title: Donor 75, 3D Collagen Untreated

description: gene expression data from monocyte derived iDCs cultured for two days in 3D collagen

value: Untreated iDCs in 3D collagen


title: Donor 71, 2D suspension HIV-1 infected + Vpx and Raltegravir

status: Public on Mar 28 2023

type: RNA

city: Heidelberg

first: Lara

last: Gallucci

address: Neuenheimer Feld

department: Department of Infectious Diseases, Integrative Virology

country: Germany

institute: University Hospital Heidelberg

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and Raltegravir and cultured for two days in 2D suspension

hyb_protocol: Standard Affymetrix protocols

scan_protocol: Standard Affymetrix protocols

data_processing: The data were analyzed with GeneChip Command Console

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: monocyte derived dendritic cells

label_protocol: Standard Affymetrix protocols

growth_protocol: Monocytes, isolated from PBMCs of healthy donors, were differentiated into iDCs for six days by the addition of IL-4/GM-CSF. Once differentiated, iDCs were cultured for two days either in 3D collagen matrix or in 2D suspension cultures under the respective conditions

extract_protocol: RNA was extracted using “Macherey-Nagel NucleoSpin RNA kit according to the manufacturer's instructions.

treatment_protocol: Two days post culturing iDCs were treated with collagenase I (100U Worthington) for 30-45 min at 37°C, were extensively washed in PBS and RNA was extracted.

tag: tissue

value: monocyte derived dendritic cells

tag: treatment

value: iDC spin-transduced with VLPs_Vpx, infected with HIV-1 and treated with raltegravir in 2D suspension

tag: donor


title: E14.5_Control_03

type: SRA

city: San Francisco

first: Julie

middle: B

last: Sneddon

state: California

address: 500 Parnassus Ave.

country: USA

institute: UCSF

description:
E14_C3
Bulk RNA-Seq

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the reference genome (mm10-2020-A) using TopHat.
Gene expression quantification was performed using HTSeq.
Differential gene expression analysis was performed using DESeq2.
Assembly: mm10-2020-A
Supplementary files format and content: E13.5_E14.5_Control_Null_Counts.xls: Excel processed data file contains a gene by sample matrix of counts.

organism: Mus musculus

source_name: Pancreas

growth_protocol: Fgf9 LacZ mice were maintained on a C57BL/6J background.

extract_protocol:
Dissected pancreata were placed in TriZol reagent. Total RNA was extracted using Zymo Directzol Microprep (R2060) according to the manufacturer's instructions.
Libraries were constructed using the Illumina NEBNext Ultra II RNA library prep kit following manufacturer's instructions for the NEBNext Poly(A) mRNA magnetic isolation module.

value: Pancreas

tag: pancreata per sample

tag: developmental stage

value: Embryonic day 14.5

tag: genotype


title: Donor 71, 2D suspension HIV-1 infected i+ Vpx

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and cultured for two days in 2D suspension

value: iDC spin-transduced with VLPs_Vpx and infected with HIV-1 in 2D suspension


title: iUC5, male, 67 years old

city: Chengdu

first: Yun

last: Yang

state: Sichuan

address: 37 Guoxue Lane

department: Colorectal Cancer Center, Department of General Surgery

country: China

institute: West China Hospital, Sichuan University

description:
inflamed colon segmetns from ulcerative colitis
FPKM_allsamples.txt
counts_allsamples.txt
UC5

data_processing:
1.Data preprocessing:  Raw reads generated during high-throughput sequencing were fastq format sequences. In   order to get high-quality reads that could be used for later analysis, raw reads needed to be further   quality filtered. Trimmomatic software was first used for adpter removing, And then low-quality   bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
2.Genomic alignment:    Using hisat2 to align clean reads to the reference genome of the experimental specie, the   sample should be assessed by genomic and gene alignment.
3.Differential screening analysis and Functional Analysis  Using the estimateSizeFactors function of the DESeq (2012) R package to normalize the counts, and using nbinomTest function to calculate pvalue and flodchange values for the difference comparison. Selecting differential transcripts with p-values <= 0.05 and flodchange >= 2，and analysising differential mRNA GO and KEGG enrichment by Hypergeometric Distribution Test.
4. Gene set expression analysis (GSEA)  Gene set expression analysis (GSEA) of molecular pathways affected by differentially expressed genes (DEGs) was performed by GSEA R (v1.2) with weighted enrichment statistic and Signal2Noise for gene ranking
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each samples
Supplementary files format and content: tab-delimited text files include Counts values for each samples

source_name: colon,  intact bowel wall

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA   Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times.   Leave the mixture on ice for 10 min.  B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition   of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate   the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the   lower phase, and transfer it to a fresh tube.  C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase.  D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up   to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass   the mixture through the filter. Discard the flow-through.  E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at   13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into   the same Collection Tube.  F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the   mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min.  G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at   13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube.  H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through   the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3.  I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter   Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the   center of the filter. Leave it at the room temperature for 2 min. Spin for 20–30 sec at maximum speed   to recover the RNA. Collect the eluate (which contains the RNA) and store it at -70°C.
1 Ribo-Zero Deplete and Fragment RNA  a. Add 5 μL rRNA Binding Buffer and 5 μL rRNA Removal Mix-Gold to each well with 10 μL total RNA (1 μg). Gently pipette the entire volume up and down 6 times to mix thoroughly.  b. Incubate the PCR plate at 68°C for 5 min, and then place at room temperature for 1 min.  c. Add 35 μL of rRNA Removal Beads to each well of the new PCR plate. Adjust the pipette to 45 μL, then with the tip of the pipette at the bottom of the well, pipette quickly up and down 20 times to mix thoroughly. Incubate at room temperature for 1 min. Place the PCR plate on the magnetic stand at room temperature for 1 min. Transfer all of the supernatant from each well to the corresponding well of the new PCR plate.  d. Add 99 μL of RNAClean XP beads (If starting with degraded total RNA, add 193 μL of RNAClean XP beads to each well) to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the PCR plate at room temperature for 15 min.   e. Place the PCR plate on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well of the PCR plate.  f. Add 200 μL freshly prepared 70% EtOH to each well. Incubate the PCR plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. Let the PCR plate stand at room temperature for 15 min to dry.  g. Add 11 μL Elution Buffer to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the PCR plate at room temperature for 2 min. Place the PCR plate on the magnetic stand at room temperature for 5 min. Transfer 8.5 μL supernatant from the PCR plate to the new 0.2 ml tube.  h. Add 8.5 μL Elute, Prime, Fragment High Mix to each well of the plate. Gently pipette the entire volume up and down 6 times to mix thoroughly.  i. Incubate at 94°C for 8 min, hold at 4°C, and then centrifuge shortly    2 Synthesize First Strand cDNA  a. Add 8 μL First Strand Synthesis Act D Mix and SuperScript II Reverse   Transcriptase in each well of the PCR plate. Gently pipette the entire volume up and down 6 times to mix thoroughly.  b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C   for 15 min, 70°C for 15 min, hold at 4°C.    3 Synthesize Second Strand cDNA  a. Add 5 μL End Repair Control (2 μL End Repair Control + 98 μL  Resuspension Buffer) in each well of the PCR plate.  b. Add 20 μL Second Strand Marking Master Mix. Gently pipette the entire volume up and down 6 times to mix thoroughly.  c. Incubate at 16°C for 60 min. Remove the plate from the thermal cycler.    4 Purification  a. Add 90 μL mixed AMPure XP beads to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the plate at room temperature for 15 min.  b. Place it on the magnetic stand at room temperature for 5 min.  c. Remove and discard 135 μL supernatant from each well of the plate.  d. With the plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well.  e. Repeat step d one time.  f. Let the plate stand at room temperature for 15 min to dry, and then remove the plate from the magnetic stand.  g. Add 17.5 μL Resuspension Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly.  h. Incubate the plate at room temperature for 2 min. Then place the plate on the magnetic stand at room temperature for 5 min.  i. Transfer 15 μL supernatant from the plate to the new PCR plate.    5 Adenylate 3’ Ends  a. Add 2.5 μL of diluted A-Tailing Control (1 μL A-Tailing Control + 99 μL Resuspension Buffer) to each well of the plate.  b. Add 12.5 μL of A-Tailing Mix to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly.  c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C.    6 Ligate Adapters  a. Add 2.5 μL of diluted Ligation Control (1 μL Ligation Control + 99 μLResuspension Buffer) to each well of the plate.  b. Add 2.5 μL of Ligation Mix to each well of the plate.  c. Add 2.5 μL of RNA Adapter Index to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly.  d. Incubate at 30°C for 10 min.  e. Add 5 μL of Stop Ligation Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly.    7 Purification  a. Add 42 μL of mixed AMPure XP Beads to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the plate at room temperature for 15 min.  b. Place the plate on the magnetic stand at room temperature for 15 min or until the liquid is clear.  c. Remove and discard 79.5 μL supernatant from each well of the plate.   d. With the plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well.  e. Repeat step d one time for a total of two 80% EtOH washes.  f. With the plate on the magnetic stand, let the samples air-dry at room temperature for 15 min. Remove the plate from the magnetic stand.  g. Add 52.5 μL Resuspension Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly.  h. Incubate the plate at room temperature for 2 min. Place the plate on the magnetic stand at room temperature for 5 minutes or until the liquid is clear.  i. Transfer 50 μL supernatant from each well of the plate to the corresponding well of the new PCR plate.  j. Add 50 μL of mixed AMPure XP Beads to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the plate at room temperature for 15 min.  k. Place the plate on the magnetic stand at room temperature for 15 min or until the liquid is clear.  l. Remove and discard 95 μL supernatant from each well of the plate.   m. With the plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well.   n. Repeat step m one time for a total of two 80% EtOH washes.  o. With the plate on the magnetic stand, let the samples air-dry at room temperature for 15 min, and then remove the plate from the magnetic stand.  p. Add 22.5 μL Resuspension Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly.  q. Incubate the plate at room temperature for 2 min. Place the plate on the magnetic stand at room temperature for 5 min or until the liquid is clear.  r. Transfer 20 μL supernatant from each well of the plate to the corresponding well of the new PCR plate    8 Enrich DNA Fragments  a. Add 5 μL of PCR Primer Cocktail to each well of the PCR plate.  b. Add 25 μL of PCR Master Mix to each well of the PCR plate. Gently pipette the entire volume up and down to mix thoroughly.  c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 s; 15 cycles 98°C for 10 s, 60°C for 30 s, 72°C for 30 s; 1 cycle 72°C for 5 min; hold at 10°C    9 Purification  a. Add 50 μL of the mixed AMPure XP Beads to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the PCR plate at room temperature for 15 min.  b. Place the plate on the magnetic stand at room temperature for 15 min or until the liquid is clear.  c. Remove and discard 95 μL supernatant from each well of the PCR plate.  d. With the PCR plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the PCR plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well.  e. Repeat step d one time for a total of two 80% EtOH washes.  f. With the PCR plate on the magnetic stand, let the samples air-dry at room temperature for 15 min, and then remove the plate from the magnetic stand.  g. Add 32.5 μL Resuspension Buffer to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly.  h. Incubate the PCR plate at room temperature for 2 min. Place the PCR plate on the magnetic stand at room temperature for 5 min or until the liquid is clear.  i. Transfer 30 μL supernatant from each well of the PCR plate to the corresponding well of the new PCR plate    10 Validate library  a. Load 1 μL sample on an Agilent Technologies 2100 Bioanalyze.  b. Check the size and purity of the sample.

value: colon,  intact bowel wall

tag: disease state

value: ulcerative colitis


title: iUC4, male, 56 years old

description:
inflamed colon segmetns from ulcerative colitis
FPKM_allsamples.txt
counts_allsamples.txt
UC4


title: iUC3, male, 67 years old

description:
inflamed colon segmetns from ulcerative colitis
FPKM_allsamples.txt
counts_allsamples.txt
UC3


title: JW1899

city: Beijing

first: Feifei

last: Ma

address: Road 2 Yabao

institute: Capital Institue of Pediatrics

description: miRNAs expression in Peripheral Blood between obesity and lean of children

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section.

