title: Ca9-22 rep4

description:
CA922_4
counts.Cell.Lines.txt


title: Mhc2_hi_0h_44

status: Public on Jul 07 2023

type: SRA

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description:
Mhc2_hi_0h
Mhc2_Cd206_baseline_raw_expression_matrix.csv

library_source: transcriptomic single cell

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v3.1.1). Then, low quality cells (expressing less than 500 genes or more than 9000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for dural Cd206_hi cells and Mhc2_hi cells at base line condition.

molecule: total RNA

organism: Mus musculus

source_name: mouse dura mhc2_hi cell

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted dural Cd206_hi cells and Mhc2_hi cells were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

tag: cell type

value: mouse dura mhc2_hi cell

tag: strain

tag: treatment

value: FACS sorted

tag: molecule type

value: single cell RNA


title: Ca9-22 rep3

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description:
CA922_3
counts.Cell.Lines.txt

library_source: transcriptomic

data_processing:
bcl2fastq2 v2.20 was used to convert BCL files generated by Illumina NextSeq to standard FASTQ file formats
Alignment to GRCm38.p5 was done using STAR v2.5.3a (Dobin A, Bioinformatics, 2013) with default settings except for the following ones: --sjdbOverhang 74 --quantMode GeneCounts.
The resulting gene counts were further processed and normalised using DESeq2 R package v1.20 (Love M, Genome Biology, 2014).
Assembly: hg38
Supplementary files format and content: count tables (.txt) and metadata tables (.txt)

organism: Homo sapiens

growth_protocol: Cells were maintained in Dulbecco´s Eagle Modified (DMEM) RPMI-1640, Ham´s Nutrient F10 Mixture (F10) and Ham´s Nutrient F12 Mixture (F12) growth medium supplemented with 10% (v/v) FBS, Glutamax and Penicillin/Streptomycin solution (100U/ml penicillin, 100mg/ml streptomycin). All cells were cultured in humid environment at 37°C and 5% CO2. Human embryonic fibroblasts (HEF) were grown on plates coated with 0.1% gelatine and maintained in Dulbecco´s Eagles Modified growth medium supplemented with 10% FBS, Glutamax and 1% penicillin/streptomycin.

extract_protocol:
To profile reprogramming-induced transcriptomic changes in human cancer cell lines and human embryonic fibroblasts (HEF), total RNA from 3,000–5,000 FACS-sorted cells was extracted using TRIzol Reagent (ThermoFischer Scientific) following the manufacturer’s protocol. cDNA was transcribed with SMARTSeq v4 Ultra low input RNA kit (TakaraBio), amplified with 8 PCR cycles and purified with AMPure XP beads. The cDNA was quantified using High sensitivity DNA kit (Agilent) on Bioanalyzer 2100 (Agilent).
Sequencing library was prepared using Nextera XT DNA library preparation kit (Illumina) according to the manufacturer´s instructions. Briefly, cDNA was enzymatically tagmented, followed by indexing via 12 cycles of PCR. The library was normalized with beads, pooled and sequenced on Illumina NextSeq 500 platform (75bp paired-end).

treatment_protocol: Cells were sorted by FACS.

tag: cell line

tag: tumor type

value: oral cavity carcinoma

tag: transduction

value: The cells were transduced with control SFFV-MCS-EGFP lentiviral particles (4h to overnight).

tag: time point

value: Cells were collected 9 days after viral transduction

tag: sorted cells

value: GFP+

tag: agent


title: Mhc2_hi_0h_43


title: Mhc2_hi_0h_52


title: Ca9-22 rep1

description:
CA922_1
counts.Cell.Lines.txt


title: MKN74 d9 CD45+HLA-DR+ rep4

description:
MKN74_8
counts.Cell.Lines.txt

value: gastric tubullar adenocarcinoma

value: The cells were transduced with SFFV-hPIB-EGFP lentiviral particles to induce reprogramming (4h to overnight).


