title: CAF3 control

city: Okayama

first: Shuta

last: Tomida

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

institute: Okayama University Hospital

data_processing:
RNA sequencing was performed on a Illumina HiSeq 2500 sequencer via PE150 setting.
Sequencing data were mapped and analyzed to calculate TPM (Transcripts Per Kilobase Million) values using the CLC Genomics Workbench (CLC bio, Aarhus, Denmark).
Assembly: Homo Sapience GRCh38
Supplementary files format and content: tab-delimited text files includeTPM values for each sample

source_name: fibroblast

growth_protocol: Cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).  20ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Access Library Prep Kit following manufacturer's protocols.

treatment_protocol: Normal fibroblasts (NFs) and cancer-associated fibroblasts (CAFs) were cultured in 1:1 mixture of fresh RPMI media and cancer conditioned media obtained from A549 or HCC827.

tag: condition

value: CAF3 control

tag: cell type

value: fibroblast

value: WT

value: no treatment (control)


title: CAF3 HCC827CM

status: Public on Jun 10 2023

type: SRA

country: Japan

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: CAF3 HCC827CM

tag: genotype

tag: treatment

value: cultured with conditioned media obtained from HCC827 for 48 hours


title: 140Ru_NM2

city: Dijon

first: Pierre-Emmanuel

last: COURTY

address: 17 rue Sully

country: France

institute: INRAE Dijon

data_processing:
CLC genomics work bench 12.0.4
Sequences were trimmed for adaptator/lowquality sequence using CLC genomics benchwork (parameter - qualitit limit 0,05)
Trimmed sequence reads were mapped to vitis vinifera genome ( Vvinifera_457_v2.1 from phytozome (https://phytozome-next.jgi.doe.goc/info/Vvinifera_2_1) using CLC genomics benchwork (parameters - mismatch cost: 2 insertion cost: 3 deletion cost:3 length fraction 0.8 similarity fraction : 0.8)
Read counts extraction and normalization were performed using CLC genomics bench work
Assembly: Vvinifera_457_v2.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Vitis vinifera

source_name: grapevine rootstock 140Ru

growth_protocol: Rootstocks of seven hybrids (110 Richter, 140 Ruggeri, 1103 Paulsen, Selection Oppenheim4, 420A Millardet et de Grasset, 41B Millardet et de Grasset and 101.14 Millardet et de Grasset) and some of their parentals (V. riparia, V. rupestris and V. berlandieri) were chosen. Hybrids were chosen according to (i) their parentals, (ii) their use at the French vineyard scale, (iii) their tolerance to drought, active limestone and the chlorosis power index (CPI), and the vigor conferred to the scion (Figure 1, Table 1). Herbaceous cuttings of rootstocks were dipped into water-saturated clumps of peat (Jiffy) and grown in a mini greenhouse at 25 °C for 4 weeks. Well-rooted plants with homogenous growth were transplanted individually in 1L pots filled with clay beads at their bottom and a mix of sterile sand/zeolite (1:1). From the first week on, 20 mL of modified Hoagland solution (Gamborg et al. 1976) were applied weekly.

extract_protocol:
RNA was extracted using protocol from sportes et al 2022
genewiz

treatment_protocol: Plantlets were watered twice a week. After two weeks of growth, about 200 spores of the AMF strain R. irregularis (Ri) DAOM197198 (spore suspension, Premier tech, Canada) were added directly in contact with the root system of half of the plants. inoculation was repeated one times, a month after the first inoculation. The plants were grown in a glasshouse with day - night temperatures of ca. 24 - 18 °C. Sixty pots were prepared.

tag: tissue

value: grapevine root

value: rootstock 140Ru

value: control


title: CAF3 A549CM

value: CAF3 A549CM

value: cultured with conditioned media obtained from A549 for 48 hours


title: NF3 A549CM

value: NF3 A549CM


title: NF3 HCC827CM

value: NF3 HCC827CM


title: 140Ru_NM1


title: 3E-005Hb

type: RNA

city: Boston

first: Ionita

middle: Calin

last: Ghiran

state: MA

address: 3 Blackfan Circle

department: Medicine

country: USA

institute: Beth Israel Deaconess Medical Center

description: Healthy Subject

data_processing:
Non-normalized were obtained from raw CT values
Normalized were obtained from substracting the mean of raw CT values by 25
ExpressionSuite Software v1.3

source_name: Plasma

label_protocol: As per TaqMan Advanced miRNA Assays protocol

extract_protocol: RNA was extracted from serum/plasma using Qiagen miRNeasy Serum/Plasma Advanced Kit

tag: Sex

value: Male

tag: age

tag: anticoagulant

value: E

tag: anatomical location

value: Entire cardiovascular system

tag: sample collection method

value: Peripheral venous cannula insertion - forearm


title: 140Ru_M3

value: Mycorrhization with rhizophagus irregularis


title: 2S-0Hb

description: Healthy Subject

source_name: Serum

value: S


title: 2S-5Hb

description: Healthy Subject


title: 140Ru_M1


title: 3E-5Hb

description: Healthy Subject


title: NF3 control

value: NF3 control

value: fibroblast

value: WT


title: CAF2 HCC827CM

value: CAF2 HCC827CM

value: cultured with conditioned media obtained from HCC827 for 48 hours


title: 2S-05Hb

description: Healthy Subject


title: 2S-005Hb

description: Healthy Subject


title: CAF2 A549CM

value: CAF2 A549CM


title: 140Ru_M2

value: grapevine root

value: rootstock 140Ru


title: 110R_NM3

source_name: grapevine rootstock 110R

value: rootstock 110R

value: control


title: THP-1 cells, LDL plus LL37 treatment 1

city: La Jolla

first: Yoahiyuki

last: Nakamura

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow
Trimmed sequence reads were mapped to STAR using Partek Flow
Read count extraction and normalization were performed using Partek Flow
Assembly: STAR
Supplementary files format and content: Excel files for treatments comparing no treatment with LSMean of each samples

growth_protocol: THP-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using PURELINK RNA MINI KIT (Thermo Fisher). Around 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared in IGM of UCSD

treatment_protocol: THP-1 cells were treated with LL37 and/or LDL for 24 hours.

tag: cell line

value: Macrophages

tag: time

value: Day 1


title: THP-1 cells, LDL plus LL37 treatment 3


title: 2H-5Hb

description: Healthy Subject

value: Male

value: H


title: THP-1 cells, LL37 treatment 1


title: THP-1 cells, LDL treatment 2

value: LDL


title: THP-1 cells, LDL treatment 3


title: THP-1 cells, LDL plus LL37 treatment 2


title: THP-1 cells, LL37 treatment 2


title: THP-1 cells, LL37 treatment 3


title: 2H-0Hb

description: Healthy Subject

value: Entire cardiovascular system

value: Peripheral venous cannula insertion - forearm


title: THP-1 cells, LDL treatment 1


title: NF2 HCC827CM

value: NF2 HCC827CM


title: 110R_NM2


title: NF2 A549CM

value: NF2 A549CM

value: fibroblast

value: cultured with conditioned media obtained from A549 for 48 hours


title: 110R_NM1


title: THP-1 cells, no treatment 2

value: WT

value: No treatment


title: 110R_M3

value: grapevine root

value: Mycorrhization with rhizophagus irregularis


title: THP-1 cells, no treatment 3


title: NF2 control

value: NF2 control

value: no treatment (control)


title: 2H-05Hb

description: Healthy Subject


title: 2E-5Hb

description: Healthy Subject

value: E


title: 110R_M2

value: rootstock 110R


title: 110R_M1


title: 2H-005Hb

description: Healthy Subject

value: Male


title: Normal-9

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

country: China

institute: The Second Military Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh_38
Supplementary files format and content: TXT file contain counts for each sample

source_name: blood

growth_protocol: No growth protocolt avaliable

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment avaliable

value: peripheral blood mononuclear cells

value: primary cell

value: blood


title: CAF1 HCC827CM

value: CAF1 HCC827CM

value: cultured with conditioned media obtained from HCC827 for 48 hours


title: 2E-0Hb

description: Healthy Subject

value: Entire cardiovascular system

value: Peripheral venous cannula insertion - forearm


title: CAF2 control

value: CAF2 control

value: fibroblast


title: CAF1 control

value: CAF1 control

value: WT


title: CAF1 A549CM

value: CAF1 A549CM

value: cultured with conditioned media obtained from A549 for 48 hours


title: Normal-8


title: NF1 HCC827CM

value: NF1 HCC827CM


title: 2E-05Hb

description: Healthy Subject

value: E


title: Normal-6


title: 41B_NM3

source_name: grapevine rootstock 41B

value: grapevine root

value: rootstock 41B

value: control


title: 41B_NM2


title: 2E-005Hb

description: Healthy Subject

value: Male


title: Normal-7

value: peripheral blood mononuclear cells

value: primary cell

value: blood


title: 41B_NM1


title: NF1 A549CM

value: NF1 A549CM


title: 1S-5Hb

description: Healthy Subject

value: Female

value: S

value: Entire cardiovascular system

value: Peripheral venous cannula insertion - forearm


title: Normal-5


title: NF1 control

value: NF1 control

value: fibroblast

value: WT

value: no treatment (control)


title: Normal-4


title: 41B_M2

value: Mycorrhization with rhizophagus irregularis


title: THP-1 cells, no treatment 1

value: Macrophages

value: No treatment

value: Day 1


title: 41B_M3

value: grapevine root

value: rootstock 41B


title: 1S-0Hb

description: Healthy Subject


title: Normal-3

value: peripheral blood mononuclear cells

value: primary cell


title: 1S-05Hb

description: Healthy Subject


title: Normal-2

value: blood


title: 1S-005Hb

description: Healthy Subject

value: Female


title: 41B_M1


title: Rv189

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

country: United Kingdom

institute: University of Glasgow

library_source: genomic

data_processing:
fastQ files were assessed using FastP
Data was aligned to the C. difficile R20291 (NCBI: NC_013316.1) reference genome using Bowtie2, under default settings.
VCF files were created from the BAM files using FreeBayes, under default settings.
Assembly: C. difficile R20291 (accession number NC_013316)
Supplementary files format and content: Unfiltered VCF file generated using FreeBayes.
Library strategy: DNA-seq

molecule: genomic DNA

organism: Clostridioides difficile

source_name: Clostridioides difficile

extract_protocol:
Individual clones of bacteria, recovered from faecal or tissue associated material that showed different morphology on ChromID plates, where subject to at least two rounds of clonal selection. Genomic DNA was isolated from a 20 ml culture grown anaerobically for 18 h in tryptic soya broth (TSB). Bacterial cells were initially disrupted enzymatically by resuspending the pellet in lysis buffer (20 mM Tris-Cl, pH8.0, 2 mM Na EDTA, 1.2 % Triton X-100, lysozyme 200 mg ml-1), and incubated at 56 oC for 90 min. The DNA was recovered using the DNeasy Blood and Tissue Kit (Qiagen), following manufacturer’s instructions.
Genomic DNA recovered from R20291, FM2.5, FM2.5varA, FM2.5varB were sequenced by MicrobesNG (Birmingham UK) using Illumina next-seq 500 with 250bp paired read length.