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: Peripheral Blood

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Normal environment

extract_protocol: Total RNA was extracted and purified using mirVanaTM PARISTM (Cat#AM1556, Ambion, Austin, TX, US) in accordance with the manufacturer’s instructions and checked for the RIN number to inspect RNA integration with an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Blood samples were centrifuged. Plasma and red blood cells were separated.

value: plasma

tag: gender

value: boy

tag: phenotype

value: obesity


title: BJ0598

value: lean


title: E14.5_Control_02

description:
E14_C2
Bulk RNA-Seq


title: Donor 71, 2D suspension LPS treated

description: gene expression data from monocyte derived iDCs trated with LPS and cultured for two days in 2D suspension

value: LPS treated iDCs in 2D suspension


title: iUC1, male, 65 years old

description:
inflamed colon segmetns from ulcerative colitis
FPKM_allsamples.txt
counts_allsamples.txt
UC1


title: iUC2, male, 75 years old

description:
inflamed colon segmetns from ulcerative colitis
FPKM_allsamples.txt
counts_allsamples.txt
UC2


title: Donor 71, 2D suspension Untreated

description: gene expression data from monocyte derived iDCs cultured for two days in 2D suspension

value: Untreated iDCs in 2D suspension


title: Donor 71, 2D suspension HIV-1 infected

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5 and cultured for two days in 2D suspension

value: HIV-1 infected iDCs in 2D suspension


title: E14.5_Null_02

description:
E14_M2
Bulk RNA-Seq


title: E13.5_Null_02

description:
E13_M2
Bulk RNA-Seq

value: Embryonic day 13.5


title: niBD4, male,  56 years old

description:
non-inflamed colon segments
FPKM_allsamples.txt
counts_allsamples.txt
CTR4

value: non-inflamed colon


title: niBD5, male,  67 years old

description:
non-inflamed colon segments
FPKM_allsamples.txt
counts_allsamples.txt
CTR5


title: JW1690

value: girl


title: JW1272


title: JW1363


title: Donor 71, 3D Collagen HIV-1 infected + Vpx and Raltegravir

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and Raltegravir and cultured for two days in 3D collagen

value: monocyte derived dendritic cells

value: iDC spin-transduced with VLPs_Vpx, infected with HIV-1 and treated with raltegravir in 3D collagen


title: E13.5_Null_01

description:
E13_M1
Bulk RNA-Seq

value: Pancreas


title: niBD3, male,  24 years old

description:
non-inflamed colon segments
FPKM_allsamples.txt
counts_allsamples.txt
CTR3


title: E13.5_Control_03

description:
E13_C3
Bulk RNA-Seq


title: E13.5_Control_01

description:
E13_C1
Bulk RNA-Seq


title: JW1827


title: E14.5_Control_01

description:
E14_C1
Bulk RNA-Seq

value: Embryonic day 14.5


title: JW0988


title: Donor 71, 3D Collagen LPS treated

description: gene expression data from monocyte derived iDCs trated with LPS and cultured for two days in 3D collagen

value: LPS treated iDCs in 3D collagen


title: Mouse_BCC_CD45.2+

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

description: single cell RNA-seq

library_source: transcriptomic single cell

data_processing:
scRNA data was processed using the 10x Genomics CellRanger pipeline
Seurat was used to call cluster and generate UMAPs
Monocle was used to perform pseudotime analysis
Assembly: mm10
Supplementary files format and content: count matrix

source_name: mouse BCC

growth_protocol: Ptch1+/-;p53f/f;K14CreER mice were induced to form tumors (Whitson et al., 2018; PMID: 29400712)

extract_protocol:
Tumors were dissociated by first mincing into pieces smaller than 1 mm in diameter and then incubated in 40 mL of a 0.5% collagenase solution (Gibco; 25200056) for 1hrs with rotation at 37°C . 5 mL of 0.25% Trypsin was then added and incubated for an additional 15min with rotation at 37°C . For Sample1/Mouse_BCC_CD45+_Primary_Tumor  cells were FACS sorted for CD45+ cells. For Sample 2/Mouse_BCC_CD45.2+ and Sample 3/Mouse_BCC_CD45.2-, cells were  FACS sorted for CD45+CD45.2+ or CD45+CD45.2-. Cells were then processed using the 10X Genomics Next GEM scRNA-Seq solution.
Library construction followed the 10X Genomics Next GEM scRNA-Seq pipeline.

treatment_protocol: No additional treatment for Sample 1/mBCC sample. For Sample 2/Mouse_BCC_CD45.2+ and Sample 3/Mouse_BCC_CD45.2-, primary Ptch1+/-;p53f/f;K14CreER tumor cells were transplanted into NodScid host, which then formed tumors. Once tumors were formed, mice were either treated with Vismodegib (100 mg/kg) or DMSO control for 2 weeks and then harvested.

value: Ptch1+/-;p53f/f;K14CreER model transplanted into NOD SCID

value: mouse basal cell carcinoma (BCC) tumor


title: iCD5, male, 46 years old

description:
inflamed colon segments from Crohn’s disease
FPKM_allsamples.txt
counts_allsamples.txt
CD5

value: colon,  intact bowel wall

value: Crohn’s disease


title: E13.5_Control_02

description:
E13_C2
Bulk RNA-Seq


title: JW0761

value: plasma

value: obesity


title: Donor 71, 3D Collagen Untreated

description: gene expression data from monocyte derived iDCs cultured for two days in 3D collagen

value: Untreated iDCs in 3D collagen


title: JW0563

value: boy


title: Donor 71, 3D Collagen HIV-1 infected + Vpx

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and cultured for two days in 3D collagen

value: iDC spin-transduced with VLPs_Vpx and infected with HIV-1 in 3D collagen


title: JW0306


title: niBD1, male,  32 years old

description:
non-inflamed colon segments
FPKM_allsamples.txt
counts_allsamples.txt
CTR1


title: Donor 70, 2D suspension LPS treated

value: LPS treated iDCs in 2D suspension


title: Donor 71, 3D Collagen HIV-1 infected

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5 and cultured for two days in 3D collagen

value: HIV-1 infected iDCs in 3D collagen


title: Donor 75, 3D Collagen HIV-1 infected + Vpx and Raltegravir


title: iCD3, male, 24 years old

description:
inflamed colon segments from Crohn’s disease
FPKM_allsamples.txt
counts_allsamples.txt
CD3


title: Donor 70, 2D suspension HIV-1 infected + Vpx and Raltegravir

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and Raltegravir and cultured for two days in 2D suspension

value: iDC spin-transduced with VLPs_Vpx, infected with HIV-1 and treated with raltegravir in 2D suspension


title: Donor 70, 2D suspension HIV-1 infected

value: monocyte derived dendritic cells

value: HIV-1 infected iDCs in 2D suspension


title: Donor 70, 2D suspension HIV-1 infected + Vpx

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and cultured for two days in 2D suspension

value: iDC spin-transduced with VLPs_Vpx and infected with HIV-1 in 2D suspension


title: iCD6, male, 25 years old

description:
inflamed colon segments from Crohn’s disease
FPKM_allsamples.txt
counts_allsamples.txt
CD6


title: JW0439

description: miRNAs expression in Peripheral Blood between obesity and lean of children


title: Mouse_BCC_CD45.2-

description: single cell RNA-seq


title: Mouse_BCC_CD45+_Primary_Tumor_Rep2

description: single cell ATAC-seq

library_source: genomic single cell

data_processing:
scATAC data is processed using ArchR
ArchR was used to cluster and generate UMAPs. Using MACS2 peaks are called and homer is used to find cluster specific Motifs.
ArchR was used to perform pseudotime analysis and Integration analysis with the respective scRNA data
Assembly: mm10
Supplementary files format and content: Fragment file

molecule: genomic DNA

extract_protocol:
Tumors were dissociated by first mincing into pieces smaller than 1 mm in diameter and then incubated in 40 mL of a 0.5% collagenase solution (Gibco; 25200056) for 1hrs with rotation at 37°C . 5 mL of 0.25% Trypsin was then added and incubated for an additional 15min with rotation at 37°C . Cells were then processed using the 10X Genomics  scATAC-Seq solution.
Library construction followed the 10X Genomics scATAC-Seq pipeline.

treatment_protocol: No additional treatment for either samples.

value: Mouse tumor from Ptch1+/-;p53f/f;K14CreER model


title: iCD1, male, 32 years old

description:
inflamed colon segments from Crohn’s disease
FPKM_allsamples.txt
counts_allsamples.txt
CD1


title: JW0212


title: Donor 70, 2D suspension Untreated

description: gene expression data from monocyte derived iDCs cultured for two days in 2D suspension

value: Untreated iDCs in 2D suspension


title: niBD2, male,  23 years old

description:
non-inflamed colon segments
FPKM_allsamples.txt
counts_allsamples.txt
CTR2

value: non-inflamed colon


title: Mouse_BCC_CD45+_Primary_Tumor_Rep1

description: single cell ATAC-seq


title: Mouse_BCC_CD45+_Primary_Tumor

description: single cell RNA-seq

value: Ptch1+/-;p53f/f;K14CreER model

value: mouse basal cell carcinoma (BCC) tumor


title: JW0299

value: girl


title: JW0035

value: plasma


title: iCD2, male, 23 years old

description:
inflamed colon segments from Crohn’s disease
FPKM_allsamples.txt
counts_allsamples.txt
CD2

value: colon,  intact bowel wall

value: Crohn’s disease


title: CD_F6

status: Public on Mar 27 2023

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

data_processing:
Reads were aligned to the musmusculus reference genome version mm10 using STAR (v2.5.2) with default parameters. SAM files were converted to BAM and sorted using Sambamba (v0.7.1)
Count matrices were generated using The Rsubread R package with the Gencode Mus_musculus v.M25  custom annotation
Assembly: mm10
Supplementary files format and content: Raw count matrix in xls format

source_name: epididymal white adipose tissue

extract_protocol:
RNA was extracted using TRIzol reagent and further purified/DNase treated with the RNeasy Kit cleanup protocol (Qiagen, Hilden, Germany). 300 ng of total RNA were used for the construction of the sequencing libraries.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep kit  (Human/Mouse/Rat 96 samples ref. 20020597, Illumina) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing.

tag: condition

value: control Sucnr1fl/fl mice

tag: strain


title: CD_F5


title: CD_F4


title: Donor 70, 3D Collagen LPS treated

value: LPS treated iDCs in 3D collagen


title: CD_F2


title: CD_A5

value: adipocyte cell-specific Sucnr1 knockout (Ad-Sucnr1 KO) mice


title: JW0132

value: obesity


title: cDC2s

city: Bethesda

first: Katherine

last: Goldfarbmuren

state: MD

address: 41 Center Dr

department: Advanced Biomedical Computational Science

institute: NCI, Frederick National Laboratory for Cancer Research

data_processing:
CCBR Pipeliner (https://github.com/CCBR/Pipeliner)
Supplementary files format and content: comma-delimited text file includes matrix with CPM values for all 4 samples

source_name: EO771 tumor

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen) and removal of genomic DNA was performed with the DNase I enzyme (Qiagen), acccording to manufacturer's recommendations
Library preparation was performed using NEBNext® Ultra™ II Directional RNA Library Prep Kit

value: EO771 tumor

tag: cell type


title: cDC1s


title: Macrophages

value: macrophage


title: NewDCs


title: Tgfb_rep2 [11_TGF_B]

city: Aurora

first: Mary

last: Weiser-Evans

state: CO

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

institute: University of Colorado Anschutz Medical Campus

data_processing:
Paired-end RNA-Seq reads were obtained using Illumina analysis Pipeline.
Fastq files were preprocessed with Flexbar 3.5.0 to trim 12 bases at the left side of reads and remove adapter sequences.
The fastq files were were aligned to the Mus musculus GRCm39 reference genome (Ensembl, release 104) using HISAT2 version 2.2.1 with the following options: -p 8 --dta --rna-strandness RF
Samtools 1.13 were used to sort the aligned reads and HTSeq 0.11.3 were used to produce raw counts uniquely mapping to genes for each samples.
Assembly: GRCm39 (Ensembl release 104)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Aorta and carotid artery

growth_protocol: AdvSca1-SM cells were maintained in alpha-MEM GlutaMAX media supplemented with 10% mesenchymal stem cell-qualified fetal bovine serum (FBS), 1ng/mL murine basic fibroblast growth factor, 5ng/mL murine epidermal growth factor, and 1x penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C. Prior to treatment, AdvSca1-SM cells were maintained in alpha-MEM GlutaMAX media supplemented with 0.1% mesenchymal stem cell-qualified fetal bovine serum (FBS), 1ng/mL murine basic fibroblast growth factor, 5ng/mL murine epidermal growth factor, and 1x penicillin/streptomycin for 24hrs to growth arrest cells

extract_protocol:
RNA was isolated from hepatic tissue using QIAshredders and RNeasy Plus mini kit (Qiagen). RNA quality and quantity were analyzed using TapeStation Systems (Agilent)
Ribo Depleted total RNA library preparation and sequencing (Paired end 150 cycle 2x150, using NovaSEQ 6000) were conducted at The Genomics Shared Resource at the University of Colorado Cancer Center.

treatment_protocol: On the day of treatment, growth-arrested AdvSca1-SM cells were switched to DMEM media supplemented with 0.1% FBS and 1x penicillin/streptomycin and treated with either 5ng/mL TGF-B by adding a 5ug/mL stock solution of TGFB at a 1:1000 dilution (diluted in serum-free DMEM) to the cells, or treated with 5ng/mL TGF-B + 50uM PFI-3. For cells treated with PFI-3, a 50mM stock was applied at a 1:1000 dilution in DMSO. All cells received 0.1% DMSO as vehicle control. Cells were incubated for 72 hours.

