title: Pt33_D_63_PBMC

city: Tampa

first: Chao

last: Wang

address: 12902 USF Magnolia Dr

department: Immunology

institute: H Lee Moffitt Cancer Center & Research Institute

description: Library name: Sample174

data_processing:
Raw data preprocessed by Adaptive Biotechnologies
Assembly: Assembly: hg18 (NCBI 36)
Supplementary files format and content: Processed data are presented in .tsv files containing the CDR3B sequences, counts and frequencies, VDJ gene usage, etc.
Library strategy: TCR-Seq

source_name: PBMC

extract_protocol:
DNA was extracted using Qiagen DNeasy Blood & Tissue Kit
Library was constructed according to manufacture's protocols (Adaptive Biotechnologies)

value: PBMC


title: Pt32_D_63_PBMC

status: Public on Mar 12 2025

type: SRA

country: USA

description: Library name: Sample173

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue


title: mTEChi, neonate, EED-cKO, cell163

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

library_source: transcriptomic single cell

data_processing:
Trimming reads to 50bp by fastx_trimmer if needed (FASTX Toolkit v0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/)
Trimming low-quality parts and adapter sequences by fastp (v0.20.0, Chen et al., fastp: an ultra-fast all-in-one FASTQ preprocessor, 2018)
Mapping to the mm10 genome using STAR (v2.7.3a, Dobin et al., STAR: ultrafast universal RNA-seq aligner, 2013) with a GTF file downloaded from http://www.ensembl.org (GRCm38.99)
Removing unmapped reads and reads mapped with low-quality scores (MAPQ < 5) by SAMtools (v1.9, Li et al., The Sequence Alignment/Map format and SAMtools, 2009)
Removing duplicated reads using Picard Tools (v2.21.1, http://broadinstitute.github.io/picard/)
Counting mapped reads on each gene using htseq-count (v0.11.2, Anders et al., HTSeq--a Python framework to work with high-throughput sequencing data, 2015) using a --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
Normalization of the count data for each cell, dividing by the total counts for that cell and multipling by the scale.factor 10000. This is then natural-log transformed using log1p
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw read counts for each gene by each sample
Supplementary files format and content: comma-separated values file includes normalized values for each gene by each sample

molecule: total RNA

organism: Mus musculus

source_name: thymus

extract_protocol:
Mouse thymus was enzymatically digested and CD45+ cells were depleted using mouse CD45 MicroBeads and a LS Column (Miltenyi Biotec). After staining with an antibody cocktail, mTEChi (DAPI-CD45-EpCAM+Ly51-MHCII-high), mTEClo (DAPI-CD45-EpCAM+Ly51-MHCII-low), and cTEC (DAPI-CD45-EpCAM+Ly51+) were sorted by FACSAria into a 96well plate containing 1uL of lysis buffer (0.3% NP40; Thermo Scientific, 1U/uL RNasinPlus; Promega in 1x Lysis Buffer, Takara)
scRNA-seq libraries were prepared by a RamDA-seq method (Hayashi et al., Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, 2018). Specifically, RNA was denatured by incubating at 70C for 90sec, then placed on ice and treated with DNaseI (0.1U/uL DNase I, Amplification Grade, Invitrogen) in 0.25xRT Buffer (PrimeScript RT reagent Kit, Takara) at 30C for 5min. Then cDNA was synthesized in 3uL of 1xRT Buffer containing RT Enzyme Mix (0.15uL of PrimeScript RT Enzyme Mix I, Takara), oligo(dT)-RT primer (0.2uM Oligo(dT)18 Primer, Thermo Scientific), T4 gene 32 protein (0.033mg/mL, NEB) and 1st-NSR primer for mouse (2.7uM, SIGMA custom DNA oligos) by incubating 10min at 25C, 10min at 30C, 30min at 37C, 5min at 50C and 5min at 94C. Next, the second strand was synthesized by adding 0.5uL of 10x NEB buffer2 (NEB), 0.125uL of dNTP mix (10mM each nt, NEB), 0.15uL of Klenow Fragment (3'→5' exo-, NEB), 0.4uL of 2nd-NSR primer for mouse (100uM, SIGMA custom DNA oligos), and 0.825uL of DW and incubating 60min at 16C followed by 10min at 70C. The double-stranded cDNA (ds-cDNA) was purified using the AMPure XP beads (Beckman Coulter) and applied for Tn5 tagmentation in a 5uL reaction with a homemade Tn5 enzyme prepared as previously described (Picelli et al., Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, 2014 and Hennig et al., Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol, 2018). After dissociating Tn5 protein by adding SDS (0.04% in final), tagmented DNA was amplified by 17 cycles of PCR using indexed primers and KAPA HiFi DNA Polymerase (Roche). The libraries were purified using AMPure XP beads (x1.0 vol), quantified by MultiNA (SHIMADZU) and pooled for next-generation sequencing.