value: Clostridioides difficile

tag: strain


title: Rv9


title: 1H-05Hb

description: Healthy Subject

value: H

value: Entire cardiovascular system


title: R20291


title: Normal-15


title: Normal-14


title: Normal-13


title: 1H-5Hb

description: Healthy Subject

value: Peripheral venous cannula insertion - forearm


title: 1H-0Hb

description: Healthy Subject


title: Rv189 sample 6 [Rv189_3_S44]

data_processing:
fastQ files were assessed using FastP
Data was aligned to the C. difficile R20291 (NCBI: NC_013316.1) reference genome using STAR (Dobin et al., 2013) (v2.6) with –quantMode GeneCounts –outFilterMultimapNmax 1 and –outFilterMatchNmin 35. We used a Star index with a –sjdbOverhang of the maximum read length − 1.
Read count files were merged and genes with mean of < 1 read per sample were excluded.
The expression and differential expression values were generated using DESeq2 (Love, Huber and Anders, 2014) (v1.24). For differential comparisons we used an A versus B model with no additional covariates. All other parameters were left to default.
Assembly: C. difficile R20291 (NCBI: NC_013316.1)
Supplementary files format and content: Raw per gene read counts (read_counts.csv)

source_name: bacterial cell

growth_protocol: RNA was recovered from C. difficile strains R20291, FM2.5, RvA and RvB which had been cultured in vitro in TY broth.

extract_protocol:
Briefly, bacterial cells reaching an OD620nm = 0.6 were pelleted (5000 x g, 15 min) and immediately fixed in 1.5 ml RNA-protect (Qiagen) for 10 min before being processed using a PureLink RNA mini kit (Ambion) to extract total RNA. To ensure maximal lysis of bacteria and recovery of RNA the bacterial pellet was additionally subject to treatment with 100 ml lysozyme solution (10 mg/ml in 10 mM Tris-HCl [pH8.0] 0.1 mM EDTA), 0.5 ml 10% SDS solution and 350 ml of Lysis Buffer (Invitrogen PureLink RNA Mini Kit) containing 2-mercaptoethanol. Cells were then homogenised using MP Biomedical beads (0.1 mm) and bead beater (MP Biomedical FastPrep24) with cells subject to 2 cycles of 60 s beating followed by incubation on ice for 2 min. Total RNA was then extracted using the standard PureLink RNA mini kit protocol, according to the manufacturer’s specifications. Genomic DNA was removed using a TURBO DNase kit (Ambion) and samples were tested for efficient removal of DNA using PCR.
Illumina library preparation of mRNA samples for RNA-Seq was prepared using a TruSeq Stranded mRNA library prep kit (Illumina) according to the manufacturer’s instructions.
Sequencing was performed on the Illumina NextSeq 500 platform (75 bp length; single-end). Library generation, optimisation of amplification and sequencing were performed at the University of Glasgow Polyomics facility. Quality control of sequencing data was performed using FastQC (Babraham Bioinformatics) to assess the minimum Phred threshold of 20 and potential data contamination.

value: bacterial cell


title: Normal-12


title: Normal-11


title: 1E-5Hb

description: Healthy Subject

value: E


title: 1H-005Hb

description: Healthy Subject


title: Rv189 sample 4 [Rv189_1_S42]


title: Rv189 sample 5 [Rv189_2_S43]


title: Normal-10


title: 1E-05Hb

description: Healthy Subject


title: 1E-005Hb

description: Healthy Subject


title: Normal-1


title: FM2-5


title: Rv9 sample 6 [Rv9_3_S47]


title: P9-rep0 LD8


title: P9-rep2 LD9


title: GSC456 cells, Erlotinib-3

city: Wuhan

first: Wei

last: Wang

state: Hubei

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

data_processing:
The raw reads were quality-controlled and trimmed using Fastp (v0.20.1) with default parameters.
The resulting Clean RNA-seq reads were aligned to the human reference genome (GRCh38) using Hisat2 (v2.2.1), sorted and indexed using Samtools (v1.14).
The number of reads (raw_counts) per gene was determined using featureCounts (v2.0.1)
Assembly: Homo sapiens
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: GSC456 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using the Trizol Reagent.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment Selection. After purification and fragment selection, the products were amplified and enriched by PCR. Qubit was used for quantitative .  The target region library of the duplex was denatured, cycled, and digested to yield a single-stranded circular DNA. Single-stranded circular DNA is amplified by a rolling circle amplification (RCA), known as DNA nano balls (DNB). After library construction, Qubit was used for quantitative.

value: GBM stem cell

value: Erlotinib treatment

value: 12 hours


title: 1E-0Hb

description: Healthy Subject


title: Rv9 sample 5 [Rv9_2_S46]


title: GSC456 cells, Erlotinib-1


title: P10-rep1 LD2


title: R20291 sample 6 [R20291_3_S41]


title: Rv9 sample 4 [Rv9_1_S45]


title: GSC456 cells, DMSO-3

value: DMSO; control


title: P9-rep3 LD14


title: R20291 sample 5 [R20291_2_S40]


title: GSC456 cells, Erlotinib-2


title: 256740610833_1_3,SS9,hacase

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

description:
SS9
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh patients with essential hypertension was detected by gene chip technology.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software was used to preprocess tiff image data, and GeneSpring GX software was used to calculate gene expression difference and statistical significance p value. The tiff image is scanned on the chip and FeatureExtraction software is used to obtain a raw data file (.txt).mport the original data file (.txt) into GeneSpring software and write the grouping and other parameter information. Data normalization and QC analysis were performed for each sample. Cluster3.0 software is used for Cluster analysis and graphical presentation.

source_name: lymphocytes, Kazakh, essential hypertension

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
5µL Total RNA (100-500 ng) was taken and added to 0.2 mL nuclease-free centrifuge tube.
All samples were added to Spike A (Agilent) 2.0µL or Spike B (Agilent) 2.0µL.
Prepare reverse transcription Master Mix on ice, mix gently, centrifuge briefly and place on ice bath.
5µL of reverse transcription Master Mix was added to a 0.2mL centrifuge tube containing the Total RNA sample. Reverse transcription
The final reaction volume is 10µL.
Gently blow and mix for 2-3 times, centrifuge instantaneously, and place on ice.
The reverse transcription centrifuge tube was placed on the PCR apparatus, and the reaction time was 1h at 25℃, 1h at 42℃, and kept at 4℃ for more than 5min.
The reverse transcription centrifuge tube was removed, centrifuged instantaneously and placed on ice to prepare for the Second Strand cDNA synthesis reaction.

tag: population

value: Xinjiang Kazakh

tag: diagnosis

value: essential hypertension

value: peripheral blood lymphocytes

tag: gender

value: male


title: R20291 sample 4 [R20291_1_S39]


title: P3-rep0 LD13

value: peripheral blood mononuclear cells

value: primary cell


title: Y CHROMOSOME  positive cell line

city: los Angeles

first: Hany

middle: A

last: Abdel-Hafiz

state: California

address: 110 N George Burns RD, DRoom 3057

department: Medicine/ Medical Oncology

institute: Cedars-Sinai Medical Center

description: MBN

data_processing:
We mapped the paired-end clean reads to the mouse reference genome (Mouse, NCBI37/mm9) using BWA, sorted them with Sambamba, and marked duplicates with Picard.
Finally, we computed the coverage and depth, and tested for SNP and InDel detection.
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain annotation information for INDELs

organism: Mus musculus

growth_protocol: MB49 bladder cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)  in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Genomic DNA was isolated from parental, Y-, and Y+ MB49 cell lines by Invitrogen Kit (catalog No K1820) according to the manufacturer’s instructions
The genomic DNA was randomly sheared into short fragments, end-repaired, A-tailed, and ligated with Illumina adapters. After PCR amplification, size selection, and purification, we proceeded with the hybridization capture of libraries. The captured libraries were enriched by PCR amplification and checked with Qubit and bioanalyzer for quality control. The libraries were then pooled and sequenced on Illumina platforms using the PE150 strategy.

value: bladder cancer cell line

value: Y positive


title: 256740610834_1_4,sd6,hacontrol

description:
sd6
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh healthy participants was detected by gene chip technology.

source_name: lymphocytes, Kazakh, healthy control

value: healthy

value: female


title: 256740610832_1_4,Sd13,hacontrol

description:
Sd13
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh healthy participants was detected by gene chip technology.


title: MB49 parental cell line

value: parental


title: 256740610832_1_3,SS8,hacase

description:
SS8
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh patients with essential hypertension was detected by gene chip technology.


title: 256740610833_1_4,Sd7,hacontrol

description:
Sd7
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh healthy participants was detected by gene chip technology.


title: 256740610834_1_3,SS10,hacase

description:
SS10
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh patients with essential hypertension was detected by gene chip technology.


title: P5-rep5 LD10

value: blood


title: 256740610806_1_4,Sd10,hacontrol

description:
Sd10
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh healthy participants was detected by gene chip technology.


title: 256740610807_1_4,Sd11,hacontrol

description:
Sd11
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh healthy participants was detected by gene chip technology.


title: P5-rep5 L8


title: Lung, Adult mouse, Itgb1 iKO, LPS 21 days

city: Nashville

first: Jennifer

last: Sucre

state: TN

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger Count v3.1 (10X Genomics) was used to align reads onto the mm10 reference genome. Feature barcodes (hashing antibodies) were used for mouse demultiplexing: 1) anti-mouse-1 (BioLegend cat # 155861: ACCCACCAGTAAGAC); 2) anti-mouse-2 (BioLegend cat # 155863: GGTCGAGAGCATTCA); 3) anti-mouse-3 (BioLegend cat # 155865: CTTGCCGCATGTCAT); 4) anti-mouse-4 (BioLegend cat # 155867: AAAGCATTCTTCACG); 4) anti-mouse-5 (BioLegend cat # 155869: CTTTGTCTTTGTGAG)
Ambient background RNA were cleaned from the scRNA-seq data with “SoupX” (version 1.2.2) using the following genes to estimate ambient RNA contamination: Dcn, Bgn, Aspn, Ecm2, Fos, Hbb-bs, Hbb-bt, Hba-a1, Hba-a2, Lyz1, Lyz2, Mgp, Postn, Scgb1a1.
Data integration and clustering was performed using a standard Seurat (v4.1.0) / SCTransform (v0.3.3) workflow. Individual SoupX “cleaned” libraries were concatenated and analyzed jointly. After quality filtering (removal of cells with <700 , or >15% mitochondrial gene expression), data were normalized,  highly-variable genes were identified, and percent mitochondrial gene expression and sequencing batch were regressed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files from Cellranger count.

source_name: Lung

extract_protocol:
Lung lobes were harvested, minced, and incubated for 30 minutes at 37°C in dissociation media (RPMI-1640 with 0.7 mg/ml collagenase XI and 30 mg/ml type IV bovine pancreatic DNase). After incubation, lobes were passed through a wide bore pipet tip and filtered through a 40 μm filter. Single cell lung suspension was then counted, aliquoted, and blocked with CD-32 Fc block (BD cat #553142) for 20 minutes on ice. After 2% FBS staining buffer wash, cells were incubated with the conjugated primary antibodies anti-CD45 (BD cat # 559864) and anti-Ter119 (BD cat# 116211). In the same manner, fluorescence minus one controls were blocked and stained with the appropriate antibody controls. Cells from individual mice were then incubated with identifiable hashtags, resuspended in staining buffer, and treated with PI viability dye. CD45 negative, Ter119 negative, viable cells were collected by fluorescence associated cell sorting using a 70 μm nozzle on a 4-laser FACSAria III Cell Sorter. Both single and fluorescence-minus-one controls were used for compensation. Samples collected at the 21-day post treatment timepoint were EPCAM eiriched by adding approximately 1/3 EPCAM positive cells to the suspension for sequencing.
ScRNA-seq libraries were generated using the 10X Chromium platform 5’ library preparation kits (10X Genomics) following the manufacturer's recommendations and targeting 10,000 - 20,000 cells per sample.