value: Aorta and carotid artery

tag: cell line

value: AdvSca1-SM cells

value: Resident vascular progenitor

value: Tgfb


title: Donor 70, 3D Collagen HIV-1 infected + Vpx and Raltegravir

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and Raltegravir and cultured for two days in 3D collagen

value: monocyte derived dendritic cells

value: iDC spin-transduced with VLPs_Vpx, infected with HIV-1 and treated with raltegravir in 3D collagen


title: Donor 70, 3D Collagen HIV-1 infected + Vpx

value: iDC spin-transduced with VLPs_Vpx and infected with HIV-1 in 3D collagen


title: CD_A2


title: Tmem161a-KO-2

city: Miyazaki

first: TAKUYA

last: NAGAI

state: Miyazaki

address: Kiyotake Kihara 5200

department: Department of Medicine of Sensory and Motor Organs, Faculty of Medicine,

country: Japan

institute: University of MIyazaki

hyb_protocol: Fifteen micrograms of fragmented cRNA from each sample was hybridized to a pre-equilibrated Clariom S mouse microarray chip, which was then washed and stained.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, USA)

data_processing: Normalization and expression value calculations were performed using Genespring. (Agilent Technologies, Santa Clara, CA, USA). Fold change 2 or more are considered to be changed.

source_name: Tmem161a knockout MC3T3-e1 cells

label_protocol: Amplification and biotin labeling of fragmented cDNA was performed using the biotin labeling system (WT PLUS Reagent Kit, Thermo Fisher Scientific, Rockford, IL, USA) in duplicate.

extract_protocol: Total RNA was prepared using Trizol (Invitrogen, Carlsbad, CA, USA).

value: MC3T3-e1 cells


title: CD_F3


title: CD_A6


title: TIR-STING induced, harvested at 18 hr, replicate 2

city: Los Angeles

first: Douglas

middle: Edmund

last: Feldman

address: 2011 Zonal Avenue

department: Pathology

institute: USC Keck School of Medicine

description: Double-stranded gene fragments and pooled, single-stranded DNA oligonucleotides encoding phage ORFs with 20-25 nt flanking regions of homology to the pET-SUMO2 vector flanking the NdeI and NotI sites were purchased from IDT (eBlocks and oPools). ssDNA oligos were converted to dsDNA through isotheral extension of a primer complementary to the 3’ flanking region  (sparQ HiFi PCR Master Mix, Quantabio), and products purified with a DNA spin column. Pooled ORFs were inserted into pET-SUMO2 by DNA assembly (NEBuilder HiFi) and transformed into E. coli (NEB DH5a). Colonies were scraped from plates, combined and inoculated into 10 ml liquid cultures. Plasmid DNA encoding the pooled ORF library was then prepared and used to transform BL21 (DE3) Rosetta 2 competent cells (MilliporeSigma) together with pET30a encoding Flag-TIR-STING or empty vector control. 100 ml of overnight cultures were diluted 1:20 and grown in M9 media supplemented with 0.25% CAA and 1% glycerol, and induced at A600=0.3-0.4 through the addition of 0.5mM IPTG. Samples were taken immediately prior to induction and at 18 h post-induction. Plasmid DNA was recovered by miniprep, and library inserts amplified by PCR using primers flanking the ORF insertion site in pET-SUMO2. Bar-coded libraries for Illumina sequencing were generated using the sparQ DNA Library Kit (Quantabio) and 50 bp reads generated using a HiSeq3000 sequencing system. Raw reads were trimmed to remove adapters and low-quality reads using Trim Galore (v0.3.5). Bowtie 1.3.1 (Langmead et al. 2009) was used to align reads and Cufflinks (v2.2.1) (Trapnell et al. 2010) was used to estimate read abundances and test for differential expression.

library_source: other

data_processing:
Raw reads were trimmed to remove adapters and low-quality reads using Trim Galore (v0.3.5).
Bowtie 1.3.1 (Langmead et al. 2009) was used to align reads and Cufflinks (v2.2.1) (Trapnell et al. 2010) was used to estimate read abundances and test for differential expression.
Assembly: Reads aligned to attached fasta file "amplicon_sequence.fa" - a custom library encoding bacteriophage genes.

molecule: other

organism: Bacteriophage sp.

source_name: phage ORF library

value: phage ORF library

tag: construct

value: pET30a encoding Flag-TIR-STING

value: TIR-STING induced, harvested at 18 hr


title: WT-1

source_name: intact MC3T3-e1 cells

value: WT


title: Tmem161a-KO-3


title: WT-2


title: WT-3


title: Tmem161a-KO-1


title: CD_A4


title: CD_A3


title: TIR-STING induced, harvested at 18 hr, replicate 1

growth_protocol: Plasmid DNA encoding the pooled ORF library was then prepared and used to transform BL21 (DE3) Rosetta 2 competent cells (MilliporeSigma) together with pET30a encoding Flag-TIR-STING or empty vector control. 100 ml of overnight cultures were diluted 1:20 and grown in M9 media supplemented with 0.25% CAA and 1% glycerol, and induced at A600=0.3-0.4 through the addition of 0.5mM IPTG. Samples were taken immediately prior to induction and at 18 h post-induction.

extract_protocol:
Plasmid DNA was recovered by miniprep, and library inserts amplified by PCR using primers flanking the ORF insertion site in pET-SUMO2.
Bar-coded libraries for Illumina sequencing were generated using the sparQ DNA Library Kit (Quantabio) and 50 bp reads generated using a HiSeq3000 sequencing system.


title: TIR-STING, baseline- 0 hr

value: TIR-STING, baseline- 0 hr


title: shMETTL14_01_01

city: Shanghai

first: Yichao

last: Hou

address: 639 Zhi Zao Ju Road

institute: Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) were processed using Trimmomatic.The reads containing ploy-N and the low quality reads were removed to obtain the clean reads
Then the clean reads were mapped to reference genome using hisat2.
FPKM and read counts value of each transcript was calculated using bowtie2 and eXpress.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HT29 human colon cancer cells

growth_protocol: HT29 human colon cancer cells were maintained in McCoy’s 5A supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’ s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: stably infected with lentivirus carrying control shRNA or shMETTL14

value: p53 mutant

value: HT29 human colon cancer cells

value: stably infected with lentivirus carrying control shMETTL14_01


title: shMETTL14_02_02

value: stably infected with lentivirus carrying control shMETTL14_02


title: Donor 70, 3D Collagen HIV-1 infected

value: HIV-1 infected iDCs in 3D collagen


title: shMETTL14_01_02


title: EV, harvested at 18 hr, replicate 2

value: empty vector (EV)

value: EV, harvested at 18 hr


title: Donor 70, 3D Collagen Untreated

value: Untreated iDCs cells in 3D collagen


title: EV, harvested at 18 hr, replicate 1


title: shNC_02

value: stably infected with lentivirus carrying control shRNA


title: shMETTL14_02_01


title: shNC_04


title: sh_MET_04

data_processing:
Raw data (raw reads) were processed using Trimmomatic.The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM and read counts value of each transcript was calculated using bowtie2 and eXpress.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HCT116 human colon cancer cells

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’ s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HCT116 human colon cancer cells

value: stably infected with lentivirus carrying METTL14 shRNA


title: sh_NC_04


title: sh_MET_03


title: sh_MET_02


title: sh_NC_02


title: sh_NC_01


title: sh_MET_01


title: GAN, biol reps 1-3, anti-TGFβ, scRNAseq

city: Cambridge

first: Ken

last: Dower

state: MA

address: 1 Portland St.

department: Inflammation and Immunology Research Unit

institute: Pfizer, Inc.

description:
10x Genomics
XC43_3

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were performed using Cell Ranger software (multiple versions) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Demultiplexing of lipid hashtag oligos was performed as described in PMID 31209384 and only cells mapping to a single hashtag oligo were retained for downstream processing.
Spliced and unspliced read counts were generated from Cell Ranger outputs using the run10x wrapper in the velocyto CLI as described in PMID 30089906 and at http://velocyto.org/velocyto.py/tutorial/cli.html#run10x-run-on-10x-chromium-samples.
Demultiplexed gene counts, hashtag counts and spliced/unspliced counts were merged in R. Only cells mapping to a single hashtag oligo were retained for downstream processing.
Additional details of data processing are described in the publication and are available from the authors upon inquiry.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Murine livers were collected in RPMI1640 media on ice, minced and digested in 100 U/mL collagenase (Sigma-Aldrich) at 37°C for 1 hour with shaking. Digested tissue was filtered through 70 μm nylon mesh and hepatocytes removed by spinning at 50xg for 3 minutes. The remaining cells were passed through a 25 % Percoll (GE Life Sciences) cushion and erythrocytes were lysed with ammonium-chloride-potassium buffer. Isolated cells were stained with 30 μg/mL Hoechst 33342 (Miltenyi) and Zombie NIR viability dye (diluted 1:250 in PBS; Biolegend) before FACS sorting (Sony SH800) to obtain live, single cells. These were methanol fixed based on the 10x Genomics recommended fixation protocol and stored at -80°C.
Library was performed according to the manufacter’s instructions for methanol fixed samples (single cell 3’ v2 or v3.1 protocols, 10x Genomics). Briefly, hepatic cells in methanol were pelleted, counted, washed and resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. For samples that were lipid hashed, library construction was performed as described in PMID 31209384 (McGinnis, Gartner et al., 2019).

value: Liver

value: Hepatic cells

tag: Sex

value: Male

value: anti-TGFβ

value: Fibrosis

tag: mmpsense signal

tag: age

value: 50-52 weeks


title: NPCs in co-culture - p53

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

library_source: genomic

data_processing:
Processing was adapted from the CUT&RUNTools pipeline with the following steps:
Fastq files were trimmed with Trimmomatic (0.36)
Alignment to mm10 with Bowtie2 (2.3.4.3) with --dovetail
Coversion of aligned bam to bed format with bedtools (2.26.0) using bamtobed with -bedpe
Filtering to remove fragments larger than 120bp
Normalisation of each sample to sequencing read depth using bedtools (2.26.0) genomecov. -scale Scale factor used was generated by division of an arbitrary large number by read.   depth for each sample
Peak calling with MACS2 (2.1.1) bdgpeakcall
Genome_build: Mus musculus GRCm38 (mm10)
Supplementary_files_format_and_content: Bigwig files of normalised data

source_name: Neural progenitor cells

growth_protocol: NPCs were isolated from the SVZ of P9–P12 mouse brains and routinely grown DMEM/F12supplemented with 0.25% FBS, N2 ), 20 ng/ml EGF, 10 ng/ml bFGF and 35 μg/ml bovine pituitary extract.

extract_protocol:
Chromatin was purified by performing Phenol Chloroform Extraction
CUT&RUN barcoded libraries for Illumina sequencing were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645) accordingly with Zhu et al. (Zhu et al., 2019).
CUT&RUN

treatment_protocol: NPCs were plated either alone or onto endothelial monolayers for 48h before collection

tag: culture condition

value: co-culture for 48h

tag: cnr antibody

value: p53 Ab Leica, NCL-p53-CM5p


title: EV, baseline- 0 hr

tag: tissue

value: phage ORF library

value: EV, baseline- 0 hr


title: sh_NC_03

tag: treatment


title: GAN, biol reps 1-3, isotype, scRNAseq

description:
10x Genomics
XC43_2

value: Isotype


title: Olive oil, biol rep 1, MMPsense positive, scRNAseq

description:
10x Genomics
OliveMMPPos

value: Control

value: Positive

value: 12-14 weeks


title: Olive oil, biol rep 1, MMPsense negative, scRNAseq

description:
10x Genomics
OliveMMPNeg


title: Chow, biol reps 1-3, isotype, scRNAseq

description:
10x Genomics
XC43_1


title: CCl4, biol rep 1, MMPsense positive, scRNAseq

description:
10x Genomics
CCL4MMPPos


title: CCl4, biol rep 1, MMPsense negative, scRNAseq

description:
10x Genomics
CCL4MMPNeg

value: Negative


title: shNC_03

value: p53 mutant

value: HT29 human colon cancer cells

value: stably infected with lentivirus carrying control shRNA


title: shNC_01


title: NPCs in co-culture - IgG

value: Rabbit IgG Millipore PP64


title: H37L7DSX2-IDT-DUI-NXT-305

first: Pere

last: Santamaria

address: C/Rosselló 149-153

institute: IDIBAPS

description:
Tetramer+ CD4+ T cells from Fla501-515/IAb-NP-treated B6 mice
Raw_counts_FLA2(501)_SMARTseq2.txt

data_processing:
Quality check with FastQC v0.11.8
Alignment to the mouse genome mm10 with STAR v2.5.4b
Gene expression estimation with RSEM v1.3.0
QC filtering of low quality cells
TCR sequences reconstructed to infer clonality with TraCeR v.0.5.1
Genome_build: mm10
Supplementary_files_format_and_content: txt (Raw counts for each cell)

extract_protocol:
Single-cell sorting in SMARTseq2 plates
Smart-seq protocol (Picelli et al., 2013)
SMARTseq2

treatment_protocol: Treated samples are obtained from mice that have received intravenously 10 doses of FLA2(501-515)/IAb-NPs.

