title: 973-hCS-6mo

first: Yu

last: Fan

state: NY

address: 1425 madison Ave

institute: Icahn school of medicine at mount sinai

description: Library name: 973-hCS

data_processing:
The raw sequencing data, represented as base call (BCL) files produced by the Illumina sequencing platform, were subjected to demultiplexing and subsequent conversion into FASTQ format using CellRanger software (version 6.0.0, 10x Genomics) with default parameters. The software then mapped the FASTQ reads to the human reference genome (GRCh38) with default parameters. Following this, the ‘count’ command in the Cell Ranger (v6.0.0) software was utilized for the quantification of gene expression. For alignment and counting, the reference genome refdata-gex-GRCh38-2020-A was used, which was procured from the official 10x Genomics website.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Cortical organoids were generated according to the protocol described by Sloan et. al.63, with several modifications. hiPSCs were first aggregated into embryoid bodies (EBs) using an AggreWell™800 Microwell Culture Plate system (Stemcell Tech #34850). Expanded hiPSCs were rinsed twice with DPBS without Ca/Mg, and then dissociated using accutase. 3x10E6 hiPSCs were added to a single well in the prepared AggreWell and allowed to aggregate in a 37 °C incubator for 24 hours. The following day (day 0), EBs were dislodged from the AggreWell plate using a cut p1000 pipette tip and passed over a 40μm strainer, and washed with excess DMEM. The strainer was inverted over an Ultra-Low Attachment 10 cm culture dish and the EBs were collected in spheroid induction media, which contained Stemflex supplemented with two SMAD inhibitors, SB-431542 (SB) and LDN193189 (LDN), and THX. The following day (day 1), the media THX was withdrawn. From d2-d6, induction media was replaced daily, and no longer contained the Stemflex supplement (only base Stemflex media with SB and LDN). On day 6, the media was replaced with organoid patterning media, formulated with Neurobasal-A medium, 1x B-27 minus Vitamin A, 1x GlutaMAX, and 1x Antibiotic-Antimycotic. From d6-d24, organoid maturation media was supplemented with 20 ng/ml of EGF (R&D Systems, #236-EG) and 20 ng/ml FGF2 (R&D Systems, #233-FB-01M). Media was changed every day from d6 – d15, after which media was changed every other day. From d25-d43, the organoid maturation media was supplemented with 20 ng/ml of NT-3 (PeproTech, #450-03) and 20 ng/ml BDNF. From d43 onwards, organoids received organoid maturation media with no supplements, and media was changed every 4 days or as needed. Subpallial organoids were generated in the same way as cortical organoids, but with additions in media formulations. From d4-d23, hSOs received spheroid induction media or organoid maturation media supplemented with 5 µM of the Wnt inhibitor, IWP-2 (Selleckchem, #S7085). From d12-d23, hSO organoids received neuronal differentiation media supplemented with 100 nM of the SHH agonist, SAG (Selleckchem, #S7779).

extract_protocol:
scRNA-seq was performed on 4-6 pooled 6-month-old organoids per donor line, per condition (hCS or hSS) for a total of 48 organoids. A minimum of 10,000 dissociated cells were submitted for sequencing. The library was prepared using the Chromium platform (10x Genomics) with the 3’ gene expression (3’ GEX) V3/V3.1 kit.
The library was prepared using the Chromium platform (10x Genomics) with the 3’ gene expression (3’ GEX) V3/V3.1 kit, according to the manufacturer's instructions.

treatment_protocol: Whole organoids were dissociated to the single cell level in preparation for single-cell RNA sequencing using the Papain Worthington Kit (Worthington, LK003150). All solutions included in the kit were prepared according to the manufacturer’s instructions. 4-6 organoids were transferred to one well of a low attachment 6 well plate and were washed with PBS without Ca2+ and Mg2+. Organoids were cut with a small scalpel into smaller pieces for easier dissociation. 800 µl of papain solution (supplied in the kit) was added per well. Samples were incubated at 37°C for about two hours or until single cell suspension was achieved. Every 15 minutes, the mixture was pipetted up and down with a cut P1000 pipette tip. Once single cell suspension was reached, 500 µl of inhibitor solution (supplied in the kit) was added to the well. The solution was gently mixed, filtered through a 70 µm-pore sieve, and transferred to a 15 ml centrifuge tube. The cells were pelleted by centrifugation at 300 x g for 5 minutes at room temperature. Cell pellets were resuspended in 500 µl of ice-cold 0.04% BSA diluted in PBS without Ca2+ and Mg2+.

value: hiPSC-derived-hCS

tag: time

value: 6 months

tag: experimental batch

value: Case-Control-Organoid


title: R62-Kidney-PreTx_TCRB

status: Public on Feb 10 2025

type: SRA

city: Chicago

first: James

last: Mathew

state: IL

address: 300 E Superior

department: Department of Surgery, Division of Organ Transplantation, Comprehensive Transplant Center

country: USA

institute: Northwestern University Feinberg School of Medicine

description: Library name: R62-Kidney-PreTx_TCRB

library_source: genomic

data_processing:
raw data preprocessed by Adaptive Biotechnologies
Assembly: hg18 (NCBI 36)
Supplementary files format and content: sample level TSV files (unique per sample) are tab deliminated and contain the T-cell receptor rearrangement sequences, their observed counts and frequencies in the sample, as well as information relating to rearrangement length, V,D,J gene usage and their respective indices along the nucleotide rearrangement, and whether the sequence was in frame for transcription/translation and thus productive
Supplementary files format and content: project level TSV file (one containing data from all samples) is tab deliminated and contains sample level metrics including the numbers of T-cell receptor rearrangements and templates observed, the total number of nucleated cells observed, the T-cell content of the sample i.e. the fraction of T-cell templates observed divided by the total number of nucleated cells observed, the fraction of T-cell receptors that are productive or in-frame, Simpson clonality of the observed productive T-cells, the sequencing locus TCRB, and the estimated gDNA mass sequenced
Library strategy: TCR-Seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Kidney

extract_protocol:
QIAamp DNA blood Mini kit (Qiagen)
Bias-controlled multiplex PCR using forward and reverse primers specific to CDR3 Vβ and Jβ region (Adaptive Biotechnologies)

tag: tissue

value: Kidney

tag: subject

tag: visit

value: PreTx

tag: diagnosis 3_months

value: Reject

tag: induction

value: Simulect


title: R62-CD8-DRTC_TCRB

description: Library name: R62-CD8-DRTC_TCRB

source_name: DRTC

value: DRTC


title: Rgs9+/- Cortex male mRNA rep1 [Msh2]

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
M2R22_1CTX
mRNA

library_source: transcriptomic

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: Semicolon-delimited csv files include FPKM and Count values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Cerebral Cortex

extract_protocol:
Brain striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).

value: Cerebral Cortex

tag: genotype

tag: strain/background

tag: age

value: 12 months

tag: Sex

value: male

tag: well address


title: R62-CD4-DRTC_TCRB

description: Library name: R62-CD4-DRTC_TCRB


title: 972-hSS-6mo

city: New York

description: Library name: 972-hSS

library_source: transcriptomic single cell

tag: cell line

tag: cell type

value: hiPSC-derived-hSS


title: 972-hCS-6mo

description: Library name: 972-hCS


title: R59-Urine_Pellet-12M_TCRB

description: Library name: R59-Urine_Pellet-12M_TCRB

source_name: Urine Pellet

value: Urine Pellet

value: 12 Month

value: Borderline


title: R59-Urine_Pellet-6M_TCRB

description: Library name: R59-Urine_Pellet-6M_TCRB

value: 6 Month


title: 641-hSS-6mo

description: Library name: 641-hSS


title: Rgs9+/- Cortex female mRNA rep4 [Msh2]

description:
MRQ8_3CTX
mRNA

value: female


description: Library name: R62-Urine_Pellet-for_cause_Jun_18_2019_TCRB

value: 1 Month

tag: rejection episode


title: Rgs9+/- Cortex female mRNA rep3 [Msh2]

description:
MRQ4_3CTX
mRNA


title: R59-Urine_Pellet-2W_TCRB

description: Library name: R59-Urine_Pellet-2W_TCRB

value: 2 Week


title: R59-PBMC-12M_TCRB

description: Library name: R59-PBMC-12M_TCRB

source_name: PBMC

value: PBMC


title: Rgs9+/- Cortex male mRNA rep4 [Msh2]

description:
MRQ7_3CTX
mRNA


title: R59-PBMC-6M_TCRB

description: Library name: R59-PBMC-6M_TCRB


title: R62-PBMC-for_cause_Jun_18_19_TCRB

description: Library name: R62-PBMC-for_cause_Jun_18_19_TCRB


title: R59-Urine_Pellet-3M_TCRB

description: Library name: R59-Urine_Pellet-3M_TCRB

value: 3 Month


title: 641-hCS-6mo

description: Library name: 641-hCS

value: hiPSC-derived-hCS

value: 6 months

value: Case-Control-Organoid


title: Rgs9+/- Cortex male mRNA rep3 [Msh2]

description:
MRQ5_4CTX
mRNA


title: 973-hSS-6mo

description: Library name: 973-hSS


title: 581-hSS-6mo

description: Library name: 581-hSS


title: R59-PBMC-PreTx_TCRB

description: Library name: R59-PBMC-PreTx_TCRB

value: PreTx

value: Simulect


title: R59-Kidney-3M_TCRB

description: Library name: R59-Kidney-3M_TCRB

value: Kidney


title: R59-Kidney-12M_TCRB

description: Library name: R59-Kidney-12M_TCRB


title: 581-hCS-6mo

description: Library name: 581-hCS


title: 2607-hSS-6mo

description: Library name: 2607-hSS

value: Control


title: R59-Kidney-PreTx_TCRB

description: Library name: R59-Kidney-PreTx_TCRB


title: Het (Q140) KI X Msh2-/- Striatum male mRNA rep3 [Msh2]

description:
MRQ46_2str
mRNA

source_name: Corpus Striatum

value: Corpus Striatum

value: Het (Q140) KI X Msh2-/-

value: 12 months

value: male


title: R59-CD8-DRTC_TCRB

description: Library name: R59-CD8-DRTC_TCRB

value: DRTC

value: Borderline


title: R59-CD4-DRTC_TCRB

description: Library name: R59-CD4-DRTC_TCRB


title: 2607-hCS-6mo

description: Library name: 2607-hCS


title: R57-Urine_Pellet-12M_TCRB

description: Library name: R57-Urine_Pellet-12M_TCRB

value: Urine Pellet

value: 12 Month


title: R57-Urine_Pellet-6M_TCRB

description: Library name: R57-Urine_Pellet-6M_TCRB

value: 6 Month


title: Rgs9+/- Cortex female mRNA rep2 [Msh2]

description:
MRQ35_1CTX
mRNA

value: Cerebral Cortex

value: female


title: Het (Q140) KI X Msh2-/- Striatum male mRNA rep1 [Msh2]

description:
MRQ33_1str
mRNA


title: R57-Urine_Pellet-3M_TCRB

description: Library name: R57-Urine_Pellet-3M_TCRB

value: 3 Month


title: R59-PBMC-3M_TCRB

description: Library name: R59-PBMC-3M_TCRB

value: PBMC


title: Rgs9+/- Cortex female mRNA rep1 [Msh2]

description:
MRQ23_4CTX
mRNA


title: R57-PBMC-6M_TCRB

description: Library name: R57-PBMC-6M_TCRB


title: R57-Urine_Pellet-2W_TCRB

description: Library name: R57-Urine_Pellet-2W_TCRB

value: 2 Week


title: Het (Q140) KI X Msh2-/- Striatum female mRNA rep5 [Msh2]

description:
MRQ40_5str
mRNA


title: Het (Q140) KI X Msh2-/- Striatum female mRNA rep3 [Msh2]

description:
MRQ33_2str
mRNA


title: R57-PBMC-12M_TCRB

description: Library name: R57-PBMC-12M_TCRB

value: Simulect


title: 2D_PX43_48h_3

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

description:
Library name: 2D_PX43_48h_3
PX43_48h_3

data_processing:
Raw sequencing data was pseudo-aligned against the human transcriptome (Ensembl GRCh38.105) using kallisto (v0.45.0) with 20 bootstraps. Gene expression was summarized from the scaledTPM values of the transcripts using tximport (v1.30.0).
Assembly: Ensembl GRCh38 version 105.
Supplementary files format and content: Excel file with scaled TPM values summarized to gene expression using tximport (v1.30.0).

source_name: Human Primary Epidermis Keratinocyte

growth_protocol: Triplicates (denoted as donors X, Y, Z) of normal human epidermal keratinocyte (NHEK) juvenile single-donor cells (#HPEKs, lot nos. ES1503029, CP1911101, MC1706096) were purchased from CELLnTEC (Bern, Switzerland) at passage 2. The cells were expanded to passage 4 and cryopreserved at a density of 1×106 cells per vial using CnT-CRYO Defined medium (CELLnTEC, #CnT-CRYO-50) for later use.

extract_protocol:
RNA was isolated following the manufacturer’s protocol for the RNeasy Mini Kit (Qiagen, #74104), and residual DNA was removed using the RNase-Free DNase Set (Qiagen, #79254). RNA quality was assessed using the NanoDrop™ 2000 spectrophotometer (Thermo Fisher Scientific, #ND-2000), and samples were stored at −20°C until sequencing.
Illumina TruSeq Stranded Total RNA Library Prep Kit with RiboZero Plus rRNA depletion.

treatment_protocol: For experiments, HPEKs were cultured starting at passage 4 by seeding at an initial density of 4×104 cells/cm² in CnT-07 medium (CELLnTEC, #CnT-07) at 37°C and 5% CO₂. Once the cells reached 80% confluency, they were detached from the culture dish using Accutase Cell Detachment Solution (CELLnTEC, #CnT-Accutase-100) and seeded for experiments. For experiments cells were seeded at passage 5 at a density of 4×104 cells/cm². Upon reaching 85% confluency, calcium concentration was increased to 1.2 mM using CaCl₂ (Merck, #102382) to establish cell-cell adhesion and synchronize differentiation. Six hours after the calcium switch, cells were stimulated using PX43 or hIgG (control antibody). Then cells were harvested at 5, 10, 24, and 48 hours post scFv or antibody stimulation.