value: thymus

tag: cell type

value: epitherial cells

value: mTEChi

tag: strain

tag: genotype

value: EED-cKO

tag: age

tag: Sex

value: unknown

tag: exp. batch


title: mTEChi, neonate, EED-cKO, cell142


title: mTEChi, neonate, EED-cKO, cell141


title: SU2C1-PD-tu-frozen-DNA

description: Library name: Sample172

source_name: Progressive Tumor

value: Progressive Tumor


title: mTEChi, neonate, EED-cKO, cell139


title: mTEChi, neonate, EED-cKO, cell159


title: Pt-31-Wk1

description: Library name: Sample171


title: mTEChi, neonate, EED-cKO, cell157


title: mTEChi, neonate, EED-cKO, cell138


title: Pt-4-Wk2

description: Library name: Sample169


title: SU2C4-PD-tu-frozen-DNA

description: Library name: Sample168


title: mTEChi, neonate, EED-cKO, cell137


title: mTEChi, neonate, EED-cKO, cell136


title: mTEChi, neonate, EED-cKO, cell135


title: Pt31_Wk16_PBMC

description: Library name: Sample167


title: mTEChi, neonate, EED-cKO, cell149


title: Pt31-AU-LN

description: Library name: Sample166

source_name: Lymph node

value: Lymph node


title: mTEChi, neonate, EED-cKO, cell134


title: SU2C-No2-bl-DNA_TCRB

description: Library name: Sample165


title: mTEChi, neonate, EED-cKO, cell133


title: mTEChi, neonate, EED-cKO, cell132


title: PT3_TIL_preREP_Pool

description: Library name: Sample164

source_name: TIL

value: TIL


title: mTEChi, neonate, EED-cKO, cell131


title: PT1_SCR_BL_HLA_lab

description: Library name: Sample163


title: mTEChi, neonate, EED-cKO, cell140


title: Pt-16-Wk64

description: Library name: Sample161


title: mTEChi, neonate, EED-cKO, cell130


title: Pt32_Wk16_PBMC

description: Library name: Sample170


title: PT16_D-35_PBMC

description: Library name: Sample159


title: mTEChi, neonate, EED-cKO, cell127


title: mTEChi, neonate, EED-cKO, cell129


title: mTEChi, neonate, EED-cKO, cell128


title: mTEChi, neonate, EED-cKO, cell126


title: mTEChi, neonate, EED-cKO, cell125


title: mTEChi, neonate, EED-cKO, cell124


title: PT14_Wk16_PBMC

description: Library name: Sample158


title: SU2C16-tu-frozen-DNA

description: Library name: Sample157

source_name: Baseline Tumor

value: Baseline Tumor


title: Pt25-Wk10

description: Library name: Sample156


title: SU2C25_D-63_PBMC_DNA

description: Library name: Sample155


title: Pt25-Wk16

description: Library name: Sample154


title: mTEChi, neonate, EED-cKO, cell121


title: mTEChi, neonate, EED-cKO, cell123


title: mTEChi, neonate, EED-cKO, cell120


title: PT2-wk-8_TCRB

description: Library name: Sample152


title: PT8_REP_TIL

description: Library name: Sample153


title: PT2-wk-6_TCRB

description: Library name: Sample162


title: mTEChi, neonate, EED-cKO, cell122


title: mTEChi, neonate, EED-cKO, cell118


title: PT3_PBMC_Wk1

description: Library name: Sample160


title: mTEChi, neonate, EED-cKO, cell116


title: PT8_Wk4_PBMC

description: Library name: Sample149


title: mTEChi, neonate, EED-cKO, cell119


title: SU2C-4-tu-DNA

description: Library name: Sample151


title: PT5_Wk1_BL

description: Library name: Sample147


title: Pt32_Wk2_PBMC

description: Library name: Sample145


title: mTEChi, neonate, EED-cKO, cell114


title: mTEChi, neonate, EED-cKO, cell112


title: PT1_REP_TIL

description: Library name: Sample146


title: mTEChi, neonate, EED-cKO, cell113


title: mTEChi, neonate, EED-cKO, cell115


title: SU2C-No2-tu-DNA_TCRB

description: Library name: Sample144


title: PT2-day-8_TCRB

description: Library name: Sample148


title: Pt9-Wk2

description: Library name: Sample143


title: mTEChi, neonate, EED-cKO, cell109


title: mTEChi, neonate, EED-cKO, cell110


title: mTEChi, neonate, EED-cKO, cell111


title: SU2C8-PD-tu-frozen-DNA

description: Library name: Sample141


title: Pt-33-Wk2

description: Library name: Sample142


title: mTEChi, neonate, EED-cKO, cell108


title: PT3_Wk60_PBMC

description: Library name: Sample140


title: mTEChi, neonate, EED-cKO, cell107


title: Pt32_D_35_PBMC

description: Library name: Sample139


title: Pt7-postTIL-wk14

description: Library name: Sample150


title: mTEChi, neonate, EED-cKO, cell117


title: PT16_Wk20_PBMC

description: Library name: Sample138


title: mTEChi, neonate, EED-cKO, cell106


title: Pt-2-Wk16

description: Library name: Sample137


title: mTEChi, neonate, EED-cKO, cell105


title: Pt-32-Wk1

description: Library name: Sample136


title: mTEChi, neonate, EED-cKO, cell104


title: mTEChi, neonate, EED-cKO, cell103


title: PT14_D-8_PBMC

description: Library name: Sample135


title: Pt-3-Wk108-FU

description: Library name: Sample134


title: mTEChi, neonate, EED-cKO, cell102


title: SU2C25-tu-frozen-DNA

description: Library name: Sample133


title: mTEChi, neonate, EED-cKO, cell101


title: Pt-4-Wk1

description: Library name: Sample131


title: SU2C-9-tu-DNA

description: Library name: Sample132


title: mTEChi, neonate, EED-cKO, cell100


title: mTEChi, neonate, EED-cKO, cell98


title: mTEChi, neonate, EED-cKO, cell99


title: Pt-16-Wk8

description: Library name: Sample130


title: mTEChi, neonate, EED-cKO, cell97


title: mTEChi, neonate, EED-cKO, cell96


title: SU2C-5-tu-DNA

description: Library name: Sample127


title: mTEChi, neonate, EED-cKO, cell94


title: PT3_PBMC_Wk26

description: Library name: Sample126


title: mTEChi, neonate, EED-cKO, cell93


title: PT7_D-63_PBMC

description: Library name: Sample125


title: Pt-14-Wk56

description: Library name: Sample124


title: mTEChi, neonate, EED-cKO, cell92


title: Pt25-D-35

description: Library name: Sample123


title: mTEChi, neonate, EED-cKO, cell91


title: mTEChi, neonate, EED-cKO, cell90


title: PT9_REP_TIL

description: Library name: Sample122


title: mTEChi, neonate, EED-cKO, cell89


title: mTEChi, neonate, EED-cKO, cell88


title: SU2C32_tu_frozen

description: Library name: Sample121


title: PT2_Wk20_PD_Tumor_TCRB

description: Library name: Sample120


title: Pt32_Wk4_PBMC

description: Library name: Sample119


title: Pt7-postTIL-wk10

description: Library name: Sample118


title: mTEChi, neonate, EED-cKO, cell87


title: mTEChi, neonate, EED-cKO, cell86


title: PT14_REP_TIL

description: Library name: Sample129


title: PT8_D-63_BL

description: Library name: Sample117


title: PT2_Wk10_BL_TCRB

description: Library name: Sample128


title: mTEChi, neonate, EED-cKO, cell84


title: mTEChi, neonate, EED-cKO, cell83


title: mTEChi, neonate, EED-cKO, cell95


title: Pt33_D_35_PBMC

description: Library name: Sample115


title: mTEChi, neonate, EED-cKO, cell82


title: PT4_D-8_PBMC

description: Library name: Sample114


title: mTEChi, neonate, EED-cKO, cell80


title: Pt-8-Wk10

description: Library name: Sample112


title: mTEChi, neonate, EED-cKO, cell79


title: Pt33_D_8_PBMC

description: Library name: Sample111


title: Pt9-Wk4

description: Library name: Sample110


title: PT9_D-63_BL

description: Library name: Sample109


title: mTEChi, neonate, EED-cKO, cell78


title: mTEChi, neonate, EED-cKO, cell77


title: mTEChi, neonate, EED-cKO, cell76


title: PT7_D-35_BL

description: Library name: Sample108


title: SU2C-14-tu-DNA

description: Library name: Sample107


title: mTEChi, neonate, EED-cKO, cell75


title: mTEChi, neonate, EED-cKO, cell85


title: mTEChi, neonate, EED-cKO, cell74


title: Pt7-PD2-tumor

description: Library name: Sample106


title: mTEChi, neonate, EED-cKO, cell73


title: PT1_D-8_PBM

description: Library name: Sample116


title: PT9_D-8_PBMC

description: Library name: Sample105


title: Pt31-AU-LUNG-Redo

description: Library name: Sample104

source_name: Lung Autopsy

value: Lung Autopsy


title: mTEChi, neonate, EED-cKO, cell72


title: PT14_D-63_PBMC

description: Library name: Sample103