value: T cell

value: pMHCII-NPs


title: H37L7DSX2-IDT-DUI-NXT-300

source_name: Tetramer+ CD4+ T cells from Fla501-515/IAb-NP-treated B6 mice


title: H37L7DSX2-IDT-DUI-NXT-306


title: NPCs - IgG

value: laminin coated plates for 48h


title: H37L7DSX2-IDT-DUI-NXT-298


title: H37L7DSX2-IDT-DUI-NXT-294


title: H37L7DSX2-IDT-DUI-NXT-304


title: H37L7DSX2-IDT-DUI-NXT-303


title: H37L7DSX2-IDT-DUI-NXT-301


title: H37L7DSX2-IDT-DUI-NXT-292


title: NPCs - p53


title: H37L7DSX2-IDT-DUI-NXT-297


title: H37L7DSX2-IDT-DUI-NXT-295


title: H37L7DSX2-IDT-DUI-NXT-299


title: H37G7DSX2-IDT-DUI-NXT-288

description:
Tetramer- CD4+ T cells from Fla501-515/IAb-NP-treated B6 mice
Raw_counts_FLA2(501)_SMARTseq2.txt


title: H37G7DSX2-IDT-DUI-NXT-285

source_name: Tetramer- CD4+ T cells from Fla501-515/IAb-NP-treated B6 mice


title: H37L7DSX2-IDT-DUI-NXT-289


title: H37G7DSX2-IDT-DUI-NXT-282


title: H37G7DSX2-IDT-DUI-NXT-287


title: H37G7DSX2-IDT-DUI-NXT-286


title: H37G7DSX2-IDT-DUI-NXT-281


title: H37L7DSX2-IDT-DUI-NXT-290


title: H37G7DSX2-IDT-DUI-NXT-284


title: H37L7DSX2-IDT-DUI-NXT-302


title: H37L7DSX2-IDT-DUI-NXT-296


title: H37L7DSX2-IDT-DUI-NXT-293


title: H37G7DSX2-IDT-DUI-NXT-272


title: H37L7DSX2-IDT-DUI-NXT-291


title: H37G7DSX2-IDT-DUI-NXT-283


title: H37G7DSX2-IDT-DUI-NXT-278


title: H37G7DSX2-IDT-DUI-NXT-279


title: H37G7DSX2-IDT-DUI-NXT-280


title: H37G7DSX2-IDT-DUI-NXT-270


title: H37G7DSX2-IDT-DUI-NXT-277


title: H37G7DSX2-IDT-DUI-NXT-276


title: H37G7DSX2-IDT-DUI-NXT-275


title: H37G7DSX2-IDT-DUI-NXT-274


title: H37G7DSX2-IDT-DUI-NXT-273


title: H37G7DSX2-IDT-DUI-NXT-269


title: H37G7DSX2-IDT-DUI-NXT-265


title: H37G7DSX2-IDT-DUI-NXT-263


title: H37G7DSX2-IDT-DUI-NXT-271


title: H37G7DSX2-IDT-DUI-NXT-259


title: H37G7DSX2-IDT-DUI-NXT-266


title: H37G7DSX2-IDT-DUI-NXT-264


title: H37G7DSX2-IDT-DUI-NXT-258


title: H37G7DSX2-IDT-DUI-NXT-262


title: H37G7DSX2-IDT-DUI-NXT-268


title: H37G7DSX2-IDT-DUI-NXT-261


title: H37G7DSX2-IDT-DUI-NXT-257


title: H37G7DSX2-IDT-DUI-NXT-256


title: H37G7DSX2-IDT-DUI-NXT-260


title: H37G7DSX2-IDT-DUI-NXT-255


title: H37G7DSX2-IDT-DUI-NXT-253


title: H37G7DSX2-IDT-DUI-NXT-254


title: H37G7DSX2-IDT-DUI-NXT-251


title: H37G7DSX2-IDT-DUI-NXT-248


title: H37G7DSX2-IDT-DUI-NXT-247


title: H37G7DSX2-IDT-DUI-NXT-249


title: H37G7DSX2-IDT-DUI-NXT-250


title: H37G7DSX2-IDT-DUI-NXT-246


title: H37G7DSX2-IDT-DUI-NXT-267


title: H37G7DSX2-IDT-DUI-NXT-244


title: H37G7DSX2-IDT-DUI-NXT-238


title: H37G7DSX2-IDT-DUI-NXT-245


title: H37G7DSX2-IDT-DUI-NXT-240


title: H37G7DSX2-IDT-DUI-NXT-242


title: H37G7DSX2-IDT-DUI-NXT-241


title: H37G7DSX2-IDT-DUI-NXT-235


title: H37G7DSX2-IDT-DUI-NXT-234


title: H37G7DSX2-IDT-DUI-NXT-233


title: H37G7DSX2-IDT-DUI-NXT-236


title: H37G7DSX2-IDT-DUI-NXT-231


title: H37G7DSX2-IDT-DUI-NXT-229


title: H37G7DSX2-IDT-DUI-NXT-226


title: H37G7DSX2-IDT-DUI-NXT-232


title: H37G7DSX2-IDT-DUI-NXT-224


title: H37G7DSX2-IDT-DUI-NXT-237


title: H37G7DSX2-IDT-DUI-NXT-230


title: H37G7DSX2-IDT-DUI-NXT-227


title: H37G7DSX2-IDT-DUI-NXT-252


title: H37G7DSX2-IDT-DUI-NXT-223


title: H37G7DSX2-IDT-DUI-NXT-228


title: H37G7DSX2-IDT-DUI-NXT-222


title: H37G7DSX2-IDT-DUI-NXT-225


title: H37G7DSX2-IDT-DUI-NXT-218


title: H37G7DSX2-IDT-DUI-NXT-243


title: H37G7DSX2-IDT-DUI-NXT-220


title: H37G7DSX2-IDT-DUI-NXT-217


title: H37G7DSX2-IDT-DUI-NXT-221


title: H37G7DSX2-IDT-DUI-NXT-219


title: H37G7DSX2-IDT-DUI-NXT-239


title: H37G7DSX2-IDT-DUI-NXT-216


title: H37G7DSX2-IDT-DUI-NXT-214


title: H37G7DSX2-IDT-DUI-NXT-215


title: H37G7DSX2-IDT-DUI-NXT-212


title: H37G7DSX2-IDT-DUI-NXT-213


title: H37G7DSX2-IDT-DUI-NXT-205


title: H37G7DSX2-IDT-DUI-NXT-209


title: H37G7DSX2-IDT-DUI-NXT-206


title: H37G7DSX2-IDT-DUI-NXT-207


title: H37G7DSX2-IDT-DUI-NXT-211


title: H37G7DSX2-IDT-DUI-NXT-210


title: H37G7DSX2-IDT-DUI-NXT-204


title: H37G7DSX2-IDT-DUI-NXT-201


title: H37G7DSX2-IDT-DUI-NXT-202


title: H37G7DSX2-IDT-DUI-NXT-199


title: H37G7DSX2-IDT-DUI-NXT-196


title: H37G7DSX2-IDT-DUI-NXT-203


title: H37G7DSX2-IDT-DUI-NXT-208


title: H37G7DSX2-IDT-DUI-NXT-194


title: H37G7DSX2-IDT-DUI-NXT-197


title: H37G7DSX2-IDT-DUI-NXT-198


title: H37G7DSX2-IDT-DUI-NXT-195


title: HK53TBBXY_5_IDT-DUI-NXT-192

description:
Tetramer+ CD4+ T cells from FLA2(501-515)/IAb-NP-treated NOD mice
Raw_counts_FLA2(501)_SMARTseq2.xlsx

data_processing:
Quality check with FastQC v0.11.8
Alignment to the mouse genome mm10 with STAR v2.5.4b
Gene expression estimation with RSEM v1.3.0
QC filtering of low quality cells
TCR sequences reconstructed to infer clonality with TraCeR v.0.5.1
Genome_build: mm10
Supplementary_files_format_and_content: xlsx (Raw counts for each cell)

source_name: Tetramer+ CD4+ T cells

extract_protocol:
Single-cell sorting in SMARTseq2 plates
Smart-seq protocol (Picelli et al., 2013)

treatment_protocol:
Treated samples are obtained from mice that have received intravenously 10 doses of FLA2(501-515)/IAb-NPs.
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.


title: HK53TBBXY_5_IDT-DUI-NXT-191


title: HK53TBBXY_5_IDT-DUI-NXT-189


title: HK53TBBXY_5_IDT-DUI-NXT-188


title: HK53TBBXY_5_IDT-DUI-NXT-190


title: HK53TBBXY_5_IDT-DUI-NXT-186


title: HK53TBBXY_5_IDT-DUI-NXT-187


title: HK53TBBXY_5_IDT-DUI-NXT-185


title: HK53TBBXY_5_IDT-DUI-NXT-184


title: HK53TBBXY_5_IDT-DUI-NXT-182


title: HK53TBBXY_5_IDT-DUI-NXT-181


title: HK53TBBXY_5_IDT-DUI-NXT-180


title: H37G7DSX2-IDT-DUI-NXT-200


title: HK53TBBXY_5_IDT-DUI-NXT-179


title: HK53TBBXY_5_IDT-DUI-NXT-177


title: HK53TBBXY_5_IDT-DUI-NXT-178


title: HK53TBBXY_5_IDT-DUI-NXT-175


title: HK53TBBXY_5_IDT-DUI-NXT-173


title: HK53TBBXY_5_IDT-DUI-NXT-176


title: HK53TBBXY_5_IDT-DUI-NXT-174


title: H37G7DSX2-IDT-DUI-NXT-193


title: HK53TBBXY_5_IDT-DUI-NXT-172


title: HK53TBBXY_5_IDT-DUI-NXT-170


title: HK53TBBXY_5_IDT-DUI-NXT-168


title: HK53TBBXY_5_IDT-DUI-NXT-169


title: HK53TBBXY_5_IDT-DUI-NXT-166


title: HK53TBBXY_5_IDT-DUI-NXT-167


title: HK53TBBXY_5_IDT-DUI-NXT-171


title: HK53TBBXY_5_IDT-DUI-NXT-163


title: HK53TBBXY_5_IDT-DUI-NXT-161


title: HK53TBBXY_5_IDT-DUI-NXT-160


title: HK53TBBXY_5_IDT-DUI-NXT-183


title: HK53TBBXY_5_IDT-DUI-NXT-159


title: HK53TBBXY_5_IDT-DUI-NXT-164


title: HK53TBBXY_5_IDT-DUI-NXT-157


title: HK53TBBXY_5_IDT-DUI-NXT-165


title: HK53TBBXY_5_IDT-DUI-NXT-158


title: HK53TBBXY_5_IDT-DUI-NXT-156


title: HK53TBBXY_5_IDT-DUI-NXT-155


title: HK53TBBXY_5_IDT-DUI-NXT-152


title: HK53TBBXY_5_IDT-DUI-NXT-154


title: HK53TBBXY_5_IDT-DUI-NXT-153


title: HK53TBBXY_5_IDT-DUI-NXT-151


title: HK53TBBXY_5_IDT-DUI-NXT-150


title: HK53TBBXY_5_IDT-DUI-NXT-147


title: HK53TBBXY_5_IDT-DUI-NXT-145


title: HK53TBBXY_5_IDT-DUI-NXT-143


title: HK53TBBXY_5_IDT-DUI-NXT-148


title: HK53TBBXY_5_IDT-DUI-NXT-149


title: HK53TBBXY_5_IDT-DUI-NXT-141


title: HK53TBBXY_5_IDT-DUI-NXT-142


title: HK53TBBXY_5_IDT-DUI-NXT-146


title: HK53TBBXY_5_IDT-DUI-NXT-144


title: HK53TBBXY_5_IDT-DUI-NXT-139


title: HK53TBBXY_5_IDT-DUI-NXT-138


title: HK53TBBXY_5_IDT-DUI-NXT-140


title: HK53TBBXY_5_IDT-DUI-NXT-137


title: HK53TBBXY_5_IDT-DUI-NXT-136


title: HK53TBBXY_5_IDT-DUI-NXT-135


title: HK53TBBXY_5_IDT-DUI-NXT-134


title: HK53TBBXY_5_IDT-DUI-NXT-133


title: HK53TBBXY_5_IDT-DUI-NXT-132


title: HK53TBBXY_5_IDT-DUI-NXT-131


title: HK53TBBXY_5_IDT-DUI-NXT-128


title: HK53TBBXY_5_IDT-DUI-NXT-129


title: HK53TBBXY_5_IDT-DUI-NXT-127


title: HK53TBBXY_5_IDT-DUI-NXT-125


title: HK53TBBXY_5_IDT-DUI-NXT-123


title: HK53TBBXY_5_IDT-DUI-NXT-124


title: HK53TBBXY_5_IDT-DUI-NXT-120


title: HK53TBBXY_5_IDT-DUI-NXT-119


title: HK53TBBXY_5_IDT-DUI-NXT-121


title: HK53TBBXY_5_IDT-DUI-NXT-122


title: HK53TBBXY_5_IDT-DUI-NXT-117


title: HK53TBBXY_5_IDT-DUI-NXT-112


title: HK53TBBXY_5_IDT-DUI-NXT-113


title: HK53TBBXY_5_IDT-DUI-NXT-115


title: HK53TBBXY_5_IDT-DUI-NXT-114


title: HK53TBBXY_5_IDT-DUI-NXT-130


title: HK53TBBXY_5_IDT-DUI-NXT-126


title: HK53TBBXY_5_IDT-DUI-NXT-109


title: HK53TBBXY_5_IDT-DUI-NXT-111


title: HK53TBBXY_5_IDT-DUI-NXT-110


title: HK53TBBXY_5_IDT-DUI-NXT-108


title: HK53TBBXY_5_IDT-DUI-NXT-103


title: HK53TBBXY_5_IDT-DUI-NXT-106


title: HK53TBBXY_5_IDT-DUI-NXT-99


title: HK53TBBXY_5_IDT-DUI-NXT-102


title: HK53TBBXY_5_IDT-DUI-NXT-104


title: HK53TBBXY_5_IDT-DUI-NXT-101


title: HK53TBBXY_5_IDT-DUI-NXT-100


title: HK53TBBXY_5_IDT-DUI-NXT-105


title: HK53TBBXY_5_IDT-DUI-NXT-98


title: HK53TBBXY_5_IDT-DUI-NXT-118


title: HK53TBBXY_5_IDT-DUI-NXT-116


title: HFJ75BBXY_8_IDT-DUI-NXT-95

description:
Tetramer+ CD4+ T cells from FLA2(462-472)/IAb-NP-treated NOD mice
Raw_counts_FLA2(462)_SMARTseq2.xlsx

treatment_protocol:
Treated samples are obtained from mice that have received intravenously 10 doses of FLA2(462-472)/IAb-NPs.
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.