value: Human Primary Epidermis Keratinocyte

tag: treatment

tag: replicate

value: replicate 3


title: R57-PBMC-3M_TCRB

description: Library name: R57-PBMC-3M_TCRB


title: Het (Q140) KI X Msh2-/- Striatum female mRNA rep4 [Msh2]

description:
MRQ34_2str
mRNA

value: Corpus Striatum


title: 2D_PX43_48h_2

description:
Library name: 2D_PX43_48h_2
PX43_48h_2

tag: time

value: replicate 2


title: 2D_PX43_48h_1

description:
Library name: 2D_PX43_48h_1
PX43_48h_1

value: replicate 1


title: Het (Q140) KI X Msh2-/- Striatum female mRNA rep2 [Msh2]

description:
MRQ29_5str
mRNA

value: Het (Q140) KI X Msh2-/-

value: 12 months


title: R57-PBMC-PreTx_TCRB

description: Library name: R57-PBMC-PreTx_TCRB

value: PreTx

value: Borderline


title: Het (Q140) KI X Msh2-/- Striatum male mRNA rep2 [Msh2]

description:
MRQ33_3str
mRNA

value: male


title: 2D_hIgG_48h_3

description:
Library name: 2D_hIgG_48h_3
hIgG_48h_3

value: hIgG


title: Het (Q140) KI X Msh2-/- Striatum female mRNA rep1 [Msh2]

description:
MRQ26_1str
mRNA


title: 2D_hIgG_48h_1

description:
Library name: 2D_hIgG_48h_1
hIgG_48h_1


title: 2D_hIgG_48h_2

description:
Library name: 2D_hIgG_48h_2
hIgG_48h_2


title: R57-Kidney-3M_TCRB

description: Library name: R57-Kidney-3M_TCRB

value: Kidney


title: R57-Kidney-PreTx_TCRB

description: Library name: R57-Kidney-PreTx_TCRB


title: R57-CD8-DRTC_TCRB

description: Library name: R57-CD8-DRTC_TCRB

value: DRTC


title: R57-CD4-DRTC_TCRB

description: Library name: R57-CD4-DRTC_TCRB


title: 2D_PX43_24h_3

description:
Library name: 2D_PX43_24h_3
PX43_24h_3


title: R53-Urine_Pellet-12M_TCRB

description: Library name: R53-Urine_Pellet-12M_TCRB

value: Urine Pellet

value: 12 Month

value: Stable

value: Campath


title: R53-Urine_Pellet-6M_TCRB

description: Library name: R53-Urine_Pellet-6M_TCRB

value: 6 Month


title: R53-Urine_Pellet-3M_TCRB

description: Library name: R53-Urine_Pellet-3M_TCRB

value: 3 Month


title: Het (Q140) KI X Msh2-/- Cortex male mRNA rep3 [Msh2]

description:
MRQ40_5CTX
mRNA

value: Cerebral Cortex


description: Library name: R53-Urine_Pellet-for_cause_May_9_2019_TCRB

value: 1.7 Months


title: 2D_PX43_24h_2

description:
Library name: 2D_PX43_24h_2
PX43_24h_2

value: Human Primary Epidermis Keratinocyte

value: replicate 2


title: Het (Q140) KI X Msh2-/- Cortex male mRNA rep2 [Msh2]

description:
MRQ34_2CTX
mRNA

value: Het (Q140) KI X Msh2-/-

value: 12 months


title: 2D_hIgG_24h_3

description:
Library name: 2D_hIgG_24h_3
hIgG_24h_3

value: replicate 3


title: R53-Urine_Pellet-2W_TCRB

description: Library name: R53-Urine_Pellet-2W_TCRB

value: 2 Week


title: R53-PBMC-for_cause_May_9_19_TCRB

description: Library name: R53-PBMC-for_cause_May_9_19_TCRB

value: PBMC


title: Het (Q140) KI X Msh2-/- Cortex male mRNA rep1 [Msh2]

description:
MRQ26_1CTX
mRNA

value: male


title: Het (Q140) KI X Msh2-/- Cortex female mRNA rep4 [Msh2]

description:
MRQ33_3CTX
mRNA

value: female


title: R57-Kidney-12M_TCRB

description: Library name: R57-Kidney-12M_TCRB

value: Kidney

value: Borderline

value: Simulect


title: R53-PBMC-3M_TCRB

description: Library name: R53-PBMC-3M_TCRB

value: Stable

value: Campath


title: R53-PBMC-6M_TCRB

description: Library name: R53-PBMC-6M_TCRB

value: 6 Month


title: 2D_hIgG_24h_2

description:
Library name: 2D_hIgG_24h_2
hIgG_24h_2

value: hIgG


title: Het (Q140) KI X Msh2-/- Cortex female mRNA rep3 [Msh2]

description:
MRQ33_2CTX
mRNA

value: Cerebral Cortex


title: R53-Kidney-12M_TCRB

description: Library name: R53-Kidney-12M_TCRB

value: 12 Month


title: R53-PBMC-PreTx_TCRB

description: Library name: R53-PBMC-PreTx_TCRB

value: PreTx


title: R53-Kidney-_for_cause_May_9_2019_TCRB

description: Library name: R53-Kidney-_for_cause_May_9_2019_TCRB

value: 1.7 Months


title: Het (Q140) KI X Msh2-/- Cortex male mRNA rep4 [Msh2]

description:
MRQ46_2CTX
mRNA

value: Het (Q140) KI X Msh2-/-

value: 12 months


title: R53-Kidney-PreTx_TCRB

description: Library name: R53-Kidney-PreTx_TCRB


title: 2D_hIgG_24h_1

description:
Library name: 2D_hIgG_24h_1
hIgG_24h_1

value: Human Primary Epidermis Keratinocyte

value: replicate 1


title: Het (Q140) KI X Msh2-/- Cortex female mRNA rep1 [Msh2]

description:
MRQ29_5CTX
mRNA


title: 2D_PX43_10h_3

description:
Library name: 2D_PX43_10h_3
PX43_10h_3

value: replicate 3


title: R53-CD8-DRTC_TCRB

description: Library name: R53-CD8-DRTC_TCRB

value: DRTC


title: 2D_PX43_24h_1

description:
Library name: 2D_PX43_24h_1
PX43_24h_1


title: R53-CD4-DRTC_TCRB

description: Library name: R53-CD4-DRTC_TCRB


title: R52-Urine_Pellet-6M_TCRB

description: Library name: R52-Urine_Pellet-6M_TCRB

value: Urine Pellet


title: R52-Urine_Pellet-3M_TCRB

description: Library name: R52-Urine_Pellet-3M_TCRB

value: 3 Month

value: Borderline


title: R52-PBMC-12M_TCRB

description: Library name: R52-PBMC-12M_TCRB

value: PBMC

value: Simulect


title: R52-PBMC-6M_TCRB

description: Library name: R52-PBMC-6M_TCRB

value: 6 Month


title: 2D_hIgG_10h_3

description:
Library name: 2D_hIgG_10h_3
hIgG_10h_3

value: hIgG


title: Msh2-/- Striatum male mRNA rep3 [Msh2]

description:
MRQ39_4str
mRNA

value: Corpus Striatum

value: male


title: 2D_hIgG_10h_2

description:
Library name: 2D_hIgG_10h_2
hIgG_10h_2

value: replicate 2


title: R52-PBMC-3M_TCRB

description: Library name: R52-PBMC-3M_TCRB


title: 2D_PX43_10h_1

description:
Library name: 2D_PX43_10h_1
PX43_10h_1


title: Msh2-/- Striatum male mRNA rep2 [Msh2]

description:
MRQ36_2str
mRNA


title: R52-Kidney-3M_TCRB

description: Library name: R52-Kidney-3M_TCRB

value: Kidney


title: Het (Q140) KI X Msh2-/- Cortex female mRNA rep2 [Msh2]

description:
MRQ33_1CTX
mRNA

value: Cerebral Cortex

value: Het (Q140) KI X Msh2-/-

value: female


title: 2D_hIgG_10h_1

description:
Library name: 2D_hIgG_10h_1
hIgG_10h_1

value: Human Primary Epidermis Keratinocyte

value: replicate 1


title: R53-PBMC-12M_TCRB

description: Library name: R53-PBMC-12M_TCRB

value: 12 Month

value: Stable

value: Campath


title: R52-Kidney-12M_TCRB

description: Library name: R52-Kidney-12M_TCRB

value: Borderline


title: R52-Kidney-PreTx_TCRB

description: Library name: R52-Kidney-PreTx_TCRB

value: PreTx


title: Msh2-/- Striatum male mRNA rep1 [Msh2]

description:
MRQ24_5str
mRNA

value: 12 months


title: R52-PBMC-PreTx_TCRB

description: Library name: R52-PBMC-PreTx_TCRB

value: PBMC

value: Simulect


title: R52-CD8-DRTC_TCRB

description: Library name: R52-CD8-DRTC_TCRB

value: DRTC


title: 2D_PX43_5h_3

description:
Library name: 2D_PX43_5h_3
PX43_5h_3

value: replicate 3


title: R49-Urine_Pellet-6M_TCRB

description: Library name: R49-Urine_Pellet-6M_TCRB

value: Urine Pellet

value: 6 Month


title: R52-CD4-DRTC_TCRB

description: Library name: R52-CD4-DRTC_TCRB


title: 2D_PX43_5h_2

description:
Library name: 2D_PX43_5h_2
PX43_5h_2

value: replicate 2


title: 2D_PX43_10h_2

description:
Library name: 2D_PX43_10h_2
PX43_10h_2


title: Msh2-/- Striatum male mRNA rep5 [Msh2]

description:
MRQ55_1str
mRNA

value: Corpus Striatum

value: male


title: Msh2-/- Striatum female mRNA rep2 [Msh2]

description:
MRQ53_2str
mRNA

value: female


title: 2D_PX43_5h_1

description:
Library name: 2D_PX43_5h_1
PX43_5h_1

value: Human Primary Epidermis Keratinocyte

value: replicate 1


title: R49-Urine_Pellet-2W_TCRB

description: Library name: R49-Urine_Pellet-2W_TCRB

value: 2 Week

value: Stable


title: R49-Urine_Pellet-3M_TCRB

description: Library name: R49-Urine_Pellet-3M_TCRB

value: 3 Month


title: Msh2-/- Striatum male mRNA rep4 [Msh2]

description:
MRQ49_1str
mRNA


title: Msh2-/- Striatum female mRNA rep1 [Msh2]

description:
MRQ16_4str
mRNA


description: Library name: R49-Urine_Pellet-for_cause_Mar_19_2019_TCRB

value: 5 days


title: R49-PBMC-6M_TCRB

description: Library name: R49-PBMC-6M_TCRB


title: R49-PBMC-for_cause_Mar_19_19_TCRB

description: Library name: R49-PBMC-for_cause_Mar_19_19_TCRB


title: Msh2-/- Cortex male mRNA rep4 [Msh2]

description:
MRQ55_4CTX
mRNA

value: Cerebral Cortex

value: 12 months


title: Msh2-/- Cortex male mRNA rep3 [Msh2]

description:
MRQ55_1CTX
mRNA


title: R49-PBMC-PreTx_TCRB

description: Library name: R49-PBMC-PreTx_TCRB

value: PBMC

value: PreTx

value: Simulect


title: R49-Kidney-_for_cause_Mar_18_2019_TCRB

description: Library name: R49-Kidney-_for_cause_Mar_18_2019_TCRB

value: Kidney

value: 4 days


title: Msh2-/- Cortex male mRNA rep2 [Msh2]

description:
MRQ53_2CTX
mRNA


title: R49-CD8-DRTC_TCRB

description: Library name: R49-CD8-DRTC_TCRB

value: DRTC


title: Msh2-/- Cortex male mRNA rep1 [Msh2]

description:
MRQ24_5CTX
mRNA


title: R48-Urine_Pellet-12M_TCRB

description: Library name: R48-Urine_Pellet-12M_TCRB

value: Urine Pellet

value: 12 Month

value: solumedrol


title: Msh2-/- Cortex female mRNA rep4 [Msh2]

description:
MRQ49_1CTX
mRNA

value: female


title: R49-Kidney-PreTx_TCRB

description: Library name: R49-Kidney-PreTx_TCRB


title: iPSC_TSZ_3

city: Cambridge

first: Timothy

middle: R

last: Hammond

state: MA

address: 350 Water Street

institute: Sanofi

description: Library name: s8

data_processing:
cellranger-5.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: .h5 matrix files

molecule: polyA RNA

source_name: iPSC tri-culture

extract_protocol:
Four hours after treatment, cells were washed twice with PBS then treated with 0.25% trypsin-EDTA solution (Sigma-Aldrich, T4049) and transcription/translation inhibitors: 5 μg/mL actinomycin D (Sigma-Aldrich, A1410), 10 μM triptolide (Sigma-Aldrich, T3652), and 27.1 μg/mL anisomycin (Sigma-Aldrich, A9789) for 6 minutes at 37 °C in a 5% CO2 incubator. Then, 1 volume of PBS with 2% FBS (Gibco, A38400-01), the transcription/translation inhibitors, and 1:100 DNAse (Worthington, LS002007) was added to quench. Cells from two wells were combined for each technical replicate and put through 40 μm cell strainers (BD Falcon, 352235). Cells were counted and spun at 4 °C for 5 minutes at 1500 rpm. Supernatant was removed and cells were resuspended at 1,000 cells/μL in ice-cold PBS. Cells were loaded onto the 10x Genomics Next GEM Single Cell 3′ v3.1 sample chip and run following the manufacturerʼs protocols.
10x Genomics Next GEM Single Cell 3′ v3.1

value: iPSC tri-culture


title: iPSC_TSZ+GSK547_3

description: Library name: s10


title: R49-PBMC-3M_TCRB

description: Library name: R49-PBMC-3M_TCRB


title: R48-Urine_Pellet-3M_TCRB

description: Library name: R48-Urine_Pellet-3M_TCRB


title: 2D_hIgG_5h_1

description:
Library name: 2D_hIgG_5h_1
hIgG_5h_1

value: Human Primary Epidermis Keratinocyte

value: hIgG

value: replicate 1


title: Msh2-/- Cortex female mRNA rep2 [Msh2]

description:
MRQ36_2CTX
mRNA


title: iPSC_GSK547_2

description: Library name: s7


title: R49-CD4-DRTC_TCRB

description: Library name: R49-CD4-DRTC_TCRB

value: Stable


title: 2D_hIgG_5h_2

description:
Library name: 2D_hIgG_5h_2
hIgG_5h_2

value: replicate 2


title: R48-Urine_Pellet-2W_TCRB

description: Library name: R48-Urine_Pellet-2W_TCRB

value: 2 Week


title: iPSC_DMSO_2

description: Library name: s6


title: Msh2-/- Cortex female mRNA rep3 [Msh2]

description:
MRQ39_4CTX
mRNA

value: Cerebral Cortex

value: 12 months


title: Msh2-/- Striatum female mRNA rep3 [Msh2]

description:
MRQ55_4str
mRNA

value: Corpus Striatum


title: R48-Urine_Pellet-6M_TCRB

description: Library name: R48-Urine_Pellet-6M_TCRB

value: 6 Month


title: R48-PBMC-3M_TCRB

description: Library name: R48-PBMC-3M_TCRB

value: PBMC

value: 3 Month


title: R48-PBMC-12M_TCRB

description: Library name: R48-PBMC-12M_TCRB


title: Msh2-/- Cortex female mRNA rep1 [Msh2]

description:
MRQ16_4CTX
mRNA


title: R48-PBMC-6M_TCRB

description: Library name: R48-PBMC-6M_TCRB


title: R48-PBMC-PreTx_TCRB

description: Library name: R48-PBMC-PreTx_TCRB

value: PreTx


title: iPSC_TSZ+GSK547_2

description: Library name: s9


title: iPSC_TSZ_2

description: Library name: s4


title: WT Striatum male mRNA rep4 [Mlh1]

description:
MLQ84_4_STR
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: Semicolon-delimited csv files include FPKM and Count values for each Sample.

