21). scRNAseq analysis of all MTs was performed after 21 days.

value: hiPSC-derived PMEC

tag: time

value: differentiation day6

tag: batch


title: SUB21, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: D28_1_D11

description:
hiPSC_derived_PMEC_day8_batch6
RPKM_normalized_CMEC_PMEC_bulk.csv

value: differentiation day8


title: D28_1_C1

description:
hiPSC_derived_CMEC_day6_batch6
RPKM_normalized_CMEC_PMEC_bulk.csv

value: hiPSC-derived CMEC


title: Liver, Late ACR, Patient6-BX5, GEX

description: 10x Genomics


title: E17-5_LSK_WT_GEX

description:
17WT_mRNA
17W_barcodes.tsv.gz
17W_features.tsv.gz
17W_matrix.mtx.gz

value: E17.5 fetal liver


title: HSC_WT_RNA-seq_rep2


title: N283_Control_Heme

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

address: 1 Hoppin St., Coro West, 5th Fl., Suite 5.36

department: Division of Hematology/Oncology, Department of Medicine

institute: Warren Alpert Medical School of Brown University and Rhode Island Hospital

data_processing:
Adapter and quality read trimming was performed using Skewer (version 0.2.1) and alignments were performed using Star Aligner (v2.7.3a) against the murine primary assembly transcriptome (GRCm39 v110). Counts tables were then generated using featureCounts (subread v1.6.2).
For only the stroma samples, since these libraries were run twice (technical replicates), the total counts from the two runs were combined for the raw counts table.
Assembly: GRCm39 v110
Supplementary files format and content: tab-delimited text file includes raw counts

source_name: Bone Marrow

extract_protocol:
RNA was isolated using guanidinium thiocyanate-phenol-chloroform extraction (TRIzol®) from sorted BM samples. Due to the low numbers of cells isolated from the sorted bone marrow stroma RNA, samples was concentrated using SPRIselect magnetic beads (Beckman Coulter).
For the hematopoietic samples: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq6000 at PE150. Each library was sequenced to 6G (20 million paired-end reads).  For the Stromal Samples: Libraries were created using the NEBNext Low Input RNA Library Prep Kit (E6420S, New England Biolabs) and indexed using the NEBNext Multiplex Oligos dual index primers (E6440S, New England Biolabs). Libraries were sequenced at Novogene (Sacramento, CA) using the NovaSeq X system to generate 150bp paired end reads.