title: mTEChi, neonate, EED-cKO, cell81


title: PT5_D-8_BL

description: Library name: Sample102


title: mTEChi, neonate, EED-cKO, cell70


title: mTEChi, neonate, EED-cKO, cell69


title: SU2C33_tu_frozen

description: Library name: Sample113


title: Pt-16-Wk32

description: Library name: Sample101


title: mTEChi, neonate, EED-cKO, cell68


title: mTEChi, neonate, EED-cKO, cell71


title: PT2_Wk24_EOT30_PBMC_TCRB

description: Library name: Sample100


title: Pt33_Wk8_PBMC

description: Library name: Sample99


title: mTEChi, neonate, EED-cKO, cell66


title: PT16_REP_TIL

description: Library name: Sample98


title: mTEChi, neonate, EED-cKO, cell67


title: mTEChi, neonate, EED-cKO, cell65


title: PT16_D-8_PBMC

description: Library name: Sample97


title: Pt-8-Wk52

description: Library name: Sample96


title: mTEChi, neonate, EED-cKO, cell64


title: PT8_Wk16_PBMC

description: Library name: Sample95


title: PT4_REP_TIL

description: Library name: Sample94


title: mTEChi, neonate, EED-cKO, cell62


title: Pt-5-Wk14

description: Library name: Sample93


title: mTEChi, neonate, EED-cKO, cell61


title: PT2-wk-14_TCRB

description: Library name: Sample92


title: PT1_Wk35_EOT90_PBMC

description: Library name: Sample91


title: mTEChi, neonate, EED-cKO, cell60


title: Pt31-AU-LIVER-Redo

description: Library name: Sample90

source_name: Liver Autopsy

value: Liver Autopsy


title: mTEChi, neonate, EED-cKO, cell59


title: Pt-3-postTIL-NT

description: Library name: Sample89

source_name: Normal Lung

value: Normal Lung


title: mTEChi, neonate, EED-cKO, cell58


title: mTEChi, neonate, EED-cKO, cell55


title: SU2C31_tu_frozen

description: Library name: Sample87


title: mTEChi, neonate, EED-cKO, cell57


title: mTEChi, neonate, EED-cKO, cell54


title: Pt-8-Wk1

description: Library name: Sample86


title: mTEChi, neonate, EED-cKO, cell53


title: PT4_Wk4_PBMC

description: Library name: Sample85


title: SU2C14_PD_tu_frozen

description: Library name: Sample88


title: mTEChi, neonate, EED-cKO, cell52


title: mTEChi, neonate, EED-cKO, cell63


title: mTEChi, neonate, EED-cKO, cell51


title: PT3_PBMC_D-35

description: Library name: Sample84


title: mTEChi, neonate, EED-cKO, cell49


title: mTEChi, neonate, EED-cKO, cell50


title: PT2-TILpool_TCRB

description: Library name: Sample81


title: PT25_REP_TIL

description: Library name: Sample82


title: mTEChi, neonate, EED-cKO, cell48


title: mTEChi, neonate, EED-cKO, cell47


title: Pt-5-Wk10

description: Library name: Sample80


title: PT8_D-8_PBMC

description: Library name: Sample79


title: Pt7-postTIL-Day14

description: Library name: Sample78


title: mTEChi, neonate, EED-cKO, cell56


title: Pt-16-Wk1

description: Library name: Sample77


title: mTEChi, neonate, EED-cKO, cell43


title: Pt31_D_35_PBMC

description: Library name: Sample76


title: mTEChi, neonate, EED-cKO, cell46


title: mTEChi, neonate, EED-cKO, cell45


title: PT1_Wk4_PBMC

description: Library name: Sample75


title: Pt31_Wk22_PBMC

description: Library name: Sample74


title: mTEChi, neonate, EED-cKO, cell41


title: Pt25-Wk34

description: Library name: Sample72


title: mTEChi, neonate, EED-cKO, cell40


title: mTEChi, neonate, EED-cKO, cell39


title: mTEChi, neonate, EED-cKO, cell42


title: PT16_D-63_PBMC

description: Library name: Sample73


title: Pt-2-Wk20

description: Library name: Sample71


title: SU2C-7-tu-DNA

description: Library name: Sample70


title: PT3_PBMC_Wk16

description: Library name: Sample68


title: PT3_PBMC_Wk4

description: Library name: Sample83


title: Pt31_Wk10_PBMC

description: Library name: Sample69


title: mTEChi, neonate, EED-cKO, cell37


title: mTEChi, neonate, EED-cKO, cell34


title: mTEChi, neonate, EED-cKO, cell36


title: mTEChi, neonate, EED-cKO, cell35


title: PT3_PBMC_Wk6

description: Library name: Sample66


title: mTEChi, neonate, EED-cKO, cell44


title: mTEChi, neonate, EED-cKO, cell33


title: mTEChi, neonate, EED-cKO, cell32


title: Pt-14-Wk4

description: Library name: Sample65


title: Pt7-postTIL-wk22

description: Library name: Sample64


title: Pt32-PD-tumor

description: Library name: Sample63


title: Pt9-Wk16

description: Library name: Sample62


title: mTEChi, neonate, EED-cKO, cell30


title: mTEChi, neonate, EED-cKO, cell29


title: mTEChi, neonate, EED-cKO, cell38


title: mTEChi, neonate, EED-cKO, cell31


title: Pt33_Wk4_PBMC

description: Library name: Sample61


title: PT1_Wk16_PBMC

description: Library name: Sample59


title: PT2-Aph_TCRB

description: Library name: Sample58

source_name: Apheresis

value: Apheresis


title: mTEChi, neonate, EED-cKO, cell26


title: mTEChi, neonate, EED-cKO, cell27


title: mTEChi, neonate, EED-cKO, cell28


title: Pt31_Wk2_PBMC

description: Library name: Sample60


title: PT3_TIL_postREP

description: Library name: Sample57


title: PT5_Wk17_EOT60_PBMC

description: Library name: Sample67


title: SU2C-8-tu-DNA

description: Library name: Sample56


title: mTEChi, neonate, EED-cKO, cell23


title: mTEChi, neonate, EED-cKO, cell24


title: mTEChi, neonate, EED-cKO, cell22


title: Pt33_TIL

description: Library name: Sample53


title: Pt25-Wk4

description: Library name: Sample52


title: mTEChi, neonate, EED-cKO, cell20


title: Pt-16-Wk4

description: Library name: Sample54


title: Pt31-CC

description: Library name: Sample55


title: mTEChi, neonate, EED-cKO, cell18


title: Pt9-Wk1

description: Library name: Sample48


title: mTEChi, neonate, EED-cKO, cell21


title: mTEChi, neonate, EED-cKO, cell16


title: mTEChi, neonate, EED-cKO, cell17


title: mTEChi, neonate, EED-cKO, cell15


title: Pt31_TIL

description: Library name: Sample51


title: Pt16-PD-tumor

description: Library name: Sample50


title: Pt33-PD-tumor

description: Library name: Sample49


title: mTEChi, neonate, EED-cKO, cell13


title: mTEChi, neonate, EED-cKO, cell25


title: SU2C9-PD-tu-frozen-DNA

description: Library name: Sample44


title: mTEChi, neonate, EED-cKO, cell19


title: PT16_Wk2_PBMC

description: Library name: Sample45


title: mTEChi, neonate, EED-cKO, cell14


title: mTEChi, neonate, EED-cKO, cell11


title: PT3_PBMC_Baseline

description: Library name: Sample47


title: Pt32_D_8_PBMC

description: Library name: Sample46


title: PT2-day-35_TCRB

description: Library name: Sample43


title: mTEChi, neonate, EED-cKO, cell10


title: Pt25-Wk1

description: Library name: Sample42


title: mTEChi, neonate, EED-cKO, cell9


title: Pt7-postTIL-Day-8

description: Library name: Sample41


title: mTEChi, neonate, EED-cKO, cell12


title: Pt33_Wk16_PBMC

description: Library name: Sample40


title: mTEChi, neonate, EED-cKO, cell8


title: mTEChi, neonate, EED-cKO, cell7


title: Pt25_Wk52_PBMC

description: Library name: Sample38


title: Pt25-PD-tumor

description: Library name: Sample39


title: mTEChi, neonate, EED-cKO, cell6


title: mTEChi, neonate, EED-cKO, cell4


title: Pt9-Wk52

description: Library name: Sample37


title: Pt7-postTIL-Day7

description: Library name: Sample36


title: PT14_Wk2_PBMC

description: Library name: Sample35


title: mTEChi, neonate, EED-cKO, cell2


title: PT5_Wk24_EOT90_PBMC

description: Library name: Sample32


title: mTEChi, neonate, EED-cKO, cell1


title: mTEChi, neonate, EED-cKO, cell3


title: Sample 30: Bulk, Mouse, NUGC3, shIQGAP3-3

city: Singapore

first: Mitsuhiro

last: Shimura

address: 14 Medical Drive

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. [1] Li R, Li Y, Kristiansen K, Wang J. (2008). SOAP: short oligonucleotide alignment program. Bioinformatics. 24(5):713-4
Assembly: you can refer the genome information in Dr. tom.
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: Mouse stromal cells