title: HFJ75BBXY_8_IDT-DUI-NXT-94


title: HFJ75BBXY_8_IDT-DUI-NXT-91


title: HFJ75BBXY_8_IDT-DUI-NXT-92


title: HFJ75BBXY_8_IDT-DUI-NXT-89


title: HFJ75BBXY_8_IDT-DUI-NXT-88


title: HFJ75BBXY_8_IDT-DUI-NXT-90


title: HK53TBBXY_5_IDT-DUI-NXT-107


title: HFJ75BBXY_8_IDT-DUI-NXT-87


title: HFJ75BBXY_8_IDT-DUI-NXT-86


title: HFJ75BBXY_8_IDT-DUI-NXT-85


title: HFJ75BBXY_8_IDT-DUI-NXT-83


title: HFJ75BBXY_8_IDT-DUI-NXT-84


title: HFJ75BBXY_8_IDT-DUI-NXT-82


title: HFJ75BBXY_8_IDT-DUI-NXT-81


title: HFJ75BBXY_8_IDT-DUI-NXT-79


title: HFJ75BBXY_8_IDT-DUI-NXT-96


title: HFJ75BBXY_8_IDT-DUI-NXT-73


title: HFJ75BBXY_8_IDT-DUI-NXT-71


title: HFJ75BBXY_8_IDT-DUI-NXT-72


title: HFJ75BBXY_8_IDT-DUI-NXT-80


title: HFJ75BBXY_8_IDT-DUI-NXT-77


title: HK53TBBXY_5_IDT-DUI-NXT-97


title: HFJ75BBXY_8_IDT-DUI-NXT-69


title: HFJ75BBXY_8_IDT-DUI-NXT-76


title: HFJ75BBXY_8_IDT-DUI-NXT-68


title: HFJ75BBXY_8_IDT-DUI-NXT-70


title: HFJ75BBXY_8_IDT-DUI-NXT-75


title: HFJ75BBXY_8_IDT-DUI-NXT-93


title: HFJ75BBXY_8_IDT-DUI-NXT-78


title: HFJ75BBXY_8_IDT-DUI-NXT-74


title: HFJ75BBXY_8_IDT-DUI-NXT-67


title: HFJ75BBXY_8_IDT-DUI-NXT-66


title: HFJ75BBXY_8_IDT-DUI-NXT-64


title: HFJ75BBXY_8_IDT-DUI-NXT-63


title: HFJ75BBXY_8_IDT-DUI-NXT-62


title: HFJ75BBXY_8_IDT-DUI-NXT-61


title: HFJ75BBXY_8_IDT-DUI-NXT-60


title: HFJ75BBXY_8_IDT-DUI-NXT-59


title: HFJ75BBXY_8_IDT-DUI-NXT-58


title: HFJ75BBXY_8_IDT-DUI-NXT-57


title: HFJ75BBXY_8_IDT-DUI-NXT-56


title: HFJ75BBXY_8_IDT-DUI-NXT-53


title: HFJ75BBXY_8_IDT-DUI-NXT-51


title: HFJ75BBXY_8_IDT-DUI-NXT-49


title: HFJ75BBXY_8_IDT-DUI-NXT-46


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title: HFJ75BBXY_8_IDT-DUI-NXT-47


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title: HFJ75BBXY_8_IDT-DUI-NXT-42


title: HFJ75BBXY_8_IDT-DUI-NXT-65


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title: HFJ75BBXY_8_IDT-DUI-NXT-37


title: HFJ75BBXY_8_IDT-DUI-NXT-32


title: HFJ75BBXY_8_IDT-DUI-NXT-34


title: HFJ75BBXY_8_IDT-DUI-NXT-33


title: HFJ75BBXY_8_IDT-DUI-NXT-36


title: HFJ75BBXY_8_IDT-DUI-NXT-35


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title: HFJ75BBXY_8_IDT-DUI-NXT-17


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title: HFJ75BBXY_8_IDT-DUI-NXT-10


title: HFJ75BBXY_8_IDT-DUI-NXT-8


title: HFJ75BBXY_8_IDT-DUI-NXT-6


title: HFJ75BBXY_8_IDT-DUI-NXT-5


title: HFJ75BBXY_8_IDT-DUI-NXT-7


title: HFJ75BBXY_8_IDT-DUI-NXT-4


title: HFJ75BBXY_8_IDT-DUI-NXT-1


title: HFJ75BBXY_8_IDT-DUI-NXT-3


title: HFJ75BBXY_8_IDT-DUI-NXT-25


title: HFJ75BBXY_7_IDT-DUI-NXT-384


title: HFJ75BBXY_8_IDT-DUI-NXT-19


title: HFJ75BBXY_7_IDT-DUI-NXT-383


title: HK53TBBXY_5_IDT-DUI-NXT-162


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title: HFJ75BBXY_7_IDT-DUI-NXT-372


title: HFJ75BBXY_7_IDT-DUI-NXT-371


title: HFJ75BBXY_8_IDT-DUI-NXT-9


title: HFJ75BBXY_7_IDT-DUI-NXT-373


title: HFJ75BBXY_7_IDT-DUI-NXT-367


title: HFJ75BBXY_8_IDT-DUI-NXT-2


title: HFJ75BBXY_7_IDT-DUI-NXT-368


title: HFJ75BBXY_7_IDT-DUI-NXT-365


title: HFJ75BBXY_7_IDT-DUI-NXT-363


title: HFJ75BBXY_7_IDT-DUI-NXT-364


title: HFJ75BBXY_7_IDT-DUI-NXT-362


title: HFJ75BBXY_7_IDT-DUI-NXT-360


title: HFJ75BBXY_7_IDT-DUI-NXT-359


title: HFJ75BBXY_7_IDT-DUI-NXT-378


title: HFJ75BBXY_7_IDT-DUI-NXT-356


title: HFJ75BBXY_7_IDT-DUI-NXT-358


title: HFJ75BBXY_7_IDT-DUI-NXT-357


title: HFJ75BBXY_7_IDT-DUI-NXT-355


title: HFJ75BBXY_7_IDT-DUI-NXT-351


title: HFJ75BBXY_7_IDT-DUI-NXT-353


title: HFJ75BBXY_7_IDT-DUI-NXT-352


title: HFJ75BBXY_7_IDT-DUI-NXT-350


title: HFJ75BBXY_7_IDT-DUI-NXT-354


title: HFJ75BBXY_7_IDT-DUI-NXT-370


title: HFJ75BBXY_7_IDT-DUI-NXT-349


title: HFJ75BBXY_7_IDT-DUI-NXT-369


title: HFJ75BBXY_7_IDT-DUI-NXT-347


title: HFJ75BBXY_7_IDT-DUI-NXT-348


title: HFJ75BBXY_7_IDT-DUI-NXT-346


title: HFJ75BBXY_7_IDT-DUI-NXT-345


title: HFJ75BBXY_7_IDT-DUI-NXT-366


title: HFJ75BBXY_7_IDT-DUI-NXT-341


title: HFJ75BBXY_7_IDT-DUI-NXT-340


title: HFJ75BBXY_7_IDT-DUI-NXT-339


title: HFJ75BBXY_7_IDT-DUI-NXT-342


title: HFJ75BBXY_7_IDT-DUI-NXT-344


title: HFJ75BBXY_7_IDT-DUI-NXT-361


title: HFJ75BBXY_7_IDT-DUI-NXT-338


title: HFJ75BBXY_7_IDT-DUI-NXT-343


title: HFJ75BBXY_7_IDT-DUI-NXT-337


title: HFJ75BBXY_7_IDT-DUI-NXT-334


title: HFJ75BBXY_7_IDT-DUI-NXT-335


title: HFJ75BBXY_7_IDT-DUI-NXT-336


title: HFJ75BBXY_7_IDT-DUI-NXT-332


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title: HFJ75BBXY_7_IDT-DUI-NXT-330