value: Wild type

value: 6 months

value: male


title: R48-Kidney-_for_cause_Jan_2_2020_TCRB

description: Library name: R48-Kidney-_for_cause_Jan_2_2020_TCRB

value: Kidney

value: 10.7 Months

value: solumedrol


title: WT Striatum male mRNA rep3 [Mlh1]

description:
MLQ76_2_STR
mRNA


title: R48-Kidney-3M_TCRB

description: Library name: R48-Kidney-3M_TCRB


title: iPSC_TSZ_1

description: Library name: s3

value: iPSC tri-culture


title: R48-CD8-DRTC_TCRB

description: Library name: R48-CD8-DRTC_TCRB

value: DRTC

value: Stable


title: WT Striatum male mRNA rep2 [Mlh1]

description:
MLQ73_5_STR
mRNA


title: R46-Urine_Pellet-12M_TCRB

description: Library name: R46-Urine_Pellet-12M_TCRB

value: Urine Pellet

value: 12 Month

value: Campath


title: WT Striatum male mRNA rep1 [Mlh1]

description:
MLQ65_5_STR
mRNA

value: Corpus Striatum


title: R48-CD4-DRTC_TCRB

description: Library name: R48-CD4-DRTC_TCRB


title: R48-PBMC-for_cause_Jan_2_20_TCRB

description: Library name: R48-PBMC-for_cause_Jan_2_20_TCRB


title: R46-Urine_Pellet-6M_TCRB

description: Library name: R46-Urine_Pellet-6M_TCRB

value: 6 Month


title: iPSC_DMSO_1

description: Library name: s1


title: R46-Urine_Pellet-2W_TCRB

description: Library name: R46-Urine_Pellet-2W_TCRB

value: 2 Week


title: WT Striatum female mRNA rep3 [Mlh1]

description:
MLQ73_2BC_STR
mRNA

value: female


title: iPSC_TSZ+GSK547_1

description: Library name: s5


description: Library name: R48-Urine_Pellet-for_cause_Jan_2_2020_TCRB


title: R46-Urine_Pellet-3M_TCRB

description: Library name: R46-Urine_Pellet-3M_TCRB

value: 3 Month


title: WT Striatum female mRNA rep2 [Mlh1]

description:
MLQ69_1_STR
mRNA

value: Wild type


title: R46-PBMC-12M_TCRB

description: Library name: R46-PBMC-12M_TCRB

value: PBMC


title: R46-PBMC-6M_TCRB

description: Library name: R46-PBMC-6M_TCRB


title: R46-PBMC-3M_TCRB

description: Library name: R46-PBMC-3M_TCRB


title: R46-CD8-DRTC_TCRB

description: Library name: R46-CD8-DRTC_TCRB


title: R46-CD4-DRTC_TCRB

description: Library name: R46-CD4-DRTC_TCRB


title: WT Striatum female mRNA rep4 [Mlh1]

description:
MLQ85_2_STR
mRNA

value: 6 months


title: R46-PBMC-PreTx_TCRB

description: Library name: R46-PBMC-PreTx_TCRB

value: PreTx


title: R46-Kidney-PreTx_TCRB

description: Library name: R46-Kidney-PreTx_TCRB

value: Kidney


title: R45-Urine_Pellet-6M_TCRB

description: Library name: R45-Urine_Pellet-6M_TCRB

value: Borderline


title: R45-Urine_Pellet-3M_TCRB

description: Library name: R45-Urine_Pellet-3M_TCRB


title: R45-Urine_Pellet-12M_TCRB

description: Library name: R45-Urine_Pellet-12M_TCRB


title: iPSC_GSK547_1

description: Library name: s2

value: iPSC tri-culture


title: R48-Kidney-PreTx_TCRB

description: Library name: R48-Kidney-PreTx_TCRB

value: solumedrol


title: WT Cortex male mRNA rep2 [Mlh1]

description:
MLQ73_5_CTX
mRNA

value: Cerebral Cortex

value: male


title: WT Cortex male mRNA rep4 [Mlh1]

description:
MLQ84_4_CTX
mRNA


title: R45-Urine_Pellet-2W_TCRB

description: Library name: R45-Urine_Pellet-2W_TCRB

value: Urine Pellet


title: R45-PBMC-6M_TCRB

description: Library name: R45-PBMC-6M_TCRB

value: Campath


title: R45-PBMC-12M_TCRB

description: Library name: R45-PBMC-12M_TCRB

value: 12 Month


title: R45-PBMC-3M_TCRB

description: Library name: R45-PBMC-3M_TCRB


title: WT Cortex female mRNA rep4 [Mlh1]

description:
MLQ85_2_CTX
mRNA


title: WT Striatum female mRNA rep1 [Mlh1]

description:
MLQ56_1_STR
mRNA

value: Corpus Striatum


title: WT Cortex female mRNA rep3 [Mlh1]

description:
MLQ73_2BC_CTX
mRNA


title: R45-CD8-DRTC_TCRB

description: Library name: R45-CD8-DRTC_TCRB

value: DRTC


title: R45-Kidney-PreTx_TCRB

description: Library name: R45-Kidney-PreTx_TCRB


title: R44-Urine_Pellet-12M_TCRB

description: Library name: R44-Urine_Pellet-12M_TCRB

value: Stable


title: R45-CD4-DRTC_TCRB

description: Library name: R45-CD4-DRTC_TCRB


title: WT Cortex female mRNA rep1 [Mlh1]

description:
MLQ56_1_CTX
mRNA

value: female


title: R44-Urine_Pellet-6M_TCRB

description: Library name: R44-Urine_Pellet-6M_TCRB

value: 6 Month


title: R44-Urine_Pellet-3M_TCRB

description: Library name: R44-Urine_Pellet-3M_TCRB

value: 3 Month


title: Het (Q140) KI Striatum male mRNA rep5 [Mlh1]

description:
MLQ84_2_STR
mRNA

value: Het (Q140) KI

value: 6 months


title: R44-PBMC-12M_TCRB

description: Library name: R44-PBMC-12M_TCRB

value: PBMC


title: WT Cortex male mRNA rep3 [Mlh1]

description:
MLQ76_2_CTX
mRNA

value: Wild type


title: R44-PBMC-6M_TCRB

description: Library name: R44-PBMC-6M_TCRB


title: R44-PBMC-3M_TCRB

description: Library name: R44-PBMC-3M_TCRB


title: Het (Q140) KI Striatum male mRNA rep3 [Mlh1]

description:
MLQ75_5_STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep4 [Mlh1]

description:
MLQ76_3_STR
mRNA


title: R44-PBMC-PreTx_TCRB

description: Library name: R44-PBMC-PreTx_TCRB

value: PreTx


title: R44-Kidney-12M_TCRB

description: Library name: R44-Kidney-12M_TCRB

value: Kidney


title: R44-CD8-DRTC_TCRB

description: Library name: R44-CD8-DRTC_TCRB


title: Het (Q140) KI Striatum male mRNA rep1 [Mlh1]

description:
MLQ75_1_STR
mRNA


title: R44-Kidney-PreTx_TCRB

description: Library name: R44-Kidney-PreTx_TCRB


title: R45-PBMC-PreTx_TCRB

description: Library name: R45-PBMC-PreTx_TCRB

value: Borderline


title: Het (Q140) KI Striatum male mRNA rep2 [Mlh1]

description:
MLQ15_2_STR
mRNA

value: male


title: R44-CD4-DRTC_TCRB

description: Library name: R44-CD4-DRTC_TCRB


title: R42-Urine_Pellet-12M_TCRB

description: Library name: R42-Urine_Pellet-12M_TCRB

value: Urine Pellet

value: Simulect


title: WT Cortex female mRNA rep2 [Mlh1]

description:
MLQ69_1_CTX
mRNA

value: Cerebral Cortex


title: WT Cortex male mRNA rep1 [Mlh1]

description:
MLQ65_5_CTX
mRNA


title: R42-PBMC-12M_TCRB

description: Library name: R42-PBMC-12M_TCRB

value: 12 Month


title: Het (Q140) KI Striatum female mRNA rep3 [Mlh1]

description:
MLQ85_4_STR
mRNA

value: Corpus Striatum


title: R45-Kidney-12M_TCRB

description: Library name: R45-Kidney-12M_TCRB

value: Campath


title: R42-Urine_Pellet-6M_TCRB

description: Library name: R42-Urine_Pellet-6M_TCRB

value: Stable


title: R42-PBMC-3M_TCRB

description: Library name: R42-PBMC-3M_TCRB


title: R42-Urine_Pellet-2W_TCRB

description: Library name: R42-Urine_Pellet-2W_TCRB

value: 2 Week


title: R42-Urine_Pellet-3M_TCRB

description: Library name: R42-Urine_Pellet-3M_TCRB

value: 3 Month


title: Het (Q140) KI Cortex male mRNA rep5 [Mlh1]

description:
MLQ84_2_CTX
mRNA

value: Het (Q140) KI


title: Het (Q140) KI Striatum female mRNA rep1 [Mlh1]

description:
MLQ12_4_STR
mRNA

value: 6 months

value: female


title: R42-Kidney-12M_TCRB

description: Library name: R42-Kidney-12M_TCRB


title: R44-Urine_Pellet-2W_TCRB

description: Library name: R44-Urine_Pellet-2W_TCRB


title: R42-Kidney-PreTx_TCRB

description: Library name: R42-Kidney-PreTx_TCRB


title: Het (Q140) KI Cortex male mRNA rep4 [Mlh1]

description:
MLQ76_3_CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep3 [Mlh1]

description:
MLQ75_5_CTX
mRNA


title: R42-CD4-DRTC_TCRB

description: Library name: R42-CD4-DRTC_TCRB

value: DRTC


title: R42-CD8-DRTC_TCRB

description: Library name: R42-CD8-DRTC_TCRB


title: R42-PBMC-PreTx_TCRB

description: Library name: R42-PBMC-PreTx_TCRB

value: PBMC

value: PreTx


title: 37R-Urine-pellet-3-Month_TCRB

description: Library name: 37R-Urine-pellet-3-Month_TCRB

value: Borderline


title: 37R-Urine-pellet-12-Month_TCRB

description: Library name: 37R-Urine-pellet-12-Month_TCRB


title: Het (Q140) KI Cortex male mRNA rep1 [Mlh1]

description:
MLQ75_1_CTX
mRNA

value: male


title: 37R-Urine-pellet-6-Month_TCRB

description: Library name: 37R-Urine-pellet-6-Month_TCRB

value: Urine Pellet

value: 5.6 Months


title: HepG2-IGF1R-KO_insulin-resistant-media_human-insulin-stimulation_72hr_BiolRep9

city: Copenhagen

first: Andreas

last: Constantinou

address: Malov

department: Diabetes Pharmacology, Liver & Gut Biology

country: Denmark

institute: Novo Nordisk

description: Library name: 1918125_D5

data_processing:
RNA-sequencing reads were aligned to GRCh37 using STAR and quantification was performed using Salmon.
Assembly: GRCh37
Supplementary files format and content: Comma-separated values (CSV) file with raw read counts per gene (rows) by sample (columns).

source_name: liver

growth_protocol: HepG2-IGF1R-KO cells were cultured and maintained in DMEM supplemented with 10% FBS. Medium was aspirated and replaced with fresh medium every 2-3 days. Cells were split 1:4 every 3 days by aspiration of medium, washing once with PBS and trypsinization (0.25% Trypsin-EDTA solution, #T4049, Sigma).

extract_protocol:
RNA for bulk RNA-seq was isolated using RNeasy Mini Kit with DNase treatment according to manufacturer’s instructions (Qiagen, Hilden, Germany)
The sequencing library was prepared by purification of poly-A containing mRNAs, mRNA fragmentation, strand-specific random primed cDNA synthesis, and adapter ligation and adapter specific PCR amplification using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765, New England BioLabs, Ipswich, Massachusetts, USA)

treatment_protocol: For insulin stimulation, cells were incubated with 3 nM human insulin for 18 h. For culturing in insulin resistant medium, HepG2-IGF1R-KO cells were exposed to 1 nM human insulin, 0.5 mM palmitic, linoleic, and oleic acids, and 20 mM glucose for 72 h prior to insulin stimulation.