title: Mhc2_hi_0h_41


title: Mhc2_hi_0h_42


title: MKN74 d9 CD45+HLA-DR+ rep2

description:
MKN74_6
counts.Cell.Lines.txt


title: MKN74 d9 CD45+HLA-DR+ rep3

description:
MKN74_7
counts.Cell.Lines.txt


title: Mhc2_hi_0h_38


title: MKN74 d9 CD45+HLA-DR+ rep1

description:
MKN74_5
counts.Cell.Lines.txt


title: MKN74 rep4

description:
MKN74_4
counts.Cell.Lines.txt


title: Mhc2_hi_0h_37


title: MKN74 rep3

description:
MKN74_3
counts.Cell.Lines.txt


title: Mhc2_hi_0h_36


title: Mhc2_hi_0h_48


title: MKN74 rep2

description:
MKN74_2
counts.Cell.Lines.txt


title: Mhc2_hi_0h_35


title: MKN74 rep1

description:
MKN74_1
counts.Cell.Lines.txt


title: HUCCT1 d9 CD45+HLA-DR+ rep4

description:
HUCCT1_8
counts.Cell.Lines.txt

value: bile duct carcinoma


title: HUCCT1 d9 CD45+HLA-DR+ rep3

description:
HUCCT1_7
counts.Cell.Lines.txt


title: Ca9-22 rep2

description:
CA922_2
counts.Cell.Lines.txt


title: Mhc2_hi_0h_34


title: Mhc2_hi_0h_31


title: Mhc2_hi_0h_33


title: HUCCT1 d9 CD45+HLA-DR+ rep2

description:
HUCCT1_6
counts.Cell.Lines.txt


title: HUCCT1 rep4

description:
HUCCT1_4
counts.Cell.Lines.txt


title: Mhc2_hi_0h_30


title: Mhc2_hi_0h_40


title: Mhc2_hi_0h_39


title: Mhc2_hi_0h_29


title: HUCCT1 rep3

description:
HUCCT1_3
counts.Cell.Lines.txt


title: HUCCT1 d9 CD45+HLA-DR+ rep1

description:
HUCCT1_5
counts.Cell.Lines.txt


title: Mhc2_hi_0h_27


title: HUCCT1 rep1

description:
HUCCT1_1
counts.Cell.Lines.txt


title: Mhc2_hi_0h_26


title: HUCCT1 rep2

description:
HUCCT1_2
counts.Cell.Lines.txt


title: ECC4 d9 CD45+HLA-DR+ rep4

description:
ECC4_6
counts.Cell.Lines.txt

value: rectal adenocarcinoma


title: ECC4 d9 CD45+HLA-DR+ rep3

description:
ECC4_5
counts.Cell.Lines.txt


title: Mhc2_hi_0h_23


title: Mhc2_hi_0h_24


title: ECC4 d9 CD45+HLA-DR+ rep2

description:
ECC4_4
counts.Cell.Lines.txt


title: Mhc2_hi_0h_22


title: ECC4 rep2

description:
ECC4_2
counts.Cell.Lines.txt


title: Mhc2_hi_0h_32


title: Mhc2_hi_0h_21


title: Mhc2_hi_0h_20


title: ECC4 rep1

description:
ECC4_1
counts.Cell.Lines.txt


title: Mhc2_hi_0h_28


title: PK-59 d9 CD45+HLA-DR+ rep4

description:
PK59_11
counts.Cell.Lines.txt

value: pancreatic adenocarcinoma


title: PK-59 d9 CD45+HLA-DR+ rep3

description:
PK59_10
counts.Cell.Lines.txt


title: Mhc2_hi_0h_19


title: Mhc2_hi_0h_18


title: ECC4 d9 CD45+HLA-DR+ rep1

description:
ECC4_3
counts.Cell.Lines.txt


title: PK-59 d9 HLA-DR+ rep4

description:
PK59_7
counts.Cell.Lines.txt

value: HLA-DR+


title: Mhc2_hi_0h_25


title: PK-59 d9 CD45+HLA-DR+ rep1

description:
PK59_8
counts.Cell.Lines.txt


title: Mhc2_hi_0h_17


title: Mhc2_hi_0h_16


title: PK-59 d9 HLA-DR+ rep2

description:
PK59_5
counts.Cell.Lines.txt


title: PK-59 d9 CD45+HLA-DR+ rep2

description:
PK59_9
counts.Cell.Lines.txt


title: Mhc2_hi_0h_15


title: PK-59 rep3

description:
PK59_3
counts.Cell.Lines.txt


title: PK-59 d9 HLA-DR+ rep3

description:
PK59_6
counts.Cell.Lines.txt


title: PK-59 d9 HLA-DR+ rep1

description:
PK59_4
counts.Cell.Lines.txt


title: Mhc2_hi_0h_13


title: Mhc2_hi_0h_11


title: Mhc2_hi_0h_12


title: Mhc2_hi_0h_14


title: PK-59 rep1

description:
PK59_1
counts.Cell.Lines.txt


title: Mhc2_hi_0h_10


title: PK-59 rep2

description:
PK59_2
counts.Cell.Lines.txt


title: 888-MEL d9 CD45+HLA-DR+ rep4

description:
888MEL_12
counts.Cell.Lines.txt

value: melanoma


title: Mhc2_hi_0h_8


title: 888-MEL d9 CD45+HLA-DR+ rep3

description:
888MEL_11
counts.Cell.Lines.txt


title: Mhc2_hi_0h_7


title: Mhc2_hi_0h_9


title: Mhc2_hi_0h_6


title: Mhc2_hi_0h_5


title: 888-MEL d9 CD45+HLA-DR+ rep2

description:
888MEL_10
counts.Cell.Lines.txt


title: 888-MEL d9 CD45+HLA-DR+ rep1

description:
888MEL_9
counts.Cell.Lines.txt


title: Mhc2_hi_0h_4


title: 888-MEL d9 HLA-DR+ rep4

description:
888MEL_8
counts.Cell.Lines.txt


title: Mhc2_hi_0h_3


title: 888-MEL d9 HLA-DR+ rep3

description:
888MEL_7
counts.Cell.Lines.txt


title: Mhc2_hi_0h_2


title: Cd206_hi_0h_192

description:
Cd206_hi_0h
Mhc2_Cd206_baseline_raw_expression_matrix.csv

source_name: mouse dural cd206_hi cell

value: mouse dural cd206_hi cell


title: 888-MEL d9 HLA-DR+ rep2

description:
888MEL_6
counts.Cell.Lines.txt


title: Cd206_hi_0h_191


title: Mhc2_hi_0h_1


title: Cd206_hi_0h_188


title: Cd206_hi_0h_190


title: HMV-II d9 CD45+HLA-DR+ rep4

description:
HMVII_12
counts.Cell.Lines.txt

source_name: HMV-II

value: HMV-II


title: 888-MEL rep4

description:
888MEL_4
counts.Cell.Lines.txt


title: 888-MEL d9 HLA-DR+ rep1

description:
888MEL_5
counts.Cell.Lines.txt


title: Cd206_hi_0h_189


title: Cd206_hi_0h_187


title: 888-MEL rep3

description:
888MEL_3
counts.Cell.Lines.txt


title: 888-MEL rep2

description:
888MEL_2
counts.Cell.Lines.txt


title: 888-MEL rep1

description:
888MEL_1
counts.Cell.Lines.txt


title: Cd206_hi_0h_186


title: HMV-II d9 CD45+HLA-DR+ rep3

description:
HMVII_11
counts.Cell.Lines.txt


title: Cd206_hi_0h_185


title: HMV-II d9 CD45+HLA-DR+ rep1

description:
HMVII_9
counts.Cell.Lines.txt


title: HMV-II d9 HLA-DR+ rep4

description:
HMVII_8
counts.Cell.Lines.txt


title: HMV-II d9 HLA-DR+ rep3

description:
HMVII_7
counts.Cell.Lines.txt


title: Cd206_hi_0h_184


title: HMV-II d9 HLA-DR+ rep2

description:
HMVII_6
counts.Cell.Lines.txt


title: Cd206_hi_0h_183


title: Cd206_hi_0h_182


title: Cd206_hi_0h_180


title: Cd206_hi_0h_181


title: HMV-II d9 HLA-DR+ rep1

description:
HMVII_5
counts.Cell.Lines.txt


title: HMV-II rep4

description:
HMVII_4
counts.Cell.Lines.txt


title: HMV-II rep3

description:
HMVII_3
counts.Cell.Lines.txt


title: HMV-II rep2

description:
HMVII_2
counts.Cell.Lines.txt


title: Cd206_hi_0h_178


title: Cd206_hi_0h_179


title: HMV-II d9 CD45+HLA-DR+ rep2

description:
HMVII_10
counts.Cell.Lines.txt


title: Cd206_hi_0h_176


title: HMV-II rep1

description:
HMVII_1
counts.Cell.Lines.txt


title: Cd206_hi_0h_177


title: HEF d9 CD45+HLA-DR+ rep4

description:
HEF_29
counts.Time.Course.txt

source_name: HEF

value: HEF


title: Cd206_hi_0h_174


title: Cd206_hi_0h_175


title: Cd206_hi_0h_173


title: HEF d9 CD45+ rep4

description:
HEF_25
counts.Time.Course.txt


title: HEF d9 CD45+HLA-DR+ rep2

description:
HEF_27
counts.Time.Course.txt


title: HEF d9 CD45+ rep2

description:
HEF_23
counts.Time.Course.txt


title: HEF d9 CD45+HLA-DR+ rep3

description:
HEF_28
counts.Time.Course.txt


title: Cd206_hi_0h_172


title: HEF d9 CD45+ rep3

description:
HEF_24
counts.Time.Course.txt


title: HEF d9 CD45+HLA-DR+ rep1

description:
HEF_26
counts.Time.Course.txt


title: HEF d9 CD45+ rep1

description:
HEF_22
counts.Time.Course.txt


title: HEF d7 CD45+HLA-DR+ rep3

description:
HEF_21
counts.Time.Course.txt

value: Cells were collected 7 days after viral transduction


title: HEF d7 CD45+HLA-DR+ rep2

description:
HEF_20
counts.Time.Course.txt


title: Cd206_hi_0h_168

value: FACS sorted


title: HEF d7 CD45+HLA-DR+ rep1

description:
HEF_19
counts.Time.Course.txt


title: Cd206_hi_0h_167

value: single cell RNA


title: Cd206_hi_0h_165


title: Cd206_hi_0h_166


title: Cd206_hi_0h_164


title: HEF d7 CD45+ rep4

description:
HEF_18
counts.Time.Course.txt


title: HEF d7 CD45+ rep3

description:
HEF_17
counts.Time.Course.txt


title: HEF d7 CD45+ rep2

description:
HEF_16
counts.Time.Course.txt


title: Cd206_hi_0h_171


title: Cd206_hi_0h_163


title: HEF d7 CD45+ rep1

description:
HEF_15
counts.Time.Course.txt


title: Cd206_hi_0h_161


title: Cd206_hi_0h_162


title: HEF d5 CD45+HLA-DR+ rep3

description:
HEF_14
counts.Time.Course.txt

value: Cells were collected 5 days after viral transduction


title: HEF d5 CD45+HLA-DR+ rep2

description:
HEF_13
counts.Time.Course.txt


title: Cd206_hi_0h_158


title: Cd206_hi_0h_160


title: Cd206_hi_0h_169


title: HEF d5 CD45+ rep3

description:
HEF_11
counts.Time.Course.txt


title: HEF d5 CD45+HLA-DR+ rep1

description:
HEF_12
counts.Time.Course.txt


title: HEF d5 CD45+ rep1

description:
HEF_9
counts.Time.Course.txt


title: HEF d5 CD45+ rep2

description:
HEF_10
counts.Time.Course.txt


title: Cd206_hi_0h_156


title: HEF d3 CD45+ rep3

description:
HEF_7
counts.Time.Course.txt

value: Cells were collected 3 days after viral transduction


title: HEF d3 CD45+ rep4

description:
HEF_8
counts.Time.Course.txt


title: Cd206_hi_0h_154


title: HEF d3 CD45+ rep2

description:
HEF_6
counts.Time.Course.txt


title: Cd206_hi_0h_153


title: HEF rep4

description:
HEF_4
counts.Time.Course.txt

value: The cells were transduced with control SFFV-MCS-EGFP lentiviral particles (4h to overnight).

value: Cells were collected 9 days after viral transduction


title: HEF d3 CD45+ rep1

description:
HEF_5
counts.Time.Course.txt


title: Cd206_hi_0h_151


title: HEF rep3

description:
HEF_3
counts.Time.Course.txt

value: GFP+


title: Cd206_hi_0h_159


title: CD140+/PDGFRa+ CON RNA-seq

city: nanjing

first: yifan

last: lv

state: jiangsu

address: 300 Guangzhou Road

department: Department of Geriatrics

country: China

institute: the First Affiliated Hospital to Nanjing Medical University

data_processing:
We used cufflinks and cuffdiff analysis module to analyze gene differential expression between samples or under different conditions
Genome_build: mm10

source_name: PDGFRa+ adipocyte progenitor subgroup with PBS treatment-1

growth_protocol: CD137+ and PDGFRα+ cells were isolated from SAT or VAT by MACS. Cells were cultured in cultured under growth condition and then exposed toadipogenesis cocktail.

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

treatment_protocol: Differentiated CD137+ and PDGFRα+ cells were treated with PBS or Dexamethasone(DEX,1μM).

tag: tissue

value: adipose tissue

value: adipose progenitors

value: PBS treatment


title: HEF rep2

description:
HEF_2
counts.Time.Course.txt


title: CD140+/PDGFRa+ DEX RNA-seq

source_name: PDGFRa+ adipocyte progenitor subgroup with dex treatment

value: DEX treatment


title: Cd206_hi_0h_148


title: Cd206_hi_0h_155


title: T98G d9 CD45+HLA-DR+ rep2

description:
T98G_33
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt

value: glioblastoma

value: The cells were transduced with SFFV-hPIB-EGFP lentiviral particles to induce reprogramming (4h to overnight).


title: Cd206_hi_0h_150

value: mouse dural cd206_hi cell


title: HEF rep1

description:
HEF_1
counts.Time.Course.txt


title: T98G d9 CD45+HLA-DR+ rep1

description:
T98G_32
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: T98G d9 CD45+HLA-DR+ rep4

description:
T98G_35
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: Cd206_hi_0h_147


title: Cd206_hi_0h_149


title: Cd206_hi_0h_157


title: T98G d9 CD45+HLA-DR+ rep3

description:
T98G_34
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: CD140+/PDGFRa+ DEX ATAC-seq

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
After cell lysis, a transposase library construction kit was used to construct the library. Translocase was used for the first interrupt. After the interrupt VAHTS DNA Clean Beads were purified. The purified products could be directly used in PCR amplification. The PCR products were purified again to obtain the final library. The built library is checked with Agilent 2100 Bioanalyzer. Illumina HiSeq sequencing will be performed after pooling different libraries according to the effective concentration and the target data volume
Genome_build: ATAC-seq reads were aligned to the mm10 genome
Supplementary_files_format_and_content: Use The peak-Calling software Macs 1.4.2 to scan PEAK in the whole gene range to obtain the location information of peak on the genome and the length information of peak

molecule: genomic DNA

source_name: PDGFRa+ adipocyte progenitor subgroup with DEX treatment

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification

treatment_protocol: Differentiated CD137+ and PDGFRα+ cells were treated with Dexamethasone(DEX,1μM).

value: adipose


title: CD137+-DEX RNA-seq

source_name: CD137+ adipocyte progenitor subgroup with dex treatment


title: Cd206_hi_0h_152


title: CD137+-CON RNA-seq

source_name: CD137+ adipocyte progenitor subgroup with PBS treatment-1


title: CD137+ DEX ATAC-seq

source_name: CD137+ adipocyte progenitor subgroup with DEX treatment


title: T98G d7 CD45+HLA-DR+ rep3

description:
T98G_28
counts.Time.Course.txt
counts.VPA.txt


title: T98G d7 CD45+HLA-DR+ rep2

description:
T98G_27
counts.Time.Course.txt
counts.VPA.txt


title: Cd206_hi_0h_146


title: T98G d7 HLA-DR+ rep4

description:
T98G_25
counts.Time.Course.txt
counts.VPA.txt

value: HLA-DR+


title: T98G d7 HLA-DR+ rep3

description:
T98G_24
counts.Time.Course.txt
counts.VPA.txt

value: Cells were collected 7 days after viral transduction


title: Cd206_hi_0h_144

value: FACS sorted


title: CD140+/PDGFRa+ BS-seq

data_processing:
Here is DMR identification with the DSSv2.14.0 software, it is based on strict Wald beta binomial model test
Genome_build: mm10

extract_protocol:
After extracting the sample DNA, DNA concentration and integrity were detected by electrophoresis. After passing the detection, the database was built.
The DNA was randomly interrupted to about 350BP by ultrasound. After terminal repair, base A was added, and sequencing joint was added, the unmethylated C in the disulfite DNA fragment was converted into U, and then fragment screening and PCR amplification were performed to complete the preparation of DNA methylated library. After the library quality control, the library can be sequenced.