treatment_protocol: To isolate bone marrow (BM) from bone marrow transplant (BMT) recipients and donor animals they were euthanized via CO2 administration and secondary cervical dislocation. Bones were isolated, manually cleaned with sterile gauze, and stored in 4C dissection media (phosphate buffered saline without calcium and magnesium (1x PBS, Corning), 0.5% albumin bovine fraction V (BSA, RPI research products international), and 2mM EDTA (Invitrogen)).  Bones included were pelvic (2x), fibula (2x), tibia (2x), femur (1x), humerus (2x), scapula (2x), and sternum (1x).  After extraction of bones from euthanized animals, they were lightly crushed once in a mortar and pestle and collected into 3ml of Liberace TM (0.2 mg/ml), DNase I (200 U/ml, benzonase) and 1x PBS. Bones and cell suspension were then allowed to digest in an incubator at 37°C for 60 min on a tube rotator in a 5mL conical tube. Contents were then poured through a 70µm filter on a 50mL conical tube and washed with additional 45ml dissection media to collect released BM cells and quench the digestion. This was followed by peleting the cells at 485g for 10 minutes at 4C. Supernatant was discarded, and the cell pellet was resuspended into 7mL of  RBC lysis buffer for mouse (Boston BioProducts) and incubated on a tube rotator (Rotator Genie) for 15 minutes at room temperature. RBC lysis was quenched with the addition of 43mL of dissection media, tubes were lightly inverted to mix, and the suspension was spun down again at 485g for 5-10 minutes at 4C. Cells were resuspended into 3ml 1x PBS + 1µL/mL benzonase and counted to determine concentration.  Once cells were counted, they were concentrated into 1mL of 1x PBS where they were stained with zombie violet viability dye for 10 minutes at room temperature in the dark followed by quenching in FACS buffer (0.5% FBS in 1X PBS) and pelleted at 300g at 4C for 5 minutes. Cells were then resuspended into 15ml conical tubes at concentrations of 2.0x10^6 cells/100µL and blocked with Rat anti-mouse CD16/CD32 (Fc Block, BD Biosciences) for 10 minutes at room temperature in the dark on a tube revolver (FisherBrand). The samples were then diluted with an antibody cocktail to a concentration of 1.0x10^6 cells/100µL. This cocktail contained anti-CD45.1 (A20)-FITC (BioLegend), and anti-CD45.2 (104)-APC (BioLegend) along with biotinylated lineage markers: anti-B220 (RA3-6B2, BioLegend), CD4, (GK1.5, BioLegend), CD8 (53-6.7, BioLegend), NK1.1 (PK136, BioLegend), Ly-6G/Ly-6C (RB6-8C5, BioLegend), TER119 (BioLegend), and CD11b (M1/70, BioLegend).  Cell suspension was allowed to incubate on a tube revolver in the dark at room temperature for 30 minutes. Cells were then spun down (300g for 5min) and washed. Cells were spun down again and resuspended at 1.0x10^6 cells/100µL of FACs buffer with PE streptavidin (BD Biosciences) and allowed to incubate at room temperature on a rotator in the dark for 15 minutes. Cells were again spun down, washed, and resuspended into FACs buffer for sorting. Matched unstained BM was also kept aside to be run alongside the stained BM during sorting. Stained BM was then put through FACs tube 35µm strainer caps (Alkali Scientific) just prior to cell sorting. All sorted cells were collected into collection media. The workflow for sorting the BM proceeded as follows. To isolate hematopoietic BM, live singlets were sorted using gates that isolated CD45.2 donor-derived (FITC-positive/APC-negative) or CD45.1 recipient-derived (FITC-negative/APC-positive) BM. Concurrently, CD45.1/CD45.2 double negative cells were gated to observe the PE-stained combined lineage makers. A sorting gate was then used to collect the lineage-negative stromal-enriched cells. While performing the sorting only two populations were being isolated at a time to reduce the chance of contamination by positioning the collection tubes on either side of the sorting stream. The stromal isolation tube was always present during the sorting on one side since the frequency was always very low, while the other side would be used for the hematopoietic donor- or recipient-derived collection tubes. Starting with the recipient-derived material we would sort until 5.0x106 cells were collected before pausing the sorting and switching out collection tubes to collect 4.0-5.0x106 donor-derived cells. Wild-type no-BMT cells were sorted with the same gating paradigm but no CD45.2 cells were collected. Once isolated, cells were pelleted down (300g for 10 minutes) and resuspended into 1mL of TRIZOL and stored at -80C until RNA isolation.

value: Bone Marrow

value: FEMALE

tag: animal id

tag: source

value: Wild-type Control Cells

value: Wild-Type Control

tag: euthanasia date

tag: final peripheral_blood_chimerism


title: SUB10, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2

value: peripheral blood mononuclear cells


title: Liver, Late ACR, Patient6-BX5, TCR

description: 10x Genomics

value: Liver

tag: library type

value: mRNA


title: Liver, No ACR, Patient7-BX2, BCR

description: 10x Genomics

tag: baseline immunosuppression

value: TAC+steroids+RAPA


title: N280_Control_Heme

tag: Sex


title: D28_1_C11

description:
hiPSC_derived_CMEC_day8_batch6
RPKM_normalized_CMEC_PMEC_bulk.csv


title: BxPC3 Rep2

description: Library name: AH790 BxPC3 replica 2 ATAC-Seq

value: Human pancreatic cell line


title: SUB40, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1

tag: tissue


title: D27_1_D1

description:
hiPSC_derived_PMEC_day6_batch5
RPKM_normalized_CMEC_PMEC_bulk.csv

tag: cell type


title: SUB11, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2

tag: treatment


title: SUB31, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2

tag: day


title: Liver, Late ACR, Patient6-BX4, BCR

description: 10x Genomics

tag: rejection treatment

value: TAC+steroids


title: E17-5_LSK_WT_ADT

description:
17WT_ADT
17W_barcodes.tsv.gz
17W_features.tsv.gz
17W_matrix.mtx.gz

value: LSK (Lineage- Sca1+ c-Kit+)