growth_protocol: Hs746T was cultured in DMEM (Dulbecco’s Modified Medium, Nacalai Tesque) supplemented with 10% FBS (Fetal bovine serum, biowest) and penicillin (100 IU/ml), and streptomycin (100 µg/ml) (Thermo Fisher Scientific) at 37oC in a humidified 5% CO2 incubator. The other GC cell lines were cultured similarly, except that RPMI-1640 (Nacalai Tesque) was used instead of DMEM.

extract_protocol:
Total RNA from AGS, NUGC3, Hs746T, and NUGC3 subcutaneous tumors were extracted using RNeasy Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq using MGIEasy RNA Directional Library Prep Set（1000006385，made in MGI）following manufacturer’s protocols.

treatment_protocol: ON-TARGET plus SMARTpool siRNAs targeting human IQGAP3 (Horizon Discovery, L-009077-00-0005) and a non-targeting siRNA pool (Horizon Discovery, D001810-10-50) as the control siRNA were used for the siRNA knockdown experiments. At 24 hours after seeding 1.0 x 106 AGS and NUGC3 cells and 2.0 x 106 Hs746T cells onto a 10 cm dish, cells were transfected with 35 nM of siRNAs using jetPRIME (Polypus, 101000046) according to the manufacturer’s protocol. At 72 hours after the transfection, the medium was changed and then transfected in a similar manner as a 2nd siRNA knockdown. Cells were harvested 48 hours after the 2nd siRNA transfection. Total RNA from AGS, NUGC3, Hs746T, and NUGC3 subcutaneous tumors were extracted using RNeasy Kit (Qiagen) according to the manufacturer’s instructions. RNA from AGS, NUGC3, Hs746T, and bulk tumors from NUGC3 shCtrl/shIQGAP3 (bulk RNA-sequence) were sent to Beijing Genomics Institute (BGI) for PCR amplification, transcriptome library preparation, sequencing, and analysis.

value: Mouse stromal cells

value: shIQGAP3 knockdown

tag: treatment

value: shIQGAP3 transfected stable cell


title: PT3_PBMC_D-8

description: Library name: Sample30

value: PBMC


title: Sample 29: Bulk, Mouse, NUGC3, shIQGAP3-2


title: SU2C-1-tu-DNA

description: Library name: Sample33


title: PT8_D-35_BL

description: Library name: Sample31


title: PT5_SCR_PBMC

description: Library name: Sample29


title: Pt-2-Wk2

description: Library name: Sample28


title: Sample 25: Bulk, Mouse, NUGC3, shCtrl-1

value: WT

value: shContorol transfected stable cell


title: Sample 28: Bulk, Mouse, NUGC3, shIQGAP3-1


title: PT4_Wk10_EOT60_PBMC

description: Library name: Sample25


title: Pt31-PD-tumor

description: Library name: Sample27


title: mTEChi, neonate, EED-cKO, cell5

value: thymus

value: epitherial cells

value: mTEChi


title: cTEC, neonate, WT, cell137

data_processing:
Trimming reads to 50bp by fastx_trimmer if needed (FASTX Toolkit v0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/)
Trimming low-quality parts and adapter sequences by fastp (v0.20.0, Chen et al., fastp: an ultra-fast all-in-one FASTQ preprocessor, 2018)
Mapping to the mm10 genome using STAR (v2.7.3a, Dobin et al., STAR: ultrafast universal RNA-seq aligner, 2013) with a GTF file downloaded from http://www.ensembl.org (GRCm38.99)
Removing unmapped reads and reads mapped with low-quality scores (MAPQ < 5) by SAMtools (v1.9, Li et al., The Sequence Alignment/Map format and SAMtools, 2009)
Removing duplicated reads using Picard Tools (v2.21.1, http://broadinstitute.github.io/picard/)
Counting mapped reads on each gene using htseq-count (v0.11.2, Anders et al., HTSeq--a Python framework to work with high-throughput sequencing data, 2015) using a --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
GeTMM (Gene length corrected trimmed mean of M-values) normalization by edgeR package in R programming language (Robinson et al., edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, 2010) and gene length data obtained from EMBL-EBI, as described by Smid et al. (Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons, 2018)
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw read counts for each gene by each Sample
Supplementary files format and content: comma-separated values file includes GeTMM normalized values for each gene by each Sample