title: Cd206_hi_0h_145

value: single cell RNA


title: T98G d7 CD45+HLA-DR+ rep1

description:
T98G_26
counts.Time.Course.txt
counts.VPA.txt


title: T98G d7 HLA-DR+ rep2

description:
T98G_23
counts.Time.Course.txt
counts.VPA.txt


title: T98G d7 HLA-DR+ rep1

description:
T98G_22
counts.Time.Course.txt
counts.VPA.txt


title: Cd206_hi_0h_143


title: PMCA-3_CTL3

city: HOUSTON

first: John Paul

last: Shen

state: TX

address: 1515 Holcombe Blvd

department: Gastrointestinal Medical Oncology

country: USA

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Raw FASTQ files were mapped to the human reference genome (hg38) using STAR (version 2.7.2b) RNASeq alignment tool. Biobambam (version 0.0.191) was used to mark duplicates and index raw files before alignment.
Xenome (version 1.0.1-r) was used to segregate mouse and human reads from raw RNAseq files of PDX models. Mouse reference genome (GRCm39) and gene annotation file (Gencode.vM26) were used for mapping and annotating mouse reads. Extracted human reads for each PDX sample were stored in FASTQ files and input to the downstream STAR (version 2.7.2b) RNASeq alignment tool.
HTSeq (version 0.11.0) was utilized to extract raw read counts from STAR-aligned RNAseq files of PDX models.
Assembly: hg38
Supplementary files format and content: tab-delimited csv file include raw counts of human reads for each sample

source_name: PMCA-3 PDX Model of Appendiceal Adenocarcinoma tumor treated with Saline control (Replicate 3)

growth_protocol: Two Appendiceal cancer tissues (TM00351 from Jackson Laboratory, and PMCA-3 generously provided by Dr. Kjersti Flatmark (University of Oslo)), were implanted in the peritoneal space of NSG mice. In these PDX models tumor did not spread beyond the peritoneal space. The tumors were passaged 3 times to establish PDX models in NSG mice. The tumors grew as a mucinous disease in NSG mice and were diffusely disseminated within the entire peritoneal cavity. Quantitative changes in mucinous peritoneal disease were visualized by MRI. Tumor volume in each mouse was measured by taking the sum of the total area tumor from 5 fixed MRI sections in the peritoneum using OsiriX Lite software v12.0.1 (Pixmeo, Switzerland).

extract_protocol:
RNA was extracted using RNAqueous™ Total RNA Isolation Kit (Catalog number: AM1912). RNA concentraction ≥ 20 ng/µl for each sample was used for library construction.
Before library construction, quality control for each RNA samples was performed to guarantee the reliability of the data. RNA degradation and potential contamination were tested by Agarose Gel Electrophoresis. Agilent 2100 was used to check the RNA integrity and quantitation. After the QC procedures, mRNA from each smaple was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: Paclitaxel, dissolved in castor oil, citric acid, and dehydrated alcohol USP, was obtained from residual unused doses from the Mays clinic pharmacy at the University of Texas MD Anderson Cancer Center. Paclitaxel was freshly diluted 5-fold with physiological saline. PDX mice were IP injected with diluted paclitaxel (0.5 ml) with a dose range from 6.25 to 25.0 mg/kg mouse body weight. PDX models were treated with paclitaxel weekly (3 weekly treatments and 1 week off, for two cycles) or biweekly (up to 6 biweekly treatments). We confirmed that the inactive components in the solvents [castor oil (105.4 mg/ml), citric acid (0.4 mg/ml), and dehydrated alcohol USP (9.94% v/v)] did not have a significant effect on tumor growth or body weight in PDX mice.

value: Appendiceal Adenocarcinoma

value: Saline control


title: T98G d5 CD45+HLA-DR+ rep3

description:
T98G_21
counts.Time.Course.txt
counts.VPA.txt

value: Cells were collected 5 days after viral transduction


title: CD137+ BS-seq


title: PMCA-3_CTL2

source_name: PMCA-3 PDX Model of Appendiceal Adenocarcinoma tumor treated with Saline control (Replicate 2)


title: T98G d5 CD45+HLA-DR+ rep1

description:
T98G_19
counts.Time.Course.txt
counts.VPA.txt


title: Cd206_hi_0h_141


title: T98G d5 HLA-DR+ rep2

description:
T98G_17
counts.Time.Course.txt
counts.VPA.txt


title: T98G d5 HLA-DR+ rep3

description:
T98G_18
counts.Time.Course.txt
counts.VPA.txt


title: T98G d5 CD45+HLA-DR+ rep2

description:
T98G_20
counts.Time.Course.txt
counts.VPA.txt


title: T98G d3 HLA-DR+ rep7

description:
T98G_11
counts.Time.Course.txt
counts.VPA.txt

value: Cells were collected 3 days after viral transduction


title: PMCA-3_PTX1

source_name: PMCA-3 PDX Model of Appendiceal Adenocarcinoma tumor treated with Intraperitoneal paclitaxel (Replicate 1)

value: Intraperitoneal paclitaxel


title: Cd206_hi_0h_140

description:
Cd206_hi_0h
Mhc2_Cd206_baseline_raw_expression_matrix.csv


title: PMCA-3_CTL1

source_name: PMCA-3 PDX Model of Appendiceal Adenocarcinoma tumor treated with Saline control (Replicate 1)


title: T98G d5 HLA-DR+ rep1

description:
T98G_16
counts.Time.Course.txt
counts.VPA.txt


title: T98G d3 HLA-DR+ rep5

description:
T98G_9
counts.Time.Course.txt
counts.VPA.txt


title: TM00351_CTL2

source_name: TM00351 PDX Model of Appendiceal Adenocarcinoma tumor treated with Saline control (Replicate 2)


title: PMCA-3_PTX3

source_name: PMCA-3 PDX Model of Appendiceal Adenocarcinoma tumor treated with Intraperitoneal paclitaxel (Replicate 3)


title: PMCA-3_PTX2

source_name: PMCA-3 PDX Model of Appendiceal Adenocarcinoma tumor treated with Intraperitoneal paclitaxel (Replicate 2)


title: Cd206_hi_0h_135


title: T98G d3 HLA-DR+ rep2

description:
T98G_6
counts.Time.Course.txt
counts.VPA.txt


title: Cd206_hi_0h_139


title: Cd206_hi_0h_138


title: TM00351_CTL1

source_name: TM00351 PDX Model of Appendiceal Adenocarcinoma tumor treated with Saline control (Replicate 1)


title: Cd206_hi_0h_134

source_name: mouse dural cd206_hi cell


title: Cd206_hi_0h_142


title: Cd206_hi_0h_137


title: T98G rep4

description:
T98G_4
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt

value: The cells were transduced with control SFFV-MCS-EGFP lentiviral particles (4h to overnight).

value: Cells were collected 9 days after viral transduction

value: GFP+


title: T98G rep3

description:
T98G_3
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: TM00351_PTX2

source_name: TM00351 PDX Model of Appendiceal Adenocarcinoma tumor treated with Intraperitoneal paclitaxel (Replicate 2)


title: T98G d3 HLA-DR+ rep6

description:
T98G_10
counts.Time.Course.txt
counts.VPA.txt


title: TM00351_CTL3

source_name: TM00351 PDX Model of Appendiceal Adenocarcinoma tumor treated with Saline control (Replicate 3)


title: Cd206_hi_0h_132


title: Cd206_hi_0h_136


title: T98G d3 HLA-DR+ rep4

description:
T98G_8
counts.Time.Course.txt
counts.VPA.txt


title: T98G d3 HLA-DR+ rep3

description:
T98G_7
counts.Time.Course.txt
counts.VPA.txt


title: Cd206_hi_0h_131


title: A172 d9 CD45+HLA-DR+ rep2

description:
A172_6
counts.Cell.Lines.txt


title: LO-Pool1, replicate 1, scRNA-seq

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

description: 10x Genomics

data_processing:
Reads were aligned to the GRCh38 human genome (2020-A, 10x Genomics) using Cell Ranger (v6.0.2, 10x Genomics) with an include-introns parameter. Donors were demultiplexed using souporcell (v2.0) (1) to two clusters based on common variants. Ambient RNA counts were eliminated with CellBender (v0.2.1) (2).
Filtered count matrices were further processed with Scanpy (v1.9.1) (3). Low quality cells with < 2,000 total counts, < 500 number of genes, > 15% mitochondrial gene counts, and > 0.4 Scrublet (v0.2.3) (4) doublet detection scores were filtered out, and only souporcell singlets were retained. Raw counts were normalized per cell to 10,000 and ln(x+1) transformed, which were further used as gene expression values.
Data was splitted into two donors based on souporcell assignment for downstream analyses. Top 2,000 highly variable genes were selected with scanpy.pp.highly_variable_genes function with seurat_v3 method (5) for each data. After data scaling to unit variance, principal component analysis (PCA) was performed over selected highly variable genes. Neighborhood graph was built from top 50 principle components and visualized using uniform manifold approximation and projection (UMAP) (6).
Clustering was performed with Leiden method (7) with 2.0 resolution. Low quality and stressed clusters displaying low total counts, low number of genes and high mitochondrial gene counts were discarded and remaining data were reprocessed from the highly variable gene selection step. Cell cycle scores were calculated with scanpy.tl.score_genes_cell_cycle function. Each cluster was manually annotated by inspecting marker genes.
Copy number variation (CNV) was inferred using infercnvpy (v0.1.0) (8) with a 100 running window size. Normal cell types were provided as a reference.
Assembly: GRCh38
Supplementary files format and content: h5ad file of processed single-cell RNA-sequencing data from normal lung organoid sample; found in LO-normal.h5ad
Supplementary files format and content: h5ad file of processed single-cell RNA-sequencing data from lung cancer organoid sample; found in LO-cancer.h5ad

source_name: Lung cancer organoid

growth_protocol: Lung cancer tissues stored in DMEM/F12 media (Gibco) containing 1% Penicillin and streptomycin (Gibco) were transported to the laboratory and processed within 12 hours of removal from the patients. Upon arrival, the lung cancer tissues were photographed, and volume measured. For mechanical dissociation, the tissues were as small as possible with surgical scissors and handy micro-tube homogenizer on ice after then re-suspended in DMEM/F12 containing 1% penicillin and streptomycin. The suspension was filtered through a 70㎛ strainer (SPL). After the membrane rinsing, the residual impurities on the membrane were discarded together with the strainer. The strained cells were centrifuged at 500× g for 5 min at 4℃, discarding the supernatant. Incubate the pellet with RBC lysis buffer (Biolegend) for 10min at room temperature. Add the cold-DPBS containing 10% FBS (WELGENE) and centrifuged at 500× g for 5 min at 4℃. The cell pellet was washed once with cold-DPBS and centrifuged again for enzyme digestion. Organoid culture media contains FGF 7/10, Noggin, R-spondin, and etc (supple table 1). To culture Lung cancer organoids (LCOs) in a multi-well plate, LCOs re-suspended in the cold reduced growth factor Basement Membrane Extract Type 2 (BME, R&D system). Then, the seeding density was adjusted to ~1000 single cell per 20ul drops of the BME suspension into 48-well plate (SPL) and were allowed to solidify at 37℃ for 10min. After gelation, 120ul of LCOs culture medium was added to the well and the plate was transferred to an organoid culture incubator at 37℃ with 5% CO2. The composition of the LCOs culture medium table 1 and the medium was refreshed weekly. For passage, organoids (2-3 weeks after starting the culture) were harvested of cold-DPBS (WELGENE) from the plate and centrifuged at 500× g for 5 min at 4℃. The supernatant was discarded and the BME was digested with 200ul TrypLE express (Gibco) for ~10min at 37℃. The trypsinization was stopped by the addition of 1ml cold-DPBS containing 10% FBS (WELGENE). Organoids were centrifuged at 500× g for 5 min at 4℃ and washed once with cold-DPBS and centrifuged again. The pellets were resuspended in cold-BME to allow the formation of new organoids.