tag: genotype

value: WT

value: ADT


title: D27_1_D11

description:
hiPSC_derived_PMEC_day8_batch5
RPKM_normalized_CMEC_PMEC_bulk.csv

value: hiPSC-derived PMEC


title: Liver, Late ACR, Patient6-BX4, GEX

description: 10x Genomics


title: SUB13, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: N002_Control_Heme

value: MALE


title: Liver, Late ACR, Patient11-BX2, GEX

description: 10x Genomics

value: TAC


title: Liver, Late ACR, Patient6-BX3, BCR

description: 10x Genomics


title: N093_Control_Heme


title: D27_1_C1

description:
hiPSC_derived_CMEC_day6_batch5
RPKM_normalized_CMEC_PMEC_bulk.csv

value: hiPSC-derived CMEC

value: differentiation day6


title: Liver, Late ACR, Patient6-BX3, TCR

description: 10x Genomics


title: SUB18, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: SUB16, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: N288_Control_Heme

value: Bone Marrow

value: FEMALE


title: D27_1_C11

description:
hiPSC_derived_CMEC_day8_batch5
RPKM_normalized_CMEC_PMEC_bulk.csv

value: differentiation day8


title: Liver, Late ACR, Patient6-BX3, GEX

description: 10x Genomics


title: N208_Control_Heme

value: Wild-type Control Cells

value: Wild-Type Control


title: D26_1_D11

description:
hiPSC_derived_PMEC_day8_batch4
RPKM_normalized_CMEC_PMEC_bulk.csv


title: D26_1_D1

description:
hiPSC_derived_PMEC_day6_batch4
RPKM_normalized_CMEC_PMEC_bulk.csv


title: N277_Control_Heme


title: Liver, Late ACR, Patient6-BX4, TCR

description: 10x Genomics

value: Liver

value: mRNA


title: Liver, Late ACR, Patient6-BX2, BCR

description: 10x Genomics

value: TAC+Rituximab


title: Liver, Late ACR, Patient6-BX2, TCR

description: 10x Genomics


title: D26_1_C1

description:
hiPSC_derived_CMEC_day6_batch4
RPKM_normalized_CMEC_PMEC_bulk.csv


title: SUB04, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1

value: peripheral blood mononuclear cells


title: N269_Donor_Heme

value: Donor-Derived Cells

value: Bone Marrow Transplant


title: SUB16, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: N051_Control_Heme


title: D26_1_C11

description:
hiPSC_derived_CMEC_day8_batch4
RPKM_normalized_CMEC_PMEC_bulk.csv


title: Liver, Pre-TXP, Patient6-Pre-TXP, BCR

description: 10x Genomics


title: N279_Donor_Heme


title: Liver, Late ACR, Patient6-BX2, GEX

description: 10x Genomics


title: SUB17, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: N005_Donor_Heme


title: D25_1_D1

description:
hiPSC_derived_PMEC_day6_batch3
RPKM_normalized_CMEC_PMEC_bulk.csv


title: Liver, Pre-TXP, Patient6-Pre-TXP, TCR

description: 10x Genomics


title: D25_1_D11

description:
hiPSC_derived_PMEC_day8_batch3
RPKM_normalized_CMEC_PMEC_bulk.csv


title: N203_Donor_Heme


title: SUB27, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: Liver, Pre-TXP, Patient6-Pre-TXP, GEX

description: 10x Genomics


title: D25_1_C11

description:
hiPSC_derived_CMEC_day8_batch3
RPKM_normalized_CMEC_PMEC_bulk.csv


title: Liver, No ACR, Patient5-BX1, BCR

description: 10x Genomics


title: SUB02, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: N014_Donor_Heme


title: N204_Donor_Heme

value: Recipient-Derived Cells


title: Liver, No ACR, Patient5-BX1, TCR

description: 10x Genomics


title: D24_1_D1

description:
hiPSC_derived_PMEC_day6_batch2
RPKM_normalized_CMEC_PMEC_bulk.csv

value: hiPSC-derived PMEC


title: SUB31, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Liver, No ACR, Patient5-BX1, GEX

description: 10x Genomics


title: SUB08, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: NP

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and GRCh38. genome.
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Exosomes