value: Lung

value: Adult

value: Itgb1 iKO

value: LPS

tag: time post_treatment

value: 21 days

tag: epithelial enriched

value: yes


title: 256740610831_1_3,ss5,hacase

description:
ss5
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh patients with essential hypertension was detected by gene chip technology.

value: Xinjiang Kazakh

value: essential hypertension

tag: cell type


title: 256740610807_1_3,ss4,hacase

description:
ss4
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh patients with essential hypertension was detected by gene chip technology.

value: peripheral blood lymphocytes


title: FM2-5 sample 5 [FM2_5_3_S37]

value: bacterial cell


title: 256740610806_1_3,ss3,hacase

description:
ss3
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh patients with essential hypertension was detected by gene chip technology.

value: male


title: 256740610831_1_4,Sd12,hacontrol

description:
Sd12
The expression level of lncRNA in peripheral blood lymphocytes of Kazakh healthy participants was detected by gene chip technology.


title: Y CHROMOSOME  NEGATIVE cell line

description: MBP

value: bladder cancer cell line

tag: genotype

value: Y NEGATIVE


title: FM2-5 sample 4 [FM2_5_1_S36]


title: GSC456 cells, DMSO-2

value: GBM stem cell

tag: treatment

value: DMSO; control

value: 12 hours


title: MB49 Y CHROMOSOME POSITIVE tumor (MP9)

data_processing:
Illumina Truseq adapter, polyA, and polyT sequences were trimmed with cutadapt v2.3
Trimmed reads were aligned to mouse genome version 38 (mm10) using STAR aligner v2.7.0d_022152 with parameters according to the ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline).
Gene expression levels were quantified using RSEM v1.3.1
Ensembl gene annotations (version 84) were used in the alignment and quantification steps
RNA-seq sequence, alignment, and quantification quality was assessed using FastQC v0.11.5 and MultiQC v1.8
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and read_count values for each Sample

growth_protocol: MB49 bladder cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C. subcutaneous Y+ and Y- tumors were grown in WT C57BL/6 male mice.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 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 at Novogene.

value: bladder cancer

value: Y POSITIVE

tag: sample type

value: subcutaneous tumor


title: Lung, Adult mouse, Itgb1 fl/fl, LPS 21 days

description: 10x Genomics

tag: tissue

value: Lung

value: Adult

value: Itgb1 fl/fl


title: Lung, Adult mouse, Itgb1 iKO, LPS 7 days

description: 10x Genomics

tag: age

value: Itgb1 iKO

value: LPS

value: 7 days

value: no


title: P1-rep0 L4

value: peripheral blood mononuclear cells

value: primary cell

value: blood


title: MB49 Y CHROMOSOME POSITIVE tumor (MP8)


title: FM2-5 sample 6 [FM2_5_5_S38]

value: bacterial cell


title: MB49 Y CHROMOSOME POSITIVE tumor (MP10)


title: P5-rep1 H5


title: Lung, Adult mouse, Itgb1 iKO, PBS 7 days

description: 10x Genomics

value: PBS


title: Lung, Adult mouse, Itgb1 fl/fl, LPS 7 days

description: 10x Genomics


title: MB49 Y CHROMOSOME POSITIVE tumor (MP6)


title: MB49 Y CHROMOSOME POSITIVE tumor (MP7)


title: Rv189 sample 2 [Rv189_2_S41]

description: Bulk RNA-seq of clostridium difficile

data_processing:
FastQ files were assessed using FastP (Chen et al., 2018)
Data was aligned to the C. difficile R20291 (NCBI: NC_013316.1) reference genome using STAR (Dobin et al., 2013) (v2.6) with –quantMode GeneCounts –outFilterMultimapNmax 1 and –outFilterMatchNmin 35. We used a Star index with a –sjdbOverhang of the maximum read length − 1.
Read count files were merged and genes with mean of < 1 read per sample were excluded.
The expression and differential expression values were generated using DESeq2 (Love, Huber and Anders, 2014) (v1.24). For differential comparisons we used an A versus B model with no additional covariates. All other parameters were left to default.
Assembly: C. difficile R20291 (NCBI: NC_013316.1)
Supplementary files format and content: Raw per gene read counts (read_counts.csv)


title: Rv189 sample 1 [Rv189_1_S34]

description: Bulk RNA-seq of clostridium difficile


title: IP-GFP_DOX+_PMA_2h

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt v1.13.
Mapping to the hg38 genome was performed with STAR v2.6.1d.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1.
Mapped reads were de-duplicated with Picard (ChIP-seq and DRIP-seq).
Reads mapping to the DAC Exclusion List Regions (accession: ENCSR636HFF) were removed with Bedtools version 2.29.2.
FPKM-normalized bigwig files were created with deepTools version 2.5.0.1 b.
ChIP-seq and DRIPseq peaks were called with MACS2 version 2.2.6.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples.
Supplementary_files_format_and_content: txt files: Text files of the called peaks (IP vs. Input, MACS2).

growth_protocol: MCF10A WT and KO cells (DRIP) were maintained in DMEM/F12 (Invitrogen, 11330-032) supplemented with 5% horse serum (Invitrogen, 16050-122), 20ng/mL EGF (Peprotech), 0.5mg/mL hydrocortisone (Sigma, H-0888), 100ng/mL cholera toxin (Sigma, C-8052), 10ug/mL insulin (Sigma, I-9278) and 0.5% pen/strep. MCF10A-TREx-A3B-eGFP (ChIP) Same medium and culture conditions but with addition of Normocin (100 ug/ml).

extract_protocol:
DNA were purified from chromatin IP products.
For ChIP-seq and DRIP-seq, libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions.

treatment_protocol: Cells were treated with Doxycycline at 1 ug/ml for 24 hours. In case of PMA (Thermo Fisher, BP685), the cells were treated with 25ng/mL for the indicated time.

tag: genotype/variation

value: DOX+ PMA 2h

tag: antibody

value: Anti-GFP antibody - ChIP Grade (ab290, Abcam)


title: MB49 Y CHROMOSOME NEGATIVE tumor (MN15)

value: bladder cancer

value: Y NEGATIVE


title: M12-HI-control-5dpi

city: New York

first: Franco

last: Izzo

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Indexed genome versions were generated using STAR (v2.5.2) genomeGenerate function and gencode vM25 annotation. Reads were aligned using STAR (v2.5.2) with twopassMode = basic.
Assembly: Concatenated mm10 and CHIKV genome (AM258994)
Supplementary files format and content: Comma separated values file containing gene counts

molecule: polyA RNA

source_name: Heart

growth_protocol: C57BL/6(027) male wild type mice (Charles River Laboratories)

extract_protocol:
Hearts were collected in 500 μl of TRIzolTM (Invitrogen) with one 5 mm stainless steel bead and processed as described above. RNA was extracted using Zymo direct-zol RNA purification kit (Zymo research, #R2072) according to the manufacturer’s instructions
A total of 500 ng per sample was sent to the NYU Genome Technology Center for quality control assessment and automated TruSeq stranded total RNA with RiboZero Gold library preparation.
Illumina Novaseq600 sequencing (single pair 100)

treatment_protocol: Mice were infected intravenously with 10^5 PFU of CHIKV or HI control, and hearts were perfused with 30 ml of PBS and then collected at either 2 and 5 dpi.

value: Heart

tag: infection

value: Heat-inactivated control

value: 5 dpi

tag: Sex

value: Male


title: IP-GFP_DOX+_DMSO

tag: cell line

value: DOX+ DMSO


title: M11-HI-control-5dpi

tag: strain

tag: time


title: P5-rep4 L3


title: MB49 Y CHROMOSOME NEGATIVE tumor (MN14)

value: subcutaneous tumor


title: IP-GFP_DOX-_DMSO

value: DOX- DMSO


title: M10-IOL-5dpi

value: Chikungunya-infected


title: Rv9 sample 2 [Rv9_2_S20]

description: Bulk RNA-seq of clostridium difficile


title: Rv9 sample 3 [Rv9_3_S27]

description: Bulk RNA-seq of clostridium difficile


title: Rv189 sample 3 [Rv189_3_S48]

description: Bulk RNA-seq of clostridium difficile


title: Input_DRIP_WT_PMA_6h

data_processing:
Library strategy: DRIP-seq
Adapters were trimmed with Cutadapt v1.13.
Mapping to the hg38 genome was performed with STAR v2.6.1d.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1.
Mapped reads were de-duplicated with Picard (ChIP-seq and DRIP-seq).
Reads mapping to the DAC Exclusion List Regions (accession: ENCSR636HFF) were removed with Bedtools version 2.29.2.
FPKM-normalized bigwig files were created with deepTools version 2.5.0.1 b.
ChIP-seq and DRIPseq peaks were called with MACS2 version 2.2.6.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples.
Supplementary_files_format_and_content: txt files: Text files of the called peaks (IP vs. Input, MACS2).

value: Wild-type

value: PMA 6h


title: M9-IOL-5dpi


title: M8-IOL-5dpi


title: Rv9 sample 1 [Rv9_1_S13]

description: Bulk RNA-seq of clostridium difficile


title: MB49 Y CHROMOSOME NEGATIVE tumor (MN12)


title: R20291 sample 3 [R20291_3_S12]

description: Bulk RNA-seq of clostridium difficile


title: Input_DRIP_WT_DMSO

value: DMSO


title: Input_DRIP_WT_PMA_2h

value: PMA 2h


title: R20291 sample 2 [R20291_2_S6]

description: Bulk RNA-seq of clostridium difficile

value: bacterial cell


title: M7-IOL-5dpi


title: MB49 Y CHROMOSOME POSITIVE cell line (MB34)

value: Y POSITIVE

value: cell line


title: Input_DRIP_KO_PMA_6h

value: APOBEC3B KO


title: R20291 sample 1 [R20291_1_S50]

description: Bulk RNA-seq of clostridium difficile


title: M6-HI-control-2dpi

value: 2 dpi


title: MB49 Y CHROMOSOME POSITIVE cell line (MB19)

value: bladder cancer


title: MB49 Y CHROMOSOME NEGATIVE tumor (MN13)

value: Y NEGATIVE


title: FM2-5 sample 3 [FM2_5_3_S54]

description: Bulk RNA-seq of clostridium difficile


title: MB49 Y CHROMOSOME NEGATIVE tumor (MN11)


title: MB49 Y CHROMOSOME POSITIVE cell line (MB17)


title: Input_DRIP_KO_DMSO


title: FM2-5 sample 2 [FM2_5_2_S47]

description: Bulk RNA-seq of clostridium difficile


title: M4-IOL-2dpi

value: Heart


title: Input_DOX+_PMA_2h

value: DOX+ PMA 2h


title: FM2-5 sample 1 [FM2_5_1_S40]

description: Bulk RNA-seq of clostridium difficile


title: MB49 Y CHROMOSOME POSITIVE cell line (MB11)


title: MB49 Y CHROMOSOME POSITIVE cell line (MB8)


title: Input_DOX+_DMSO

value: DOX+ DMSO


title: M2-IOL-2dpi

value: Male


title: MB49 Y CHROMOSOME NEGATIVE cell line (BN10)


title: TPM_E2Fi&STAT3i_2

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads preprocessing was performed by Trimmomatic (version 0.36) with the parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50.
Mapping of RNA-seq reads was done using STAR (version 020201, Dobin et al., 2013) with default parameters for RNA-seq data; the human ENSEMBL gene annotation model (GRCh38).
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Genome_build: hg38
Supplementary_files_format_and_content: txt format; TPM values for four experimental conditions with 2 replicates each.