extract_protocol:
Cryopreserved initial passage organoid cell stocks were thawed in a 37 °C water bath for 1 min and transferred to DMEM/F-12 (Gibco) followed by centrifugation at 500× g for 5 min at 4℃. Cells were further washed twice with cold DPBS (Gibco) containing 0.04% BSA (Miltenyi Biotec) and filtered through 40 µm cell strainers (Flowmi). Cell suspensions from two different donors were pooled to equal cell concentrations.
Pooled cell suspensions were then loaded targeting recovery of 10,000 cells per channel to construct single-cell RNA sequencing (scRNA-seq) libraries using Chromium Next GEM Single Cell 5' v2 kit (10x Genomics) according to the manufacturer’s instructions. Generated libraries were sequenced on a Illumina NovaSeq 6000 at a paired-end, 150 bp reads configuration aiming 400 million reads per library.

value: Lung cancer organoid


title: T98G d3 HLA-DR+ rep1

description:
T98G_5
counts.Time.Course.txt
counts.VPA.txt

value: glioblastoma


title: Cd206_hi_0h_130


title: TM00351_PTX3

source_name: TM00351 PDX Model of Appendiceal Adenocarcinoma tumor treated with Intraperitoneal paclitaxel (Replicate 3)


title: A172 rep4

description:
A172_4
counts.Cell.Lines.txt


title: Cd206_hi_0h_129


title: Cd206_hi_0h_170


title: Cd206_hi_0h_133


title: A172 rep3

description:
A172_3
counts.Cell.Lines.txt


title: T98G rep1

description:
T98G_1
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: A172 d9 CD45+HLA-DR+ rep4

description:
A172_8
counts.Cell.Lines.txt

value: The cells were transduced with SFFV-hPIB-EGFP lentiviral particles to induce reprogramming (4h to overnight).


title: T98G rep2

description:
T98G_2
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: A172 rep2

description:
A172_2
counts.Cell.Lines.txt


title: A172 d9 CD45+HLA-DR+ rep3

description:
A172_7
counts.Cell.Lines.txt


title: U3P2E2 day9

description: sorted EGFP+ cells expressing at least one of the reprogramming markers (CD45 or HLA-DR)

data_processing:
The Cell Ranger v6.0.1 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated. This pipeline was used with a hg38 genome.
R1 read is technical; R2 is biological. Barcode position in R1 is 1-16bp; UMI - 17-28bp.
The resulting expression matrix was used as input to the Seurat library v4.1.0
Assembly: hg38
Supplementary files format and content: 10x Gene Expression matrix

source_name: Bladder tumor

extract_protocol:
Single cells were isolated using 10x Chromium by 10x Genomics.
scRNA-seq libraries were prepared with Dual Index Chromium Next GEM Single Cell 3ʹ Kit v3.1 (Dual Index) (10x Genomics) according to manufacturer’s instructions. Library size and quality check was performed using High Sensitivity D1000 ScreenTape with High Sensitivity D1000 Reagents (Agilent) in a 4200 TapeStation System (Agilent), according to the manufacturer’s protocol.

tag: donor

value: Bladder tumor

value: Bladder carcinoma

value: Cells were sorted by FACS

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP

tag: time

tag: sorted cell_type

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: Cd206_hi_0h_127

value: mouse dural cd206_hi cell

value: FACS sorted

value: single cell RNA


title: IGR-39 d9 CD45+HLA-DR+ rep4

description:
IGR39_8
counts.Cell.Lines.txt

value: melanoma


title: Cd206_hi_0h_126


title: L6903 day9

source_name: Lung tumor

value: Lung tumor

value: Lung carcinoma


title: Cd206_hi_0h_125


title: U3P2E2 day0

description: sorted EGFP+ cells

value: Cells were transducted with EGFP

value: sorted live(DAPI-) and EGFP+


title: A172 rep1

description:
A172_1
counts.Cell.Lines.txt

value: The cells were transduced with control SFFV-MCS-EGFP lentiviral particles (4h to overnight).

value: Cells were collected 9 days after viral transduction

value: GFP+


title: Cd206_hi_0h_124


title: Cd206_hi_0h_128


title: L2404 day9


title: K562 d9 CD45+HLA-DR+ rep2

description:
K562_5
counts.Cell.Lines.txt

value: chronic myeloid leukaemia

value: The cells were transduced with SFFV-hPIB-EGFP lentiviral particles to induce reprogramming (4h to overnight).


title: IGR-39 d9 CD45+HLA-DR+ rep3

description:
IGR39_7
counts.Cell.Lines.txt


title: A172 d9 CD45+HLA-DR+ rep1

description:
A172_5
counts.Cell.Lines.txt

value: glioblastoma


title: B8317 day9

source_name: Breast tumor

value: Breast tumor

value: Breast carcinoma

value: Cells were sorted by FACS


title: IGR-39 d9 CD45+HLA-DR+ rep2

description:
IGR39_6
counts.Cell.Lines.txt


title: L2061 day0

description: sorted EGFP+ cells


title: TM00351_PTX1

source_name: TM00351 PDX Model of Appendiceal Adenocarcinoma tumor treated with Intraperitoneal paclitaxel (Replicate 1)

value: Appendiceal Adenocarcinoma

value: Intraperitoneal paclitaxel


title: K562 rep2

description:
K562_2
counts.Cell.Lines.txt


title: L2404 day0

description: sorted EGFP+ cells


title: L6903 day0

description: sorted EGFP+ cells


title: IGR-39 d9 CD45+HLA-DR+ rep1

description:
IGR39_5
counts.Cell.Lines.txt


title: IGR-39 rep4

description:
IGR39_4
counts.Cell.Lines.txt


title: B8317 day0

description: sorted EGFP+ cells


title: Cd206_hi_0h_120

value: mouse dural cd206_hi cell

value: FACS sorted

value: single cell RNA


title: IGR-39 rep3

description:
IGR39_3
counts.Cell.Lines.txt

value: melanoma


title: CDC1 rep6

description:
CDC1_6
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: IGR-39 rep1

description:
IGR39_1
counts.Cell.Lines.txt


title: Cd206_hi_0h_123


title: IGR-39 rep2

description:
IGR39_2
counts.Cell.Lines.txt


title: K562 d9 CD45+HLA-DR+ rep3

description:
K562_6
counts.Cell.Lines.txt


title: K562 d9 CD45+HLA-DR+ rep1

description:
K562_4
counts.Cell.Lines.txt


title: L2061 day9

value: Lung tumor

value: Lung carcinoma

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: K562 rep3

description:
K562_3
counts.Cell.Lines.txt

value: The cells were transduced with control SFFV-MCS-EGFP lentiviral particles (4h to overnight).

value: Cells were collected 9 days after viral transduction

value: GFP+


title: K562 rep1

description:
K562_1
counts.Cell.Lines.txt

value: chronic myeloid leukaemia


title: CDC1 rep8

description:
CDC1_8
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: Cd206_hi_0h_121


title: Cd206_hi_0h_119


title: CDC1 rep3

description:
CDC1_3
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: B3376 day0

description: sorted EGFP+ cells

value: Breast tumor

value: Cells were transducted with EGFP

value: sorted live(DAPI-) and EGFP+


title: CDC1 rep5

description:
CDC1_5
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: B0763 day0

description: sorted EGFP+ cells

value: Breast carcinoma

value: Cells were sorted by FACS


title: Cd206_hi_0h_118

description:
Cd206_hi_0h
Mhc2_Cd206_baseline_raw_expression_matrix.csv

value: mouse dural cd206_hi cell


title: CDC1 rep2

description:
CDC1_2
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: CDC1 rep7

description:
CDC1_7
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: SL_55

city: Toronto

first: Shahrzad

last: Ghazisaeidi

state: Ontario

address: 250 College Street

department: Krembil Centre for Neuroinformatics

country: Canada

institute: Centre for Addiction and Mental Health

data_processing:
Quality control check for fastq files
The filtered reads are aligned to a reference genome using STAR
Trimmed sequences were alligned to genome assemblies
Assembly: Mus musculus (GRCm38-mm10.0) and Rattus Norvegicus assembly (Rnor_6.0)
Supplementary files format and content: raw counts- text file csv

molecule: polyA RNA

source_name: L4:L5- Spinal cord dorsal horn-ipsi

extract_protocol:
RNA was extracted from the tissue using Rneasy kit Qiagen and preserved in RNALater
cDNA library was prepared using High Capacity RNA-to cDNA kit, ThermoFisher according to manufactorer's instructions and sequenced at TCAG at The Hospital for Sick Children.

treatment_protocol: Spared nerve injury (SNI) and Sham Surgery , Post operative day 7.

value: L4:L5- Spinal cord dorsal horn-ipsi

tag: genotype

value: WT

tag: Sex

value: Female

value: SNI


title: B3376 day9


title: CDC2 rep15

description:
CDC2_15
counts.Cell.Lines.txt


title: SL_56

source_name: L4:L5- Spinal cord dorsal horn-contra

value: L4:L5- Spinal cord dorsal horn-contra


title: B0763 day9

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP


title: Cd206_hi_0h_122

value: FACS sorted

value: single cell RNA


title: CDC1 rep1

description:
CDC1_1
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: SL_54

value: SHAM


title: Cd206_hi_0h_116


title: P1021 day9

source_name: Pancreatic tumor

value: Pancreatic tumor

value: Pancreatic carcinoma

value: Cells were collected 9 days after viral transduction

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: Cd206_hi_0h_115


title: CDC2 rep14

description:
CDC2_14
counts.Cell.Lines.txt


title: CDC1 rep4

description:
CDC1_4
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: Ceder5 day9