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
AF,NP; Proton Sequencing Protocol
AF-IL,AF-TNF,NP-IL,NP-TNF: HiSeq Sequencing Protocol

tag: subject status

value: spine fracture patients who underwent discectomy

value: primary nuclues pulposus (NP) cells


title: N204_Recipient_Heme


title: Liver, Pre-TXP, Patient5-Pre-TXP, BCR

description: 10x Genomics


title: SUB13, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: D24_1_C11

description:
hiPSC_derived_CMEC_day8_batch2
RPKM_normalized_CMEC_PMEC_bulk.csv

value: hiPSC-derived CMEC


title: D24_1_C1

description:
hiPSC_derived_CMEC_day6_batch2
RPKM_normalized_CMEC_PMEC_bulk.csv

value: differentiation day6


title: N005_Recipient_Heme

value: Bone Marrow

value: MALE


title: D25_1_C1

description:
hiPSC_derived_CMEC_day6_batch3
RPKM_normalized_CMEC_PMEC_bulk.csv


title: N203_Recipient_Heme


title: Liver, No ACR, Patient4-BX2, BCR

description: 10x Genomics

value: TAC+MMF


title: Liver, Pre-TXP, Patient5-Pre-TXP, TCR

description: 10x Genomics


title: SUB06, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: D23_1_D1

description:
hiPSC_derived_PMEC_day6_batch1
RPKM_normalized_CMEC_PMEC_bulk.csv


title: AF

value: primary annulus fibrosis (AF)


title: N032_Donor_Heme


title: N269_Recipient_Heme

value: FEMALE


title: H4

city: Houston

first: HONG

last: ZHAO

address: 6565 Fannin Street

institute: Houston Methodist Hospital

description:
Library name: H4
fresh frozen spatial transcriptomic sequnecing

data_processing:
raw sequnecing data were processed using the 10X Genomics Space Ranger pipeline to generate FASTQ files
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
fresh frozen tissue were OCT embedded, 10um frozen sections were cut with cryostat
spatial transcriptome sequencing libraries were prepared with 10X Genomics Spatial Gene Expression Slides and Reagent kit according to manufractuer's construction