source_name: Cancer stem cells

growth_protocol: The GSCs were cultured in human neural stem cell Maintenance Media (Millipore), 1% Penicillin-Streptomycin (PS) supplemented with EGF and  FGF (20 ng/ml each) to maintain stemness.

extract_protocol:
Tree days after treatment, cells were harvested and total RNA were extracted with RNeasy® Micro Kit (Qiagen).
A modified NEBNext RNA Ultra protocol is used to prepare the libraries for mRNA sequencing. The first step is selectively purifying the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented using divalent cations under elevated temperature. Next, the cDNA is synthesized using Reverse transcriptase and random hexamers in a first strand synthesis reaction. Subsequently, the cDNA is converted to double stranded cDNA in a DNA polymerase based reaction. These DNA molecules are then subjected to a series of enzymatic steps for end repair, A-Tailing and ligation with NEB adapters. Finally, these adapter ligated molecules are enriched in a limited cycle PCR with indexed primers and purified using AMPure beads to create final cDNA library for sequencing.

treatment_protocol: TS543 cells were treated with either DMSO, 10 uM of HLM006474, 75 uM of S3I-201 or 10 uM of HLM006474 with 75 uM of S3I-201.

value: Glioblastoma patient derived cancer stem cell

tag: passage


title: Input_DOX-_DMSO

value: DOX- DMSO


title: MB49 Y CHROMOSOME NEGATIVE cell line (BN9)


title: M1-IOL-2dpi

value: Chikungunya-infected


title: DRIP_WT_PMA_6h

value: Wild-type

value: PMA 6h

value: S9.6 mouse monoclonal antibody; Gromak lab; RRID:AB_2810829


title: Input_DRIP_KO_PMA_2h

value: PMA 2h


title: Wound bed of dorsal skin, PWD7

city: Xiamen

first: Lingjuan

last: Zhang

address: Xiangan South Street

institute: Xiamen University

data_processing:
The raw sequencing data was demultiplexed and aligned to the reference genome mm10-1.2.0 using Cell Ranger v3.0.2 pipiline(10x Genomics).
The generated raw gene expression matrix was converted into Seurat objects using the R package Seurat v3.0.
To remove doublets and poor-quality cells, we utilized the following procedures to control for cell quality: >200 genes/cell, <5000 genes/cell; >25,000 unique molecular identifiers(UMIs)； and <8% mitochondrial gene expression.
After low quality cells and outliers were discarded, 10233 cells from non-lesional skin, 7807 cells from wound beds at post-wounding day 2 (PWD2), and 4925 cells from wound tissue at PWD7 were used for downstream analysis.
Unsupervised clustering and gene expression were visualized with the Seurat 3.0 on R studio, and assignment of cell clusters was based on expression of validated marker genes.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Wound bed of dorsal skin

extract_protocol:
Skin biopsies were minced and digested with collagenase D and DNase1 to isolate single skin cells as previously described (Zhang et al., 2019; Zhang et al., 2021).
Libraries were generated from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v2. cDNA libraries were sequenced on an Illumina Novaseq6000 platform (Illumina).

value: male

value: wound bed at post-wounding day 7

tag: tissue details

value: full-thickness wound (1.0 cm x 0.5 cm in size) was generated at post-wounding day 0

value: 7-9 weeks


title: M5-HI-control-2dpi

value: Heat-inactivated control

value: 2 dpi


title: MB49 Y CHROMOSOME NEGATIVE cell line (BN6)

value: bladder cancer

value: Y NEGATIVE

value: cell line


title: MB49 Y CHROMOSOME NEGATIVE cell line (BN3)


title: DRIP_WT_DMSO

value: DMSO


title: TPM_E2Fi&STAT3i_1

value: Glioblastoma patient derived cancer stem cell


title: TPM1_STAT3i_2


title: TPM1_STAT3i_1


title: DRIP_WT_PMA_2h


title: Non-lesional dorsal skin, CTRL

source_name: Non-lesional dorsal skin

value: dorsal skin

value: Non-lesional


title: M3-IOL-2-dpi

value: Heart

value: Chikungunya-infected

value: Male


title: TPM_E2Fi_1


title: DRIP_KO_PMA_6h

value: APOBEC3B KO

value: PMA 6h

value: S9.6 mouse monoclonal antibody; Gromak lab; RRID:AB_2810829


title: Adult

data_processing:
The raw sequencing data was demultiplexed and aligned to the reference genome mm10-1.2.0 using Cell Ranger v3.0.2 pipiline(10x Genomics).
The generated raw gene expression matrix was converted into Seurat objects using the R package Seurat v2.0.
Low quality cells and outliers were discarded, and only ～24,409 viable cells were used for downstream analysis. These included ~7,483 cells – NB; ~8,235 cells – young(3weeks mice); ~8,691cells-adult (2month mice).
Unsupervised clustering and gene expression were visualized with the Seurat 2.0 on R studio, and assignment of cell clusters was based on expression of validated marker genes.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: dorsal skin

extract_protocol:
Skin biopsies were minced and digested with collagenase D and DNase1 to isolate single skin cells as previously described (Zhang et al., 2019; Zhang et al., 2021).
Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v 2. cDNA libraries were sequenced on an Illumina Novaseq6000 platform (Illumina).

value: skin

value: 2 month


title: DRIP_KO_PMA_2h

value: PMA 2h


title: Young

value: 3 weeks


title: DRIP_KO_DMSO


title: TPM_DMSO_1


title: AI_2

city: Portland

first: Claudio

last: Mello

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health & Science University

data_processing:
Reads were aligned to the zebra finch genome (Taegut1) using CellRanger with include-introns.
SnRNA-seq data was processed using a standard Seurat workflow (Stuart, Butler et al. 2019). Clusters were resolved using FindClusters() with a resolution of 0.25 and visualized with a UMAP projection. Differential gene expression was defined using FindMarkers() with min.pct of 0.25.
Supplementary files format and content: Processed data file corresponds to the two combined samples. One cluster exhibited differential markers with low percent of cells (<50%) exhibiting the defining marker and with a majority of markers having a negative average logFC, suggesting low quality nuclei and was excluded from further analysis. This processed data file was used to generate the R Shiny app available on www.zebrafinchatlas.org.

molecule: nuclear RNA

organism: Taeniopygia guttata

source_name: Brain

growth_protocol: Birds were sacrificed within 20 min of lights-on and no singing was observed in any individual.

extract_protocol:
Frontal slices (400 μm thick, one slice per hemisphere) containing RA, AId, and AIv were cut on a Leica VT1200S vibratome in an ice-cold cutting solution containing 119 mM NaCl, 2.5 mM KCl, 8 mM MgSO4, 16.2 mM NaHCO3, 10 mM HEPES, 1 mM NaH2PO4, 0.5 mM CaCl2, 11 mM D-Glucose, 35 mM Sucrose with a pH of 7.3-7.4 when bubbled with carbogen (95% O2, 5% CO2; ~330-340 mOsm). Slices were then transferred to an incubation chamber containing artificial cerebral spinal fluid with 119 mM NaCl, 2.5 mM KCl, 1.3 mM MgSO4, 26.2 mM NaHCO3, 1 mM NaH2PO4, 1.5 mM CaCl2, 11 mM D-Glucose, 35 mM Sucrose with a pH of 7.3-7.4 when bubbled with carbogen (95% O2, 5% CO2; ~330-340 mOsm) at 37°C. Microbiopsies containing RA, AId, and AIv were dissected using a scalpel and angled forceps and flash frozen in a dry ice/isopropyl alcohol slurry. Tissue was homogenized in 300 µL of nuclei lysis buffer (10 mM Tris pH 8.0, 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 0.1% Triton-X 100, 0.5% RNasin, and 0.1 mM DTT). 700 µL of lysis buffer was added to the homogenate and the sample was incubated on ice for 5 min. The sample was transferred to a 15 ml conical tube and centrifuged at 500 x g for 5 min at 4°C. The supernatant was discarded, 1 ml of ice-cold lysis buffer was added, and the mix was incubated on ice for 5 min. The sample then was centrifuged at 500 x g for 5 min at 4°C. The pellet was resuspended in 1 ml of nuclei suspension buffer (1x PBS, 0.01% BSA, and 0.1% RNasin), and filtered through a FLOWMI 40 μm tip strainer (Bel-Art) and centrifuged at 500 x g for 5 min at 4°C. The pelleted nuclei were resuspended in nuclei suspension buffer.
Libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) according to the manufacturer’s instructions

value: Brain

value: Wild type


title: AI_1


title: NB

value: neonatal


title: Wound bed of dorsal skin, PWD2

value: male

value: wound bed at post-wounding day 2

value: full-thickness wound (1.0 cm x 0.5 cm in size) was generated at post-wounding day 0

value: 7-9 weeks


title: TPM_E2Fi_2

value: Glioblastoma patient derived cancer stem cell


title: MB49 Y CHROMOSOME NEGATIVE cell line (BN2)

value: bladder cancer

value: Y NEGATIVE

value: cell line


title: TPM_DMSO_2

value: DMSO


title: INPUT, 1014 sgKdm6a, DMSO, rep1

status: Public on Jun 09 2023

first: Leslie

last: Duplaquet

state: Massachusetts

address: 360 Longwood Ave

department: Medical Oncology

institute: DFCI

data_processing:
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75)
Assembly: mm10
Supplementary files format and content: tdf

source_name: mouse small cell lung cancer (SCLC) tumor

growth_protocol: Cells were counted and plated at 0.1x106 per mL in 100 mLs (10 X 107 cells total) for each condition.

extract_protocol:
DNA was purified with AMPure XP beads (Beckman Coulter). DNA fragments were quantified by TapeStation 4200 (Agilent) using HSD1000 Tape and Reagent (Agilent) and Qubit (ThermoFisher).
1-10 ng of DNA was used in preparation of Illumina compatible libraries using SMARTer ThruPLEX DNA-Seq Kit (Takara) followed by sequencing using NextSeq550 (Illumina) to obtain 20-30 million 37bp, paired-end reads. Reads (paired-end 37mers) were aligned to the mouse (Gencode M24/mm10) genome using STAR (v2.7.5a; params –alignIntronMax 1 –alignEndsType EndToEnd – alignMatesGapMax 2000 for ChIP-seq analysis), sorted, and duplicates were marked/removed with picard pipeline tools (v2.9.4). Final “deduped” .BAM files were indexed using SAMtools (v1.95)

treatment_protocol: Cells were treated with VTP-50469 (500 nM) or DMSO for 5 days for each replicate

value: 1014 sgKdm6a

value: mouse small cell lung cancer tumor-derived cells

value: pure congenic Lox-stop-lox (LSL) Cas9 BL6J mice

tag: chip antibody


title: INPUT, 1014 sgKdm6a, DMSO, rep2

value: mouse small cell lung cancer (SCLC) tumor


title: Menin-ChIP, 1014 sgKdm6a, DMSO, rep1

value: Menin (Bethyl, A300-105A)


title: INPUT, 1014 sgKdm6a, VTP, rep1


title: Menin-ChIP, 1014 sgKdm6a, VTP, rep1


title: Menin-ChIP, 1014 sgKdm6a, VTP, rep2


title: INPUT, 1014 sgKdm6a, VTP, rep2


title: Menin-ChIP, 1014 sgKdm6a, DMSO, rep2


title: breast tumor tissue, J03_118

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

institute: Osaka University

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized overnight at 46C on Affymetrix U133 plus2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000.