title: SL_52

value: Male


title: CDC2 rep13

description:
CDC2_13
counts.Cell.Lines.txt


title: CDC2 rep12

description:
CDC2_12
counts.Cell.Lines.txt


title: Cd206_hi_0h_117


title: Ceder5 day0

description: sorted EGFP+ cells

value: Cells were transducted with EGFP

value: sorted live(DAPI-) and EGFP+


title: SL_51


title: CDC2 rep11

description:
CDC2_11
counts.Cell.Lines.txt


title: OCL10 day9

source_name: Tongue tumor

value: Tongue tumor

value: Tongue carcinoma

value: Cells were sorted by FACS


title: Cd206_hi_0h_112

value: mouse dural cd206_hi cell


title: CDC2 rep10

description:
CDC2_10
counts.Cell.Lines.txt


title: SL_49

value: L4:L5- Spinal cord dorsal horn-ipsi

value: WT

value: SNI


title: Cd206_hi_0h_111

value: FACS sorted


title: CDC2 rep9

description:
CDC2_9
counts.Cell.Lines.txt


title: P1021 day0

description: sorted EGFP+ cells


title: Cd206_hi_0h_114

value: single cell RNA


title: OCL07 day9

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP


title: SL_53

value: Female

value: SHAM


title: OCL07 day0

description: sorted EGFP+ cells

value: Cells were collected 9 days after viral transduction


title: SL_47


title: SL_48

value: L4:L5- Spinal cord dorsal horn-contra


title: Cd206_hi_0h_109


title: Cd206_hi_0h_108


title: CDC2 rep7

description:
CDC2_7
counts.Cell.Lines.txt


title: CDC2 rep8

description:
CDC2_8
counts.Cell.Lines.txt


title: Cd206_hi_0h_113


title: OCL06 day9

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: SL_46


title: Cd206_hi_0h_110


title: Cd206_hi_0h_105


title: SL_44


title: OCL2206 day0

description: sorted EGFP+ cells

source_name: Tonsil tumor

value: Tonsil tumor

value: Tonsil carcinoma

value: Cells were transducted with EGFP


title: SL_43


title: OCL06 day0

description: sorted EGFP+ cells

value: Tongue tumor

value: Tongue carcinoma

value: sorted live(DAPI-) and EGFP+


title: SL_50

value: Male


title: SL_45

value: L4:L5- Spinal cord dorsal horn-ipsi

value: WT


title: T6051 day9

value: Cells were sorted by FACS


title: SL_42


title: CDC2 rep6

description:
CDC2_6
counts.Cell.Lines.txt


title: OCL10 day0

description: sorted EGFP+ cells


title: OCL2206 day9


title: CDC2 rep4

description:
CDC2_4
counts.Cell.Lines.txt


title: Cd206_hi_0h_104

value: mouse dural cd206_hi cell

value: FACS sorted

value: single cell RNA


title: Cd206_hi_0h_107


title: CDC2 rep3

description:
CDC2_3
counts.Cell.Lines.txt


title: CDC2 rep2

description:
CDC2_2
counts.Cell.Lines.txt


title: Cd206_hi_0h_103


title: Cd206_hi_0h_102


title: TC48 day9

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP


title: CDC2 rep1

description:
CDC2_1
counts.Cell.Lines.txt


title: Cd206_hi_0h_101


title: CDC2 rep5

description:
CDC2_5
counts.Cell.Lines.txt


title: Cd206_hi_0h_106


title: PDC rep16

description:
PDC_16
counts.Cell.Lines.txt

source_name: PDC

value: PDC


title: Cd206_hi_0h_100


title: TC48 day0

description: sorted EGFP+ cells

value: Cells were collected 9 days after viral transduction


title: PDC rep15

description:
PDC_15
counts.Cell.Lines.txt


title: SL_40

value: L4:L5- Spinal cord dorsal horn-contra

value: SHAM


title: SL_37


title: SL_41

value: Female


title: SL_39


title: T6051 day0

description: sorted EGFP+ cells

value: Tonsil tumor

value: Tonsil carcinoma

value: Cells were transducted with EGFP


title: PDC rep12

description:
PDC_12
counts.Cell.Lines.txt


title: TCA17 day9

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: Cd206_hi_0h_99


title: SL_38

value: Male


title: Cd206_hi_0h_98


title: PDC rep14

description:
PDC_14
counts.Cell.Lines.txt


title: PDC rep13

description:
PDC_13
counts.Cell.Lines.txt


title: G2572 day9

source_name: Brain tumor

value: Brain tumor

value: Glioblastoma


title: TCA17 day0

description: sorted EGFP+ cells

value: Cells were sorted by FACS

value: sorted live(DAPI-) and EGFP+


title: SL_34

value: WT


title: SL_36

value: SNI


title: M0008 day9

source_name: Skin tumor

value: Skin tumor

value: Melanoma

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP


title: Cd206_hi_0h_97

source_name: mouse dural cd206_hi cell

value: mouse dural cd206_hi cell

value: FACS sorted

value: single cell RNA


title: PDC rep9

description:
PDC_9
counts.Cell.Lines.txt

value: PDC


title: G2572 day0

description: sorted EGFP+ cells

value: Cells were collected 9 days after viral transduction


title: SL_35

value: L4:L5- Spinal cord dorsal horn-ipsi


title: Cd206_hi_0h_93


title: PDC rep11

description:
PDC_11
counts.Cell.Lines.txt


title: Cd206_hi_0h_96


title: G1933 day9

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: Cd206_hi_0h_95


title: PDC rep10

description:
PDC_10
counts.Cell.Lines.txt


title: as3mtmut_male_liver1

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads where first assessed for quality using FastQC v0.11.5. Trimmomatic v0.36 was used for quality trimming and adapter sequence removal, with the parameters (ILLUMINACLIP: trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36)
The resulting transcripts from the raw counts were used for further downstream analysis
Assembly: NOT PROVIDED
Supplementary files format and content: txt containing raw counts

organism: Danio rerio

growth_protocol: Zebrafish larvae were kept in 6-well plate at a density of 2 larvae/ per 1 mL embyro medium in a 10:14 light/dark cycle

extract_protocol:
TRIzol/Choloform Extraction
RNA-seq libraries were prepared with Illumina TruSeq V2 RNA kit for Poly A by the staff in the NYUAD genomics facility and quality controled by Bioanalyzer.

value: male

value: liver


title: Cd206_hi_0h_92


title: SL_33

value: Male

value: SHAM


title: Cd206_hi_0h_94


title: Cd206_hi_0h_91


title: as3mtmut_male_liver2


title: PDC rep6

description:
PDC_6
counts.Cell.Lines.txt


title: Cd206_hi_0h_90


title: G1933 day0

description: sorted EGFP+ cells

value: Brain tumor

value: Glioblastoma

value: Cells were sorted by FACS

value: Cells were transducted with EGFP

value: sorted live(DAPI-) and EGFP+


title: PDC rep8

description:
PDC_8
counts.Cell.Lines.txt


title: PDC rep5

description:
PDC_5
counts.Cell.Lines.txt


title: M0006 day9

value: Skin tumor

value: Melanoma

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP


title: Cd206_hi_0h_89

value: mouse dural cd206_hi cell

value: FACS sorted

value: single cell RNA


title: M0008 day0

description: sorted EGFP+ cells

value: Cells were collected 9 days after viral transduction


title: PDC rep7

description:
PDC_7
counts.Cell.Lines.txt

value: PDC


title: M0007 day9

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: Cd206_hi_0h_87


title: as3mtmut_female_liver2

value: female

value: liver


title: M0007 day0

description: sorted EGFP+ cells


title: M0004 day0

description: sorted EGFP+ cells


title: wttab14_male_liver2

value: male


title: as3mtmut_female_liver1


title: PDC rep4

description:
PDC_4
counts.Cell.Lines.txt


title: Cd206_hi_0h_86


title: M0006 day0

description: sorted EGFP+ cells


title: wttab14_female_liver1


title: wttab14_male_liver1


title: Cd206_hi_0h_88


title: M0003 day9


title: PDC rep2

description:
PDC_2
counts.Cell.Lines.txt


title: Supraspinatus day 3 Bursa intact, rep 6

city: New York

first: Stavros

last: Thomopoulos

state: NY

institute: Columbia University

description:
SB046
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv

data_processing:
Libaries were sequenced using Illumina NovaSeq 6000.
Samples were multiplex samples in each lane, yielding targeted number of paired-end 100bp reads for each sample.
Used RTA (Illumina) base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
Performed pseudoalignment to a kallisto index created from transcriptomes (Ensembl v92) using kallisto (0.44.0)
Tested for differentially expressed genes using DESeq2
Supplementary files format and content: Tab delimited data file containing raw counts for each sample
Supplementary files format and content: Tab delimited data file containing DESeq2 expression results per study design

organism: Rattus norvegicus

source_name: supraspinatus tendon

extract_protocol:
Rats were sacrificed at 3- or 14-days post-operation. Bursa and supraspinatus tendon were dissected and stored in AllProtect reagent for 24 hours at room temperature before transfer to -80deg storage until further processing steps. Before RNA isolation, AllProtect was removed via centrifugation in nested Eppendorf tubes (inner tube punctured with hole to drain off AllProtect). Tissues were then snap frozen and homogenized using a ball mill homogenizer. RNA extraction QIAzol lysis reagent and Maxtract high density phase lock gel tubes. RNA purification was confucted using the RNeasy Mini Kit spin columns. RNA concentraiton was then quantified and checked for quality using the Bioanalyzer (Agilent) prior to sequencing.
used poly-A pull-down to enrich mRNAs from total RNA samples, then proceeded with library construction using Illumina TruSeq chemistry

treatment_protocol: Rat supraspinatus tendons were tenotomized and bursa was either removed or kept in tact; tissues (both supraspinatus and the remaining bursa of each rat) were dissected 3 or 14 days post-operation

value: supraspinatus tendon

value: tenotomy and bursa intact, 3 days post op


title: M0003 day0

description: sorted EGFP+ cells

value: Cells were sorted by FACS


title: Late OA, chondrocytes #5

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

description:
Counts_Matrix.txt
LateOA2_S5

data_processing:
Alignment using HISAT2 2.1.0 build of Ensembl GRCh38 of primary assembly with default paired-end unstranded parameters and converting to sorted bam files using Samtools 1.9
Counts were generated using HT-Seq 0.11.2 using Ensembl GRCh38 as GTF file and using unstranded strandedness, gene_id GFF attribute, union mode, and exon feature type as parameters
edgeR in Rstudio using R version 4.0 including CPM values for each sample
Genome_build: GRCh38

source_name: damaged cartilage from osteoarthritic knee joint

extract_protocol:
Total RNA extracted by Qiazol, RNeasy® Plus Universal Mini Kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cartilage was digested by type 2 collagenase at 170 RPM at 37°C for 16 hours, then chondrocytes were harvested.