title: HFJ75BBXY_7_IDT-DUI-NXT-329


title: HFJ75BBXY_7_IDT-DUI-NXT-327


title: HFJ75BBXY_7_IDT-DUI-NXT-324


title: HFJ75BBXY_7_IDT-DUI-NXT-326


title: HFJ75BBXY_7_IDT-DUI-NXT-323


title: HFJ75BBXY_7_IDT-DUI-NXT-325


title: HFJ75BBXY_7_IDT-DUI-NXT-333


title: HFJ75BBXY_7_IDT-DUI-NXT-322


title: HFJ75BBXY_7_IDT-DUI-NXT-321


title: HFJ75BBXY_7_IDT-DUI-NXT-320


title: HFJ75BBXY_7_IDT-DUI-NXT-319


title: HFJ75BBXY_7_IDT-DUI-NXT-318


title: HFJ75BBXY_7_IDT-DUI-NXT-317


title: HFJ75BBXY_7_IDT-DUI-NXT-316


title: HFJ75BBXY_7_IDT-DUI-NXT-309


title: HFJ75BBXY_7_IDT-DUI-NXT-313


title: HFJ75BBXY_7_IDT-DUI-NXT-312


title: HFJ75BBXY_7_IDT-DUI-NXT-315


title: HFJ75BBXY_7_IDT-DUI-NXT-311


title: HFJ75BBXY_7_IDT-DUI-NXT-314


title: HFJ75BBXY_7_IDT-DUI-NXT-310


title: HFJ75BBXY_7_IDT-DUI-NXT-307


title: HFJ75BBXY_7_IDT-DUI-NXT-328


title: HFJ75BBXY_7_IDT-DUI-NXT-308


title: HFJ75BBXY_7_IDT-DUI-NXT-306


title: HFJ75BBXY_7_IDT-DUI-NXT-303


title: HFJ75BBXY_7_IDT-DUI-NXT-304


title: HFJ75BBXY_7_IDT-DUI-NXT-302


title: HFJ75BBXY_7_IDT-DUI-NXT-297


title: HFJ75BBXY_7_IDT-DUI-NXT-299


title: HFJ75BBXY_7_IDT-DUI-NXT-300


title: HFJ75BBXY_7_IDT-DUI-NXT-301


title: HFJ75BBXY_7_IDT-DUI-NXT-296


title: HFJ75BBXY_7_IDT-DUI-NXT-295


title: HFJ75BBXY_7_IDT-DUI-NXT-293


title: HFJ75BBXY_7_IDT-DUI-NXT-290


title: HFJ75BBXY_7_IDT-DUI-NXT-294


title: HFFTNBBXY_8_IDT-DUI-NXT-384


title: HFFTNBBXY_8_IDT-DUI-NXT-383


title: HFJ75BBXY_7_IDT-DUI-NXT-292


title: HFJ75BBXY_7_IDT-DUI-NXT-289


title: HFFTNBBXY_8_IDT-DUI-NXT-382


title: HFJ75BBXY_7_IDT-DUI-NXT-305


title: HFFTNBBXY_8_IDT-DUI-NXT-378


title: HFFTNBBXY_8_IDT-DUI-NXT-377


title: HFFTNBBXY_8_IDT-DUI-NXT-379


title: HFFTNBBXY_8_IDT-DUI-NXT-376


title: HFFTNBBXY_8_IDT-DUI-NXT-375


title: HFFTNBBXY_8_IDT-DUI-NXT-381


title: HFJ75BBXY_7_IDT-DUI-NXT-298


title: HFFTNBBXY_8_IDT-DUI-NXT-372


title: HFFTNBBXY_8_IDT-DUI-NXT-380


title: HFFTNBBXY_8_IDT-DUI-NXT-370


title: HFFTNBBXY_8_IDT-DUI-NXT-369


title: HFFTNBBXY_8_IDT-DUI-NXT-371


title: HFFTNBBXY_8_IDT-DUI-NXT-373


title: HFFTNBBXY_8_IDT-DUI-NXT-374


title: HFFTNBBXY_8_IDT-DUI-NXT-367


title: HFFTNBBXY_8_IDT-DUI-NXT-366


title: HFJ75BBXY_7_IDT-DUI-NXT-291


title: HFFTNBBXY_8_IDT-DUI-NXT-362


title: HFFTNBBXY_8_IDT-DUI-NXT-365


title: HFFTNBBXY_8_IDT-DUI-NXT-361


title: HFFTNBBXY_8_IDT-DUI-NXT-364


title: HFFTNBBXY_8_IDT-DUI-NXT-359


title: HFFTNBBXY_8_IDT-DUI-NXT-358


title: HFFTNBBXY_8_IDT-DUI-NXT-360


title: HFFTNBBXY_8_IDT-DUI-NXT-356


title: HFFTNBBXY_8_IDT-DUI-NXT-357


title: HFFTNBBXY_8_IDT-DUI-NXT-368


title: HFFTNBBXY_8_IDT-DUI-NXT-354


title: HFFTNBBXY_8_IDT-DUI-NXT-353


title: HFFTNBBXY_8_IDT-DUI-NXT-352


title: HFFTNBBXY_8_IDT-DUI-NXT-350


title: HFFTNBBXY_8_IDT-DUI-NXT-351


title: HFFTNBBXY_8_IDT-DUI-NXT-349


title: HFFTNBBXY_8_IDT-DUI-NXT-348


title: HFFTNBBXY_8_IDT-DUI-NXT-346


title: HFFTNBBXY_8_IDT-DUI-NXT-343


title: HFFTNBBXY_8_IDT-DUI-NXT-347


title: HFFTNBBXY_8_IDT-DUI-NXT-344


title: HFFTNBBXY_8_IDT-DUI-NXT-345


title: HFFTNBBXY_8_IDT-DUI-NXT-341


title: HFFTNBBXY_8_IDT-DUI-NXT-363


title: HFFTNBBXY_8_IDT-DUI-NXT-342


title: HFFTNBBXY_8_IDT-DUI-NXT-339


title: HFFTNBBXY_8_IDT-DUI-NXT-340


title: HFFTNBBXY_8_IDT-DUI-NXT-335


title: HFFTNBBXY_8_IDT-DUI-NXT-334


title: HFFTNBBXY_8_IDT-DUI-NXT-337


title: HFFTNBBXY_8_IDT-DUI-NXT-336


title: HFFTNBBXY_8_IDT-DUI-NXT-338


title: HFFTNBBXY_8_IDT-DUI-NXT-333


title: HFFTNBBXY_8_IDT-DUI-NXT-355


title: HFFTNBBXY_8_IDT-DUI-NXT-332


title: HFFTNBBXY_8_IDT-DUI-NXT-328


title: HFFTNBBXY_8_IDT-DUI-NXT-331


title: HFFTNBBXY_8_IDT-DUI-NXT-330


title: HFFTNBBXY_8_IDT-DUI-NXT-327


title: HFFTNBBXY_8_IDT-DUI-NXT-325


title: HFFTNBBXY_8_IDT-DUI-NXT-326


title: HFFTNBBXY_8_IDT-DUI-NXT-324


title: HFFTNBBXY_8_IDT-DUI-NXT-320


title: HFFTNBBXY_8_IDT-DUI-NXT-323


title: HFFTNBBXY_8_IDT-DUI-NXT-322


title: HFFTNBBXY_8_IDT-DUI-NXT-313


title: HFFTNBBXY_8_IDT-DUI-NXT-314


title: HFFTNBBXY_8_IDT-DUI-NXT-315


title: HFFTNBBXY_8_IDT-DUI-NXT-321


title: HFFTNBBXY_8_IDT-DUI-NXT-312


title: HFFTNBBXY_8_IDT-DUI-NXT-319


title: HFFTNBBXY_8_IDT-DUI-NXT-317


title: HFFTNBBXY_8_IDT-DUI-NXT-318


title: HFFTNBBXY_8_IDT-DUI-NXT-311


title: HFFTNBBXY_8_IDT-DUI-NXT-309


title: HFFTNBBXY_8_IDT-DUI-NXT-307


title: HFFTNBBXY_8_IDT-DUI-NXT-306


title: HFFTNBBXY_8_IDT-DUI-NXT-308


title: HFFTNBBXY_8_IDT-DUI-NXT-329


title: HFFTNBBXY_8_IDT-DUI-NXT-302


title: HFFTNBBXY_8_IDT-DUI-NXT-303


title: HFFTNBBXY_8_IDT-DUI-NXT-304


title: HFFTNBBXY_8_IDT-DUI-NXT-299


title: HFFTNBBXY_8_IDT-DUI-NXT-301


title: HFFTNBBXY_8_IDT-DUI-NXT-297


title: HFFTNBBXY_8_IDT-DUI-NXT-300


title: HFFTNBBXY_8_IDT-DUI-NXT-294


title: HFFTNBBXY_8_IDT-DUI-NXT-298


title: HFFTNBBXY_8_IDT-DUI-NXT-310


title: HFFTNBBXY_8_IDT-DUI-NXT-292


title: HFFTNBBXY_8_IDT-DUI-NXT-296


title: HFFTNBBXY_8_IDT-DUI-NXT-293


title: HFFTNBBXY_8_IDT-DUI-NXT-291


title: HFFTNBBXY_8_IDT-DUI-NXT-290


title: HFFTNBBXY_8_IDT-DUI-NXT-289


title: HFFTNBBXY_8_IDT-DUI-NXT-286


title: HFFTNBBXY_8_IDT-DUI-NXT-282


title: HFFTNBBXY_8_IDT-DUI-NXT-281


title: HFFTNBBXY_8_IDT-DUI-NXT-305


title: HFFTNBBXY_8_IDT-DUI-NXT-285


title: HFFTNBBXY_8_IDT-DUI-NXT-284


title: HFFTNBBXY_8_IDT-DUI-NXT-279


title: HFFTNBBXY_8_IDT-DUI-NXT-283


title: HFFTNBBXY_8_IDT-DUI-NXT-277


title: HFFTNBBXY_8_IDT-DUI-NXT-278


title: HFFTNBBXY_8_IDT-DUI-NXT-287


title: HFFTNBBXY_8_IDT-DUI-NXT-276


title: HFFTNBBXY_8_IDT-DUI-NXT-273


title: HFFTNBBXY_8_IDT-DUI-NXT-275


title: HFFTNBBXY_8_IDT-DUI-NXT-268


title: HFFTNBBXY_8_IDT-DUI-NXT-270


title: HFFTNBBXY_8_IDT-DUI-NXT-274


title: HFFTNBBXY_8_IDT-DUI-NXT-295


title: HFFTNBBXY_8_IDT-DUI-NXT-272


title: HFFTNBBXY_8_IDT-DUI-NXT-264


title: HFFTNBBXY_8_IDT-DUI-NXT-265


title: HFFTNBBXY_8_IDT-DUI-NXT-271


title: HFFTNBBXY_8_IDT-DUI-NXT-267


title: HFFTNBBXY_8_IDT-DUI-NXT-288


title: HFFTNBBXY_8_IDT-DUI-NXT-269


title: HFFTNBBXY_8_IDT-DUI-NXT-266


title: HFFTNBBXY_8_IDT-DUI-NXT-280


title: HFFTNBBXY_8_IDT-DUI-NXT-261


title: HFFTNBBXY_8_IDT-DUI-NXT-260


title: HFFTNBBXY_8_IDT-DUI-NXT-259


title: HFFTNBBXY_8_IDT-DUI-NXT-256


title: HFFTNBBXY_8_IDT-DUI-NXT-257


title: HFFTNBBXY_8_IDT-DUI-NXT-255


title: HFFTNBBXY_8_IDT-DUI-NXT-254


title: HFFTNBBXY_8_IDT-DUI-NXT-252


title: HFFTNBBXY_8_IDT-DUI-NXT-258


title: HFFTNBBXY_8_IDT-DUI-NXT-244


title: HFFTNBBXY_8_IDT-DUI-NXT-248


title: HFFTNBBXY_8_IDT-DUI-NXT-245


title: HFFTNBBXY_8_IDT-DUI-NXT-250


title: HFFTNBBXY_8_IDT-DUI-NXT-249


title: HFFTNBBXY_8_IDT-DUI-NXT-246


title: HFFTNBBXY_8_IDT-DUI-NXT-243


title: HFFTNBBXY_8_IDT-DUI-NXT-263


title: HFFTNBBXY_8_IDT-DUI-NXT-242


title: HFFTNBBXY_8_IDT-DUI-NXT-262


title: HFFTNBBXY_8_IDT-DUI-NXT-247


title: HFFTNBBXY_8_IDT-DUI-NXT-240


title: HFFTNBBXY_8_IDT-DUI-NXT-241


title: HFFTNBBXY_8_IDT-DUI-NXT-238


title: HFFTNBBXY_8_IDT-DUI-NXT-253


title: HFFTNBBXY_8_IDT-DUI-NXT-233


title: HFFTNBBXY_8_IDT-DUI-NXT-236


title: HFFTNBBXY_8_IDT-DUI-NXT-235


title: HFFTNBBXY_8_IDT-DUI-NXT-231


title: HFFTNBBXY_8_IDT-DUI-NXT-239


title: HFFTNBBXY_8_IDT-DUI-NXT-251


title: HFFTNBBXY_8_IDT-DUI-NXT-234


title: HFFTNBBXY_8_IDT-DUI-NXT-226


title: HFFTNBBXY_8_IDT-DUI-NXT-230


title: HFFTNBBXY_8_IDT-DUI-NXT-221


title: HFFTNBBXY_8_IDT-DUI-NXT-228


title: HFFTNBBXY_8_IDT-DUI-NXT-223


title: HFFTNBBXY_8_IDT-DUI-NXT-219


title: HFFTNBBXY_8_IDT-DUI-NXT-232


title: HFFTNBBXY_8_IDT-DUI-NXT-237


title: HFFTNBBXY_8_IDT-DUI-NXT-227


title: HFFTNBBXY_8_IDT-DUI-NXT-217


title: HFFTNBBXY_8_IDT-DUI-NXT-215


title: HFFTNBBXY_8_IDT-DUI-NXT-224


title: HFFTNBBXY_8_IDT-DUI-NXT-218


title: HFFTNBBXY_8_IDT-DUI-NXT-222


title: HFFTNBBXY_8_IDT-DUI-NXT-213


title: HFFTNBBXY_8_IDT-DUI-NXT-216


title: HFFTNBBXY_8_IDT-DUI-NXT-214


title: HFFTNBBXY_8_IDT-DUI-NXT-212


title: HFFTNBBXY_8_IDT-DUI-NXT-225


title: HFFTNBBXY_8_IDT-DUI-NXT-209


title: HFFTNBBXY_8_IDT-DUI-NXT-211


title: HFFTNBBXY_8_IDT-DUI-NXT-208


title: HFFTNBBXY_8_IDT-DUI-NXT-206


title: HFFTNBBXY_8_IDT-DUI-NXT-204


title: HFFTNBBXY_8_IDT-DUI-NXT-205


title: HFFTNBBXY_8_IDT-DUI-NXT-220


title: HFFTNBBXY_8_IDT-DUI-NXT-229


title: HFFTNBBXY_8_IDT-DUI-NXT-201


title: HFFTNBBXY_8_IDT-DUI-NXT-210


title: HFFTNBBXY_8_IDT-DUI-NXT-197


title: HFFTNBBXY_8_IDT-DUI-NXT-196


title: HFFTNBBXY_8_IDT-DUI-NXT-202


title: HFFTNBBXY_8_IDT-DUI-NXT-194


title: HFFTNBBXY_8_IDT-DUI-NXT-199


title: HFFTNBBXY_8_IDT-DUI-NXT-193


title: HFFTNBBXY_8_IDT-DUI-NXT-198


title: HFFTNBBXY_8_IDT-DUI-NXT-195


title: P2149_N712-S506

description:
Tetramer+ CD4+ T cells from BDC 2.5mi/IAg7-NP-treated NOD mice
Raw_counts_BDC_SMARTseq2.xlsx

treatment_protocol:
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.