data_processing: Probe intensities were normalized with MAS5.

label: biotin

source_name: fresh frozen tumor samples obtained from radical breast cancer surgery

label_protocol: RNA (1 μg; RIN value >6) was used for generation of second-strand cDNA, and cRNA was amplified with the Oligo dT primer, then biotinated and fragmented with One-Cycle Target Labeling and control reagents (Affymetrix, Santa Clara, CA).

extract_protocol: RNA was extracted from tumor tissues obtained at the surgery with the aid of the Qiagen RNeasy® mini kit (QIAGEN Sciences, Germantown, MD).

treatment_protocol: The patients agreed to have their research specimens cryopreserved for future use after undergoing radical breast cancer surgery, and also received endocrine therapy and/or adjuvant chemotherapy following the surgery.

value: breast tumor

tag: menopause

value: postmenopausal

tag: ct

value: No

tag: er

value: Positive

tag: pgr

value: Negative

tag: hg


title: breast tumor tissue, J03_113

tag: tissue

value: premenopausal


title: breast tumor tissue, J03_116

tag: age


title: MDA-MB-231_sh3_rep2

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Human Genome microarry 4x44K Ver. 2.0 (G4845A, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih three filters with GeneSpring software 14.9 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was exluded. After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: MDA-MB-231, the ASH2L sh3 knockdown cells, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 10% FBS, DMEM + 1%penicillin/streptomycin

extract_protocol: Total RNA was extracted with Rneasy Mini Kit(QIAGEN) according to the manufacturer's instructions.

tag: cell type

value: breast cancer cell line


title: MDA-MB-231_CTL_rep1

source_name: MDA-MB-231, negative control cell, replicate 1


title: breast tumor tissue, J03_117


title: breast tumor tissue, J03_120


title: breast tumor tissue, J03_119


title: breast tumor tissue, J03_109

value: Yes


title: breast tumor tissue, J03_114


title: breast tumor tissue, J03_111


title: breast tumor tissue, J03_115


title: breast tumor tissue, J03_105


title: breast tumor tissue, J03_106


title: MDA-MB-231_sh3_rep1

source_name: MDA-MB-231, the ASH2L sh3 knockdown cells, replicate 1


title: MDA-MB-231_CTL_rep2

source_name: MDA-MB-231, negative control cell, replicate 2


title: breast tumor tissue, J03_104


title: breast tumor tissue, J03_107


title: breast tumor tissue, J03_112


title: breast tumor tissue, J03_108


title: breast tumor tissue, J03_102


title: breast tumor tissue, J03_103


title: breast tumor tissue, J03_099


title: breast tumor tissue, J03_101


title: breast tumor tissue, J03_110


title: breast tumor tissue, J03_098


title: breast tumor tissue, J03_096


title: breast tumor tissue, J03_100


title: breast tumor tissue, J03_095


title: breast tumor tissue, J03_097


title: breast tumor tissue, J03_091


title: breast tumor tissue, J03_089


title: breast tumor tissue, J03_088


title: breast tumor tissue, J03_090


title: breast tumor tissue, J03_093


title: breast tumor tissue, J03_094


title: breast tumor tissue, J03_085


title: breast tumor tissue, J03_079


title: breast tumor tissue, J03_080


title: breast tumor tissue, J03_084


title: breast tumor tissue, J03_086


title: breast tumor tissue, J03_092


title: breast tumor tissue, J03_082


title: breast tumor tissue, J03_087


title: breast tumor tissue, J03_081


title: breast tumor tissue, J03_078


title: breast tumor tissue, J03_075


title: breast tumor tissue, J03_077


title: breast tumor tissue, J03_071


title: breast tumor tissue, J03_076


title: breast tumor tissue, J03_070


title: breast tumor tissue, J03_073


title: breast tumor tissue, J03_072


title: breast tumor tissue, J03_074


title: breast tumor tissue, J03_068


title: breast tumor tissue, J03_083


title: breast tumor tissue, J03_066


title: breast tumor tissue, J03_069


title: breast tumor tissue, J03_063


title: breast tumor tissue, J03_065


title: WCL, rep1

city: Uppsala

first: Siv

last: Andersson

address: Husargatan 3

country: Sweden

institute: Uppsala University

description:
WCL1.raw/WCL1
RNAseq.raw.read.counts.csv
RNAseq.DESeq2.csv

data_processing:
read mapping using hisat2 v2.2.1
read quantification using FeatureCounts v2.0.1
Differential analysis with DESEq2
Assembly: A1401.gff, in-house genome assembly
Supplementary files format and content: RNAseq.raw.read.counts.csv; raw read counts after mapping with hisat and read counting with featurecounts; columns: locus tag, gene length, feature, raw read counts for 6 samples, mean read counts for CFP and WCL group, gene length adjusted mean read counts for CFP and WCL group
Supplementary files format and content: RNAseq.DESeq2.csv; read counts from DESeq2 and additional information for data analysis; columns: locus tag; log2-ratio (CFP vs WCL); raw and adjusted p-values; gene length; feature; normalized and corrected read counts from DESeq2; mean read counts for for CFP and WCL group; gene length adjusted mean read counts for CFP and WCL group; type of enrichment based on DESeq2 (adjusted p-value < 0.05, absolut log2-ratio > 1); genomic position; annotation; COG cateogry; COG family; prediction of signal peptides; prediction of transmembrane domains and signal peptides by Phobius

organism: Apilactobacillus kunkeei

source_name: whole cell lysate

growth_protocol: The A. kunkeei strain and A1401 was cultivated in MRS-medium (Sigma Aldrich) according to (De Man et al., 1960) supplemented with 0.5% (w/v) D-Fructose (Sigma Aldrich) and 0.1% (v/v) Tween-80 (Sigma Aldrich), in the following referred to as fMRS. Batch-cultivation was performed at 35°C and 5% CO2 in batch-cultures of 100–150 mL fMRS medium and the cells were harvested during exponential growth phase at OD600 ≈ 0.3.

extract_protocol:
The RNA extraction was performed using the RiboPure-Bacteria Kit including DNAse I treatment (LifeTechnologies)
Sequencing libraries were prepared from 500 ng total RNA using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina, cat#20040525).

treatment_protocol: Cell suspensions were pelleted by centrifugation, the supernatant was filtered and ultracentrifuged to obtain the cell-free pellet (CFP), the pellet was washed to further obtain the Whole-cell lysate

value: whole cell lysate

value: gram-positive

tag: treatment


title: breast tumor tissue, J03_061


title: breast tumor tissue, J03_060


title: breast tumor tissue, J03_059


title: WCL, rep2

description:
WCL2.raw/WCL1
RNAseq.raw.read.counts.csv
RNAseq.DESeq2.csv


title: CFP, rep3

description:
CFP3.raw/CFP3
RNAseq.raw.read.counts.csv
RNAseq.DESeq2.csv

source_name: extracellular cell-free pellet

value: extracellular cell-free pellet


title: breast tumor tissue, J03_057


title: CFP, rep1

description:
CFP1.raw/CFP1
RNAseq.raw.read.counts.csv
RNAseq.DESeq2.csv


title: breast tumor tissue, J03_055


title: breast tumor tissue, J03_058


title: WCL, rep3

description:
WCL3.raw/WCL3
RNAseq.raw.read.counts.csv
RNAseq.DESeq2.csv


title: breast tumor tissue, J03_056


title: breast tumor tissue, J03_064


title: breast tumor tissue, J03_062


title: CFP, rep2

description:
CFP2.raw/CFP2
RNAseq.raw.read.counts.csv
RNAseq.DESeq2.csv


title: breast tumor tissue, J03_054


title: breast tumor tissue, J03_048


title: breast tumor tissue, J03_053


title: breast tumor tissue, J03_049


title: breast tumor tissue, J03_046


title: breast tumor tissue, J03_051


title: breast tumor tissue, J03_052


title: Abeta_Propolis_Hippocampus_04

city: Tomata

first: Nobuaki

last: Okumura

state: Okayama

address: 194 Ichiba Kagamino

institute: Yamada Bee Company, Inc.

hyb_protocol: Applied BiosystemsTM Genechipr® Hybridization oven 640

scan_protocol: Applied BiosystemsTM Genechip® scanner 30007G system

data_processing: Applied BiosystemsTM Genechip® consoleTM softwere ver.1.3.0

source_name: Hippocampus Abeta plus Propolis, replicate4

label_protocol: Applied BiosystetnsTM Genechip@ Fluidics station 450

extract_protocol: Total RNA from the prefrontal cortex and hippocampus was purified using the Nucleospin RNA Plus kit (Takara, Shiga, Japan)

value: Slc :ddY

tag: gender

value: male


title: breast tumor tissue, J03_047


title: breast tumor tissue, J03_050


title: Abeta_Propolis_Hippocampus_08

source_name: Hippocampus Abeta plus Propolis, replicate8


title: breast tumor tissue, J03_045


title: breast tumor tissue, J03_043


title: Abeta_Propolis_Hippocampus_06

source_name: Hippocampus Abeta plus Propolis, replicate6


title: Abeta_Propolis_Hippocampus_03

source_name: Hippocampus Abeta plus Propolis, replicate3


title: breast tumor tissue, J03_044


title: Abeta_Propolis_Hippocampus_02

source_name: Hippocampus Abeta plus Propolis, replicate2


title: Abeta_Propolis_Hippocampus_05

source_name: Hippocampus Abeta plus Propolis, replicate5


title: Abeta_Propolis_Hippocampus_07

source_name: Hippocampus Abeta plus Propolis, replicate7


title: breast tumor tissue, J03_042


title: ABeta_Hippocampus_07

source_name: Hippocampus Abeta, replicate7


title: ABeta_Hippocampus_08

source_name: Hippocampus Abeta, replicate8


title: breast tumor tissue, J03_040


title: Abeta_Propolis_Hippocampus_01

source_name: Hippocampus Abeta plus Propolis, replicate1


title: breast tumor tissue, J03_041

source_name: fresh frozen tumor samples obtained from radical breast cancer surgery