tag: disease state

value: osteoarthritis

value: chondrocyte

tag: group

value: Late


title: Supraspinatus day 3 Bursa intact, rep 5

description:
SB043
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: Late OA, chondrocytes #4

description:
Counts_Matrix.txt
LateOA1_S4

tag: cell type


title: PDC rep1

description:
PDC_1
counts.Cell.Lines.txt


title: Cd206_hi_0h_85

tag: strain

tag: treatment


title: Cd206_hi_0h_84

tag: molecule type


title: Late OA, chondrocytes #6

description:
Counts_Matrix.txt
LateOA3_S6


title: M0002 day9

value: Skin tumor

value: Melanoma


title: PDC rep3

description:
PDC_3
counts.Cell.Lines.txt

tag: cell line

tag: tumor type


title: Supraspinatus day 3 Bursa intact, rep 4

description:
SB040
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: Cd206_hi_0h_83

value: mouse dural cd206_hi cell


title: wttab14_female_liver2


title: M0004 day9

tag: transduction

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP


title: M0001 day9


title: M0001 day0

description: sorted EGFP+ cells

value: Cells were transducted with EGFP

value: sorted live(DAPI-) and EGFP+


title: Supraspinatus day 3 Bursa intact, rep 1

description:
SB031
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: M2778 day9

value: Cells were collected 9 days after viral transduction


title: Supraspinatus day 3 Bursa removed, rep 6

description:
SB044
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv

value: tenotomy and bursa removed, 3 days post op


title: M0002 day0

description: sorted EGFP+ cells


title: Supraspinatus day 3 Bursa removed, rep 5

description:
SB041
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv


title: RPMI-1640-1-2_L2

city: Jinan

first: Ting

last: Yu

state: Shandong

address: No. 324, Jingwu Weiqi Road, Huaiyin District

institute: Tumor Research and Therapy Centre, Shandong Provincial Hospital Affiliated to Shandong University

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

growth_protocol: B16F10 cells were maintained in DMEM or RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using trizol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells .
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: melanoma cell

value: WT


title: DMEM-HG-3-3_L3

value: DMEM


title: Supraspinatus day 3 Bursa intact, rep 2

description:
SB034
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv

value: supraspinatus tendon


title: Supraspinatus day 3 Bursa intact, rep 3

description:
SB037
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv

value: tenotomy and bursa intact, 3 days post op


title: Supraspinatus day 3 Bursa removed, rep 2

description:
SB032
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv


title: Cd206_hi_0h_82

value: FACS sorted

value: single cell RNA


title: T98G day9

description: sorted EGFP+ cells expressing at least one of the reprogramming markers (CD45 or HLA-DR)

source_name: Brain tumor cell line

value: Brain tumor cell line

value: Glioblastoma

value: Cells were sorted by FACS

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: EarlyOA, chondrocytes #3

description:
Counts_Matrix.txt
EarlyOA3_S3

source_name: preserved cartilage from osteoarthritic knee joint

value: osteoarthritis

value: chondrocyte

value: Early


title: DMEM-HG-3-2_L2


title: Cd206_hi_0h_81

value: mouse dural cd206_hi cell


title: Supraspinatus day 3 Bursa removed, rep 1

description:
SB029
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv


title: EarlyOA, chondrocytes #2

description:
Counts_Matrix.txt
EarlyOA2_S2


title: EarlyOA, chondrocytes #1

description:
Counts_Matrix.txt
EarlyOA1_S1


title: Cd206_hi_0h_76


title: Cd206_hi_0h_80


title: RPMI-1640-1-3_L2


title: M2778 day0

description: sorted EGFP+ cells

value: Skin tumor

value: Melanoma

value: Cells were transducted with EGFP

value: Cells were collected 9 days after viral transduction

value: sorted live(DAPI-) and EGFP+


title: ChIPRx_2wk_ctx_nsd1_cKO_Input_ab2_biorep2

city: Saint Louis

first: Nicole

last: Hamagami

state: MO

address: 4487 McPherson Ave. Unit C

department: Neuroscience

institute: Washington University in St. Louis

data_processing:
library strategy: ChIP-Rx
ChIP-Rx reads were mapped to the mm9 and dm6 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated.
Bedtools coverage -counts parameter was used to quantify ChIP signal
To generate bigWig files, bedtools genomecov parameter was used to convert ChIP-seq reads to a bedgraph format and then were renormalized (to counts per million, cpm). Bedgraphs were subsequently converted to bigWigs.
ChIP-Rx ratio(Rx) was calculated by deriving the percentage of reads aligning to mm9 versus dm6, and using the equation Rx = (IP^mm9/IP^dm6)/(Input^mm9/Input^dm6). cKO tracks were normalized by multiplying by the percent difference between cKO and WT ChIP-Rx ratios.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: cerebral cortex

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the S220 Ultrasonicator (Covaris). Sonicated S2R+ chromatin was subsequently added at 5% of total chromatin.
ChIP-Rx libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) and complemented with the Accel-NGS 2S Set A adapters. Up to 4ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12-16 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent DNA D5000 Screentape Assay Kit.

value: Nsd1 flx/flx; Nestin-cre +/- (NSD1 cKO)

value: F

value: cerebral cortex

value: 2 week

tag: biological replicate

tag: chip antibody


title: Cd206_hi_0h_72

value: FACS sorted

value: single cell RNA


title: Cd206_hi_0h_78


title: M0845 day9

tag: tissue

value: Cells were sorted by FACS

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP


title: Cd206_hi_0h_77


title: RPMI-1640-1-1_L2

value: melanoma cell

value: WT


title: Supraspinatus day 3 Bursa removed, rep 4

description:
SB038
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv

value: supraspinatus tendon

value: tenotomy and bursa removed, 3 days post op


title: Supraspinatus day 3 Bursa removed, rep 3

description:
SB035
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB031_SB034_SB037_SB040_SB043_SB046-DEG_list.csv


title: M0845 day0

description: sorted EGFP+ cells

tag: donor

value: Skin tumor


title: Cd206_hi_0h_75

description:
Cd206_hi_0h
Mhc2_Cd206_baseline_raw_expression_matrix.csv

value: mouse dural cd206_hi cell


title: Cd206_hi_0h_74


title: T98G day7

value: Brain tumor cell line

value: Glioblastoma

tag: time

value: Cells were collected 7 days after viral transduction

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: Cd206_hi_0h_79


title: DMEM-HG-3-1_L2

value: DMEM


title: Cd206_hi_0h_70


title: T98G day5

value: Cells were collected 5 days after viral transduction

tag: sorted cell_type


title: Cd206_hi_0h_73


title: S-2P- B cell v2M6 Rep2 - ADT

city: Bethesda

first: Susan

last: Moir

state: Maryland

address: 9000 Rockville Pike

department: NIAID

institute: NIH

description: 10x Genomics

data_processing:
The GEX and ADT libraries were mapped to the GRCh38 human reference genome using CellRanger version 6.0.1. Data were further processed using Seurat version 4.1.0 running in R v4.1.0.
B cell receptor V(D)J data processing, B cell receptor (BCR) V(D)J repertoire data processing and analysis were carried out using tools in the Immcantation framework (www.immcantation.org). V(D)J genes were re-assigned from CellRanger output using IgBLAST v.1.15.0. Cells with multiple IGH V(D)J sequences were assigned to the most abundant IGH V(D)J sequence by UMI count. Following V(D)J gene annotation, non-functional sequences were removed from further analysis, and functional V(D)J sequences were assigned into clonal groups using Change-O v.1.0.0. Then, the immune repertoire information was added into Seurat object as meta data integrated to the transcriptome information at a per-cell level.
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files, antibody feature reference csv files

extract_protocol:
B cells of three vaccinees were isolated from thawed cryopreserved peripheral blood mononuclear cells (PBMC) by negative magnetic bead-based selection using a B cell enrichment cocktail (StemCell Technologies). The isolated B cells were stained with PE-Cy7-conjugated anti-human CD19 (ThermoFisher, cat# 25-0198-42) and APC-H7-conjugated anti-human CD20 (BD Biosciences, cat# 560734). SARS-CoV-2-specific B cells were identified using biotinylated spike protein (S-2P) tetramerized with PE-Cy5.5-labeled streptavidin (SA) (ThermoFisher, cat# SA1018) at a molar ratio of 4:1. Three B cell populations were sorted, (1) CD20+S-2P+ B cell, (2) CD20+S-2P-  B cell, and (3) CD20- B cell (plasmablast) populations, using a BD FACSAria Fusion instrument (BD Biosciences).
Isolated B cells from different donors were pooled evenly before cell sorting. Cells from each donor were demultiplexed in silico using donor-specific single nucleotide polymorphism (SNP) information collected during data analysis. Multiple cell pools were prepared, such that cells from the same donors but different time points were in different pools. After cell sorting, cell pools from v2D28 and v2M6 timepoints were Fc blocked (Human TruStain FcX, BioLegend), CITE-seq and hashtag stained with custom TotalSeq-C cocktail antibodies, (including RBD and S1 oligo-tagged tetramers, and washed 3x with staining buffer (2% BSA in PBS). Due to the lower frequency of S-2P+ B cells at earlier time points, pools from v1D14 to v2D14 timepoints were CITE-seq and hashtag (HTO) stained before cell sorting to avoid cell loss during washes. No RBD and S1 oligo-tagged tetramers could be added due to technical reasons. Final cell pools were suspended in 0.04% BSA in PBS and then counted before being immediately processed by the single cell partitioning step. Cell pools were mixed with a reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using the 10x Chromium Single Cell Immune Profiling Next GEM v2 Chemistry Kit (10x Genomics, Pleasanton, CA). The RT step was conducted using a C1000 touch Thermo Cycler (BioRad, Hercules, CA). Single-cell gene expression (GEX), cell surface protein (ADT) and B cell receptor (BCR) libraries were prepared as instructed by 10x Genomics Single Cell Immune Profiling kit v.2 user guide. A total of 84 libraries were quality control tested using a TapeStation 4200 (Agilent, Santa Clara, CA) and quantified using the KAPA Library Quantification kit (Roche, Wilmington, MA). These libraries were then pooled and sequenced on Illumina NovaSeq platform (Illumina, San Diego, CA) using the sequencing parameters recommended by the 10x Genomics user guide. The minimum sequencing depths were 50,000 read pairs/cell for the GEX library, 5,000 read pairs/cell for the BCR library, and 5,000 read pairs/cell for the ADT library. Sequencing saturation of the libraries was 80% for the GEX and 10% for the BCR and ADT libraries.

value: S-2P- B cell

tag: timepoint


title: T98G

value: Cells were transducted with EGFP

value: Cells were collected 9 days after viral transduction

value: sorted live(DAPI-) and EGFP+


title: T98G day3

value: Cells were sorted by FACS

value: Cells were transducted with PU.1, IRF8, BATF3 (PIB) and EGFP

value: Cells were collected 3 days after viral transduction


title: Cd206_hi_0h_69

value: FACS sorted

value: single cell RNA


title: Supraspinatus day 14 Bursa intact, rep 5

description:
SB025
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv

value: supraspinatus tendon

value: tenotomy and bursa intact, 14 days post op


title: Supraspinatus day 14 Bursa intact, rep 4

description:
SB022
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: Cd206_hi_0h_71

value: mouse dural cd206_hi cell


title: ChIPRx_2wk_ctx_nsd1_ctrl_Input_ab2_biorep2

tag: genotype

value: Nsd1 flx/flx; Nestin-cre -/- (NSD1 ctrl)

tag: Sex

value: F

value: cerebral cortex

value: 2 week


title: Cd206_hi_0h_67


title: Supraspinatus day 14 Bursa intact, rep 6

description:
SB028
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: ChIPRx_2wk_ctx_nsd1_ctrl_Input_ab2_biorep1

value: M


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me2_ab2_biorep2


title: Supraspinatus day 14 Bursa intact, rep 3

description:
SB019
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: ChIPRx_2wk_ctx_nsd1_cKO_Input_ab2_biorep1

value: Nsd1 flx/flx; Nestin-cre +/- (NSD1 cKO)


title: Supraspinatus day 14 Bursa intact, rep 2

description:
SB016
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me2_ab2_biorep2


title: Supraspinatus day 14 Bursa intact, rep 1

description:
SB013
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: Cd206_hi_0h_68