value: liver

value: hepatocyte

value: human-insulin-stimulation

tag: medium

value: insulin-resistant

tag: batch


title: Het (Q140) KI Cortex male mRNA rep2 [Mlh1]

description:
MLQ15_2_CTX
mRNA

tag: tissue

value: Cerebral Cortex


title: 37R-Urine-pellet-2-week_TCRB

description: Library name: 37R-Urine-pellet-2-week_TCRB

tag: subject

tag: visit

value: 2 Week

value: Campath


title: Het (Q140) KI Striatum female mRNA rep2 [Mlh1]

description:
MLQ83_4_STR
mRNA

value: Corpus Striatum

value: Het (Q140) KI


title: R42-PBMC-6M_TCRB

description: Library name: R42-PBMC-6M_TCRB

value: 6 Month

tag: diagnosis 3_months

value: Stable

tag: induction

value: Simulect


title: 37R-PBMC-12-Month_TCRB

description: Library name: 37R-PBMC-12-Month_TCRB

value: PBMC

value: 12 Month


title: 37R-PBMC-6-Month_TCRB

description: Library name: 37R-PBMC-6-Month_TCRB

value: Borderline


title: HepG2-IGF1R-KO_insulin-resistant-media_human-insulin-stimulation_72hr_BiolRep8

description: Library name: 1918125_C5

tag: genotype


title: 37R-PBMC-3-Month_TCRB

description: Library name: 37R-PBMC-3-Month_TCRB

value: 3 Month


title: HepG2-IGF1R-KO_insulin-resistant-media_human-insulin-stimulation_72hr_BiolRep7

description: Library name: 1918125_B5


title: Het (Q140) KI Cortex female mRNA rep3 [Mlh1]

description:
MLQ85_4_CTX
mRNA

tag: strain/background

tag: age

value: 6 months

value: female


title: 37R-kidney-12-month_TCRB

description: Library name: 37R-kidney-12-month_TCRB

value: Kidney


title: R42-Kidney-3M_TCRB

description: Library name: R42-Kidney-3M_TCRB


title: Het (Q140) KI Cortex female mRNA rep1 [Mlh1]

description:
MLQ12_4_CTX
mRNA

tag: Sex

tag: well address


title: HepG2-IGF1R-KO_insulin-resistant-media_human-insulin-stimulation_72hr_BiolRep6

description: Library name: 1918125_H3

value: liver

tag: cell line

tag: cell type

value: hepatocyte

value: human-insulin-stimulation


title: 37R-kidney-6-month_TCRB

description: Library name: 37R-kidney-6-month_TCRB

value: 5.6 Months


title: Het (Q140) KI X Mlh1+/- Striatum male mRNA rep4 [Mlh1]

description:
MLQ65_1_STR
mRNA

value: Het (Q140) KI X Mlh1+/-

value: male


title: Het (Q140) KI Cortex female mRNA rep2 [Mlh1]

description:
MLQ83_4_CTX
mRNA

value: Cerebral Cortex

value: Het (Q140) KI


title: 37R-kidney-PreTx_TCRB

description: Library name: 37R-kidney-PreTx_TCRB

value: PreTx

value: Campath


title: HepG2-IGF1R-KO_insulin-resistant-media_human-insulin-stimulation_72hr_BiolRep5

description: Library name: 1918125_G3

tag: treatment

value: insulin-resistant


title: 37R-CD8-DRTCs

description: Library name: 37R-CD8-DRTCs

value: DRTC


title: Het (Q140) KI X Mlh1+/- Striatum male mRNA rep3 [Mlh1]

description:
MLQ63_4_STR
mRNA

value: Corpus Striatum


title: 37R-CD4-DRTCs

description: Library name: 37R-CD4-DRTCs

value: Borderline


title: HepG2-IGF1R-KO_insulin-resistant-media_human-insulin-stimulation_72hr_BiolRep4

description: Library name: 1918125_F3


title: 35R-Urine-pellet-12-Month_TCRB

description: Library name: 35R-Urine-pellet-12-Month_TCRB

value: Urine Pellet

value: 12 Month

value: Stable

value: Simulect


title: 35R-Urine-pellet-6-Month_TCRB

description: Library name: 35R-Urine-pellet-6-Month_TCRB

value: 6 Month


title: Het (Q140) KI X Mlh1+/- Striatum male mRNA rep2 [Mlh1]

description:
MLQ50_2_STR
mRNA

value: 6 months


title: HepG2-IGF1R-KO_insulin-resistant-media_human-insulin-stimulation_72hr_BiolRep3

description: Library name: 1918125_D2

value: liver

value: hepatocyte

value: human-insulin-stimulation


title: Het (Q140) KI X Mlh1+/- Striatum male mRNA rep1 [Mlh1]

description:
MLQ50_1_STR
mRNA

value: Het (Q140) KI X Mlh1+/-

value: male


title: 35R-PBMC-12-Month_TCRB

description: Library name: 35R-PBMC-12-Month_TCRB

value: PBMC


title: 35R-Urine-pellet-3-Month_TCRB

description: Library name: 35R-Urine-pellet-3-Month_TCRB

value: 3 Month


title: HepG2-IGF1R-KO_insulin-resistant-media_human-insulin-stimulation_72hr_BiolRep2

description: Library name: 1918125_C2

value: insulin-resistant


title: 35R-PBMC-6-Month_TCRB

description: Library name: 35R-PBMC-6-Month_TCRB


title: 35R-PBMC-PreTx_TCRB

description: Library name: 35R-PBMC-PreTx_TCRB

value: PreTx


title: 35R-CD8-DRTCs

description: Library name: 35R-CD8-DRTCs

value: DRTC


title: HepG2-IGF1R-KO_insulin-resistant-media_human-insulin-stimulation_72hr_BiolRep1

description: Library name: 1918125_B2


title: 37R-PBMC-PreTx_TCRB

description: Library name: 37R-PBMC-PreTx_TCRB

value: Borderline

value: Campath


title: Het (Q140) KI X Mlh1+/- Striatum female mRNA rep4 [Mlh1]

description:
MLQ85_5_STR
mRNA

value: Corpus Striatum

value: female


title: Het (Q140) KI X Mlh1+/- Striatum female mRNA rep3 [Mlh1]

description:
MLQ79_2_STR
mRNA


title: Het (Q140) KI X Mlh1+/- Striatum female mRNA rep2 [Mlh1]

description:
MLQ74_4_STR
mRNA


title: 35R-CD4-DRTCs

description: Library name: 35R-CD4-DRTCs

value: Stable

value: Simulect


title: HepG2-IGF1R-KO_insulin-resistant-media_untreated_72hr_BiolRep9

description: Library name: 1918125_A5

value: untreated


title: 34R-Urine-pellet-3-Month_TCRB

description: Library name: 34R-Urine-pellet-3-Month_TCRB

value: Urine Pellet


title: HepG2-IGF1R-KO_insulin-resistant-media_untreated_72hr_BiolRep8

description: Library name: 1918125_H4

value: liver

value: hepatocyte


title: 34R-Urine-pellet-6-Month_TCRB

description: Library name: 34R-Urine-pellet-6-Month_TCRB

value: 6 Month


title: 34R-Urine-pellet-2-week_TCRB

description: Library name: 34R-Urine-pellet-2-week_TCRB

value: 2 Week


title: HepG2-IGF1R-KO_insulin-resistant-media_untreated_72hr_BiolRep7

description: Library name: 1918125_G4


title: 34R-PBMC-12-Month_TCRB

description: Library name: 34R-PBMC-12-Month_TCRB

value: PBMC

value: 12 Month


title: Het (Q140) KI X Mlh1+/- Striatum female mRNA rep1 [Mlh1]

description:
MLQ72_1_STR
mRNA

value: Het (Q140) KI X Mlh1+/-

value: 6 months


title: 34R-PBMC-6-Month_TCRB

description: Library name: 34R-PBMC-6-Month_TCRB


title: HepG2-IGF1R-KO_insulin-resistant-media_untreated_72hr_BiolRep6

description: Library name: 1918125_E3

value: insulin-resistant


title: 34R-PBMC-3-Month_TCRB

description: Library name: 34R-PBMC-3-Month_TCRB

value: 3 Month


title: Het (Q140) KI X Mlh1+/- Cortex male mRNA rep4 [Mlh1]

description:
MLQ65_1_CTX
mRNA

value: Cerebral Cortex

value: male


title: Het (Q140) KI X Mlh1+/- Cortex male mRNA rep3 [Mlh1]

description:
MLQ63_4_CTX
mRNA


title: 34R-CD8-DRTCs

description: Library name: 34R-CD8-DRTCs

value: DRTC

value: Campath


title: 34R-PBMC-PreTx_TCRB

description: Library name: 34R-PBMC-PreTx_TCRB

value: PreTx

value: Stable


title: HepG2-IGF1R-KO_insulin-resistant-media_untreated_72hr_BiolRep5

description: Library name: 1918125_D3

value: untreated


title: 34R-CD4-DRTCs

description: Library name: 34R-CD4-DRTCs


title: Het (Q140) KI X Mlh1+/- Cortex male mRNA rep2 [Mlh1]

description:
MLQ50_2_CTX
mRNA


title: 34R-Urine-pellet-12-Month_TCRB

description: Library name: 34R-Urine-pellet-12-Month_TCRB

value: Urine Pellet


title: 32R-Urine--12-Month_TCRB

description: Library name: 32R-Urine--12-Month_TCRB


title: HepG2-IGF1R-KO_insulin-resistant-media_untreated_72hr_BiolRep4

description: Library name: 1918125_C3

value: liver

value: hepatocyte


title: Het (Q140) KI X Mlh1+/- Cortex male mRNA rep1 [Mlh1]

description:
MLQ50_1_CTX
mRNA


title: HepG2-IGF1R-KO_insulin-resistant-media_untreated_72hr_BiolRep3

description: Library name: 1918125_A2


title: 32R-Urine-02-week_TCRB

description: Library name: 32R-Urine-02-week_TCRB

value: 2 Week


title: 32R-Urine-03-Month_TCRB

description: Library name: 32R-Urine-03-Month_TCRB


title: 32R-Urine-06-Month_TCRB

description: Library name: 32R-Urine-06-Month_TCRB

value: 6 Month


title: Het (Q140) KI X Mlh1+/- Cortex female mRNA rep4 [Mlh1]

description:
MLQ85_5_CTX
mRNA

value: female


title: HepG2-IGF1R-KO_insulin-resistant-media_untreated_72hr_BiolRep2

description: Library name: 1918125_H1


title: 32R-PBMC-06-Month_TCRB

description: Library name: 32R-PBMC-06-Month_TCRB

value: PBMC


title: Het (Q140) KI X Mlh1+/- Cortex female mRNA rep3 [Mlh1]

description:
MLQ79_2_CTX
mRNA

value: Het (Q140) KI X Mlh1+/-

value: 6 months


title: 32R-PBMC--12-Month_TCRB

description: Library name: 32R-PBMC--12-Month_TCRB

value: 12 Month


title: 32R-PBMC-03-Month_TCRB

description: Library name: 32R-PBMC-03-Month_TCRB

value: 3 Month


title: HepG2-IGF1R-KO_insulin-resistant-media_untreated_72hr_BiolRep1

description: Library name: 1918125_G1

value: insulin-resistant


title: 2D_hIgG_5h_3

description:
Library name: 2D_hIgG_5h_3
hIgG_5h_3

value: Human Primary Epidermis Keratinocyte

value: hIgG

tag: replicate

value: replicate 3


title: 32R-kidney--12-Month_TCRB

description: Library name: 32R-kidney--12-Month_TCRB

value: Kidney

value: Stable

value: Campath


title: Het (Q140) KI X Mlh1+/- Cortex female mRNA rep2 [Mlh1]

description:
MLQ74_4_CTX
mRNA

value: Cerebral Cortex


title: Het (Q140) KI X Mlh1+/- Cortex female mRNA rep1 [Mlh1]

description:
MLQ72_1_CTX
mRNA


title: 32R-kidney-00-PreTx_TCRB

description: Library name: 32R-kidney-00-PreTx_TCRB

value: PreTx


title: 32R-CD8-DRTCs

description: Library name: 32R-CD8-DRTCs

value: DRTC


title: Mlh1+/- Striatum male mRNA rep4 [Mlh1]

description:
MLQ76_1_STR
mRNA

value: Corpus Striatum

value: male


title: HepG2-IGF1R-KO_normal-media_human-insulin-stimulation_72hr_BiolRep7

description: Library name: 1918125_D4

value: liver

value: hepatocyte

value: human-insulin-stimulation

value: normal

tag: time


title: 31R-Urine-pellet-12-Month_TCRB

description: Library name: 31R-Urine-pellet-12-Month_TCRB

value: Urine Pellet

value: 12 Month

value: Reject

tag: rejection episode

value: Borderline


title: Mlh1+/- Striatum male mRNA rep3 [Mlh1]

description:
MLQ63_3_STR
mRNA

value: 6 months


title: 32R-kidney-03-Month_TCRB

description: Library name: 32R-kidney-03-Month_TCRB

value: Kidney

value: 3 Month


description: Library name: 31R-Urine-pellet-for-cause-apr-19-19_TCRB

value: 5.2 Months

value: Campath


title: 31R-Urine-pellet-6-Month_TCRB

description: Library name: 31R-Urine-pellet-6-Month_TCRB

value: 6 Month


title: HepG2-IGF1R-KO_normal-media_human-insulin-stimulation_72hr_BiolRep5

description: Library name: 1918125_A3

tag: medium

tag: batch


title: Mlh1+/- Striatum male mRNA rep2 [Mlh1]

description:
MLQ61_4_STR
mRNA

tag: tissue


title: HepG2-IGF1R-KO_normal-media_human-insulin-stimulation_72hr_BiolRep6

description: Library name: 1918125_B3


title: 31R-Urine-pellet-3-Month_TCRB

description: Library name: 31R-Urine-pellet-3-Month_TCRB

tag: subject

tag: visit

value: Rejection 1


title: Mlh1+/- Striatum male mRNA rep1 [Mlh1]

description:
MLQ61_2_STR
mRNA

value: Corpus Striatum


title: 31R-Urine-pellet-2-week_TCRB

description: Library name: 31R-Urine-pellet-2-week_TCRB

value: 2 Week

tag: diagnosis 3_months

tag: induction


title: HepG2-IGF1R-KO_normal-media_human-insulin-stimulation_72hr_BiolRep4

description: Library name: 1918125_H2

value: liver

tag: genotype


title: 31R-PBMC-6-Month_TCRB

description: Library name: 31R-PBMC-6-Month_TCRB

value: PBMC


title: HepG2-IGF1R-KO_normal-media_human-insulin-stimulation_72hr_BiolRep9

description: Library name: 1918125_F4

value: hepatocyte

value: human-insulin-stimulation


title: Mlh1+/- Striatum female mRNA rep4 [Mlh1]

description:
MLQ71_4_STR
mRNA

tag: strain/background

tag: age

value: female


title: 31R-PBMC-3-Month_TCRB

description: Library name: 31R-PBMC-3-Month_TCRB


title: HepG2-IGF1R-KO_normal-media_human-insulin-stimulation_72hr_BiolRep3

description: Library name: 1918125_F1

value: normal


title: HepG2-IGF1R-KO_normal-media_human-insulin-stimulation_72hr_BiolRep8

description: Library name: 1918125_E4


title: 31R-PBMC-PreTx_TCRB

description: Library name: 31R-PBMC-PreTx_TCRB

value: PreTx

value: Reject


title: 32R-PBMC-00-PreTx_TCRB

description: Library name: 32R-PBMC-00-PreTx_TCRB

value: Stable


title: 32R-CD4-DRTCs

description: Library name: 32R-CD4-DRTCs

value: DRTC


title: HepG2-IGF1R-KO_normal-media_human-insulin-stimulation_72hr_BiolRep2

description: Library name: 1918125_E1


title: Mlh1+/- Striatum female mRNA rep2 [Mlh1]

description:
MLQ62_5_STR
mRNA

value: 6 months

tag: Sex

tag: well address


title: 31R-kidney-PreTx_TCRB

description: Library name: 31R-kidney-PreTx_TCRB

value: Kidney


title: 31R-CD8-DRTCs

description: Library name: 31R-CD8-DRTCs

value: Campath


title: HepG2-IGF1R-KO_normal-media_human-insulin-stimulation_72hr_BiolRep1

description: Library name: 1918125_D1

tag: cell line

tag: cell type


title: HepG2-IGF1R-KO_normal-media_untreated_72hr_BiolRep9

description: Library name: 1918125_C4

tag: treatment

value: untreated


title: Mlh1+/- Striatum female mRNA rep1 [Mlh1]