title: breast tumor tissue, J03_039


title: ABeta_Hippocampus_03

source_name: Hippocampus Abeta, replicate3


title: breast tumor tissue, J03_038


title: breast tumor tissue, J03_036


title: ABeta_Hippocampus_06

source_name: Hippocampus Abeta, replicate6


title: breast tumor tissue, J03_037


title: breast tumor tissue, J03_034


title: ABeta_Hippocampus_05

source_name: Hippocampus Abeta, replicate5


title: breast tumor tissue, J03_033


title: breast tumor tissue, J03_035


title: breast tumor tissue, J03_032


title: Vehicle_Hippocampus_07

source_name: Hippocampus, Vehicle, replicate7


title: ABeta_Hippocampus_02

source_name: Hippocampus Abeta, replicate2


title: ABeta_Hippocampus_04

source_name: Hippocampus Abeta, replicate4


title: breast tumor tissue, J03_031


title: ABeta_Hippocampus_01

source_name: Hippocampus Abeta, replicate1


title: Vehicle_Hippocampus_02

source_name: Hippocampus, Vehicle, replicate2


title: breast tumor tissue, J03_030


title: breast tumor tissue, J03_028


title: breast tumor tissue, J03_029


title: Vehicle_Hippocampus_06

source_name: Hippocampus, Vehicle, replicate6


title: Vehicle_Hippocampus_03

source_name: Hippocampus, Vehicle, replicate3


title: breast tumor tissue, J03_027


title: breast tumor tissue, J03_026


title: breast tumor tissue, J03_024


title: Abeta plus Propolis_Cortex_07

source_name: Cortex Abeta plus Propolis, replicate7


title: Vehicle_Hippocampus_05

source_name: Hippocampus, Vehicle, replicate5


title: Vehicle_Hippocampus_08

source_name: Hippocampus, Vehicle, replicate8


title: breast tumor tissue, J03_022


title: breast tumor tissue, J03_025


title: Abeta plus Propolis_Cortex_03

source_name: Cortex Abeta plus Propolis, replicate3


title: breast tumor tissue, J03_020


title: Vehicle_Hippocampus_01

source_name: Hippocampus, Vehicle, replicate1


title: Vehicle_Hippocampus_04

source_name: Hippocampus, Vehicle, replicate4


title: Abeta plus Propolis_Cortex_02

source_name: Cortex Abeta plus Propolis, replicate2


title: Abeta plus Propolis_Cortex_06

source_name: Cortex Abeta plus Propolis, replicate6


title: breast tumor tissue, J03_023

source_name: fresh frozen tumor samples obtained from radical breast cancer surgery


title: ABeta_Cortex_06

source_name: Cortex Abeta, replicate6


title: breast tumor tissue, J03_018


title: breast tumor tissue, J03_015


title: Abeta plus Propolis_Cortex_08

source_name: Cortex Abeta plus Propolis, replicate8


title: ABeta_Cortex_07

source_name: Cortex Abeta, replicate7


title: ABeta_Cortex_04

source_name: Cortex Abeta, replicate4


title: ABeta_Cortex_03

source_name: Cortex Abeta, replicate3


title: breast tumor tissue, J03_017


title: breast tumor tissue, J03_021


title: ABeta_Cortex_05

source_name: Cortex Abeta, replicate5


title: Abeta plus Propolis_Cortex_05

source_name: Cortex Abeta plus Propolis, replicate5


title: Abeta plus Propolis_Cortex_01

source_name: Cortex Abeta plus Propolis, replicate1


title: breast tumor tissue, J03_019


title: ABeta_Cortex_08

source_name: Cortex Abeta, replicate8


title: breast tumor tissue, J03_067


title: breast tumor tissue, J03_013


title: breast tumor tissue, J03_014


title: Abeta plus Propolis_Cortex_04

source_name: Cortex Abeta plus Propolis, replicate4


title: breast tumor tissue, J03_012


title: breast tumor tissue, J03_011


title: breast tumor tissue, J03_016


title: RNAseqofSUIT2MRTXR:untreated (replicate 1)

first: Herve

last: Tiriac

state: CA

address: 3855 Health Sciences Drive

department: Surgery

institute: UCSD Health

data_processing:
Quality control of the raw fastq files was performed using the software tool FastQC
Sequencing reads were trimmed with Trimmomatic and aligned using the STAR aligner
Read quantification was performed with RSEM
The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis
lowly expressed genes—those not having counts per million (cpm) at least 3 in at least 3 of the samples—were filtered out and then trimmed mean of M-values (TMM)10 normalization was applied.
Assembly: GRCh38 for human and GRCm38 for mouse
Supplementary files format and content: SUIT2_RNAseq.txt (tab delimited txt file with nomalized counts)
Supplementary files format and content: FC1242_RNAseq.txt (tab delimited txt file with nomalized counts)

growth_protocol: Parental human SUIT2 or mouse Fc1242 cells and MRTXR human SUIT2 or mouse Fc1242 cells were cultured in 10 cm dishes in duplicate.

extract_protocol:
Total RNA was extracted Nucleospin® RNA isolation kit (Macherey-Nagel GmbH & Co.) following the manufacturer’s instructions.
PolyA-enriched RNA libraries were prepared according to manufacturer's protocol

treatment_protocol: Cells were left untreated or treated with 60 nM MRTX1133 for 24 hours.

value: Pancreatic cancer cell

value: untreated


title: ABeta_Cortex_01

source_name: Cortex Abeta, replicate1


title: RNAseqofSUIT2MRTXR:untreated (replicate 2)


title: RNAseqofSUIT2MRTXR:60nM MRTX1133 (replicate 2)

value: treated


title: RNAseqofSUIT2MRTXR:60nM MRTX1133 (replicate 1)


title: breast tumor tissue, J03_008


title: Wound_Control_DC

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

institute: University of Arizona

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the mm9 (mouse) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Assembly: mm9 (mouse)
Supplementary files format and content: Cell Ranger output files

source_name: wounds that had been treated with hydrogels seeded with control (untreated) dendritic cells

growth_protocol: Freshly isolated murine bone marrow cells were cultured and differentiated into dendritic cells according to Lutz et al J Immunol Methods 223, 77-92 (1999).

extract_protocol:
Tissue was enzymatically digested, cells were collected and washed. These cellular suspensions were then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) at the Stanford Functional Genomics Facility (SFGF) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: Dendritic cells were either treated with vitamin d3, CRISPR-knockout of Ndrg2 or left untreated, then submitted for scRNA-seq analysis. Wounds were treated with hydrogels seeded with Ndrg2-KO dendritic cells, control dendritic cells or blank hydrogels

tag: passages

value: freshly isolated cells from wound tissue

value: skin wound


title: Wound_CRISPR_cells

source_name: wounds that had been treated with hydrogels seeded with Ndrg2-knockout dendritic cells


title: Wound_blank_hydrogel

source_name: wounds that had been treated with blank hydrogels

value: blank hydrogels


title: DH012VitD

source_name: bone marrow-derived cultured dendritic cells after vitamin D3 treatment

value: freshly isolated and cultured according to Lutz et al J Immunol Methods 223, 77-92 (1999).

value: bone marrow

value: vitamin D3


title: Vehicle_Cortex_07

source_name: Cortex, Vehicle, replicate7


title: breast tumor tissue, J03_009

source_name: fresh frozen tumor samples obtained from radical breast cancer surgery

value: breast tumor

value: premenopausal

value: No

value: Positive

value: Negative


title: RNAseqofSUIT2PT:60nM MRTX1133 (replicate 2)

city: La Jolla

tag: cell line


title: breast tumor tissue, J03_006

value: Yes


title: DH011

source_name: bone marrow-derived cultured dendritic cells (untreated)


title: breast tumor tissue, J03_003

value: postmenopausal


title: breast tumor tissue, J03_007


title: breast tumor tissue, J03_001


title: RNAseqofSUIT2PT:60nM MRTX1133 (replicate 1)


title: breast tumor tissue, J03_010


title: RNAseqofSUIT2PT:untreated (replicate 1)


title: DH-NDRG-CRISPR

source_name: bone marrow-derived cultured dendritic cells after CRISPR-knockout of Ndrg2

value: CRISPR-knockout of Ndrg2


title: breast tumor tissue, J03_005


title: Vehicle_Cortex_08

source_name: Cortex, Vehicle, replicate8

tag: strain

value: Slc :ddY

value: male


title: WGBS_117R_O1_luminal

city: Duarte

first: Dustin

middle: E

last: Schones

address: 1500 E Duarte Rd.

institute: City of Hope

data_processing:
Raw sequencing reads were adapter trimmed and hard trimmed 8 bp from both ends using Trim Galore v0.4.5.
Trimmed reads were aligned to the human reference genome hg19 using Bismark v0.19.1 with the --bowtie1 option.
PCR duplicates were removed using Bismark. Methpipe v3.4.3 was used to determine the methylation status of individual CpG sites.
Genome_build: hg19
Supplementary_files_format_and_content: Bed format, columns: chr, CpG site, strand, cytosine context, methylation level (0 to 1), coverage

source_name: Mammary luminal epithelial cells

growth_protocol: Cells were grown in M87A medium with cholera toxin and oxytocin at 0.5 ng/ml and 0.1nM, respectively. Cells were stained with anti-human CD133-PE (Biolegend, clone 7) and anti-human CD271 (Biolegend, clone ME20.4) by following standard flow cytometry protocol. Luminal epithelial cells were enriched with Aria III (Becton Dickinson) as CD133+/CD271- fractions.

extract_protocol:
Quick-DNA Microprep kit (Zymo Research) was used to extract DNA.
Genomic DNA was bisulfite converted using the Zymo EZ DNA methylation kit (Zymo Research). Library preparation was done using TruSeq DNA Methylation Kit with 75ng of bisulfite converted DNA as per manufacturer’s recommendations.

value: Mammary luminal epithelial cells

tag: facs sort group


title: Vehicle_Cortex_04

source_name: Cortex, Vehicle, replicate4


title: Vehicle_Cortex_03

source_name: Cortex, Vehicle, replicate3


title: Vehicle_Cortex_01

source_name: Cortex, Vehicle, replicate1


title: Vehicle_Cortex_06

source_name: Cortex, Vehicle, replicate6


title: breast tumor tissue, J03_002


title: Vehicle_Cortex_02

source_name: Cortex, Vehicle, replicate2


title: WGBS_172L_Y2_luminal


title: breast tumor tissue, J03_004


title: Male, Microglia, Repopulated, Fracture, Sample 4 (V99)

city: Stanford

first: Vivianne

middle: L

last: Tawfik

address: 1291 Welch Road, Grant Building S007

department: Anesthesiology, Perioperative and Pain Medicine

institute: Stanford University

description:
Male_iDTR_fracture_V99
paired-end RNA-seq

data_processing:
Raw sequencing data was analyzed using the nf-core/rnaseq v3.5 RNA-Seq analysis pipeline with nf-core helper tools v2.2, which was run using STAR and RSEM with isoform (transcript) counts and extensive quality control.
The wrapper tool Trim Galore v0.6.7 that employs Cutadapt v3.4 and FastQC v0.11.9 was run to consistently apply quality and adapter trimming to FASTQ files.
Alignment to the GENCODE GRCm38 release M25 reference was done using STAR v2.7.6a and the aligned transcripts were quantitated by RSEM v1.3.1.
MultiQC v1.11 (https://multiqc.info/)(81) helped to aggregate results from the various bioinformatics analyses across the many samples into a single report.
Differentially expressed transcripts were detected from raw transcript counts produced by the STAR-RSEM pipeline using DESeq2 v1.34.0 running in R v4.1.3.
Assembly: GENCODE GRCm38
Supplementary files format and content: *.csv: Comma-separated values files report raw transcript counts for each Sample.

source_name: FACS-isolated microglia

extract_protocol:
Females: RNA was isolated by Azenta Life Sciences (formerly GeneWiz) using a routine protocol.
RNA libraries for RNA-seq were prepared by Azenta Life Sciences (formerly GeneWiz) using an ultra-low input protocol from Illumina.
Males: RNA was isolated using the RNeasy® Plus Micro kit then cDNA was synthesized using the SMART-Seq® v4 Ultra® Low Input RNA kit.
RNA libraries for RNA-seq were prepared using NexteraTM DNA Flex Library Prep.