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me2_ab2_biorep1


title: Cd206_hi_0h_66


title: Supraspinatus day 14 Bursa removed, rep 6

description:
SB026
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv

value: tenotomy and bursa removed, 14 days post op


title: Cd206_hi_0h_65


title: S-2P- B cell v2M6 Rep2 - GEX

description: 10x Genomics

value: S-2P- B cell


title: Cd206_hi_0h_64


title: Supraspinatus day 14 Bursa removed, rep 3

description:
SB017
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: Supraspinatus day 14 Bursa removed, rep 5

description:
SB023
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: Supraspinatus day 14 Bursa removed, rep 4

description:
SB020
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: S-2P- B cell v2M6 Rep1 - GEX

description: 10x Genomics


title: S-2P- B cell v2M6 Rep1 - ADT

description: 10x Genomics


title: Supraspinatus day 14 Bursa removed, rep 2

description:
SB014
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: S-2P+ B cell v2M6 Rep2 - ADT

description: 10x Genomics

value: S-2P+ B cell


title: Cd206_hi_0h_63


title: RNA_8wk_ctx_nsd1_cKO_biorep5

data_processing:
Sequence reads were trimmed for adaptors using Trim Galore and filtered for rRNA sequences with Bowtie.
Remaining reads were aligned to the mm9 genome with STAR. Only uniquely mapping reads were converted to BED files and separated by intronic and exonic reads.
Bedtools coverage -counts paramter was used to assess read coverage in genes.
Assembly: mm9

extract_protocol:
RNA was harvested using Allprep DNA/RNA Mini Kit (Qiagen). 250ng of total RNA was used for the construction of sequencing libraries.
RNA was rRNA depleted using NEBNext rRNA Depletion Kit (NEB). RNA libraries for RNA-seq were subsequently prepared using NEBNext Ultra Directional RNA Library Prep Kit with NEBNext Mulitplex Oligos for Illumina (NEB) following manufacturer's protocols.

value: 8 week

tag: biolgical replicate


title: Supraspinatus day 14 Bursa removed, rep 1

description:
SB011
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB011_SB014_SB017_SB020_SB023_SB026-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB013_SB016_SB019_SB022_SB025_SB028-DEG_list.csv


title: RNA_8wk_ctx_nsd1_cKO_biorep4


title: S-2P+ B cell v2M6 Rep2 - GEX

description: 10x Genomics

tag: cell type


title: RNA_8wk_ctx_nsd1_cKO_biorep2


title: Supraspinatus Control, rep 5

description:
SB010
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv

value: control


title: Cd206_hi_0h_62

tag: strain


title: RNA_8wk_ctx_nsd1_cKO_biorep1


title: S-2P+ B cell v2M6 Rep1 - ADT

description: 10x Genomics


title: RNA_8wk_ctx_nsd1_cKO_biorep3


title: Cd206_hi_0h_61

tag: treatment


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me2_ab2_biorep1


title: Cd206_hi_0h_60

tag: molecule type


title: Cd206_hi_0h_58


title: RNA_8wk_ctx_nsd1_ctrl_biorep6


title: Supraspinatus Control, rep 2

description:
SB004
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv


title: S-2P+ B cell v2M6 Rep1 - GEX

description: 10x Genomics


title: Supraspinatus Control, rep 1

description:
SB002
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv


title: Supraspinatus Control, rep 4

description:
SB008
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv


title: RNA_8wk_ctx_nsd1_ctrl_biorep5


title: Supraspinatus Control, rep 3

description:
SB006
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB031_SB034_SB037_SB040_SB043_SB046_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB029_SB032_SB035_SB038_SB041_SB044_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB013_SB016_SB019_SB022_SB025_SB028_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv
DESeq2_kallisto_SB011_SB014_SB017_SB020_SB023_SB026_vs_SB002_SB004_SB006_SB008_SB010-DEG_list.csv


title: Cd206_hi_0h_59

description:
Cd206_hi_0h
Mhc2_Cd206_baseline_raw_expression_matrix.csv


title: Plasmablast v1D14 Rep2 - ADT

description: 10x Genomics

value: Plasmablast


title: Cd206_hi_0h_57

value: FACS sorted


title: Bursa day 3 Activated, rep 5

description:
SB042
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv

source_name: subacromial bursa

value: subacromial bursa

value: activated by tenotomy, 3 days post op


title: RNA_8wk_ctx_nsd1_ctrl_biorep4


title: Cd206_hi_0h_56

value: single cell RNA


title: Bursa day 3 Activated, rep 6

description:
SB045
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: RNA_8wk_ctx_nsd1_ctrl_biorep3


title: Plasmablast v1D14 Rep2 - GEX

description: 10x Genomics


title: Cd206_hi_0h_55

value: mouse dural cd206_hi cell


title: RNA_8wk_ctx_nsd1_ctrl_biorep2

value: Nsd1 flx/flx; Nestin-cre -/- (NSD1 ctrl)


title: Cd206_hi_0h_54


title: Cd206_hi_0h_53


title: Bursa day 3 Activated, rep 3

description:
SB036
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: Bursa day 3 Activated, rep 2

description:
SB033
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: Bursa day 3 Activated, rep 4

description:
SB039
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: ChIPRx_2wk_ctx_nsd1_cKO_Input_biorep5

data_processing:
ChIP-Rx reads were mapped to the mm9 and dm6 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated.
Bedtools coverage -counts parameter was used to quantify ChIP signal
To generate bigWig files, bedtools genomecov parameter was used to convert ChIP-seq reads to a bedgraph format and then were renormalized (to counts per million, cpm). Bedgraphs were subsequently converted to bigWigs.
ChIP-Rx ratio(Rx) was calculated by deriving the percentage of reads aligning to mm9 versus dm6, and using the equation Rx = (IP^mm9/IP^dm6)/(Input^mm9/Input^dm6). cKO tracks were normalized by multiplying by the percent difference between cKO and WT ChIP-Rx ratios.
Assembly: mm9
Supplementary files format and content: bigWig
Library strategy: ChIP-Rx


title: Plasmablast v1D14 Rep1 - GEX

description: 10x Genomics


title: Cd206_hi_0h_52

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v3.1.1). Then, low quality cells (expressing less than 500 genes or more than 9000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for dural Cd206_hi cells and Mhc2_hi cells at base line condition.


title: Cd206_hi_0h_51


title: Cd206_hi_0h_50


title: ChIPRx_2wk_ctx_nsd1_cKO_Input_biorep2


title: Bursa day 3 Activated, rep 1

description:
SB030
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: ChIPRx_2wk_ctx_nsd1_cKO_Input_biorep3

value: F


title: ChIPRx_2wk_ctx_nsd1_cKO_Input_biorep1

value: cerebral cortex


title: S-2P- B cell v1D14 Rep2 - ADT

description: 10x Genomics


title: Bursa day 14 Activated rep 5

description:
SB024
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv

value: activated by tenotomy, 14 days post op


title: Plasmablast v1D14 Rep1 - ADT

description: 10x Genomics


title: ChIPRx_2wk_ctx_nsd1_ctrl_Input_biorep5

value: M

value: 2 week


title: S-2P- B cell v1D14 Rep1 - GEX

description: 10x Genomics


title: Cd206_hi_0h_49


title: ChIPRx_2wk_ctx_nsd1_ctrl_Input_biorep4


title: Cd206_hi_0h_46


title: S-2P- B cell v1D14 Rep1 - ADT

description: 10x Genomics


title: Bursa day 14 Activated, rep 2

description:
SB015
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: RNA_8wk_ctx_nsd1_ctrl_biorep1


title: Bursa day 14 Activated, rep 1

description:
SB012
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: Bursa day 14 Activated, rep 4

description:
SB021
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: Cd206_hi_0h_48


title: ChIPRx_2wk_ctx_nsd1_ctrl_Input_biorep2


title: Cd206_hi_0h_47


title: Bursa day 14 Activated, rep 3

description:
SB018
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: ChIPRx_2wk_ctx_nsd1_ctrl_Input_biorep3


title: ChIPRx_2wk_ctx_nsd1_cKO_Input_biorep4

value: Nsd1 flx/flx; Nestin-cre +/- (NSD1 cKO)


title: Cd206_hi_0h_45


title: Bursa Control, rep 5

description:
SB009
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv


title: Bursa Control, rep 4

description:
SB007
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv


title: Cd206_hi_0h_43


title: S-2P- B cell v1D14 Rep2 - GEX

description: 10x Genomics

value: S-2P- B cell


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me3_biorep5

value: H3K36me3 (Active Motif, #61101)


title: Bursa Control, rep 3

description:
SB005
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv


title: Cd206_hi_0h_42


title: ChIPRx_2wk_ctx_nsd1_ctrl_Input_biorep1


title: Cd206_hi_0h_44


title: S-2P+ B cell v1D14 - GEX

description: 10x Genomics

value: S-2P+ B cell


title: Bursa day 14 Activated, rep 6

description:
SB027
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB012_SB015_SB018_SB021_SB024_SB027-DEG_list.csv


title: RNA_8wk_ctx_nsd1_cKO_biorep6

value: 8 week


title: S-2P+ B cell v1D14 - ADT

description: 10x Genomics


title: Bursa Control, rep 2

description:
SB003
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv

value: control


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me3_biorep3


title: Cd206_hi_0h_40

description:
Cd206_hi_0h
Mhc2_Cd206_baseline_raw_expression_matrix.csv

value: FACS sorted


title: Cd206_hi_0h_41


title: Bursa Control, rep 1

description:
SB001
est_counts_transcripts_kallisto.txt
DESeq2_kallisto_SB030_SB033_SB036_SB039_SB042_SB045_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv
DESeq2_kallisto_SB012_SB015_SB018_SB021_SB024_SB027_vs_SB001_SB003_SB005_SB007_SB009-DEG_list.csv