value: cTEC

value: unknown


title: PT1_D-35_PBMC

description: Library name: Sample23


title: cTEC, neonate, WT, cell138


title: cTEC, neonate, WT, cell135


title: Pt31_D_63_PBMC

description: Library name: Sample22


title: PT3_Tumor_Baseline

description: Library name: Sample34


title: cTEC, neonate, WT, cell139


title: cTEC, neonate, WT, cell134


title: Pt25-D-8

description: Library name: Sample21


title: cTEC, neonate, WT, cell136


title: PT7_REP_TIL

description: Library name: Sample20

value: TIL


title: Pt-14-Wk20

description: Library name: Sample19


title: SU2C3-PD-tu-frozen-DNA

description: Library name: Sample18

value: Progressive Tumor


title: Sample 27: Bulk, Mouse, NUGC3, shCtrl-3


title: Sample 26: Bulk, Mouse, NUGC3, shCtrl-2


title: PT5_D-35_BL

description: Library name: Sample17


title: cTEC, neonate, WT, cell132


title: cTEC, neonate, WT, cell131


title: PT14_D-35_PBMC

description: Library name: Sample26


title: cTEC, neonate, WT, cell128


title: cTEC, neonate, WT, cell127


title: Pt7-postTIL-Day28

description: Library name: Sample14


title: PT3_PD_PreREP_pool_TIL

description: Library name: Sample24


title: cTEC, neonate, WT, cell126


title: PT5_REP_TIL

description: Library name: Sample13


title: cTEC, neonate, WT, cell125


title: PT4_D-63_PBMC

description: Library name: Sample11


title: cTEC, neonate, WT, cell124


title: cTEC, neonate, WT, cell133


title: cTEC, neonate, WT, cell130


title: Pt9-D-35

description: Library name: Sample9


title: PT3_PBMC_Wk10

description: Library name: Sample16


title: cTEC, neonate, WT, cell122


title: cTEC, neonate, WT, cell129


title: Pt-14-Wk10

description: Library name: Sample8


title: Pt9-Wk36

description: Library name: Sample10


title: cTEC, neonate, WT, cell119


title: Pt32_Wk10_PBMC

description: Library name: Sample5


title: PT5_Wk4_PBMC

description: Library name: Sample15


title: cTEC, neonate, WT, cell121


title: cTEC, neonate, WT, cell116


title: Pt-8-Wk28

description: Library name: Sample6


title: cTEC, neonate, WT, cell118


title: cTEC, neonate, WT, cell117


title: cTEC, neonate, WT, cell120


title: Pt-1-Wk10

description: Library name: Sample3


title: PT5_Wk2_PBMC

description: Library name: Sample7


title: Pt31_Wk4_PBMC

description: Library name: Sample2


title: PT3_PBMC_Wk50_sorted

description: Library name: Sample4


title: cTEC, neonate, WT, cell115


title: Pt25-Wk2

description: Library name: Sample12


title: cTEC, neonate, WT, cell114


title: Pt32_TIL

description: Library name: Sample1


title: cTEC, neonate, WT, cell123


title: cTEC, neonate, WT, cell113


title: 72hpf_8

city: Sagamihara

first: Makoto

last: Kashima

address: 5-1-16, Fuchinobe

institute: Aoyama Gakuinn University

data_processing:
Read 1 reads were processed with fastp (version 0.21.0) (S. Chen et al. 2018) using the following command: “ fastp --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31”. The trimmed reads were then mapped to a D. japonica transcriptome reference (An et al. 2018), using BWA mem (version 0.7.17-r1188) (W. Chen et al. 2013) with the default parameters. The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0) (Patro et al. 2017).
Assembly: Danio_rerio.GRCz11.cdna.all.fa
Supplementary files format and content: csv-delimited text file includes rawcnt values for each Sample

organism: Danio rerio

source_name: RNA from single embryo at mRNA

growth_protocol: The zebrafish (Danio rerio) strains RIKEN WT (RW) was maintained under a 14-h light/10-h dark cycle. The water temperature was kept at 28°C ± 1°C and water quality conditions were maintained according to The Zebrafish Book (University of Oregon Press) and the Guide for the Care and Use of Laboratory Animals 8th edition (National Research Council, 2011).

extract_protocol:
Each stage of  RW zebrafish embryos was dissected and the total RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s protocol.
3’ mRNA-Seq were conducted according to the Lasy-Seq ver. 1.1 protocol (https://sites.google.com/view/lasy-seq/) (Kamitani et al. 2019; Kashima et al. 2021). Briefly, total RNA was reverse transcribed using an RT primer with index and SuperScript IV reverse transcriptase (Thermo Fisher Scientific, Waltham, MA, USA). Then, all RT mixtures of the samples were pooled and purified using an equal volume of AMpure XP beads (Beckman Coulter, Brea, CA, USA) according to the manufacturer’s instructions. Second strand synthesis was conducted on the pooled samples using RnaseH (5 U/μL, Enzymatics, Beverly, MA, USA), and DNA polymerase I (10 U/μL, Enzymatics, Beverly, MA, USA). To avoid the carryover of large amounts of rRNAs, the mixture was subjected to Rnase treatment using Rnase T1 (Thermo Fisher Scientific, Waltham, MA, USA). Then, purification was conducted with a 0.8× volume of Ampure XP beads. Fragmentation, end-repair, and A-tailing were conducted using 5× WGS Fragmentation Mix (Enzymatics, Beverly, MA, USA). The Adapter for Lasy-Seq was ligated using 5× Ligation Mix (Enzymatics, Beverly, MA, USA), and the adapter-ligated DNA was purified twice with a 0.8× volume of Ampure XP beads. After optimisation of PCR cycles for library amplification by qPCR using Evagreen, 20× in water (Biotium, Fremont, CA, USA) and the QuantStudio5 Real-Time PCR System (Applied Biosystems, Waltham, MA, USA), the library was amplified using KAPA HiFi HotStart ReadyMix (KAPA BIOSYSTEMS, Wilmington, MA, USA) on the ProFlex PCR System (Applied Biosystems, Waltham, MA, USA). The amplified library was purified with an equal volume of Ampure XP beads. One microliter of the library was then used for electrophoresis using a Bioanalyzer 2100 with the Agilent High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA) to check for quality. Then, sequencing of 150-bp paired-end reads was performed using HiSeq X Ten (Illumina, San Diego, CA, USA) by Macrogen, Inc. (Seoul, Korea).