value: FACS-isolated microglia

tag: genotype

value: Depletion

tag: condition

value: Injury

tag: time

value: Day 14

tag: Sex

value: Male


title: Male, Microglia, Repopulated, Fracture, Sample 6 (V101)

description:
Male_iDTR_fracture_V101
paired-end RNA-seq


title: ABeta_Cortex_02

source_name: Cortex Abeta, replicate2


title: Male, Microglia, Repopulated, Fracture, Sample 5 (V100)

description:
Male_iDTR_fracture_V100
paired-end RNA-seq


title: Vehicle_Cortex_05

source_name: Cortex, Vehicle, replicate5


title: Male, Microglia, Repopulated, Fracture, Sample 2 (V68)

description:
Male_iDTR_fracture_V68
paired-end RNA-seq


title: Male, Microglia, Repopulated, Fracture, Sample 1 (V67)

description:
Male_iDTR_fracture_V67
paired-end RNA-seq


title: WGBS_240L_Y1_luminal


title: WGBS_112R_O2_luminal


title: Male, Microglia, Repopulated, Fracture, Sample 7 (V102)

description:
Male_iDTR_fracture_V102
paired-end RNA-seq


title: CAF culture from mouse # 66383 pcMicro-C replicate 1

first: Dan

last: Filipescu

state: New York

address: 1470 Madison Ave

data_processing:
library strategy: pcMicro-C
Interaction calling and significance thresholding was performed based on the workflow developed by Dovetail Genomics (https://micro-c.readthedocs.io/en/latest/) and the CHiCAGO tool recommendations. Sequenced reads were aligned using BWA v0.7.17-r1188 and filtered using PairTools v1.0.2 and SAMTools v1.9 to identify non-duplicated read-pairs. The technical replicates were merged, and significant interactions (chromatin loops) were called using CHiCAGO v1.2.0  with default parameters at 10kb resolution. Significant Interactions were defined as those with a CHiCAGO score ≥ 5 per condition.
For visualization on the UCSC Genome Browser, output loop files were converted from WashU EpiGenome Browser interactBED format to bigInteract format using BEDTools v2.30.0 and UCSC-Utils v2.9.
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: bigInteract - aligned reads pileup produced with deeptools

source_name: pcMicro-C in cultured cancer-associated fibroblasts 30 minutes after serum stimulation

extract_protocol:
10^6 short-term cultured CAFs after 30min serum stimulation were processed for Micro-C was performed using the Dovetail Micro-C Kit (Cantata Bio) according to the manufacturer’s protocol. Chromatin from 1 × 106 WT and dKO cultured CAFs, cross-linked after serum stimulation, was digested with 3 μl MNAse to obtain a mononucleosomal fraction within specifications.
Each chromatin preparation was subjected to proximity ligation and subsequent library preparation in duplicate. 400 ng of each library was pooled and subjected to promoter capture using the Dovetail Target Enrichment Kit and Mouse Pan Promoter Panel (Cantata Bio).

value: Serum-starved and stimulated cultured CAF

value: dKO

tag: assay

value: pcMicro-C


title: Male, Microglia, Repopulated, No fracture, Sample 2 (V73)

description:
Male_iDTR_control_V73
paired-end RNA-seq

value: No injury


title: Male, Microglia, Repopulated, Fracture, Sample 3 (V69)

description:
Male_iDTR_fracture_V69
paired-end RNA-seq


title: CAF culture from mouse # 66391 pcMicro-C replicate 2

value: WT


title: CAF culture from mouse # 66391 pcMicro-C replicate 1


title: Male, Microglia, Repopulated, No fracture, Sample 1 (V71)

description:
Male_iDTR_control_V71
paired-end RNA-seq


title: Male, Microglia, Resident, Fracture, Sample 5 (V110)

description:
Male_WT_fracture_V110
paired-end RNA-seq

value: No depletion


title: CAF culture from mouse # 66383 pcMicro-C replicate 2


title: Male, Microglia, Resident, Fracture, Sample 4 (V109)

description:
Male_WT_fracture_V109
paired-end RNA-seq


title: Male, Microglia, Resident, Fracture, Sample 3 (V66)

description:
Male_WT_fracture_V66
paired-end RNA-seq


title: IgG_r_Cortex

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

country: Italy

institute: University of Turin

data_processing:
The reads from sequencing were mapped to the mouse genome (mm9 assembly) using Bowtie version 0.12.7, reporting only unique hits with up to two mismatches
The redundant reads were collapsed, and peak calling was performed using MACS version 1.4.1
Assembly: mm9
Supplementary files format and content: porcessed data file contain the output of MACS peak calling

source_name: neocortex

extract_protocol:
Adult neocortical tissue was acutely isolated from two-month-old C57BL/6J mice (n=3 males). To do so, animals were deeply anesthetized with an intraperitoneal injection of a mixture of tiletamine and zolazepam (40 mg/kg; Zoletil; Virbac) and xylazine (5 mg/kg; Rompun; Bayer) and the brain removed after rapid decapitation. Neocortices from both hemispheres were microdissected and pooled together, frozen and stored at -80°C until further analysis. Around 10 mg of neural tissue were chopped with a scalpel, harvested in 5 ml of 0.01 M PBS (pH 7.4) and crosslinked by adding formaldehyde to a final concentration of 1.5%, incubated for 30 min at RT on a rotator, and quenched with 0.125 M glycine for 5 min at RT. After crosslinking, the tissue was washed twice in cold 0.01 M PBS (pH 7.4) and centrifuged at 1.000xg for 5 min at 4°C. Tissue pellet was resuspended in 0.25ml of sodium dodecyl sulfate (SDS) lysis buffer (50 mM Tris pH 8.0, 1% SDS, 10 mM EDTA, anti-proteases) and incubated on a rotator for 30 min at 4°C. Afterwards, sample was sonicated for 18 cycles on high power setting (30s ON, 30s OFF) using the Bioruptor Next Gen (Diagenode) and then centrifuged at 20.000xg for 10 min at 4°C.  The isolated chromatin was diluted 10-fold with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 0.01% SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 167 mM NaCl) (1/10 was kept as input) and incubated with 2 µg of antibody (rabbit anti-COUP-TFI/Nr2f1; Studer’s lab) overnight at 4°C on a rotator. Protein G-conjugated magnetic beads (Dynal, Thermo Fisher Scientific) were saturated with PBS/1% BSA overnight at 4°C. Next day, samples were incubated with saturated beads for two hours at 4°C on a rotator, and subsequently washed with 1 ml of cold Low salt buffer (20 mM Tris-HCl pH 8.0, 0.1 % SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), 1 ml of cold High salt buffer (20 mM Tris-HCl pH 8.0, 0.1 % SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl), 1 ml of cold LiCl buffer (10 mM Tris-HCl pH 8.0, 1% DOC, 250 mM LiCl, 1 mM EDTA, 1% NP-40), and twice with 1 ml of cold TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The immunoprecipitated chromatin was eluted with 200 µl of Elution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS, 150 mM NaCl, 5mM DTT) for 30 min at RT on a rotator, and decrosslinked at 65°C overnight. The decrosslinked DNA was purified using QIAquick PCR Purification Kit (Qiagen) according to the manufacture’s instruction.
sequencing libraries were constructed using the NEBNext ChIP-seq Library Prep Reagent Set for Illumina

value: neocortex

tag: antibody

value: IgG


title: CD8_wt_7

city: Boston

first: Linglin

last: Huang

address: 60 Fenwood Road, HBTM 10016F

department: Neurology

institute: Brigham and Women’s Hospital

data_processing:
Base-calling was performed using NextSeq Control Software 2.2.0.4 (RTA 2.4.11), and fastq files were generated using bcl2fast2 (v2.20.0.422) with default parameters.
Alignment and abundance measurement were performed using the Cumulus smartseq2 v1.1.0 workflow on Terra (https://cumulus.readthedocs.io/en/1.1.0/smart_seq_2.html). Specifically, histat2 v2.1.0 was used to align read to mm10 mouse genome, and the RSEM v1.3.3 was used to calculate gene-level raw counts and TPM. TPM-normalized count was then computed as TPM_i / 10^6 * c, rounding to nearest integer, where TPM_i is the TPM for gene i, and c is the total number of achieved reads. TPM-normalized counts from multiple lanes for the same sample were summed up to create sample-level measurements.
Assembly: mm10
Supplementary files format and content: TPM_normalized_count.txt is a tab delimited file containing a matrix of TPM-normalized counts (described in data processing step section), each column represents a sample and each row represents a gene.

source_name: MC38-OVA colon carcinoma

growth_protocol: C57BL/6J wildtype and B6.129S4-Pglyrp1tm1.1Lky/J mice were obtained from the Jackson Laboratory.

extract_protocol:
For the isolation of TILs, tumor tissue was dissociated with collagenase D (2.5mg/ml) at 37 degrees Celsius for 20 min, followed by centrifugation through a discontinuous Percoll gradient (GE Healthcare). 1,000 living CD8+ T cells (CD45+ TCRß+ CD8) were FACS-sorted immediately into TCL buffer (QIAGEN) supplemented with 1% ß-mercaptoethanol (Sigma Aldrich).
Full-length RNA-seq library preparation was performed following a modified SMART-Seq2 protocol. cDNA concentration was quantified (Quant-iT PicoGreen dsDNA Assay Kit, Thermo Fisher Scientific) and normalized to 0.25ng/ul and libraries were prepared using the Nextera XT DNA Library Preparation kit (Illumina). Using a Bioanalyzer (Agilent), the final libraries were verified to have a size of 500 bp. For sequencing, the barcoded libraries were pooled, normalized to 2 nM, and denatured using 0.1 N NaOH. Sequencing was performed following the manufacturer’s protocols using the paired-end Illumina sequencing (38bp X 2) with 75 cycle Nextseq 500 high output V2 kit (Illumina).

treatment_protocol: MC38-OVA (0.5x10^6) cells were subcutaneously injected into the right flank of mice.

value: MC38-OVA colon carcinoma

value: CD8+ T


title: CD8_wt_8


title: Male, Microglia, Resident, Fracture, Sample 1 (V64)

description:
Male_WT_fracture_V64
paired-end RNA-seq


title: Male, Microglia, Resident, No fracture, Sample 3 (V79)

description:
Male_WT_control_V79
paired-end RNA-seq


title: Male, Microglia, Resident, Fracture, Sample 2 (V65)

description:
Male_WT_fracture_V65
paired-end RNA-seq


title: Male, Microglia, Resident, No fracture, Sample 2 (V78)

description:
Male_WT_control_V78
paired-end RNA-seq


title: CD8_ko_3

value: Pglyrp1 KO


title: CD8_ko_4


title: Female, Microglia, Repopulated, Fracture, Sample 4

description:
Female_Dt_Fx_4
paired-end RNA-seq

value: Female


title: CD8_wt_6


title: CD8_wt_9


title: CD8_ko_2


title: CD8_ko_1


title: Female, Microglia, Repopulated, Fracture, Sample 2

description:
Female_Dt_Fx_2
paired-end RNA-seq

value: FACS-isolated microglia


title: K4me3_Cortex_nogel


title: E4_23_BPCE4_rep4

first: Nneoma

last: Adaku

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Reads were pseudoaligned to the mm10 mouse genome and counted using Kallisto v0.46.1
Count matrix was generated using tximport v1.18.0
Differentially expressed transcripts were determined using DESeq2 v1.28.1
Assembly: mm10
Supplementary files format and content: csv file containing normalized count matrix
Supplementary files format and content: tsv file containing abundance estimates and transcript length estimates from Kallisto pseudoalignment

source_name: melanoma primary tumor

growth_protocol: Tumors were induced with topical administration of 4-hydroxytamoxifen to shaved back skin and allowed to grow for 49 days.