value: brain

tag: cell line

value: human breast cancer

value: vehicle


title: HIPSC_MTP_BATCH2

value: hiPSC-derived MTP


title: Liver, Pre-TXP, Patient5-Pre-TXP, GEX

description: 10x Genomics

value: Liver

value: mRNA


title: H3

description:
Library name: H3
fresh frozen spatial transcriptomic sequnecing


title: D23_1_C1

description:
hiPSC_derived_CMEC_day6_batch1
RPKM_normalized_CMEC_PMEC_bulk.csv

tag: time


title: H2

description:
Library name: H2
fresh frozen spatial transcriptomic sequnecing


title: Liver, No ACR, Patient4-BX2, GEX

description: 10x Genomics


title: Liver, No ACR, Patient4-BX2, TCR

description: 10x Genomics


title: N032_Recipient_Heme

value: Recipient-Derived Cells

value: Bone Marrow Transplant


title: N014_Recipient_Heme


title: H1

description:
Library name: H1
fresh frozen spatial transcriptomic sequnecing


title: N279_Recipient_Heme


title: D24_1_D11

description:
hiPSC_derived_PMEC_day8_batch2
RPKM_normalized_CMEC_PMEC_bulk.csv

value: hiPSC-derived PMEC

value: differentiation day8

tag: batch


title: 1268

description:
Library name: 1268
fresh frozen spatial transcriptomic sequnecing

value: maraviroc


title: HIPSC_PMEC_BATCH2


title: 1267

description:
Library name: 1267
fresh frozen spatial transcriptomic sequnecing


title: H3K9me3_IP_iCKO

city: shanghai

first: Junhao

last: Xiong

address: *800 Rd dongchuan

institute: shanghai jiao tong university

data_processing:
For total RNA-seq, the resulting FASTQ files were aligned to the mm10 mouse reference genome employing HISAT2 version 2.2.1, The abundance of transcripts was quantified using the HTSeq-count tool, with expression levels reported in counts per million (CPM) to normalize for sequencing depth and gene length. Subsequently, differential expression analysis of transposable element transcripts was performed using the DESeq2 package
For ChIP-seq, the resulting FASTQ files were quality-trimmed with Trim Galore v0.6.4_dev and aligned to the mm10 genome using Bowtie2 v2.3.5.1. Genome coverage visualizations were created bigwig files with deeptools v3.5.5 bamCompare
For MeRIP-seq, the resulting FASTQ files were quality-trimmed with Trim Galore v0.6.4_dev and aligned to the mm10 genome using HISAT2 version 2.2.1. Genome coverage visualizations were created bigwig files with deeptools v3.5.5 bamCompare
Assembly: mm10
Supplementary files format and content: Total RNA-seq files are in txt format, containing the results of transcriptomic analysis statistics. ChIP- and MeRIP-seq files are in bigwig format.

source_name: Heart

growth_protocol: The animals were maintained under the standard photoperiod conditions (12-hour light/dark cycle).

extract_protocol:
For ChIP-seq, the ChIP-DNA was processed into Illumina sequencing libraries with the TIANSeq Fast DNA Library Kit (NG102, TIANGEN) and enrichment with a slight modification involving size selection on an agarose gel.
Total RNA was extracted using a RNAsimple Total RNA Kit (DP419, TIANGEN)；genomic DNA was extracted with nuclei dilution buffer (20 mM Tris Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% NP40, 1% SDS, and 1×PI).

treatment_protocol: Mice were treated with I/R or 25mg/kg tamoxifen

value: Heart

value: Male

tag: strain

value: TRIM28 iCKO

value: treatment with tamoxifen


title: Liver, Pre-TXP, Patient4-Pre-TXP, BCR

description: 10x Genomics


title: 1266

description:
Library name: 1266
fresh frozen spatial transcriptomic sequnecing


title: H3K9me3_IP_WT

value: WT


title: HIPSC_MTP_BATCH1


title: Liver, Pre-TXP, Patient4-Pre-TXP, TCR

description: 10x Genomics


title: H3K9me3_input


title: 1265

description:
Library name: 1265
fresh frozen spatial transcriptomic sequnecing


title: Liver, Pre-TXP, Patient3-Pre-TXP, BCR

description: 10x Genomics


title: HIPSC_PMEC_BATCH1


title: AE9a mBM c-Kit+ cells, C-176-3

first: Yue

last: Sun

address: 131 Dongan Road

institute: Institutes of Biomedical Sciences, Medical College of Fudan University

data_processing:
The raw pair-end RNA-seq FASTQ data were trimmed to remove low-quality bases and adaptor sequences by Trim Galore (v0.5.0) with default settings.
The clean RNA-seq FASTQ data were mapped to mouse reference genome mm10 using Hisat2 (v2.1.0) with default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: BM c-Kit+ cells

growth_protocol: Mouse bone marrow cells were maintained in SFEM supplemented with 100ng/mL mSCF, 50ng/mL mTPO, 50ng/mL mFLT3 and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
A total of 300 c-Kit+ cells per group were sorted using FACS and lysed directly with Smart-seq2 lysis buffer (Vazyme, Cat. TD502).
The RNA from the sorted cells was reverse-transcribed and amplified following the SMART-Seq2 protocol to generate sufficient cDNA. After quantifying the cDNA, 5 ng of cDNA was utilized to construct the cDNA library using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat. TD502).
SMART-seq2

treatment_protocol: Cells were treated with DMSO or 1μM C-176 for 48 hours.

value: BM c-Kit+ cells