value: RW


title: 72hpf_6


title: cTEC, neonate, WT, cell110


title: cTEC, neonate, WT, cell109


title: 72hpf_7


title: cTEC, neonate, WT, cell111


title: 72hpf_5


title: 72hpf_4


title: cTEC, neonate, WT, cell106


title: cTEC, neonate, WT, cell107


title: 72hpf_1


title: 48hpf_8


title: cTEC, neonate, WT, cell104


title: 72hpf_3


title: 48hpf_7


title: 72hpf_2


title: 48hpf_6


title: cTEC, neonate, WT, cell101


title: cTEC, neonate, WT, cell102


title: cTEC, neonate, WT, cell105


title: 48hpf_4


title: 48hpf_3


title: cTEC, neonate, WT, cell100


title: cTEC, neonate, WT, cell103


title: cTEC, neonate, WT, cell112


title: 48hpf_1


title: cTEC, neonate, WT, cell98


title: 48hpf_2


title: cTEC, neonate, WT, cell99


title: cTEC, neonate, WT, cell108


title: cTEC, neonate, WT, cell97


title: cTEC, neonate, WT, cell96


title: 32hpf_8


title: cTEC, neonate, WT, cell95


title: 32hpf_6


title: cTEC, neonate, WT, cell93


title: cTEC, neonate, WT, cell88


title: 32hpf_3


title: cTEC, neonate, WT, cell87


title: cTEC, neonate, WT, cell94


title: 32hpf_4


title: cTEC, neonate, WT, cell92


title: 24hpf_6


title: cTEC, neonate, WT, cell85


title: 24hpf_8


title: 48hpf_5


title: 32hpf_5


title: cTEC, neonate, WT, cell89


title: 32hpf_1


title: cTEC, neonate, WT, cell90


title: 24hpf_7


title: 32hpf_2


title: cTEC, neonate, WT, cell91


title: cTEC, neonate, WT, cell83


title: 24hpf_5


title: 24hpf_2


title: cTEC, neonate, WT, cell86


title: cTEC, neonate, WT, cell81


title: 24hpf_1


title: 24hpf_4


title: cTEC, neonate, WT, cell84


title: 24hpf_3


title: cTEC, neonate, WT, cell82


title: 32hpf_7


title: 20ss_8


title: 20ss_7


title: cTEC, neonate, WT, cell79


title: 20ss_5


title: cTEC, neonate, WT, cell78


title: 20ss_4


title: cTEC, neonate, WT, cell77


title: cTEC, neonate, WT, cell76


title: 20ss_6


title: 20ss_3


title: cTEC, neonate, WT, cell74


title: 20ss_1


title: 80_96hpf_S7

description: RNA from single embryo at total RNA

source_name: RW


title: cTEC, neonate, WT, cell75


title: 20ss_2


title: cTEC, neonate, WT, cell72


title: cTEC, neonate, WT, cell69


title: 78_96hpf_S5

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell71


title: cTEC, neonate, WT, cell68


title: 79_96hpf_S6

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell70


title: 76_96hpf_S3

description: RNA from single embryo at total RNA


title: 75_96hpf_S2

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell67


title: cTEC, neonate, WT, cell66


title: 74_96hpf_S1

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell80


title: cTEC, neonate, WT, cell73


title: 73_96hpf_8

description: RNA from single embryo at total RNA


title: 81_96hpf_S8

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell65


title: 72_96hpf_7

description: RNA from single embryo at total RNA


title: 71_96hpf_6

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell63


title: cTEC, neonate, WT, cell64


title: 70_96hpf_5

description: RNA from single embryo at total RNA


title: 68_96hpf_3

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell60


title: cTEC, neonate, WT, cell62


title: 67_96hpf_2

description: RNA from single embryo at total RNA


title: 77_96hpf_S4

description: RNA from single embryo at total RNA


title: 64_20ss_7

description: RNA from single embryo at total RNA


title: 69_96hpf_4

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell59


title: 65_20ss_8

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell55


title: 63_20ss_6

description: RNA from single embryo at total RNA


title: 66_96hpf_1

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell54


title: 62_20ss_5

description: RNA from single embryo at total RNA


title: 61_20ss_4

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell56


title: cTEC, neonate, WT, cell53


title: cTEC, neonate, WT, cell52


title: 60_20ss_3

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell51


title: cTEC, neonate, WT, cell61


title: cTEC, neonate, WT, cell49


title: 59_20ss_2

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell48


title: 57_72hpf_8

description: RNA from single embryo at total RNA


title: 58_20ss_1

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell50


title: cTEC, neonate, WT, cell47


title: cTEC, neonate, WT, cell58


title: 55_72hpf_6

description: RNA from single embryo at total RNA


title: 56_72hpf_7

description: RNA from single embryo at total RNA


title: 54_72hpf_5

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell57


title: cTEC, neonate, WT, cell45


title: cTEC, neonate, WT, cell46


title: 52_72hpf_3

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell44


title: cTEC, neonate, WT, cell43


title: cTEC, neonate, WT, cell42


title: 53_72hpf_4

description: RNA from single embryo at total RNA


title: 50_72hpf_1

description: RNA from single embryo at total RNA


title: 51_72hpf_2

description: RNA from single embryo at total RNA


title: 49_48hpf_8

description: RNA from single embryo at total RNA


title: 48_48hpf_7

description: RNA from single embryo at total RNA


title: 47_48hpf_6

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell40


title: cTEC, neonate, WT, cell39


title: cTEC, neonate, WT, cell38


title: cTEC, neonate, WT, cell37


title: 45_48hpf_4

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell36


title: cTEC, neonate, WT, cell34


title: cTEC, neonate, WT, cell35


title: 46_48hpf_5

description: RNA from single embryo at total RNA


title: 44_48hpf_3

description: RNA from single embryo at total RNA


title: 42_48hpf_1

description: RNA from single embryo at total RNA


title: 43_48hpf_2

description: RNA from single embryo at total RNA


title: 41_15ss_S5

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell33


title: cTEC, neonate, WT, cell31


title: cTEC, neonate, WT, cell32


title: 40_15ss_S4

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell41


title: 37_15ss_S1

description: RNA from single embryo at total RNA


title: 38_15ss_S2

description: RNA from single embryo at total RNA


title: 39_15ss_S3

description: RNA from single embryo at total RNA


title: 36_10ss_S8

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell29


title: cTEC, neonate, WT, cell27


title: 35_10ss_S7

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell28


title: 34_10ss_S6

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell25


title: 33_10ss_S5

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell24


title: 32_10ss_S4

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell23


title: 31_10ss_S3

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell22


title: 29_10ss_S1

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell21


title: 30_10ss_S2

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell30


title: cTEC, neonate, WT, cell19


title: 26_6ss_S6

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell17


title: cTEC, neonate, WT, cell18


title: 25_6ss_S5

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell16


title: 24_6ss_S4

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell15


title: 23_6ss_S3

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell14


title: cTEC, neonate, WT, cell26


title: 22_6ss_S2

description: RNA from single embryo at total RNA


title: 21_6ss_S1

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell12


title: cTEC, neonate, WT, cell13


title: 20_24hpf_8

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell11


title: 19_24hpf_7

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell10


title: 18_24hpf_6

description: RNA from single embryo at total RNA


title: 17_24hpf_5

description: RNA from single embryo at total RNA


title: 28_6ss_S8

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell20


title: cTEC, neonate, WT, cell8


title: cTEC, neonate, WT, cell9


title: cTEC, neonate, WT, cell7


title: 16_24hpf_4

description: RNA from single embryo at total RNA


title: 15_24hpf_3

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell6


title: 27_6ss_S7

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell5


title: cTEC, neonate, WT, cell4


title: 13_24hpf_1

description: RNA from single embryo at total RNA


title: 14_24hpf_2

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell3


title: cTEC, neonate, WT, cell2


title: 10_15ss_2

description: RNA from single embryo at total RNA


title: cTEC, neonate, WT, cell1


title: 12_15ss_4

description: RNA from single embryo at total RNA


title: 9_15ss_1

description: RNA from single embryo at total RNA


title: 8_6ss_8

description: RNA from single embryo at total RNA


title: 11_15ss_3

description: RNA from single embryo at total RNA


title: 6_6ss_6

description: RNA from single embryo at total RNA


title: 7_6ss_7

description: RNA from single embryo at total RNA


title: mTEChi, adult, WT, cell619

value: female


title: mTEChi, adult, WT, cell618


title: mTEChi, adult, WT, cell617


title: mTEChi, adult, WT, cell616


title: 4_6ss_4

description: RNA from single embryo at total RNA


title: mTEChi, adult, WT, cell615


title: 5_6ss_5

description: RNA from single embryo at total RNA


title: 2_6ss_2

description: RNA from single embryo at total RNA


title: mTEChi, adult, WT, cell613


title: 1_6ss_1

description: RNA from single embryo at total RNA


title: mTEChi, adult, WT, cell614


title: mTEChi, adult, WT, cell612


title: mTEChi, adult, WT, cell611


title: 3_6ss_3

description: RNA from single embryo at total RNA


title: mTEChi, adult, WT, cell609


title: Fibroblasts isolated from mouse mammary gland at adult stage (9-week-old Replicate 2)

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description:
Library name: Adult-2
10x Genomics

data_processing:
Read alignment and count summarization were performed using cellranger v8.0.1 using the Illumina BCL files as input.
Assembly: mm10
Supplementary files format and content: The barcode.tsv files contain the 10X barcodes used to identify cells.
Supplementary files format and content: The features.tsv files contain the corresponding Ensembl IDs and gene symbols as tab-delimited text.
Supplementary files format and content: The matrix.mtx files contain genewise read counts for all cells in the space-efficient matrix market format.