description:
MLQ60_1_STR
mRNA


title: 31R-CD4-DRTCs

description: Library name: 31R-CD4-DRTCs


title: 30R-Urine--12-Month_TCRB

description: Library name: 30R-Urine--12-Month_TCRB

value: Urine Pellet

value: 12 Month

value: Simulect

value: Borderline


title: 30R-Urine-06-Month_TCRB

description: Library name: 30R-Urine-06-Month_TCRB

value: 6 Month


title: Mlh1+/- Cortex male mRNA rep4 [Mlh1]

description:
MLQ76_1_CTX
mRNA

value: Cerebral Cortex

value: male


title: 31R-PBMC-12-Month_TCRB

description: Library name: 31R-PBMC-12-Month_TCRB

value: PBMC


title: 30R-Urine-02-week_TCRB

description: Library name: 30R-Urine-02-week_TCRB

value: 2 Week


title: HepG2-IGF1R-KO_normal-media_untreated_72hr_BiolRep8

description: Library name: 1918125_B4

value: liver

value: hepatocyte

value: normal

tag: time


title: Mlh1+/- Cortex male mRNA rep2 [Mlh1]

description:
MLQ61_4_CTX
mRNA


title: HepG2-IGF1R-KO_normal-media_untreated_72hr_BiolRep7

description: Library name: 1918125_A4


title: Mlh1+/- Cortex male mRNA rep3 [Mlh1]

description:
MLQ63_3_CTX
mRNA


title: 31R-PBMC-for-cause-Apr9-19_TCRB

description: Library name: 31R-PBMC-for-cause-Apr9-19_TCRB

value: 5.2 Months

value: Reject

tag: rejection episode


title: 30R-PBMC--12-Month_TCRB

description: Library name: 30R-PBMC--12-Month_TCRB


title: 30R-PBMC-06-Month_TCRB

description: Library name: 30R-PBMC-06-Month_TCRB


title: 30R-PBMC-03-Month_TCRB

description: Library name: 30R-PBMC-03-Month_TCRB

value: 3 Month

value: Rejection 1


title: 30R-PBMC-00-PreTx_TCRB

description: Library name: 30R-PBMC-00-PreTx_TCRB

value: PreTx


title: Mlh1+/- Cortex male mRNA rep1 [Mlh1]

description:
MLQ61_2_CTX
mRNA

value: 6 months


title: HepG2-IGF1R-KO_normal-media_untreated_72hr_BiolRep6

description: Library name: 1918125_G2

value: untreated

tag: medium


title: Mlh1+/- Cortex female mRNA rep4 [Mlh1]

description:
MLQ71_4_CTX
mRNA

value: female


title: HepG2-IGF1R-KO_normal-media_untreated_72hr_BiolRep5

description: Library name: 1918125_F2

tag: batch


title: Mlh1+/- Cortex female mRNA rep3 [Mlh1]

description:
MLQ64_5_CTX
mRNA

tag: tissue


title: 30R-kidney--12-Month_TCRB

description: Library name: 30R-kidney--12-Month_TCRB

value: Kidney

tag: subject

value: 12 Month

value: Simulect

value: Borderline


title: 31R-kidney-3-Month_TCRB

description: Library name: 31R-kidney-3-Month_TCRB

tag: visit

value: Campath


title: 30R-kidney-03-Month_TCRB

description: Library name: 30R-kidney-03-Month_TCRB

tag: diagnosis 3_months


title: HepG2-IGF1R-KO_normal-media_untreated_72hr_BiolRep4

description: Library name: 1918125_E2


title: HepG2-IGF1R-KO_normal-media_untreated_72hr_BiolRep3

description: Library name: 1918125_C1


title: 30R-CD4-DRTCs

description: Library name: 30R-CD4-DRTCs

value: DRTC

tag: induction


title: HepG2-IGF1R-KO_normal-media_untreated_72hr_BiolRep2

description: Library name: 1918125_B1

value: liver

tag: genotype


description: Library name: R29-EV-Urine_Pellet-for_cause_Feb_13_2020_TCRB

value: Urine Pellet

value: 2 Week

value: Stable


title: 30R-CD8-DRTCs

description: Library name: 30R-CD8-DRTCs

value: Reject


title: Mlh1+/- Cortex female mRNA rep2 [Mlh1]

description:
MLQ62_5_CTX
mRNA

value: Cerebral Cortex

tag: strain/background


title: 30R-Urine-03-Month_TCRB

description: Library name: 30R-Urine-03-Month_TCRB

value: 3 Month

value: Rejection 1


title: R29-EV-PBMC-12M_TCRB

description: Library name: R29-EV-PBMC-12M_TCRB

value: PBMC


title: Mlh1+/- Cortex female mRNA rep1 [Mlh1]

description:
MLQ60_1_CTX
mRNA

tag: age

value: 6 months


title: HepG2-IGF1R-KO_normal-media_untreated_72hr_BiolRep1

description: Library name: 1918125_A1

value: hepatocyte

value: untreated

value: normal


title: R29-EV-PBMC-for_cause_Feb_13_2020_TCRB

description: Library name: R29-EV-PBMC-for_cause_Feb_13_2020_TCRB


title: R29-EV-PBMC-PreTx_TCRB

description: Library name: R29-EV-PBMC-PreTx_TCRB

value: PreTx


title: M2.Pos.4

city: Urbana

first: Jaume

last: Amengual

address: 905 S Goodwin Ave

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina), which also trimmed adapters.
Salmon (v0.13.1) was used to quasi-map reads of the NCBI Mus musculus Annotation Release 106 transcriptome using the entire GRCm38 genome as the decoy sequence and additional options (--seqBias --gcBias --numBootstraps=30)
Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package
Gene-level counts were normalized using TMM method (edgeR v3.32.1) and genes without at least 0.4 counts per million in at least 3 samples were filtered out
Assembly: GRCm38
Supplementary files format and content: TMM-normalized, log2-tranformed (scaled.prior = 2) count per million expression values in Amengual_TMMnormValues_2021-04-25.xlsx

source_name: M2 (IL4) macrophages exposed to 1 µM retinoic acid

growth_protocol: Bone marrow cells were isolated under sterile conditions and cultured in a 5% CO2 atmosphere at 37°C for seven days in DMEM supplemented with 10% FBS, 100 U/mL penicillin, 100 µg/mL streptomycin (Corning), and 1% L‑Glutamine (Corning). For macrophage differentiation, complete growth medium was supplemented with 10 ng/mL murine M-CSF

extract_protocol:
After treatments, cells were washed with PBS and lysed with TRI reagent. RNA was isolated using Direct-zol RNA Microprep kit according to the manufacturer’s instructions, including DNase I treatment to prevent DNA contamination. RNA concentration was quantified using NanoDrop 2000 and its integrity was assessed using 2100 Bioanalyzer Instrument.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a NovaSeq 6000

treatment_protocol: BMDMs were supplemented with 20 ng/mL IL4 for 24 hours or the same medium without IL4 (control medium). Cells were then washed with PBS and treated for six hours with either 1 μM all-trans retinoic acid or DMSO alone as vehicle control.

value: Bone-marrow derived macrophages

tag: strain

value: Wild-type

tag: Sex

value: Male

tag: pre-treatment

value: Interleukin 4

tag: pre-treatment time

value: 24 hours

value: Retinoic acid

tag: treatment time

value: 6 hours


description: Library name: R29-EV-Kidney-for_cause_Feb_13_2020_TCRB

value: Kidney

value: 2 Week

value: Stable

value: Campath


title: MCF7,Hypoxia(INPUT)

city: Shenzhen

first: Rui

last: Li

address: Lishui street

country: China

institute: Peking university

description:
Library name: MCF7,INPUT,hypoxia
INPUT

data_processing:
Raw sequencing data were processed using Novogene's standard bioinformatics pipeline.
Sequencing reads were aligned to the human reference genome (hg38) using Bowtie2.
Peaks were called using MACS2 (Model-Based Analysis of ChIP-Seq).
Differential peak analysis was performed to identify hypoxia-induced changes.
Quality control metrics, including read alignment statistics and peak enrichment analysis, were conducted.
Assembly: hg38 (GRCh38)
Supplementary files format and content: BigWig files for signal tracks.

source_name: Breast

growth_protocol: MCF7 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS and 1% GlutaMAX under normoxic (21% O2) or hypoxic (1% O2) conditions.

extract_protocol:
Chromatin was extracted using the SimpleChIP Enzymatic Chromatin IP Kit with magnetic beads (Cell Signaling Technology, #9003), following the manufacturer’s protocol.
Libraries were prepared by Novogene (Sacramento, CA, USA) following their standard ChIP-Seq protocol.

treatment_protocol: Cells were treated with hypoxia (1% O2) for 24 hours prior to chromatin extraction.

value: Breast

tag: cell line

tag: cell type

value: Epithelial

value: WT

tag: treatment

value: Hypoxia (1% O2 for 24h)


title: R29-EV-CD4-DRTC_TCRB

description: Library name: R29-EV-CD4-DRTC_TCRB

value: DRTC


title: 30R-kidney-00-PreTx_TCRB

description: Library name: 30R-kidney-00-PreTx_TCRB

value: PreTx

value: Reject

value: Simulect


title: M2.Pos.2

value: Bone-marrow derived macrophages

value: Wild-type

value: Male


title: R29-EV-CD8-DRTC_TCRB

description: Library name: R29-EV-CD8-DRTC_TCRB


title: MCF7,H3K18L-la,Hypoxia biological replicate 3(ChIP)

description:
Library name: MCF7,ChIP,hypoxia_rep3
ChIP-Seq of H3K18L-la under hypoxia, replicate 3

tag: batch


title: R29-EV-Kidney-PreTx_TCRB

description: Library name: R29-EV-Kidney-PreTx_TCRB

tag: tissue


title: M2.Neg.4

source_name: M2 (IL4) macrophages exposed to vehicle (DMSO)

value: Interleukin 4

value: 24 hours

value: DMSO


title: MCF7,H3K18L-la,Hypoxia biological replicate 2(ChIP)

description:
Library name: MCF7,ChIP,hypoxia_rep2
ChIP-Seq of H3K18L-la under hypoxia, replicate 2


title: 29R-Urine-pellet-3-Month-feb-14-19_TCRB

description: Library name: 29R-Urine-pellet-3-Month-feb-14-19_TCRB

value: Urine Pellet

tag: subject

value: 3 Month


title: 29R-Urine-pellet-12-Month_TCRB

description: Library name: 29R-Urine-pellet-12-Month_TCRB

tag: visit

value: 12 Month

value: Stable


title: 29R-Urine-pellet-3-Month-mar-15-19_TCRB

description: Library name: 29R-Urine-pellet-3-Month-mar-15-19_TCRB

tag: diagnosis 3_months


title: MCF7,Normoxia(INPUT)

description:
Library name: MCF7,INPUT,normoxia
INPUT

value: Breast

value: Epithelial

value: Normoxia


title: MCF7,H3K18L-la,Hypoxia biological replicate 1(ChIP)

description:
Library name: MCF7,ChIP,hypoxia_rep1
ChIP-Seq of H3K18L-la under hypoxia, replicate 1

value: WT

value: Hypoxia (1% O2 for 24h)


title: 29R-Urine-pellet-6-Month_TCRB

description: Library name: 29R-Urine-pellet-6-Month_TCRB

value: 6 Month

tag: induction


title: 29R-PBMC-12-Month_TCRB

description: Library name: 29R-PBMC-12-Month_TCRB

value: PBMC

value: Simulect


title: M2.Neg.3

value: Bone-marrow derived macrophages

tag: genotype

value: Wild-type

value: 6 hours


title: 29R-PBMC-6-Month_TCRB

description: Library name: 29R-PBMC-6-Month_TCRB


description: Library name: 29R-Urine-pellet-for-cause-Nov-29-18_TCRB

value: 0.5 Month


title: 29R-PBMC-3-Month_TCRB

description: Library name: 29R-PBMC-3-Month_TCRB


title: M2.Neg.2

value: Male

value: Interleukin 4

value: 24 hours

value: DMSO


title: M0.Pos.4

source_name: M0 (naïve) macrophages exposed to 1 µM retinoic acid

value: PBS

value: Retinoic acid


title: 29R-kidney-12-month_TCRB

description: Library name: 29R-kidney-12-month_TCRB

value: Kidney

value: 12 Month

value: Stable


title: MCF7,H3K18L-la,Normoxia biological replicate 2(ChIP)

description:
Library name: MCF7,ChIP,normoxia_rep2
ChIP-Seq of H3K18L-la under normoxia, replicate 2

value: Breast

value: Epithelial

value: WT

value: Normoxia


title: 29R-kidney-3-Month_TCRB

description: Library name: 29R-kidney-3-Month_TCRB

value: 3 Month

value: Simulect


title: M0.Pos.3

value: Bone-marrow derived macrophages

value: Wild-type

value: 6 hours


title: M0.Pos.2

value: Male


title: M0.Neg.4

source_name: M0 (naïve) macrophages exposed to vehicle (DMSO)

value: 24 hours


title: 29R-kidney-PreTx_TCRB

description: Library name: 29R-kidney-PreTx_TCRB

value: PreTx


title: M2.Pos.3

value: Interleukin 4


title: MCF7,H3K18L-la,Normoxia biological replicate 1(ChIP)

description:
Library name: MCF7,ChIP,normoxia_rep1
ChIP-Seq of H3K18L-la under normoxia, replicate 1


title: 29R-CD8-DRTCs

description: Library name: 29R-CD8-DRTCs

value: DRTC


title: 29R-kidney-for-cause-nov29-18_TCRB

description: Library name: 29R-kidney-for-cause-nov29-18_TCRB

value: Kidney

value: 0.5 Month


title: Vandetanib_rep5

description:
Library name: HSOC_Vandetanib_rep5
E7

data_processing:
Raw sequencing data was pseudo-aligned against the human transcriptome (Ensembl GRCh38.105) using kallisto (v0.45.0) with 20 bootstraps. Gene expression was summarized from the scaledTPM values of the transcripts using tximport (v1.30.0).
Assembly: Ensembl GRCh38 version 105.
Supplementary files format and content: Excel file with scaled TPM values summarized to gene expression using tximport (v1.30.0)

source_name: human skin

growth_protocol: Human skin samples were incubated at 37°C in a humidified atmosphere with 5% CO₂ for up to 24 hours.

extract_protocol:
Basal keratinocytes were isolated for RNA extraction and sequencing using microdissection under an Olympus stereomicroscope. RNA was then extracted using the innuPREP RNA Mini Kit 2.0.
Illumina TruSeq Stranded Total RNA Library Prep Kit with RiboZero Plus rRNA depletion.