value: NOD


title: P2149_N712-S517


title: P2149_N712-S504


title: P2149_N712-S508


title: P2149_N712-S507


title: P2149_N711-S508


title: P2149_N712-S505


title: P2149_N711-S517


title: P2149_N712-S502


title: HFFTNBBXY_8_IDT-DUI-NXT-207


title: P2149_N711-S504


title: P2149_N711-S507


title: P2149_N710-S517


title: P2149_N711-S506


title: P2149_N712-S503


title: P2149_N711-S503


title: P2149_N710-S506


title: P2149_N710-S507


title: HFFTNBBXY_8_IDT-DUI-NXT-200


title: P2149_N711-S502


title: P2149_N710-S504


title: P2149_N710-S502


title: P2149_N710-S505


title: P2149_N710-S503


title: P2149_N709-S508


title: HFFTNBBXY_8_IDT-DUI-NXT-316


title: P2149_N709-S507


title: P2149_N709-S506


title: P2149_N709-S502


title: P2149_N709-S505


title: P2149_N709-S504


title: P2149_N708-S508


title: P2149_N708-S517


title: P2149_N709-S503


title: P2149_N708-S506


title: P2149_N711-S505


title: P2149_N708-S504


title: P2149_N708-S507


title: P2149_N710-S508


title: P2149_N709-S517


title: P2149_N707-S506


title: P2149_N707-S505


title: P2149_N708-S505


title: P2149_N707-S517


title: P2149_N707-S507


title: P2149_N707-S508


title: P2149_N707-S503


title: P2149_N707-S504


title: P2149_N707-S502


title: P2149_N706-S517


title: P2149_N706-S503


title: P2149_N706-S507


title: P2149_N705-S506


title: P2149_N706-S506


title: P2149_N705-S503


title: P2149_N705-S504


title: P2149_N705-S502


title: P2149_N705-S508


title: P2149_N705-S507


title: P2149_N706-S508


title: P2149_N705-S517


title: P2149_N708-S503


title: P2149_N708-S502


title: P2149_N705-S505


title: P2149_N704-S502


title: P2149_N704-S504


title: P2149_N704-S503


title: P2149_N703-S517


title: P2149_N704-S508


title: P2149_N704-S517


title: P2149_N706-S502


title: P2149_N703-S507


title: P2149_N703-S506


title: P2149_N704-S507


title: P2149_N704-S506


title: P2149_N704-S505


title: P2149_N706-S505


title: P2149_N706-S504


title: P2149_N703-S508


title: P2149_N703-S504


title: P2149_N703-S503


title: P2149_N702-S508


title: P2149_N702-S505


title: P2149_N702-S507


title: P2149_N702-S502


title: P2149_N702-S503


title: P2149_N702-S504


title: Agrp neuron20

city: Seattle

first: Linda

last: Buck

state: Washington

address: 1100 fairview ave North

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Centre

description:
single-cell RNA sequencing
P51

data_processing:
Image analysis and basecalling was performed using Illumina's Real Time Analysis v1.8.66.3 software, followed by demultiplexing of indexed reads and generation of FASTQ files with Illumina's bcl2fastq-1.8.4 software.
Sequenced reads were aligned to iGenome's UCSC mm10 using TopHat aligner v2.1.0.
Cufflinks (cuffquant followed by cuffnorm) were used to generate gene abundances
Assembly: mm10
Supplementary files format and content: tab-delimited file containing FPKM normalized gene counts per sample
Supplementary files format and content: tab-delimited file containing FPKM normalized GPCR counts per sample

molecule: polyA RNA

source_name: Brain

growth_protocol: GFP-labelled flourescent single cells were manually isolated from Agrp-Cre: Ai6 mice using a micropipette and visualizing cells under a fluorescent microscope.

extract_protocol:
Single cell cDNA libraries were prepared using oligo(dT) primed cDNA synthesis followed by PCR amplification of cDNAs,  as described in previously published methods (Hanchate et al, 2015, Science, 1251-5; Malnic et al, 1999, Cell, 96:713.)
Libraries were prepared for sequencing using the TruSeq DNA sample prep kit following the manufacturer's instructions (Illumina)

value: Brain

value: Neuron

value: Agrp-ires-Cre x Ai6


title: Agrp neuron18

description:
single-cell RNA sequencing
P42


title: P2149_N703-S502


title: P2149_N703-S505


title: P2149_N702-S517


title: Agrp neuron17

description:
single-cell RNA sequencing
P41


title: Agrp neuron16

description:
single-cell RNA sequencing
P40


title: P2149_N702-S506


title: Agrp neuron14

description:
single-cell RNA sequencing
P33


title: Agrp neuron15

description:
single-cell RNA sequencing
P36


title: Agrp neuron13

description:
single-cell RNA sequencing
P24


title: Agrp neuron19

description:
single-cell RNA sequencing
P44


title: Agrp neuron10

description:
single-cell RNA sequencing
P15


title: Agrp neuron12

description:
single-cell RNA sequencing
P23


title: Agrp neuron9

description:
single-cell RNA sequencing
P14


title: Agrp neuron5

description:
single-cell RNA sequencing
A53


title: Agrp neuron3

description:
single-cell RNA sequencing
A42


title: Agrp neuron8

description:
single-cell RNA sequencing
P12


title: Agrp neuron7

description:
single-cell RNA sequencing
A86


title: Agrp neuron6

description:
single-cell RNA sequencing
A54


title: ctrl_day_21_12b

city: Rehovot

first: Ayelet

last: Erez

state: Please Select

address: CANDIOTTI 214

country: Israel

institute: WEIZMANN INSTITUTE

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the mouse GRCm38 genome using STAR  v2.4.2a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count
Normalization was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: Excel file includes the normalized counts

extract_protocol:
RNA was extracted from dissociated hepatocytes following liver perfusion. Hepatocytes were resuspended in QIAzol and frozen at -80°C.  RNA was extracted by using QIAzol Lysis Reagent.
Inhouse poly A based RNA seq

treatment_protocol: 8 Weeks old female Balb\c mice were orthotopically injected with PBS or 4T1 BC cells for 4 or 21 days.

value: Liver

value: Hepatocytes

tag: time

value: day 21

value: Balb\c

value: female

value: PBS injection


title: Agrp neuron4

description:
single-cell RNA sequencing
A49

tag: genotype


title: 4t1_day_21_9a

value: Orthotopic 4T1 BC injection


title: ctrl_day_21_10a


title: Agrp neuron2

description:
single-cell RNA sequencing
A28


title: 4t1_day_21_8b


title: Agrp neuron11

description:
single-cell RNA sequencing
P22


title: 4t1_day_21_7


title: ctrl_day_21_11a


title: ctrl_day_4_6

value: day 4


title: 4t1_day_4_3


title: Agrp neuron1

description:
single-cell RNA sequencing
A9


title: ctrl_day_4_5


title: 4t1_day_4_2


title: 4t1_day_4_1


title: ctrl_day_4_4


title: HK53TBBXY-5-IDT-DUI-NXT-191


title: HK53TBBXY-5-IDT-DUI-NXT-187


title: HK53TBBXY-5-IDT-DUI-NXT-98


title: HK53TBBXY-5-IDT-DUI-NXT-192


title: HK53TBBXY-5-IDT-DUI-NXT-189


title: HK53TBBXY-5-IDT-DUI-NXT-186


title: HK53TBBXY-5-IDT-DUI-NXT-183


title: HK53TBBXY-5-IDT-DUI-NXT-185


title: HK53TBBXY-5-IDT-DUI-NXT-182


title: HK53TBBXY-5-IDT-DUI-NXT-181


title: HK53TBBXY-5-IDT-DUI-NXT-180


title: HK53TBBXY-5-IDT-DUI-NXT-184


title: HK53TBBXY-5-IDT-DUI-NXT-179


title: HK53TBBXY-5-IDT-DUI-NXT-178


title: HK53TBBXY-5-IDT-DUI-NXT-176


title: HK53TBBXY-5-IDT-DUI-NXT-175


title: HK53TBBXY-5-IDT-DUI-NXT-97


title: HK53TBBXY-5-IDT-DUI-NXT-174


title: HK53TBBXY-5-IDT-DUI-NXT-173


title: HFFTNBBXY_8_IDT-DUI-NXT-203


title: HK53TBBXY-5-IDT-DUI-NXT-177


title: HK53TBBXY-5-IDT-DUI-NXT-99


title: HK53TBBXY-5-IDT-DUI-NXT-172


title: HK53TBBXY-5-IDT-DUI-NXT-190


title: HK53TBBXY-5-IDT-DUI-NXT-171


title: HK53TBBXY-5-IDT-DUI-NXT-169


title: HK53TBBXY-5-IDT-DUI-NXT-188


title: HK53TBBXY-5-IDT-DUI-NXT-168


title: HK53TBBXY-5-IDT-DUI-NXT-167


title: HK53TBBXY-5-IDT-DUI-NXT-163


title: HK53TBBXY-5-IDT-DUI-NXT-161


title: HK53TBBXY-5-IDT-DUI-NXT-162


title: HK53TBBXY-5-IDT-DUI-NXT-165


title: HK53TBBXY-5-IDT-DUI-NXT-164


title: HK53TBBXY-5-IDT-DUI-NXT-166


title: HK53TBBXY-5-IDT-DUI-NXT-159


title: HK53TBBXY-5-IDT-DUI-NXT-160


title: HK53TBBXY-5-IDT-DUI-NXT-155


title: HK53TBBXY-5-IDT-DUI-NXT-157


title: HK53TBBXY-5-IDT-DUI-NXT-154


title: HK53TBBXY-5-IDT-DUI-NXT-156


title: HK53TBBXY-5-IDT-DUI-NXT-158


title: HK53TBBXY-5-IDT-DUI-NXT-147


title: HK53TBBXY-5-IDT-DUI-NXT-151


title: HK53TBBXY-5-IDT-DUI-NXT-149


title: HK53TBBXY-5-IDT-DUI-NXT-152


title: HK53TBBXY-5-IDT-DUI-NXT-145


title: HK53TBBXY-5-IDT-DUI-NXT-150


title: HK53TBBXY-5-IDT-DUI-NXT-148


title: HK53TBBXY-5-IDT-DUI-NXT-146


title: HK53TBBXY-5-IDT-DUI-NXT-170


title: HK53TBBXY-5-IDT-DUI-NXT-144


title: HK53TBBXY-5-IDT-DUI-NXT-140


title: HK53TBBXY-5-IDT-DUI-NXT-143


title: HK53TBBXY-5-IDT-DUI-NXT-142


title: HK53TBBXY-5-IDT-DUI-NXT-139


title: HK53TBBXY-5-IDT-DUI-NXT-141


title: HK53TBBXY-5-IDT-DUI-NXT-137


title: HK53TBBXY-5-IDT-DUI-NXT-135


title: HK53TBBXY-5-IDT-DUI-NXT-134


title: HK53TBBXY-5-IDT-DUI-NXT-138


title: HK53TBBXY-5-IDT-DUI-NXT-132


title: HK53TBBXY-5-IDT-DUI-NXT-133


title: HK53TBBXY-5-IDT-DUI-NXT-153


title: HK53TBBXY-5-IDT-DUI-NXT-130


title: HK53TBBXY-5-IDT-DUI-NXT-131


title: HK53TBBXY-5-IDT-DUI-NXT-126


title: HK53TBBXY-5-IDT-DUI-NXT-127


title: HK53TBBXY-5-IDT-DUI-NXT-129


title: HK53TBBXY-5-IDT-DUI-NXT-128


title: HK53TBBXY-5-IDT-DUI-NXT-125


title: HK53TBBXY-5-IDT-DUI-NXT-124


title: HK53TBBXY-5-IDT-DUI-NXT-123


title: HK53TBBXY-5-IDT-DUI-NXT-118


title: HK53TBBXY-5-IDT-DUI-NXT-120


title: HK53TBBXY-5-IDT-DUI-NXT-116


title: HK53TBBXY-5-IDT-DUI-NXT-115


title: HK53TBBXY-5-IDT-DUI-NXT-122


title: HK53TBBXY-5-IDT-DUI-NXT-112


title: HK53TBBXY-5-IDT-DUI-NXT-113


title: HK53TBBXY-5-IDT-DUI-NXT-117


title: HK53TBBXY-5-IDT-DUI-NXT-136


title: HK53TBBXY-5-IDT-DUI-NXT-111


title: HK53TBBXY-5-IDT-DUI-NXT-121


title: HK53TBBXY-5-IDT-DUI-NXT-119


title: HK53TBBXY-5-IDT-DUI-NXT-110


title: HK53TBBXY-5-IDT-DUI-NXT-114


title: HK53TBBXY-5-IDT-DUI-NXT-108


title: HK53TBBXY-5-IDT-DUI-NXT-106


title: HK53TBBXY-5-IDT-DUI-NXT-109


title: HK53TBBXY-5-IDT-DUI-NXT-105


title: HK53TBBXY-5-IDT-DUI-NXT-103


title: HK53TBBXY-5-IDT-DUI-NXT-104


title: HK53TBBXY-5-IDT-DUI-NXT-107


title: HK53TBBXY-5-IDT-DUI-NXT-102


title: HK53TBBXY-5-IDT-DUI-NXT-101


title: HK53TBBXY-5-IDT-DUI-NXT-100


title: H7YCTDSX2-IDT-DUI-NXT-99


title: H7YCTDSX2-IDT-DUI-NXT-98


title: H7YCTDSX2-IDT-DUI-NXT-97


title: H7YCTDSX2-IDT-DUI-NXT-192


title: H7YCTDSX2-IDT-DUI-NXT-191


title: H7YCTDSX2-IDT-DUI-NXT-190


title: H7YCTDSX2-IDT-DUI-NXT-188


title: H7YCTDSX2-IDT-DUI-NXT-184


title: H7YCTDSX2-IDT-DUI-NXT-181


title: H7YCTDSX2-IDT-DUI-NXT-180


title: H7YCTDSX2-IDT-DUI-NXT-187


title: H7YCTDSX2-IDT-DUI-NXT-178


title: H7YCTDSX2-IDT-DUI-NXT-183


title: H7YCTDSX2-IDT-DUI-NXT-182


title: H7YCTDSX2-IDT-DUI-NXT-176


title: H7YCTDSX2-IDT-DUI-NXT-175


title: H7YCTDSX2-IDT-DUI-NXT-173


title: H7YCTDSX2-IDT-DUI-NXT-172


title: H7YCTDSX2-IDT-DUI-NXT-174


title: H7YCTDSX2-IDT-DUI-NXT-170


title: H7YCTDSX2-IDT-DUI-NXT-189


title: H7YCTDSX2-IDT-DUI-NXT-179


title: H7YCTDSX2-IDT-DUI-NXT-171


title: H7YCTDSX2-IDT-DUI-NXT-169


title: H7YCTDSX2-IDT-DUI-NXT-168


title: H7YCTDSX2-IDT-DUI-NXT-167


title: H7YCTDSX2-IDT-DUI-NXT-165


title: H7YCTDSX2-IDT-DUI-NXT-164


title: H7YCTDSX2-IDT-DUI-NXT-163


title: H7YCTDSX2-IDT-DUI-NXT-185


title: H7YCTDSX2-IDT-DUI-NXT-161


title: H7YCTDSX2-IDT-DUI-NXT-186


title: H7YCTDSX2-IDT-DUI-NXT-160


title: H7YCTDSX2-IDT-DUI-NXT-159


title: H7YCTDSX2-IDT-DUI-NXT-177


title: H7YCTDSX2-IDT-DUI-NXT-158


title: H7YCTDSX2-IDT-DUI-NXT-155


title: H7YCTDSX2-IDT-DUI-NXT-157


title: H7YCTDSX2-IDT-DUI-NXT-152


title: H7YCTDSX2-IDT-DUI-NXT-154


title: H7YCTDSX2-IDT-DUI-NXT-153


title: H7YCTDSX2-IDT-DUI-NXT-150


title: H7YCTDSX2-IDT-DUI-NXT-151


title: H7YCTDSX2-IDT-DUI-NXT-148


title: H7YCTDSX2-IDT-DUI-NXT-145


title: H7YCTDSX2-IDT-DUI-NXT-143


title: H7YCTDSX2-IDT-DUI-NXT-142


title: H7YCTDSX2-IDT-DUI-NXT-141


title: H7YCTDSX2-IDT-DUI-NXT-166


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title: H7YCTDSX2-IDT-DUI-NXT-121