value: subacromial bursa


title: Plasmablast v2D6 Rep2 - ADT

description: 10x Genomics

value: Plasmablast


title: Cd206_hi_0h_39

value: single cell RNA


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me3_biorep2


title: Cd206_hi_0h_38

value: mouse dural cd206_hi cell


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me3_biorep1


title: Plasmablast v2D6 Rep1 - GEX

description: 10x Genomics


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me3_biorep5

value: Nsd1 flx/flx; Nestin-cre -/- (NSD1 ctrl)


title: GBC-SD_CDCA_3

first: Tianli

last: Chen

address: 107 West Wenhua Road

department: Department of General Surgery

institute: Qilu Hospital of Shandong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include FPKM values for each Sample

source_name: human gallbladder carcinoma cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (allwegene, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GBC-SD

tag: disease state

value: gallbladder carcinoma

value: CDCA stimulation for 72 hours


title: GBC-SD_CDCA_2


title: Cd206_hi_0h_37

extract_protocol:
FACS sorted dural Cd206_hi cells and Mhc2_hi cells were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)


title: GBC-SD_CDCA_4


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me3_biorep4

value: F

value: cerebral cortex


title: S-2P- B cell v2D6 Rep2 - ADT

description: 10x Genomics


title: Cd206_hi_0h_36


title: Plasmablast v2D6 Rep2 - GEX

description: 10x Genomics


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me3_biorep4

value: Nsd1 flx/flx; Nestin-cre +/- (NSD1 cKO)

value: 2 week


title: Cd206_hi_0h_35


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me3_biorep3

value: H3K36me3 (Active Motif, #61101)


title: S-2P- B cell v2D6 Rep2 - GEX

description: 10x Genomics

value: S-2P- B cell


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me3_biorep2

value: M


title: Plasmablast v2D6 Rep1 - ADT

description: 10x Genomics


title: GBC-SD_Ctrl_3

value: control group without CDCA stimulation


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me3_biorep1


title: Cd206_hi_0h_34

value: FACS sorted


title: Cd206_hi_0h_33


title: GBC-SD_Ctrl_2


title: S-2P- B cell v2D6 Rep1 - ADT

description: 10x Genomics


title: ChIPRx_2wk_ctx_nsd1_cKO_DNMT3A_biorep5

value: DNMT3A (abcam, #ab2850)


title: GBC-SD_Ctrl_1


title: Cd206_hi_0h_32


title: ChIPRx_2wk_ctx_nsd1_cKO_DNMT3A_biorep4


title: ChIPRx_2wk_ctx_nsd1_cKO_DNMT3A_biorep3


title: NCI-H889_DMSO_4h_rep2

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

data_processing:
Multiplexed samples were sequenced on an Illumina HiSeq 2500 system. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Data was processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: In brief, paired-end sequencing reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (source 1000 Genomes Project - GRCh38_full_analysis_set_plus_decoy_hla.fa,  excluding alternate contigs, chromosome mapping via grch38_ucsc2ensembl.txt) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the counts derived from featureCount using limma/voom.
Assembly: GRCh38
Supplementary files format and content: Processed data files contain sample-wise results produced by FeaturesCounts and include raw count values for each gene.

source_name: NCI-H889 cancer cell line

growth_protocol: The cell lines were grown in the media recommended by the vendor.

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
RNA-seq libraries were prepares using the TruSeq RNA Library Preparation Kit v2 according to manufacturer's instructions.

treatment_protocol: See samples section.

tag: cell line

tag: disease

value: small cell lung cancer

tag: replicate

tag: ID


title: ChIPRx_2wk_ctx_nsd1_cKO_DNMT3A_biorep2

tag: tissue

tag: biological replicate

tag: chip antibody


title: S-2P+ B cell v2D6 Rep2 - GEX

description: 10x Genomics

value: S-2P+ B cell


title: GBC-SD_CDCA_1


title: S-2P+ B cell v2D6 Rep2 - ADT

description: 10x Genomics


title: Cd206_hi_0h_29

value: mouse dural cd206_hi cell

value: single cell RNA


title: NCI-H889_BI00894999_100nM_4h_rep2


title: GBC-SD_Ctrl_4

value: GBC-SD


title: S-2P+ B cell v2D6 Rep1 - ADT

description: 10x Genomics


title: Cd206_hi_0h_28


title: NCI-H889_BI00894999_100nM_4h_rep1


title: ChIPRx_2wk_ctx_nsd1_cKO_DNMT3A_biorep1

tag: time


title: Cd206_hi_0h_27


title: NCI-H69_DMSO_4h_rep2

source_name: NCI-H69 cancer cell line


title: ChIPRx_2wk_ctx_nsd1_ctrl_DNMT3A_biorep4

value: Nsd1 flx/flx; Nestin-cre -/- (NSD1 ctrl)


title: S-2P- B cell v2D6 Rep1 - GEX

description: 10x Genomics

tag: timepoint


title: Cd206_hi_0h_31


title: NCI-H889_DMSO_4h_rep1


title: ChIPRx_2wk_ctx_nsd1_ctrl_DNMT3A_biorep3

tag: genotype


title: S-2P+ B cell v2D6 Rep1 - GEX

description: 10x Genomics


title: Cd206_hi_0h_26


title: NCI-H69_BI00894999_100nM_4h_rep1


title: Cd206_hi_0h_25


title: Cd206_hi_0h_30


title: NCI-H69_BI00894999_100nM_4h_rep2


title: Plasmablast v2D9 - ADT

description: 10x Genomics

value: Plasmablast


title: NCI-H510A_DMSO_4h_rep2

source_name: NCI-H510A cancer cell line


title: ChIPRx_2wk_ctx_nsd1_ctrl_DNMT3A_biorep2

tag: Sex


title: ChIPRx_2wk_ctx_nsd1_ctrl_DNMT3A_biorep5


title: Cd206_hi_0h_24


title: Cd206_hi_0h_23


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me2_biorep5


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me2_biorep4

value: F


title: Cd206_hi_0h_21


title: NCI-H510A_BI00894999_100nM_4h_rep2


title: Cd206_hi_0h_22


title: NCI-H510A_BI00894999_100nM_4h_rep1


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me2_biorep3

value: cerebral cortex


title: S-2P- B cell v2D9 Rep2 - GEX

description: 10x Genomics


title: Cd206_hi_0h_20


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me2_biorep2

value: Nsd1 flx/flx; Nestin-cre +/- (NSD1 cKO)


title: S-2P- B cell v2D9 Rep1 - ADT

description: 10x Genomics


title: ChIPRx_2wk_ctx_nsd1_cKO_H3K36me2_biorep1

value: 2 week


title: Cd206_hi_0h_19


title: ChIPRx_2wk_ctx_nsd1_ctrl_DNMT3A_biorep1


title: NCI-H2196_BI00894999_100nM_4h_rep2

source_name: NCI-H2196 cancer cell line


title: NCI-H2196_BI00894999_100nM_4h_rep1


title: Cd206_hi_0h_18


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me2_biorep5


title: Plasmablast v2D9 - GEX

description: 10x Genomics


title: NCI-H510A_DMSO_4h_rep1


title: NCI-H2081_DMSO_4h_rep2

source_name: NCI-H2081 cancer cell line


title: NCI-H2081_DMSO_4h_rep1


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me2_biorep4


title: Cd206_hi_0h_17


title: S-2P- B cell v2D9 Rep2 - ADT

description: 10x Genomics


title: S-2P- B cell v2D9 Rep1 - GEX

description: 10x Genomics


title: Cd206_hi_0h_16


title: NCI-H2081_BI00894999_100nM_4h_rep2


title: Cd206_hi_0h_15


title: NCI-H2196_DMSO_4h_rep1


title: S-2P+ B cell v2D9 Rep2 - ADT

description: 10x Genomics


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me2_biorep2


title: S-2P+ B cell v2D9 Rep2 - GEX

description: 10x Genomics


title: NCI-H2081_BI00894999_100nM_4h_rep1


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me2_biorep1


title: NCI-H1048_DMSO_4h_rep2

source_name: NCI-H1048 cancer cell line


title: ChIP_DIV12_NSD1-sh2_DNMT3A_biorep2

data_processing:
ChIP-seq reads were mapped to the mm9 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated.
Bedtools coverage -counts parameter was used to quantify ChIP signal
To generate bigWig files, bedtools genomecov parameter was used to convert ChIP-seq reads to a bedgraph format and then were renormalized (to counts per million, cpm). Bedgraphs were subsequently converted to bigWigs.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: cultured cortical neurons

growth_protocol: Neurobasal medium supplemented with 5% fetal bovine serum, GlutaMAX, B27 Supplement and Antibiotic-Antimycotic. Cells were maintained at 37oC with 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico sonicator (Diagenode) for 30 cycles of 30s on/ 30s off.
ChIP-seq libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) and complemented with the Accel-NGS 2S Set A adapters. Up to 4ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12-16 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent DNA D5000 Screentape Assay Kit.

treatment_protocol: Cells were treated with lentivirally expressed shRNAs at MOI of 3 on days in vitro (DIV) 1. Cells were grown in vitro until DIV 12.

value: cultured cortical neurons

value: NSD1 sh2


title: S-2P+ B cell v2D9 Rep1 - ADT

description: 10x Genomics


title: Cd206_hi_0h_12


title: NCI-H1048_DMSO_4h_rep1


title: Cd206_hi_0h_11


title: NCI-H1048_BI00894999_100nM_4h_rep2


title: ChIP_DIV12_NSD1-sh2_DNMT3A_biorep1


title: Cd206_hi_0h_10


title: ChIPRx_2wk_ctx_nsd1_ctrl_H3K36me2_biorep3


title: ChIP_DIV12_NSD1-sh1_DNMT3A_biorep2

value: NSD1 sh1


title: ChIP_DIV12_NSD1-sh1_DNMT3A_biorep1


title: DMS53_DMSO_4h_rep2

source_name: DMS 53 cancer cell line

value: DMS 53


title: ChIP_DIV12_NSD1-sh2_H3K36me2_biorep2


title: Cd206_hi_0h_9

value: FACS sorted


title: S-2P- B cell v2D14 Rep2 - ADT

description: 10x Genomics

value: S-2P- B cell


title: S-2P- B cell v2D14 Rep2 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D9 Rep1 - GEX

description: 10x Genomics


title: DMS53_DMSO_4h_rep1

value: small cell lung cancer


title: ChIP_DIV12_NSD1-sh2_H3K36me2_biorep1


title: Cd206_hi_0h_14


title: Cd206_hi_0h_8


title: DMS53_BI00894999_100nM_4h_rep2


title: Cd206_hi_0h_7


title: ChIP_DIV12_NSD1-sh1_H3K36me2_biorep2


title: DMS53_BI00894999_100nM_4h_rep1


title: Cd206_hi_0h_6


title: Cd206_hi_0h_13


title: ChIP_DIV12_NSD1-sh1_H3K36me2_biorep1


title: S-2P- B cell v2D14 Rep1 - ADT

description: 10x Genomics