treatment_protocol: Human skin samples were treated with a negative control containing only the solvent or with anti-DSG1/3 scFv in combination with one of the following inhibitors: Selumetinib, GW441756, A66, BIRB796, or Vandetanib.

value: human skin

tag: replicate

value: replicate 5


title: M0.Neg.3

value: PBS

value: DMSO


title: Selumetinib_rep5

description:
Library name: HSOC_Selumetinib_rep5
E6


title: 29R-CD4-DRTCs

description: Library name: 29R-CD4-DRTCs

value: Stable


title: 28R-Urine-pellet-12-Month_TCRB

description: Library name: 28R-Urine-pellet-12-Month_TCRB

value: Urine Pellet

value: 12 Month


title: 28R-Urine-pellet-6-Month_TCRB

description: Library name: 28R-Urine-pellet-6-Month_TCRB

value: 6 Month

value: Simulect


title: 28R-Urine-pellet-3-month_TCRB

description: Library name: 28R-Urine-pellet-3-month_TCRB

value: 3 Month


title: MCF7,H3K18L-la,Normoxia biological replicate 3(ChIP)

description:
Library name: MCF7,ChIP,normoxia_rep3
ChIP-Seq of H3K18L-la under normoxia, replicate 3

value: Breast

value: Epithelial

value: WT

value: Normoxia


title: M0.Neg.2

value: Bone-marrow derived macrophages

value: Wild-type

value: Male

value: 24 hours

value: 6 hours


title: 28R-Urine-pellet-2-week_TCRB

description: Library name: 28R-Urine-pellet-2-week_TCRB

value: 2 Week


title: 28R-PBMC-12-Month_TCRB

description: Library name: 28R-PBMC-12-Month_TCRB

value: PBMC


title: Mlh1+/- Striatum female mRNA rep3 [Mlh1]

description:
MLQ64_5_STR
mRNA

value: Corpus Striatum

tag: strain/background

tag: age

value: 6 months

value: female

tag: well address


title: A66_rep5

description:
Library name: HSOC_A66_rep5
E3

value: human skin

value: replicate 5


title: 29R-PBMC-PreTx_TCRB

description: Library name: 29R-PBMC-PreTx_TCRB

value: PreTx

value: Stable

value: Simulect


title: 28R-PBMC-6-Month_TCRB

description: Library name: 28R-PBMC-6-Month_TCRB

value: 6 Month


title: 28R-PBMC-PreTx_TCRB

description: Library name: 28R-PBMC-PreTx_TCRB


title: Zip10 cKO 3

city: Sagamihara

first: Junya

last: Ito

state: Kanagawa

address: 1-17-71 Fuchinobe, Chuo-ku

department: School of Veterinary Medicine

country: Japan

institute: Azabu university

data_processing:
The FASTQ files were processed for removal of adaptor sequences, trimmed and quality-based filtered using fastp v0.23.2
The trimmed reads were removed ribosomal RNA using SortMeRNA v4.3.6
The removed reads were mapped onto the reference genome of Mus musculus (GRCm39) using STAR v2.7.10a
Mapped reads were counted using RSEM v1.3.3.
Differential expression analysis was performed in R v4.2.1 using the EdgeR v 3.38.4 package.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: uterus

extract_protocol:
RNA was isolated using RNeasy plus mini kit (Qiagen).
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: uterus

value: Zip10 conditional knockout


title: Zip10 cKO 2


title: PC_rep5

description:
Library name: HSOC_PC_rep5
E2


title: 28R-kidney-12-Month_TCRB

description: Library name: 28R-kidney-12-Month_TCRB

value: Kidney

value: 12 Month


title: 28R-kidney-PreTx_TCRB

description: Library name: 28R-kidney-PreTx_TCRB


title: Control 3

value: WT


title: NC_rep5

description:
Library name: HSOC_NC_rep5
E1


title: Zip10 cKO 1


title: Vandetanib_rep4

description:
Library name: HSOC_Vandetanib_rep4
D7

value: replicate 4


title: GW441756_rep5

description:
Library name: HSOC_GW441756_rep5
E5


title: 27R-Urine-12-Month_TCRB

description: Library name: 27R-Urine-12-Month_TCRB

value: Urine Pellet

value: Reject

value: Campath

tag: rejection episode

value: Rejection 3


title: Selumetinib_rep4

description:
Library name: HSOC_Selumetinib_rep4
D6


title: 28R-kidney-3-Month_TCRB

description: Library name: 28R-kidney-3-Month_TCRB

value: 3 Month


title: 28R-CD8-DRTCs

description: Library name: 28R-CD8-DRTCs

value: DRTC


title: BIRB796_rep5

description:
Library name: HSOC_BIRB796_rep5
E4

value: human skin

value: replicate 5


title: Control 2


title: 27R-Urine-06-Month_TCRB

description: Library name: 27R-Urine-06-Month_TCRB


title: GW441756_rep4

description:
Library name: HSOC_GW441756_rep4
D5


title: vagina with tissue particles 9

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

institute: Statens Serum Institut

description: In the processed data, the column name of this sample is P26959_101_S64

data_processing:
The quality of the FastQ reads was controlled using FastQC. Low-quality and adapter reads were trimmed by FastP. Then, the reads were aligned to the rabbit reference genome OryCyn 2.0, using HISAT2 v2.2.1. Protein coding genes were annotated based on Ensembl release 108. A count matrix was generated by featureCounts.
Assembly: OryCyn 2.0
Supplementary files format and content: tab-separated values; The first column is gene_name. The rest of the columns are samples. The first row stores the heading. The rest of the rows store the counts.

organism: Oryctolagus cuniculus

source_name: vagina

extract_protocol:
Rabbit samples were removed from the freezer, and up to 30 mg of frozen tissue was transferred to a 2 mL tube containing steel beads and 0.5 mL lysis buffer (RLT buffer Qiagen, Valencia CA; product nr. 217684) the tubes were placed in the precooled tissue-lyser LT scaffold (Qiagen, product nr. 85600) and homogenized for 50 sec over two cycles. Each cycle was accompanied by a cooling time on ice for 30 sec. RNA was isolated from the homogenized samples by using the miRNeasy Tissue/cells advance kit (Qiagen, Valencia, CA) by following the manufacturer’s instructions. In brief, genomic DNA and proteins were eliminated by using a DNA eliminator spin column, and proteins were eliminated by using a protein precipitating reagent (PPR) and Proteinase K step. The resulting RNA solutions were next applied to a RNeasy Mini Spin Column. RNAs were eluted in 30 µl volume of RNase-Free Water. The RNA concentration and quality were evaluated using Qubit 2.0 Fluorometer and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), Respectively, at Karolinska Institutet, KIGene Core Facility.
We processed the RNA samples for sequencing using the Illumina TruSeq Stranded mRNA (polyA) library kit. These fragments underwent sequencing on a NovaSeq 6000 system. We converted Bcl files to FastQ format with the assistance of the CASAVA software. The quality measurement adhered to the Sanger / phred33 / Illumina 1.8+ scale. The National Genomics Infrastructure in Genomics Production Stockholm oversaw the quality assessment, focusing on factors like yield, read quality, and any potential cross-contamination between samples. After demultiplexing and conversion to FastQ format on location, we then uploaded the data to UPPMAX for delivery.

value: vagina

value: with tissue particles

tag: animal id


title: 27R-Urine-03-Month_TCRB

description: Library name: 27R-Urine-03-Month_TCRB

value: Rejection 1


title: BIRB796_rep4

description:
Library name: HSOC_BIRB796_rep4
D4


title: 27R-Urine-02-week_TCRB

description: Library name: 27R-Urine-02-week_TCRB

value: 2 Week


title: 28R-PBMC-3-Month_TCRB

description: Library name: 28R-PBMC-3-Month_TCRB

value: PBMC

value: Stable

value: Simulect


title: vagina without particles 8

description: In the processed data, the column name of this sample is P26959_101_S63

value: without particles


title: 27R-PBMC-12-Month_TCRB

description: Library name: 27R-PBMC-12-Month_TCRB

value: 12 Month


title: 27R-PBMC--at-Rejection-may30-19_TCRB

description: Library name: 27R-PBMC--at-Rejection-may30-19_TCRB

value: 6.9 Months

value: Rejection 2


title: A66_rep4

description:
Library name: HSOC_A66_rep4
D3

value: replicate 4


title: 27R-PBMC-06-Month_TCRB

description: Library name: 27R-PBMC-06-Month_TCRB

value: 6 Month

value: Reject

value: Campath


title: vagina control 2

description: In the processed data, the column name of this sample is P26959_101_S62

value: control


title: 27R-PBMC-03-Month_TCRB

description: Library name: 27R-PBMC-03-Month_TCRB

value: 3 Month


title: 27R-PBMC-00-PreTx_TCRB

description: Library name: 27R-PBMC-00-PreTx_TCRB

value: PreTx


title: 28R-CD4-DRTCs

description: Library name: 28R-CD4-DRTCs

value: DRTC


title: vagina control 24

description: In the processed data, the column name of this sample is P26959_101_S61

value: vagina


title: 27R-kidney--at-Rejection-may-30-19_TCRB

description: Library name: 27R-kidney--at-Rejection-may-30-19_TCRB

source_name: Kidney

value: Kidney


title: NC_rep4

description:
Library name: HSOC_NC_rep4
D1

value: human skin


title: 27R-kidney-03-Month_TCRB

description: Library name: 27R-kidney-03-Month_TCRB

value: Rejection 1


title: 27R-Urine--at-Rejection-May-30-19_TCRB

description: Library name: 27R-Urine--at-Rejection-May-30-19_TCRB

value: Urine Pellet


title: Vandetanib_rep3

description:
Library name: HSOC_Vandetanib_rep3
C7

value: replicate 3


title: vagina without particles 10

description: In the processed data, the column name of this sample is P26959_101_S60

value: without particles


title: BIRB796_rep3

description:
Library name: HSOC_BIRB796_rep3
C4


title: 27R-kidney-00-PreTx_TCRB

description: Library name: 27R-kidney-00-PreTx_TCRB


title: 27R-CD4-DRTCs

description: Library name: 27R-CD4-DRTCs

source_name: DRTC


title: 26R-Urine-pellet-3-Month_TCRB

description: Library name: 26R-Urine-pellet-3-Month_TCRB


title: 27R-CD8-DRTCs

description: Library name: 27R-CD8-DRTCs


title: GW441756_rep3

description:
Library name: HSOC_GW441756_rep3
C5


title: Control 1

value: uterus

value: WT


title: PC_rep3

description:
Library name: HSOC_PC_rep3
C2


title: 26R-PBMC--at-Rejection-july30-19_TCRB

description: Library name: 26R-PBMC--at-Rejection-july30-19_TCRB

value: PBMC

value: 9.3 Months

value: Rejection 2


title: vagina sham 14

description: In the processed data, the column name of this sample is P26959_101_S58

value: sham


title: 26R-Urine-pellet-12-Month_TCRB

description: Library name: 26R-Urine-pellet-12-Month_TCRB

value: 12 Month

value: Reject

value: Campath


title: 26R-PBMC-3-Month_TCRB

description: Library name: 26R-PBMC-3-Month_TCRB

value: 4.8 Months


description: Library name: 26R-Urine-pellet-at-Rejection-July-30-19_TCRB


title: Vandetanib_rep2

description:
Library name: HSOC_Vandetanib_rep2
B7

value: replicate 2


title: 26R-PBMC-PreTx_TCRB

description: Library name: 26R-PBMC-PreTx_TCRB

value: PreTx


title: vagina with tissue particles 5

description: In the processed data, the column name of this sample is P26959_101_S59

value: vagina

value: with tissue particles


title: vagina control 16

description: In the processed data, the column name of this sample is P26959_101_S57

value: control


title: vagina control 25

description: In the processed data, the column name of this sample is P26959_101_S53


title: 26R-Urine-pellet-6-Month_TCRB

description: Library name: 26R-Urine-pellet-6-Month_TCRB

value: Urine Pellet

value: 6 Month


title: A66_rep3

description:
Library name: HSOC_A66_rep3
C3

value: human skin

value: replicate 3


title: vagina control 9

description: In the processed data, the column name of this sample is P26959_101_S56


title: PC_rep4

description:
Library name: HSOC_PC_rep4
D2

value: replicate 4


description: Library name: 26R-kidney--at-Rejection-july-30-19_TCRB

value: Kidney

value: 9.3 Months


title: 26R-Urine-pellet-2-week_TCRB

description: Library name: 26R-Urine-pellet-2-week_TCRB

value: 2 Week


title: vagina with tissue particles 13

description: In the processed data, the column name of this sample is P26959_101_S55


title: NC_rep3

description:
Library name: HSOC_NC_rep3
C1


title: 26R-CD8-DRTCs

description: Library name: 26R-CD8-DRTCs

value: DRTC


title: 26R-PBMC-6-Month_TCRB

description: Library name: 26R-PBMC-6-Month_TCRB

value: PBMC

value: Reject


title: vagina without particles 6

description: In the processed data, the column name of this sample is P26959_101_S51

value: without particles


title: GW441756_rep2

description:
Library name: HSOC_GW441756_rep2
B5

value: replicate 2


title: vagina sham 12

description: In the processed data, the column name of this sample is P26959_101_S54

value: sham


title: R25EV-Urine_Pellet-2W_TCRB

description: Library name: R25EV-Urine_Pellet-2W_TCRB

value: Borderline

value: Campath


description: Library name: 26R-Urine-pellet--at-Rejection-mar-19-19_TCRB

value: 4.8 Months

value: Rejection 1


title: Selumetinib_rep2

description:
Library name: HSOC_Selumetinib_rep2
B6


title: 26R-kidney-PreTx_TCRB

description: Library name: 26R-kidney-PreTx_TCRB

value: PreTx


title: R25-EV-PBMC-12M_TCRB

description: Library name: R25-EV-PBMC-12M_TCRB

value: 12 Month


title: R25-EV-PBMC-3M_TCRB

description: Library name: R25-EV-PBMC-3M_TCRB

value: 3 Month


title: 26R-CD4-DRTCs

description: Library name: 26R-CD4-DRTCs


title: PC_rep2

description:
Library name: HSOC_PC_rep2
B2

value: human skin


title: R25EV_3-Urine_Pellet-12M_TCRB

description: Library name: R25EV_3-Urine_Pellet-12M_TCRB

value: Urine Pellet


title: R25EV-Urine_Pellet-3M_TCRB

description: Library name: R25EV-Urine_Pellet-3M_TCRB


title: BIRB796_rep2

description:
Library name: HSOC_BIRB796_rep2
B4


title: NC_rep2

description:
Library name: HSOC_NC_rep2
B1


title: vagina with tissue particles 1

description: In the processed data, the column name of this sample is P26959_101_S50