source_name: Mammary gland

extract_protocol:
Freshly sorted stromal fractions (Lineage–CD24–, 2 females per condition) were obtained from pubertal (4-week-old) and adult (virgin 9-week-old) mammary glands from the same mouse (n=2).
scRNA libraries were prepared using the 10x genomics Chromium GEM-X Single Cell 3’ v4 kit

value: Mammary gland

value: Stromal

value: wildtype

tag: time


title: Ntsr1

city: Charlottesville

first: Yuanming

last: Liu

state: Virginia

address: Gilmer Hall

department: Biology Department

institute: University of Virginia

description:
Library name: Sample 1
10x Genomics

data_processing:
10X Cell Ranger pipeline (version 5.0.0) was used to demultiplex and align sequencing reads
Assembly: A custom “pre-mRNA” reference genome created from mouse reference genome RGCm38.98
Supplementary files format and content: H5 file; feature-barcode matrices

molecule: polyA RNA

source_name: Superficial superior colliculus

extract_protocol:
Brains were harvested after rapid decapitation to avoid stress- or anesthesia-related changes in gene expression, cooled in ice-cold Hibernate-A for 2min, placed into a chilled stainless steel brain matrix and then sectioned coronally into 1mm thick slices containing the sSC (Bregma -3.0 mm to -5.0 mm). The sSC was then visualized under a dissecting microscope, micro-dissected approximately by knife cuts. Next, we homogenized the sSC in lysis buffer and separated nuclei from cellular debris using density gradient centrifugation. After resuspending the nuclei pellet, the concentration of nuclei was counted with propidium iodide by a CellDrop automated cell counter (DeNovix, Delaware, U.S.A.).
We used 10X Chromium Next GEM 3’ reagent kit v3.1 according to the manufacturer’s protocol (user guide revision D) to capture each nucleus’s poly-adenylated RNA in a droplet, process it into cDNA sequencing libraries, and sequenced to an average of 35,998 mean reads per cell.

value: Superficial superior colliculus

value: pooled male and female

value: Neural cells

value: Ntsr1-GN209-Cre x H2b-TRAP

value: 2-4 months

tag: batch


title: mTEChi, adult, WT, cell608

value: thymus

value: WT


title: Fibroblasts isolated from mouse mammary gland at puberty stage  (4-week-old Replicate 2)

description:
Library name: Puberty-2
10x Genomics


title: Fibroblasts isolated from mouse tumor mammary gland (Replicate 2)

description: 10x Genomics

data_processing:
Read alignment and count summarization were performed using cellranger v6.1.2 using the Illumina BCL files as input.
Assembly: mm10
Supplementary files format and content: The barcode.tsv files contain the 10X barcodes used to identify cells.
Supplementary files format and content: The features.tsv files contain the corresponding Ensembl IDs and gene symbols as tab-delimited text.
Supplementary files format and content: The matrix.mtx files contain genewise read counts for all cells in the space-efficient matrix market format.

extract_protocol:
Freshly sorted stromal fractions (Lineage–CD24–, 2 females per condition) were obtained from pubertal (4-week-old), adult (virgin 9-week-old), pregnant (14.5 days), lactating (10 days), involuting (4 days) or hormone-stimulated (MPA+E or placebo control) mammary glands as well as freshly sorted GFP+ cells from raGFP-Wnt1 mammary tumors and paired hyperplastic mammary glands from the same mouse (n=2).
scRNA libraries were prepared using the 10x genomics Chromium Single Cell 3’ v3 kit

value: Pdgfra-GFP KI/+ MMTV-Wnt1 T/+

value: raGFP-Wnt1 (C57BL/6 FVB mixed background)


title: mTEChi, adult, WT, cell620

value: epitherial cells

value: mTEChi


title: Fibroblasts isolated from mouse tumor mammary gland (Replicate 1)

description: 10x Genomics


title: mTEChi, adult, WT, cell607


title: mTEChi, adult, WT, cell606


title: mTEChi, adult, WT, cell610


title: Fibroblasts isolated from mouse hyperplastic mammary gland (Replicate 2)

description: 10x Genomics


title: Fibroblasts isolated from mouse hyperplastic mammary gland (Replicate 1)

description: 10x Genomics


title: mTEChi, adult, WT, cell605


title: Fibroblasts isolated from mouse mammary gland treated with drug (Replicate 2)

description: 10x Genomics


title: mTEChi, adult, WT, cell604


title: Fibroblasts isolated from mouse mammary gland treated with drug (Replicate 1)

description: 10x Genomics


title: mTEChi, adult, WT, cell602


title: mTEChi, adult, WT, cell601


title: Fibroblasts isolated from mouse mammary gland treated with placebo (Replicate 2)

description: 10x Genomics


title: Fibroblasts isolated from mouse mammary gland at  involution stage (4-day)

description: 10x Genomics

value: involuting 4-day


title: mTEChi, adult, WT, cell600


title: Fibroblasts isolated from mouse mammary gland at lactation stage (10-day )

description: 10x Genomics

value: lactating 10-day


title: Fibroblasts isolated from mouse mammary gland at pregnancy stage (14.5-day )

description: 10x Genomics

value: female

value: pregnant 14.5-day


title: Fibroblasts isolated from mouse mammary gland at adult stage (9-week-old)

description: 10x Genomics

value: Mammary gland

value: Stromal


title: mTEChi, adult, WT, cell597


title: Fibroblasts isolated from mouse mammary gland at puberty stage (4-week-old)

description: 10x Genomics

value: wildtype


title: mTEChi, adult, WT, cell596


title: mTEChi, adult, WT, cell595


title: TEC_neonateWT, scATACseq

data_processing:
Sequenced reads were processed using Cell Ranger ARC v2.0.0 software with a reference data refdata-cellranger-arc-mm10-2020-A-2.0.0 provided by 10x GENOMICS
Processed file format and content are described at https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/overview
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files for RNA-seq
Supplementary files format and content: Feature-barcode matrices in HDF5 formats and fragment positions in tab-separated values files for ATAC-seq

extract_protocol:
Mouse thymus was enzymatically digested and DAPI-CD45-EpCAM+ cells were sorted by FACSAria. Single‑cell emulsions were generated using a Chromium instrument from 10× GENOMICS
RNA-seq and ATAC-seq libraries were prepared for sequencing using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression v1 reagents from 10x GENOMICS
scRNA-Seq  + scATAC-Seq

value: pool of day2~4

tag: sex

value: pooled male and female


title: TEC_adultAireKO, scATACseq

value: AireKO

value: 5 weeks

value: male


title: mTEChi, adult, WT, cell593

value: thymus

value: WT


title: mTEChi, adult, WT, cell592


title: mTEChi, adult, WT, cell590


title: TEC_neonateAireKO, scRNAseq

description: nuclear RNA


title: mTEChi, adult, WT, cell591


title: mTEChi, adult, WT, cell594


title: TEC_adultWT, scATACseq


title: mTEChi, adult, WT, cell588


title: TEC_adultWT, scRNAseq

description: nuclear RNA


title: mTEChi, adult, WT, cell603


title: mTEChi, adult, WT, cell599


title: TEC_adultAireKO, scRNAseq

description: nuclear RNA


title: TEC_neonateAireKO, scATACseq


title: Fibroblasts isolated from mouse mammary gland treated with placebo (Replicate 1)

description: 10x Genomics


title: mTEChi, adult, WT, cell598


title: PBMCs profiled via Illumina PIPseq V

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description:
Library name: PIPseq-V-PBMCs
Resting PBMCs protiled via PIPseq

data_processing:
Fastqs were demultiplexed via bcl2fastq
10x Genomics data was processed via CellRanger v8
PIPseq data was processed via the pip seeker pipeline v3.3.0
Assembly: hg38
Supplementary files format and content: counts matrices of unique molecule counts per cell

source_name: peripheral blood mononuclear cells

extract_protocol: Single cell RNA-seq (10x Genomics and Illumina PIPseq)

value: peripheral blood mononuclear cells


title: PBMCs profiled via 10x Genomics 3' GEM X

description:
Library name: 10x-GEMX-PBMCs
Resting PBMCs profiled via 10x Genomics 3' GEM-X


title: TEC_neonateWT, scRNAseq

description: nuclear RNA

value: epitherial cells


title: mTEChi, adult, WT, cell586

value: mTEChi


title: mTEChi, adult, WT, cell585


title: mTEChi, adult, WT, cell589


title: Control DAP-seq Rep 3

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description: DAP-seq performed with NO HaloTagged protein. Used as background control sample for spurious Magne HaloTag pull down