title: H7YCTDSX2-IDT-DUI-NXT-102


title: H57CHDSX2-IDT-DUI-NXT-384


title: H7YCTDSX2-IDT-DUI-NXT-100


title: H7YCTDSX2-IDT-DUI-NXT-101


title: H57CHDSX2-IDT-DUI-NXT-383


title: H57CHDSX2-IDT-DUI-NXT-379


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title: H57CHDSX2-IDT-DUI-NXT-381


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title: H57CHDSX2-IDT-DUI-NXT-374


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title: H57CHDSX2-IDT-DUI-NXT-375


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title: H3CFLDSX2-IDT-DUI-NXT-227


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title: H3CFLDSX2-IDT-DUI-NXT-218


title: H3CFLDSX2-IDT-DUI-NXT-205


title: H3CFLDSX2-IDT-DUI-NXT-202


title: H3CFLDSX2-IDT-DUI-NXT-203


title: H3CFLDSX2-IDT-DUI-NXT-199


title: H3CFLDSX2-IDT-DUI-NXT-198


title: H3CFLDSX2-IDT-DUI-NXT-196


title: H3CFLDSX2-IDT-DUI-NXT-194


title: H3CFLDSX2-IDT-DUI-NXT-197


title: H3CFLDSX2-IDT-DUI-NXT-201


title: H3CFLDSX2-IDT-DUI-NXT-195


title: H37L7DSX2-IDT-DUI-NXT-382


title: H3CFLDSX2-IDT-DUI-NXT-193


title: H37L7DSX2-IDT-DUI-NXT-384


title: H37L7DSX2-IDT-DUI-NXT-383


title: H37L7DSX2-IDT-DUI-NXT-379


title: H3CFLDSX2-IDT-DUI-NXT-212


title: H37L7DSX2-IDT-DUI-NXT-377


title: H37L7DSX2-IDT-DUI-NXT-381


title: H37L7DSX2-IDT-DUI-NXT-380


title: H37L7DSX2-IDT-DUI-NXT-378


title: H37L7DSX2-IDT-DUI-NXT-376


title: H37L7DSX2-IDT-DUI-NXT-375


title: H37L7DSX2-IDT-DUI-NXT-374


title: H37L7DSX2-IDT-DUI-NXT-373


title: H3CFLDSX2-IDT-DUI-NXT-204


title: H3CFLDSX2-IDT-DUI-NXT-200


title: H37L7DSX2-IDT-DUI-NXT-370


title: H37L7DSX2-IDT-DUI-NXT-372


title: H37L7DSX2-IDT-DUI-NXT-369


title: H37L7DSX2-IDT-DUI-NXT-371


title: H37L7DSX2-IDT-DUI-NXT-368


title: H37L7DSX2-IDT-DUI-NXT-367


title: H37L7DSX2-IDT-DUI-NXT-366


title: H37L7DSX2-IDT-DUI-NXT-363


title: H37L7DSX2-IDT-DUI-NXT-364


title: H37L7DSX2-IDT-DUI-NXT-361


title: H37L7DSX2-IDT-DUI-NXT-362


title: H37L7DSX2-IDT-DUI-NXT-365


title: H37L7DSX2-IDT-DUI-NXT-360


title: H37L7DSX2-IDT-DUI-NXT-359


title: H37L7DSX2-IDT-DUI-NXT-358


title: H37L7DSX2-IDT-DUI-NXT-356


title: H37L7DSX2-IDT-DUI-NXT-355


title: H37L7DSX2-IDT-DUI-NXT-357


title: H37L7DSX2-IDT-DUI-NXT-354


title: H37L7DSX2-IDT-DUI-NXT-353


title: H37L7DSX2-IDT-DUI-NXT-352


title: H37L7DSX2-IDT-DUI-NXT-351


title: H37L7DSX2-IDT-DUI-NXT-350


title: H37L7DSX2-IDT-DUI-NXT-349


title: H37L7DSX2-IDT-DUI-NXT-347


title: H37L7DSX2-IDT-DUI-NXT-346


title: H37L7DSX2-IDT-DUI-NXT-344


title: H37L7DSX2-IDT-DUI-NXT-343


title: H37L7DSX2-IDT-DUI-NXT-339


title: H37L7DSX2-IDT-DUI-NXT-341


title: H37L7DSX2-IDT-DUI-NXT-340


title: H37L7DSX2-IDT-DUI-NXT-342


title: H37L7DSX2-IDT-DUI-NXT-338


title: H37L7DSX2-IDT-DUI-NXT-334


title: H37L7DSX2-IDT-DUI-NXT-337


title: H37L7DSX2-IDT-DUI-NXT-336


title: H37L7DSX2-IDT-DUI-NXT-335


title: H37L7DSX2-IDT-DUI-NXT-329


title: H37L7DSX2-IDT-DUI-NXT-333


title: H37L7DSX2-IDT-DUI-NXT-330


title: H37L7DSX2-IDT-DUI-NXT-328


title: H37L7DSX2-IDT-DUI-NXT-326


title: H37L7DSX2-IDT-DUI-NXT-323


title: H37L7DSX2-IDT-DUI-NXT-321


title: H37L7DSX2-IDT-DUI-NXT-325


title: H37L7DSX2-IDT-DUI-NXT-322


title: H37L7DSX2-IDT-DUI-NXT-327


title: H37L7DSX2-IDT-DUI-NXT-324


title: H37L7DSX2-IDT-DUI-NXT-320


title: H37L7DSX2-IDT-DUI-NXT-348


title: H37L7DSX2-IDT-DUI-NXT-318


title: H37L7DSX2-IDT-DUI-NXT-345


title: H37L7DSX2-IDT-DUI-NXT-316


title: H37L7DSX2-IDT-DUI-NXT-315


title: H37L7DSX2-IDT-DUI-NXT-313


title: H37L7DSX2-IDT-DUI-NXT-312


title: H37L7DSX2-IDT-DUI-NXT-314


title: H37L7DSX2-IDT-DUI-NXT-332


title: H37L7DSX2-IDT-DUI-NXT-331


title: H37L7DSX2-IDT-DUI-NXT-311


title: H37L7DSX2-IDT-DUI-NXT-308


title: H37L7DSX2-IDT-DUI-NXT-307


title: P2149_N701-S517


title: H37L7DSX2-IDT-DUI-NXT-310


title: P2149_N701-S508


title: H37L7DSX2-IDT-DUI-NXT-309


title: P2149_N701-S505


title: P2149_N701-S504


title: P2149_N701-S503


title: P2149_N701-S506


title: P2149_N701-S502


title: H37L7DSX2-IDT-DUI-NXT-319


title: P2136_N712-S508


title: P2136_N712-S507


title: P2136_N712-S506


title: P2136_N712-S505


title: P2136_N712-S504


title: H37L7DSX2-IDT-DUI-NXT-317


title: P2149_N701-S507


title: P2136_N712-S502


title: P2136_N712-S503


title: P2136_N711-S517


title: P2136_N711-S507


title: P2136_N711-S508


title: P2136_N711-S506


title: P301S Tau transgenic animals, Cdk5i peptide treated, replicate 1

first: Ravikiran

last: Raju

address: 15A Maple Ave

department: Picower Institute

institute: MIT

description: 40+40 paired-end run

data_processing:
Raw fastq files were aligned to tbe GRCm38 genome using STAR (version 2.7.9a) after 3bp were clipped off the 3p end of read 1 and 5p end of read 2 based on quality
Aligned fastq reads were mapped to genes using featureCounts within the subread package (version 2.0.0). Included flags were -t gene, -g gene_id, -p, -s 2
Raw count matrix was analyzed using DESeq2 (version 1.36.0). Genes were pre-filtered if there were less than 5 counts in fewer than 3 samples. Histogram of p-values showed an anti-conservative distribution so fdrtool (version 1.2.17) was used to correct test stastics
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Cortex

extract_protocol:
RNA was extracted from nuclei using the RecoverAll Total Nuclei Acid Isolation Kit for FFPE Tissue (ThermoFisher).
RNA libraries for RNA-seq were prepared using Clontech SMARTer Stranded Total RNAseq Kit - Pico Input following manufacturer's protocols.

value: Cortex

value: sorted cortical neurons

value: NeuN(+) cells

value: P301S Tau transgenic

value: Cdk5i peptide


title: P301S Tau transgenic animals, Cdk5i peptide treated, replicate 2

description: 40+40 paired-end run


title: P301S Tau transgenic animals, Cdk5i peptide treated, replicate 3

description: 40+40 paired-end run


title: P2136_N711-S505

value: NOD

value: T cell

value: pMHCII-NPs


title: P2136_N711-S504


title: P301S Tau transgenic animals, scrmb peptide treated, replicate 3

description: 40+40 paired-end run

value: scrmb peptide


title: P301S Tau transgenic animals, scrmb peptide treated, replicate 2

description: 40+40 paired-end run


title: P301S Tau transgenic animals, scrmb peptide treated, replicate 1

description: 40+40 paired-end run


title: wilidtype animals no treatment, replicate 3

description: 40+40 paired-end run

value: WT


title: P2136_N710-S517


title: P2136_N710-S508


title: wilidtype animals no treatment, replicate 1

description: 40+40 paired-end run


title: P2136_N710-S507


title: wilidtype animals no treatment, replicate 2

description: 40+40 paired-end run


title: 246C-N-24

city: Philadelphia

first: Hunter

last: Reavis

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Read quality was checked for each sample using FastQC
Trimmed sequence reads were mapped to GRCh38 primary assembly using STAR aligner (default parameters)
Aligned reads were quantified at the gene-level using HTSeq-count
Gene counts were then normalized using varianceStabilizingTransform method from DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized log2 abundance values for each Sample

extract_protocol:
RNA was harvested using Total RNA Purification Kit (Norgen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using th TruSeq Stranded Total RNA Library Kit (Illumina) following manufacturer's protocols.

value: immortalized fallopian tube epithelial cell

value: 10 microM norepinephrine


title: 246C-NP-24

value: 10 microM norepinephrine+10 microM propranolol


title: 246C-P-24

value: 10 microM propranolol


title: P2136_N710-S504


title: P2136_N710-S505


title: 246C-V-24

value: vehicle


title: 246C-N-4


title: P2136_N710-S502


title: 246C-V-4


title: P2136_N711-S503


title: P2136_N710-S503


title: P2136_N709-S508


title: 246B-NP-24


title: P2136_N709-S517


title: P2136_N709-S506


title: 246C-V-0


title: P2136_N712-S517


title: P2136_N709-S507


title: P2136_N711-S502


title: 246B-P-24


title: 246B-V-24


title: 246B-N-4


title: P2136_N709-S504


title: 246B-V-4


title: P2136_N709-S502


title: P2136_N709-S505


title: P2136_N710-S506


title: 246B-V-0


title: P2136_N708-S517


title: 246A-P-24


title: P2136_N708-S508


title: 246A-NP-24


title: P2136_N708-S507


title: P2136_N708-S506


title: 246A-N-24


title: 246A-N-4


title: P2136_N708-S505


title: 246A-V-24


title: 246B-N-24


title: P2136_N708-S504


title: 246A-V-4


title: P2136_N709-S503


title: 246A-V-0


title: P2136_N708-S503


title: P2136_N708-S502


title: 237C-NP-24


title: P2136_N707-S517


title: P2136_N707-S508


title: 237C-P-24