value: vagina

value: with tissue particles


title: 21T3_8

city: Planegg-Martinstied

first: Giacomo

last: Masserdotti

address: Groshaderner Strasse 9

department: ISF

institute: Helmholtz Zentrum

data_processing:
Sequencing reads were mapped to the GRCm38.101 reference genome using STAR software version 2.6.0a.
TPM expression values based on ENSEMBL annotation version GRCm38.92 were calculated with RSEM (1.3.0).
Assembly: mm10
Supplementary files format and content: txt file

source_name: brain

growth_protocol: Transgenic mice were fed ad libitum

extract_protocol:
Single cells were sucked with an electrophysiological tip and transfer to tube for subsequent analysis.
SmartSeq2 + illumina protocols

treatment_protocol: Transgenic mice were injected with Mok-LV carrying the gRNA targeting Sox9 or Trps1 or both

value: brain

value: astrocyte

tag: grna

tag: day


title: vagina control 29

description: In the processed data, the column name of this sample is P26959_101_S52

value: control


title: R25-EV-PBMC-PreTx_TCRB

description: Library name: R25-EV-PBMC-PreTx_TCRB

value: PBMC


title: R25-EV-Kidney-3M_TCRB

description: Library name: R25-EV-Kidney-3M_TCRB

value: Kidney


title: R25-EV-Kidney-12M_TCRB

description: Library name: R25-EV-Kidney-12M_TCRB


title: A66_rep2

description:
Library name: HSOC_A66_rep2
B3

value: replicate 2


title: R25-EV-Kidney-PreTx_TCRB

description: Library name: R25-EV-Kidney-PreTx_TCRB

value: Borderline


title: 21T3_7

tag: cell type


title: 21T3_10


title: 23R-Urine-pellet-3-Month_TCRB

description: Library name: 23R-Urine-pellet-3-Month_TCRB

source_name: Urine Pellet

value: Simulect


title: Vandetanib_rep1

description:
Library name: HSOC_Vandetanib_rep1
A7

value: replicate 1


title: vagina sham 11

description: In the processed data, the column name of this sample is P26959_101_S49

tag: treatment

value: sham


title: 23R-PBMC-12-Month_TCRB

description: Library name: 23R-PBMC-12-Month_TCRB

source_name: PBMC


title: 21T3_11

tag: batch


title: 23R-Urine-pellet-12-Month_TCRB

description: Library name: 23R-Urine-pellet-12-Month_TCRB

tag: tissue


title: PC_rep1

description:
Library name: HSOC_PC_rep1
A2


title: 21T3_12


title: GW441756_rep1

description:
Library name: HSOC_GW441756_rep1
A5


title: 23R-Urine-pellet-2-week_TCRB

description: Library name: 23R-Urine-pellet-2-week_TCRB

tag: subject

value: 2 Week


title: 23R-kidney-PreTx_TCRB

description: Library name: 23R-kidney-PreTx_TCRB

tag: visit

value: PreTx


title: 21T_5_b5


title: R25-EV-CD8-DRTC_TCRB

description: Library name: R25-EV-CD8-DRTC_TCRB

value: DRTC

tag: diagnosis 3_months

value: Campath


title: 23R-Urine-pellet-6-Month_TCRB

description: Library name: 23R-Urine-pellet-6-Month_TCRB

value: Urine Pellet

value: 6 Month

tag: induction


title: 23R-PBMC-3-Month_TCRB

description: Library name: 23R-PBMC-3-Month_TCRB

value: 3 Month


title: A66_rep1

description:
Library name: HSOC_A66_rep1
A3

value: human skin


title: 23R-PBMC-PreTx_TCRB

description: Library name: 23R-PBMC-PreTx_TCRB


title: 23R-PBMC-6-Month_TCRB

description: Library name: 23R-PBMC-6-Month_TCRB


title: 22R-Urine-pellet-6-Month_TCRB

description: Library name: 22R-Urine-pellet-6-Month_TCRB

value: Stable


title: 23R-kidney-12-Month_TCRB

description: Library name: 23R-kidney-12-Month_TCRB

value: 12 Month


title: hIgG_24h_5

description: Library name: HSOC_hIgG_24h_6

treatment_protocol: The human skin was injected with either 85 µg of PX43 produced in Escherichia coli,  85 µg human IgG, 85 µg  AK23, or 85  µg  mIgG.