extract_protocol:
10mg of tissue was dissected from the center of tumors on a ThermalTray (Corning, 432074) placed on dry ice. Tumor pieces were placed in homogenizer tubes containing ceramic beads along with lysis buffer from the Total RNA Purification Kit (Norgen, 37500) and RNAse inhibitors (10 μl/mL β-mercaptoethanol and 200 units/mL RNAsin Plus (Promega, N2615)), flash frozen in liquid nitrogen, and homogenized with a Beadruptor 2000 at 0°C. RNA was then purified with the Total RNA Purification Kit with on-column DNAse treatment per manufacturer’s instructions.
Libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina)

value: melanoma primary tumor


title: Female, Microglia, Repopulated, Fracture, Sample 1

description:
Female_Dt_Fx_1
paired-end RNA-seq

value: Depletion

value: Injury


title: BMAd cells, GC+GW96621 [D1]

city: baltimore

first: Mei

last: Wan

state: Maryland

address: 720 Rutland Ave,Ross research buil

department: Department of Orthopedics

institute: Johns Hopkins Hospital

data_processing:
Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast FASTQ preprocessor with useful quality
Total reads were aligned to the reference genome using HISAT2 v2.1.0
Featurecount was used to count the reads numbers mapped to each gene. And then TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Bone marrow

growth_protocol: Bone marrow stem cells were maintained in αMEM  supplemented with 15% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). At least 100 ug of total RNA was sent for further process.
Libraries were prepared using the Smart-Seq 2 protocol with a template switching oligonucleotide, followed by PCR amplification and purification.

treatment_protocol:
Adipogenic differentiation was induced by StemPro Adipogenesis Differentiation kit (Gibco) for 14 days
Cells were treated with 10−6M DEX or 10−6M DEX plus GW9662 for 24 hours.

value: Bone marrow

value: BMAd

value: Adipocyte

value: adipogenic differentiation, GC+GW9662


title: BMAd cells, GC2 [G2]

value: adipogenic differentiation, GC


title: BMAd cells, GC+GW96622 [D2]

value: WT


title: Coup-TF1_Cortex


title: E4_22_BPCE4_rep3


title: BMAd cells, GC1 [G1]


title: BMAd cells, Control2 [C3]

value: adipogenic differentiation


title: Male, Microglia, Resident, No fracture, Sample 1 (V77)

description:
Male_WT_control_V77
paired-end RNA-seq

value: No depletion

value: No injury

value: Day 14

value: Male


title: Female, Microglia, Repopulated, No fracture, Sample 3

description:
Female_Dt_Ctrl_3
paired-end RNA-seq


title: BMAd cells, Control1 [C1]


title: E4_21_BPCE4_rep2


title: Female, Microglia, Repopulated, No fracture, Sample 2

description:
Female_Dt_Ctrl_2
paired-end RNA-seq


title: E4_20_BPCE4_rep1


title: Female, Microglia, Repopulated, No fracture, Sample 1

description:
Female_Dt_Ctrl_1
paired-end RNA-seq


title: 4b

city: Frankfurt

first: Xinlai

last: Cheng

address: Max-von-Laue-Strasse 15. R. 3.652

department: Pharmaceutical Chemistry

country: Germany

institute: Goethe university Frankfurt

data_processing:
Sequencing was performed in paired-end 50 bp on an Illumina Novaseq 6000, running Novaseq Control software 1.7.0
Trimming of the adaptors was performed with cutadapt, followed by a quality control of the trimmed teads using FastQC.
Trimmed reads were aligned to the reference genome (hg38) using BWA software V.0.7.17.
Samples were filtered for regions blacklisted by the encode project.
PCR duplicates and multimapping reads were removed using samtools. Alignment coordinates were converted to BED format using BEDTools V.2.17 and peak calling was performed using MACS2. All Chip-Seq was perfomred by Diagenode Germany.
Assembly: hg38
Supplementary files format and content: BWA, samtools,
Supplementary files format and content: BEDTools, MACS2

source_name: human cancer cell line

extract_protocol:
Cells were fixed with 1% formaldehyde in cell culture medium for 15 min at room temperature. 1/10 volume of glycine was added and incubate for 5 min at RT to stop the fixation. Cells were resuspended with trypsin and cell pellets with dried ice were sent to Diagenode, Germany for ChIP-Seq.
The library was prepared with the Microplex kit. 2 µg of BRD4 antibody was used for ChIP with down to 50 pg of DNA. Shearing was performed in 0.65 ml Bioruptor with 4 min 30 s on/off condition.

value: human cancer cell line

value: lymphoblast cells

value: JQ1-FCPF +sgRNA low


title: BMAd cells, GC3 [G3]


title: 5b

value: JQ1 +sgRNA high


title: BMAd cells, GC+GW96623 [D3]


title: 3b

value: JQ1-FCPF -sgRNA low


title: pooled

value: Non treatment


title: Female, Microglia, Repopulated, Fracture, Sample 3

description:
Female_Dt_Fx_3
paired-end RNA-seq

value: FACS-isolated microglia

value: Depletion

value: Injury

value: Female


title: Female, Microglia, Resident, Fracture, Sample 4

description:
Female_Wt_Fx_4
paired-end RNA-seq


title: 5a


title: Female, Microglia, Resident, Fracture, Sample 3

description:
Female_Wt_Fx_3
paired-end RNA-seq


title: 3a


title: E2_18_BPCE2_rep4

value: melanoma primary tumor


title: 4a


title: E2_12_BPCE2_rep1


title: 2b

value: JQ1-FCPF +sgRNA high


title: E2_13_BPCE2_rep2


title: E2_14_BPCE2_rep3


title: Female, Microglia, Resident, Fracture, Sample 1

description:
Female_Wt_Fx_1
paired-end RNA-seq


title: Female, Microglia, Resident, Fracture, Sample 2

description:
Female_Wt_Fx_2
paired-end RNA-seq


title: 1b


title: 1a


title: 2a


title: B16F10_APOE3_rep5

data_processing:
Tail sequences were trimmed with bbduk v.38.31
Reads were aligned to the mm10 mouse genome with STAR v.2.6.0
Aligned reads were counted with featureCounts
Differentially expressed transcripts were determined with DESeq2 v1.28.1
Assembly: mm10
Supplementary files format and content: csv file containing normalized count matrix

source_name: lung metastasis

growth_protocol: APOE2 and APOE3 knock-in mice were injected via lateral tail vein with 1 × 10^5 B16F10-TR-shApoe cells (in PBS)

extract_protocol:
Fifteen days after injection, lungs were taken from mice and digested with collagenase. TO-PRO-3 low/CD45-/GFP+ tumor cells from the single cells suspension were sorted on a BD FACSAria II. RNA was isolated with the Norgen Total RNA Purification Kit with on-column DNAse treatment. RNA was then concentrated with a Zymo RNA Clean & Concentrator Kit.
Libraries were constructed using QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen)

value: lung metastasis

value: murine melanoma


title: B16F10_APOE3_rep4


title: Female, Microglia, Resident, No fracture, Sample 4

description:
Female_Wt_Ctrl_4
paired-end RNA-seq

value: No depletion

value: No injury


title: Female, Microglia, Resident, No fracture, Sample 2

description:
Female_Wt_Ctrl_2
paired-end RNA-seq

value: Day 14


title: B16F10_APOE3_rep2


title: B16F10_APOE3_rep3


title: BM-39c

city: West Haven

first: Sidi

state: CT

address: 850 West Campus Drive

institute: Yale University

data_processing:
raw FASTQ data were pre-processed with Cell Ranger v6.0.1.
Assembly: Ensembl GRCh38
Supplementary files format and content: filtered dataset using Cell Ranger v6.0.1

extract_protocol:
CAR-T cells were sorted using Aria II cell sorter (BD) based on mScarlet expression.
Sorted cells were washed with PBS, and cell number and viability were assessed by trypan blue (Lonza) staining. About 2,000 to 10,000 purified mScarlet+ cells were used for scRNA-seq library preparation using Chromium Next GEM Single Cell 5’ Reagent Kits V2 (10x Genomics) according to manufacturer’s instructions. The single cell libraries were sequenced by NovaSeq 6000 (Illumina) with 2x150 read length.

value: Bone Marrow


title: SP-39d

value: Spleen


title: BM-39b


title: BM-39d


title: SP-39a

source_name: CAR-T

value: CAR-T


title: BM-39a


title: Female, Microglia, Resident, No fracture, Sample 1

description:
Female_Wt_Ctrl_1
paired-end RNA-seq


title: SP-39c


title: SP-39b


title: B16F10_APOE3_rep1

city: New York


title: Female, Microglia, Resident, No fracture, Sample 3

description:
Female_Wt_Ctrl_3
paired-end RNA-seq


title: B16F10_APOE2_rep8


title: B16F10_APOE2_rep7


title: B16F10_APOE2_rep6


title: Jejunum, DKO1

city: Newark

last: Gao

state: NJ

address: 225 University Ave

department: Biological Sciences

institute: Rutgers Newark

data_processing:
Raw sequencing reads (fastq) were quality checked using fastQC (v0.11.3).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic(0.36) (parameter- reads were trimmed based on base call phred score lower than 20)
Trimmed sequence reads were mapped to mm9 using HISTAT2 (v2.1.0) using default parameters
Reads were normalized in DESeq2 (Build 3.9) using default settings in R.
Assembly: mm9
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Jejunum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Purified RNA was processed using Illumina’s TruSeq RNA Library Prep kit v2 according to manufacturer's protocol.

treatment_protocol: Adult mice were treated with tamoxifen (40mg/kg) and then subsequently sacrificed at 2 days post tamoxifen administration. Jejunal tissue was collected

value: Jejunum

value: Rab11aL/L, Rab11b-/-, VillinCreER+

value: Tamoxifen (40mg/kg)


title: Jejunum, DKO3


title: Jejunum, DKO2


title: 39C2-2

description: Biol rep2

data_processing:
Fastq files generated by sequencing were aligned and mapped using STAR with the human genome assembly version GRCh38.
Assembly: Ensembl GRCh38
Supplementary files format and content: Tab-delimited text files contain read counts after alignment.

extract_protocol:
positive CAR-T cell total RNA was extracted using RNeasy Plus mini isolation kit (Qiagen).
Library preparations were performed using a NEBNext® Ultra™RNA Library Prep Kit for Illumina according to manufacturer’s instruction.

value: 2rounds of stimulation


title: 39C2-1

description: Biol rep1


title: 39B2-2

description: Biol rep2


title: 39D2-3

description: Biol rep3


title: 39C2-3

description: Biol rep3


title: 39D2-2

description: Biol rep2


title: 39B2-3

description: Biol rep3


title: 39D2-1

description: Biol rep1


title: B16F10_APOE2_rep5


title: 39A2-3

description: Biol rep3


title: B16F10_APOE2_rep2


title: 39D0-3

description: Biol rep3

value: No stimulation


title: 39A2-2

description: Biol rep2


title: B16F10_APOE2_rep3


title: 39C0-3

description: Biol rep3


title: Jejunum, BKO2


title: Jejunum, AKO3

value: Rab11aL/L, VillinCreER+


title: Jejunum, BKO1


title: Jejunum, AKO2


title: 39C0-2

description: Biol rep2


title: Jejunum, BKO3


title: Jejunum, AKO1


title: 39B0-3

description: Biol rep3


title: 39C0-1

description: Biol rep1


title: B16F10_APOE2_rep1


title: 39B2-1

description: Biol rep1