value: Basal Human Keratinocytes

value: hIgG

tag: time

value: replicate 5


title: 21T3_6

value: brain

value: astrocyte


title: 21T_4_b5


title: NC_rep1

description:
Library name: HSOC_NC_rep1
A1

tag: replicate

value: replicate 1


title: 22R-Urine-pellet-3-Month_TCRB

description: Library name: 22R-Urine-pellet-3-Month_TCRB

value: Simulect


title: 22R-PBMC-12-Month_TCRB

description: Library name: 22R-PBMC-12-Month_TCRB

value: PBMC


title: 21T3_5


title: 23R-CD8-DRTCs

description: Library name: 23R-CD8-DRTCs

value: Borderline


title: hIgG_24h_6

description: Library name: HSOC_hIgG_24h_5

value: replicate 6


title: 22R-Urine-pellet-12-Month_TCRB

description: Library name: 22R-Urine-pellet-12-Month_TCRB


title: 23R-CD4-DRTCs

description: Library name: 23R-CD4-DRTCs

value: DRTC


title: BIRB796_rep1

description:
Library name: HSOC_BIRB796_rep1
A4


title: hIgG_24h_2

description: Library name: HSOC_hIgG_24h_2

value: replicate 2


title: 21T_3_b5


title: R25-EV-CD4-DRTC_TCRB

description: Library name: R25-EV-CD4-DRTC_TCRB

value: Campath


title: 22R-Urine-pellet-2-week_TCRB

description: Library name: 22R-Urine-pellet-2-week_TCRB

value: Urine Pellet

value: 2 Week


title: mIgG_24h_6

description: Library name: HSOC_mIgG_24h_6

value: human skin

value: mIgG


title: 23R-kidney-3-Month_TCRB

description: Library name: 23R-kidney-3-Month_TCRB

value: Kidney

value: 3 Month


title: hIgG_24h_4

description: Library name: HSOC_hIgG_24h_4

value: Basal Human Keratinocytes

value: hIgG

value: replicate 4


title: 21T_8_b5

value: brain

value: astrocyte


title: 22R-CD8-DRTCs

description: Library name: 22R-CD8-DRTCs

value: Stable

value: Simulect


title: 21T_7_b5


title: 22R-CD4-DRTCs

description: Library name: 22R-CD4-DRTCs


title: hIgG_24h_3

description: Library name: HSOC_hIgG_24h_3

value: replicate 3


title: mIgG_24h_5

description: Library name: HSOC_mIgG_24h_5

value: replicate 5


title: 22R-kidney-3-Month_TCRB

description: Library name: 22R-kidney-3-Month_TCRB


title: R20-EV-PBMC-12M_TCRB

description: Library name: R20-EV-PBMC-12M_TCRB

value: PBMC

value: 12 Month


title: mIgG_24h_4

description: Library name: HSOC_mIgG_24h_4


title: 21T_1_b5


title: b5_21S_14


title: R20-EV-PBMC-3M_TCRB

description: Library name: R20-EV-PBMC-3M_TCRB

value: Campath


title: 22R-PBMC-3-Month_TCRB

description: Library name: 22R-PBMC-3-Month_TCRB


title: 22R-PBMC-PreTx_TCRB

description: Library name: 22R-PBMC-PreTx_TCRB

value: PreTx


title: 22R-kidney-12-Month_TCRB

description: Library name: 22R-kidney-12-Month_TCRB


title: hIgG_24h_1

description: Library name: HSOC_hIgG_24h_1

value: human skin

value: replicate 1


title: R20-EV-Kidney-12M_TCRB

description: Library name: R20-EV-Kidney-12M_TCRB

value: Kidney


title: 21T_6_b5


title: Selumetinib_rep1

description:
Library name: HSOC_Selumetinib_rep1
A6


title: 21T_2_b5


title: R20-EV-Kidney-PreTx_TCRB

description: Library name: R20-EV-Kidney-PreTx_TCRB


title: 22R-kidney-PreTx_TCRB

description: Library name: 22R-kidney-PreTx_TCRB


title: mIgG_24h_2

description: Library name: HSOC_mIgG_24h_2

value: mIgG

value: replicate 2


title: 22R-PBMC-6-Month_TCRB

description: Library name: 22R-PBMC-6-Month_TCRB

value: 6 Month


title: R20-EV-CD4-DRTC_TCRB

description: Library name: R20-EV-CD4-DRTC_TCRB

value: DRTC


title: b5_21S_13

value: brain


title: mIgG_24h_1

description: Library name: HSOC_mIgG_24h_1

value: Basal Human Keratinocytes


title: R20-EV-Urine_Pellet-12M_TCRB

description: Library name: R20-EV-Urine_Pellet-12M_TCRB

value: Urine Pellet

value: Stable


title: b5_21S_10

value: astrocyte


title: R20-EV-Urine_Pellet-2W_TCRB

description: Library name: R20-EV-Urine_Pellet-2W_TCRB

value: 2 Week


title: 20R-Urine--at-Rejection-APR19-19_TCRB

description: Library name: 20R-Urine--at-Rejection-APR19-19_TCRB

value: 6.7 Months

value: Borderline

value: simulect

value: Rejection 1


title: mIgG_24h_3

description: Library name: HSOC_mIgG_24h_3

value: human skin

value: replicate 3


title: b5_21S_12


title: b5_21S_15


title: 20R-Urine-03-Month_TCRB

description: Library name: 20R-Urine-03-Month_TCRB

value: 3 Month


title: 20R-Urine-02-week_TCRB

description: Library name: 20R-Urine-02-week_TCRB


title: 20R-PBMC-at-Rejection-Sep6-19_TCRB

description: Library name: 20R-PBMC-at-Rejection-Sep6-19_TCRB

value: PBMC

value: 11.3 Months

value: Rejection 2


title: 20R-PBMC--at-Rejection-Apr19-19_TCRB

description: Library name: 20R-PBMC--at-Rejection-Apr19-19_TCRB


title: 2AG1

value: no-gRNA

value: Adult


title: PX43_24h_3

description: Library name: HSOC_PX43_24h_3

value: Basal Human Keratinocytes


title: b5_21S_11

value: brain


title: 20R-PBMC-03-Month_TCRB

description: Library name: 20R-PBMC-03-Month_TCRB


title: b5_21S_16


title: b5_21S_17


title: R20-EV-PBMC-PreTx_TCRB

description: Library name: R20-EV-PBMC-PreTx_TCRB

value: PreTx

value: Stable

value: Campath


title: R20-EV-CD8-DRTC_TCRB

description: Library name: R20-EV-CD8-DRTC_TCRB

value: DRTC


title: 20R-PBMC-00-PreTx_TCRB

description: Library name: 20R-PBMC-00-PreTx_TCRB

value: Borderline


title: AG15

value: astrocyte


title: 20R-Urine-at-Rejection-Sep6-19_TCRB

description: Library name: 20R-Urine-at-Rejection-Sep6-19_TCRB

value: Urine Pellet

value: simulect


title: 20R-kidney--at-Rejection-apr-19-19_TCRB

description: Library name: 20R-kidney--at-Rejection-apr-19-19_TCRB

value: Kidney

value: 6.7 Months

value: Rejection 1


title: PX43_24h_1

description: Library name: HSOC_PX43_24h_1

value: human skin

value: replicate 1


title: 20R-kidney-03-Month_TCRB

description: Library name: 20R-kidney-03-Month_TCRB

value: 3 Month


title: 2AG5

value: no-gRNA

value: Adult


title: PX43_24h_6

description: Library name: HSOC_PX43_24h_6

value: Basal Human Keratinocytes

value: replicate 6


title: 20R-Urine-06-Month_TCRB

description: Library name: 20R-Urine-06-Month_TCRB

value: 6 Month


title: PX43_24h_5

description: Library name: HSOC_PX43_24h_5

value: replicate 5


title: R18-EV-Urine_Pellet-12M_TCRB

description: Library name: R18-EV-Urine_Pellet-12M_TCRB

value: 12 Month

value: Stable

value: Campath


title: AK23_24h_4

description: Library name: HSOC_AK23_24h_4

value: replicate 4


title: AG12

value: brain

value: astrocyte


title: R18-EV-Urine_Pellet-3M_TCRB

description: Library name: R18-EV-Urine_Pellet-3M_TCRB

value: Urine Pellet


title: AK23_24h_5

description: Library name: HSOC_AK23_24h_5


title: R18-EV-Urine_Pellet-2W_TCRB

description: Library name: R18-EV-Urine_Pellet-2W_TCRB

value: 2 Week


title: 2AG3


title: R18-EV-PBMC-PreTx_TCRB

description: Library name: R18-EV-PBMC-PreTx_TCRB

value: PBMC

value: PreTx


title: R18-EV-Kidney-3M_TCRB

description: Library name: R18-EV-Kidney-3M_TCRB

value: Kidney

value: 3 Month


title: R18-EV-CD8-DRTC_TCRB

description: Library name: R18-EV-CD8-DRTC_TCRB

value: DRTC


title: AK23_24h_1

description: Library name: HSOC_AK23_24h_1

value: human skin

value: Basal Human Keratinocytes

value: replicate 1


title: 2AG10

value: no-gRNA

value: Adult


title: R18-EV-CD4-DRTC_TCRB

description: Library name: R18-EV-CD4-DRTC_TCRB

value: Stable


title: PX43_24h_4

description: Library name: HSOC_PX43_24h_4


title: 18R-Urine-pellet-12-Month_TCRB

description: Library name: 18R-Urine-pellet-12-Month_TCRB

value: 12 Month

value: Campath


title: 2AG2

value: brain


title: PX43_24h_2

description: Library name: HSOC_PX43_24h_2

value: replicate 2


title: b5_21S_1

value: astrocyte


title: hIgG_10h_5

description: Library name: HSOC_hIgG_10h_5

value: hIgG

value: replicate 5


title: 2AG8


title: 18R-Urine-pellet-3-Month_TCRB

description: Library name: 18R-Urine-pellet-3-Month_TCRB

value: Urine Pellet


title: 20R-PBMC-06-Month_TCRB

description: Library name: 20R-PBMC-06-Month_TCRB

value: PBMC

value: 6 Month

value: Borderline

value: simulect


title: R18-EV-Kidney-PreTx_TCRB

description: Library name: R18-EV-Kidney-PreTx_TCRB

value: Kidney

value: PreTx


title: 2AG9

value: no-gRNA


title: 18R-PBMC-12-Month_TCRB

description: Library name: 18R-PBMC-12-Month_TCRB


title: AK23_24h_6

description: Library name: HSOC_AK23_24h_6

value: human skin

value: Basal Human Keratinocytes

value: replicate 6


title: 20R-kidney-00-PreTx_TCRB

description: Library name: 20R-kidney-00-PreTx_TCRB


title: hIgG_10h_3

description: Library name: HSOC_hIgG_10h_3

value: replicate 3


title: 20R-CD4-DRTCs

description: Library name: 20R-CD4-DRTCs

value: DRTC


title: 2AG4

value: brain

value: Adult


title: AK23_24h_3

description: Library name: HSOC_AK23_24h_3


title: R18-EV-PBMC-3M_TCRB

description: Library name: R18-EV-PBMC-3M_TCRB

value: 3 Month

value: Stable

value: Campath


title: R18-EV-Kidney-12M_TCRB

description: Library name: R18-EV-Kidney-12M_TCRB

value: 12 Month


title: AG13

value: astrocyte


title: 18R-kidney-PreTx_TCRB

description: Library name: 18R-kidney-PreTx_TCRB


title: 2AG7


title: AK23_24h_2

description: Library name: HSOC_AK23_24h_2

value: replicate 2


title: 18R-CD4-DRTCs

description: Library name: 18R-CD4-DRTCs


title: hIgG_10h_6

description: Library name: HSOC_hIgG_10h_6

value: hIgG


title: 18R-Urine-pellet-6-Month_TCRB

description: Library name: 18R-Urine-pellet-6-Month_TCRB

value: Urine Pellet

value: 6 Month


title: R17-EV-Urine_Pellet-12M_TCRB

description: Library name: R17-EV-Urine_Pellet-12M_TCRB

value: Borderline


title: 18R-Urine-pellet-2-week_TCRB

description: Library name: 18R-Urine-pellet-2-week_TCRB

value: 2 Week


title: 20R-CD8-DRTCs

description: Library name: 20R-CD8-DRTCs

value: simulect


title: 18R-PBMC-6-Month_TCRB

description: Library name: 18R-PBMC-6-Month_TCRB

value: PBMC


title: R17-EV-Urine_Pellet-3M_TCRB

description: Library name: R17-EV-Urine_Pellet-3M_TCRB


title: hIgG_10h_4

description: Library name: HSOC_hIgG_10h_4

value: human skin

value: Basal Human Keratinocytes

value: replicate 4


title: mIgG_10h_5

description: Library name: HSOC_mIgG_10h_5

value: mIgG

value: replicate 5


title: 18R-PBMC-3-Month_TCRB

description: Library name: 18R-PBMC-3-Month_TCRB

value: 3 Month

value: Stable


title: R17-EV-PBMC-12M_TCRB

description: Library name: R17-EV-PBMC-12M_TCRB

value: 12 Month

value: Campath


title: 18R-PBMC-PreTx_TCRB

description: Library name: 18R-PBMC-PreTx_TCRB

value: PreTx


title: 18R-kidney-3-Month_TCRB

description: Library name: 18R-kidney-3-Month_TCRB

value: Kidney


title: 2AG6

value: brain

value: astrocyte

value: no-gRNA

value: Adult


title: R17-EV-PBMC-3M_TCRB

description: Library name: R17-EV-PBMC-3M_TCRB

value: Borderline


title: 18R-CD8-DRTCs

description: Library name: 18R-CD8-DRTCs

value: DRTC


title: hIgG_10h_2

description: Library name: HSOC_hIgG_10h_2

value: human skin

value: hIgG

value: replicate 2


title: hIgG_10h_1

description: Library name: HSOC_hIgG_10h_1

value: Basal Human Keratinocytes

value: replicate 1


title: 2AG12


title: mIgG_10h_6

description: Library name: HSOC_mIgG_10h_6

value: mIgG

value: replicate 6


title: mIgG_10h_3

description: Library name: HSOC_mIgG_10h_3

value: replicate 3


title: R17-EV-Kidney-3M_TCRB

description: Library name: R17-EV-Kidney-3M_TCRB

value: 3 Month

value: Campath


title: R17-EV-CD8-DRTC_TCRB

description: Library name: R17-EV-CD8-DRTC_TCRB


title: R17-EV-Urine_Pellet-2W_TCRB

description: Library name: R17-EV-Urine_Pellet-2W_TCRB

value: Urine Pellet

value: 2 Week


title: 2AG11

value: brain

value: astrocyte


title: mIgG_10h_4

description: Library name: HSOC_mIgG_10h_4

value: replicate 4


title: b5_21S_6


title: 17R-PBMC-12-Month_TCRB

description: Library name: 17R-PBMC-12-Month_TCRB

value: PBMC

value: 12 Month

value: Stable

value: solumedrol


title: b5_21S_4


title: 17R-PBMC-6-Month_TCRB

description: Library name: 17R-PBMC-6-Month_TCRB

value: 6 Month


title: R17-EV-PBMC-PreTx_TCRB

description: Library name: R17-EV-PBMC-PreTx_TCRB

value: PreTx

value: Borderline


title: 17R-PBMC-3-Month_TCRB

description: Library name: 17R-PBMC-3-Month_TCRB


title: PX43_10h_4

description: Library name: HSOC_PX43_10h_4

value: human skin

value: Basal Human Keratinocytes


title: 17R-PBMC-PreTx_TCRB

description: Library name: 17R-PBMC-PreTx_TCRB


title: b5_21S_9


title: mIgG_10h_2

description: Library name: HSOC_mIgG_10h_2

value: mIgG

value: replicate 2


title: 17R-Urine-pellet-12-Month_TCRB

description: Library name: 17R-Urine-pellet-12-Month_TCRB


title: R17-EV-CD4-DRTC_TCRB

description: Library name: R17-EV-CD4-DRTC_TCRB

value: DRTC

value: Campath


title: b5_21S_5


title: b5_21S_8


title: b5_21S_3


title: 17R-Urine-pellet-3-Month_TCRB

description: Library name: 17R-Urine-pellet-3-Month_TCRB

value: Urine Pellet

value: 3 Month


title: 17R-Urine-pellet-6-Month_TCRB

description: Library name: 17R-Urine-pellet-6-Month_TCRB


title: mIgG_10h_1

description: Library name: HSOC_mIgG_10h_1

value: replicate 1


title: PX43_10h_6

description: Library name: HSOC_PX43_10h_6

value: replicate 6


title: 17R-Urine-pellet-2-week_TCRB

description: Library name: 17R-Urine-pellet-2-week_TCRB

value: 2 Week


title: b5_21S_7

value: brain

value: astrocyte


title: PX43_10h_5

description: Library name: HSOC_PX43_10h_5

value: replicate 5


title: 17R-kidney-PreTx_TCRB

description: Library name: 17R-kidney-PreTx_TCRB

value: Kidney

value: Stable

value: solumedrol


title: 17R-CD8-DRTCs

description: Library name: 17R-CD8-DRTCs


title: PX43_10h_2

description: Library name: HSOC_PX43_10h_2

value: human skin


title: 21T2_23

value: in-slice control


title: R16-EV-Urine_Pellet-12M_TCRB

description: Library name: R16-EV-Urine_Pellet-12M_TCRB

value: 12 Month


title: R16-EV-Urine_Pellet-3M_TCRB

description: Library name: R16-EV-Urine_Pellet-3M_TCRB


title: 21T2_24


title: 21T3_4


title: 17R-kidney-3-Month_TCRB

description: Library name: 17R-kidney-3-Month_TCRB


title: 17R-kidney-6-Month_TCRB

description: Library name: 17R-kidney-6-Month_TCRB

value: 6 Month


title: PX43_10h_3

description: Library name: HSOC_PX43_10h_3

value: Basal Human Keratinocytes

value: replicate 3


title: R16-EV-PBMC-PreTx_TCRB

description: Library name: R16-EV-PBMC-PreTx_TCRB

value: PBMC

value: PreTx

value: Campath


title: AK23_10h_4

description: Library name: HSOC_AK23_10h_4

value: replicate 4


title: 21T2_11


title: 21T3_1


title: AK23_10h_3

description: Library name: HSOC_AK23_10h_3


title: R16-EV-CD4-DRTC_TCRB

description: Library name: R16-EV-CD4-DRTC_TCRB

value: DRTC


title: 16R-Urine-pellet-12-Month_TCRB

description: Library name: 16R-Urine-pellet-12-Month_TCRB

value: Urine Pellet

value: Simulect


title: 16R-Urine-pellet-6-Month_TCRB

description: Library name: 16R-Urine-pellet-6-Month_TCRB


title: 21T2_8

value: brain

value: astrocyte


title: 16R-Urine-pellet-2-week_TCRB

description: Library name: 16R-Urine-pellet-2-week_TCRB

value: 2 Week

value: Stable


title: 17R-CD4-DRTCs

description: Library name: 17R-CD4-DRTCs

value: solumedrol


title: b5_21S_2


title: R16-EV-Urine_Pellet-2W_TCRB

description: Library name: R16-EV-Urine_Pellet-2W_TCRB


title: 21T3_3


title: 16R-PBMC-3-Month_TCRB

description: Library name: 16R-PBMC-3-Month_TCRB

value: 3 Month


title: R16-EV-PBMC-12M_TCRB

description: Library name: R16-EV-PBMC-12M_TCRB

value: 12 Month


title: AK23_10h_6

description: Library name: HSOC_AK23_10h_6

value: human skin

value: replicate 6


title: AK23_10h_5

description: Library name: HSOC_AK23_10h_5

value: Basal Human Keratinocytes

value: replicate 5


title: 16R-PBMC-PreTx_TCRB

description: Library name: 16R-PBMC-PreTx_TCRB

value: PBMC

value: PreTx


title: hIgG_5h_5

description: Library name: HSOC_hIgG_5h_5

value: hIgG


title: R16-EV-PBMC-3M_TCRB

description: Library name: R16-EV-PBMC-3M_TCRB

value: Campath


title: R16-EV-Kidney-PreTx_TCRB

description: Library name: R16-EV-Kidney-PreTx_TCRB

value: Kidney


title: PX43_10h_1

description: Library name: HSOC_PX43_10h_1

value: replicate 1


title: 21T2_10

value: brain


title: 15R-Urine-pellet-6-Month_TCRB

description: Library name: 15R-Urine-pellet-6-Month_TCRB

value: Urine Pellet

value: 6 Month

value: campath


title: 16R-PBMC-12-Month_TCRB

description: Library name: 16R-PBMC-12-Month_TCRB

value: Stable

value: Simulect


title: AK23_10h_1

description: Library name: HSOC_AK23_10h_1


title: 21T3_2

value: astrocyte


title: 16R-PBMC-6-Month_TCRB

description: Library name: 16R-PBMC-6-Month_TCRB


title: hIgG_5h_6

description: Library name: HSOC_hIgG_5h_6

value: human skin


title: 21T2_9


title: 21T3_15

value: in-slice control


title: hIgG_5h_2

description: Library name: HSOC_hIgG_5h_2

value: Basal Human Keratinocytes

value: replicate 2


title: b5_21S_18


title: 15R-PBMC-12-Month_TCRB

description: Library name: 15R-PBMC-12-Month_TCRB

value: PBMC

value: 12 Month


title: R16-EV-CD8-DRTC_TCRB

description: Library name: R16-EV-CD8-DRTC_TCRB

value: DRTC


title: hIgG_5h_1

description: Library name: HSOC_hIgG_5h_1

value: hIgG


title: b5_21S_21


title: hIgG_5h_4

description: Library name: HSOC_hIgG_5h_4

value: replicate 4


title: 16R-CD8-DRTCs

description: Library name: 16R-CD8-DRTCs


title: 15R-PBMC-PreTx_TCRB

description: Library name: 15R-PBMC-PreTx_TCRB

value: PreTx


title: b5_21S_20

value: brain


title: b5_21S_22


title: AK23_10h_2

description: Library name: HSOC_AK23_10h_2


title: 16R-Urine-pellet-3-Month_TCRB

description: Library name: 16R-Urine-pellet-3-Month_TCRB

value: Urine Pellet

value: 3 Month


title: 15R-Urine-pellet-12-Month_TCRB

description: Library name: 15R-Urine-pellet-12-Month_TCRB

value: campath


title: 15R-Urine-pellet-3-Month_TCRB

description: Library name: 15R-Urine-pellet-3-Month_TCRB

value: Stable


title: mIgG_5h_5

description: Library name: HSOC_mIgG_5h_5

value: mIgG

value: replicate 5


title: hIgG_5h_3

description: Library name: HSOC_hIgG_5h_3

value: human skin

value: replicate 3


title: R14-EV-Urine_Pellet-12M_TCRB

description: Library name: R14-EV-Urine_Pellet-12M_TCRB

value: Campath


title: R14-EV-Urine_Pellet-3M_TCRB

description: Library name: R14-EV-Urine_Pellet-3M_TCRB


title: R14-EV-Urine_Pellet-2W_TCRB

description: Library name: R14-EV-Urine_Pellet-2W_TCRB

value: 2 Week


title: R14-EV-PBMC-12M_TCRB

description: Library name: R14-EV-PBMC-12M_TCRB

value: PBMC


title: 21T2_4

value: astrocyte


title: 16R-CD4-DRTCs

description: Library name: 16R-CD4-DRTCs

value: DRTC

value: Simulect


title: mIgG_5h_3

description: Library name: HSOC_mIgG_5h_3

value: Basal Human Keratinocytes


title: 15R-PBMC-3-Month_TCRB

description: Library name: 15R-PBMC-3-Month_TCRB


title: b5_21S_23

value: in-slice control


title: 21T2_2

value: brain


title: 15R-CD4-DRTCs

description: Library name: 15R-CD4-DRTCs


title: b5_21S_19


title: mIgG_5h_4

description: Library name: HSOC_mIgG_5h_4

value: replicate 4


title: mIgG_5h_6

description: Library name: HSOC_mIgG_5h_6

value: replicate 6


title: 21T_9


title: mIgG_5h_2

description: Library name: HSOC_mIgG_5h_2

value: replicate 2


title: mIgG_5h_1

description: Library name: HSOC_mIgG_5h_1

value: replicate 1


title: 21T2_6


title: 15R-PBMC-6-Month_TCRB

description: Library name: 15R-PBMC-6-Month_TCRB

value: 6 Month

value: Stable

value: campath


title: 21T2_3


title: R14-EV-PBMC-3M_TCRB

description: Library name: R14-EV-PBMC-3M_TCRB

value: 3 Month


title: PX43_5h_6

description: Library name: HSOC_PX43_5h_6

value: human skin


title: R13-EV-Urine_Pellet-12M_TCRB

description: Library name: R13-EV-Urine_Pellet-12M_TCRB

value: Urine Pellet

value: 12 Month

value: Campath