data_processing:
Sequencing reads for the protein-associated DNA libraries as well as the control library were trimmed to remove Illumina adapters using bbtools bbduk (v38.90, k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10). The trimmed reads were aligned to the N. aromaticivorans DSM12444 genome (GCF_000013325.1, ASM1332v1) using Bowtie2 (v2.4.2, --no-mixed --no-discordant). BigWig files were generated using deepTools (v3.5.0, --effectiveGenomeSize 4052498 --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC) All control alignment files were merged using SAMtools (v1.1.1) (13). For each TF examined, peaks were identified using macs3 (v3.0.0a6, --gsize 4052498 --call-summits --keep-dup 1).
Assembly: N. aromaticivorans DSM12444, GCF_000013325.1, ASM1332v1
Supplementary files format and content: The narrowPeak.bed files are in BED Narrowpeak format and contain genomic locations of all peaks identified with macs3 (IP vs INPUT) for each transcription factor
Supplementary files format and content: The norm_bw files are in BigWIg format and contain genomic locations of all binding sites for each transcription factor. This can be used for visualization in a genome browser such as IGV. Control (no HaloTagged protein incubated with DNA) is included for reference.

organism: Novosphingobium aromaticivorans

source_name: Bacterial cell

extract_protocol:
The transcription factor (TF) genes were synthesized and proteins expressed in vitro at the Joint Genome Institute, inclusive of an N-terminus HaloTag (Promega). N. aromaticivorans genomic DNA was purified from cultures grown in 2.5 mmol/L vanillic acid and 2.5 mmol/L glucose SMB. The genomic DNA was ultrasonically sheared to an average size of 75 bp, and 1 µg was used to create the sequencing library using the KAPA HyperPrep Kit and standard manufacturer’s protocols. The HaloTagged TFs were incubated with 1 ng of the N. aromaticivorans genomic DNA library and complexes were isolated with washed Magne HaloTag beads (Promega), which bind the HaloTagged TFs. The DNA from the protein-DNA complexes was amplified for sequencing using the KAPA High-Fidelity 2X PCR Master Mix (NEB) and the libraries were sequenced on an Illumina NovaSeq 6000 S4 instrument using 2x151 bp reads.
The DNA from the TF-DNA complexes was amplified for sequencing using the KAPA High-Fidelity 2X PCR Master Mix and the libraries were sequenced on a NovaSeq 6000 S4 instrument using 2x151 bp reads.

value: Bacterial gDNA

tag: chip antibody

value: Magne HaloTag beads but no HaloTagged protein included


title: mTEChi, adult, WT, cell583

value: female


title: mTEChi, adult, WT, cell584


title: mTEChi, adult, WT, cell582


title: Control DAP-seq Rep 1


title: SARO_RS17620 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS17620 protein with purified gDNA

value: Magne HaloTag beads used to bind HaloTagged protein/DNA complexes


title: mTEChi, adult, WT, cell580


title: SARO_RS14395 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS14395 protein with purified gDNA


title: mTEChi, adult, WT, cell587


title: mTEChi, adult, WT, cell581


title: mTEChi, adult, WT, cell578


title: SARO_RS11895 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS11895 protein with purified gDNA


title: SARO_RS14845 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS14845 protein with purified gDNA


title: SARO_RS07980 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS07980 protein with purified gDNA


title: mTEChi, adult, WT, cell575


title: mTEChi, adult, WT, cell574


title: SARO_RS13010 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS13010 protein with purified gDNA


title: mTEChi, adult, WT, cell576


title: SARO_RS09350 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS09350 protein with purified gDNA


title: mTEChi, adult, WT, cell573


title: Control DAP-seq Rep 4


title: SARO_RS07800 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS07800 protein with purified gDNA


title: SARO_RS15450 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS15450 protein with purified gDNA


title: mTEChi, adult, WT, cell572


title: Control DAP-seq Rep 2


title: SARO_RS08575 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS08575 protein with purified gDNA


title: SARO_RS00615 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS00615 protein with purified gDNA


title: SARO_RS17345 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS17345 protein with purified gDNA


title: mTEChi, adult, WT, cell570


title: mTEChi, adult, WT, cell571


title: SARO_RS11485 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS11485 protein with purified gDNA


title: mTEChi, adult, WT, cell579


title: mTEChi, adult, WT, cell569


title: SARO_RS07435 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS07435 protein with purified gDNA


title: mTEChi, adult, WT, cell577


title: mTEChi, adult, WT, cell568


title: mTEChi, adult, WT, cell567


title: SARO_RS04370 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS04370 protein with purified gDNA


title: mTEChi, adult, WT, cell566


title: SARO_RS13730 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS13730 protein with purified gDNA


title: mTEChi, adult, WT, cell563


title: SARO_RS12110 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS12110 protein with purified gDNA


title: mTEChi, adult, WT, cell562


title: SARO_RS02650 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS02650 protein with purified gDNA


title: mTEChi, adult, WT, cell561


title: mTEChi, adult, WT, cell565


title: SARO_RS07375 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS07375 protein with purified gDNA


title: SARO_RS02605 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS02605 protein with purified gDNA


title: mTEChi, adult, WT, cell559


title: SARO_RS00970 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS00970 protein with purified gDNA


title: mTEChi, adult, WT, cell558


title: mTEChi, adult, WT, cell560


title: SARO_RS06685 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS06685 protein with purified gDNA


title: mTEChi, adult, WT, cell564


title: SARO_RS00810 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS00810 protein with purified gDNA


title: mTEChi, adult, WT, cell557


title: SARO_RS05355 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS05355 protein with purified gDNA


title: SARO_RS07420 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS07420 protein with purified gDNA


title: SARO_RS08650 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS08650 protein with purified gDNA


title: mTEChi, adult, WT, cell556


title: mTEChi, adult, WT, cell555


title: SARO_RS17250 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS17250 protein with purified gDNA


title: SARO_RS20125 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS20125 protein with purified gDNA


title: SARO_RS02445 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS02445 protein with purified gDNA


title: mTEChi, adult, WT, cell552


title: SARO_RS04920 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS04920 protein with purified gDNA


title: SARO_RS03775 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS03775 protein with purified gDNA


title: mTEChi, adult, WT, cell551


title: mTEChi, adult, WT, cell553


title: mTEChi, adult, WT, cell550


title: SARO_RS20390 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS20390 protein with purified gDNA


title: SARO_RS19415 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS19415 protein with purified gDNA


title: mTEChi, adult, WT, cell549


title: SARO_RS09450 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS09450 protein with purified gDNA


title: SARO_RS04885 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS04885 protein with purified gDNA


title: mTEChi, adult, WT, cell548


title: mTEChi, adult, WT, cell547


title: mTEChi, adult, WT, cell546


title: SARO_RS19770 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS19770 protein with purified gDNA


title: SARO_RS06030 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS06030 protein with purified gDNA


title: SARO_RS10140 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS10140 protein with purified gDNA


title: mTEChi, adult, WT, cell545


title: mTEChi, adult, WT, cell544


title: mTEChi, adult, WT, cell554


title: mTEChi, adult, WT, cell543


title: SARO_RS08540 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS08540 protein with purified gDNA


title: mTEChi, adult, WT, cell541


title: SARO_RS18620 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS18620 protein with purified gDNA


title: mTEChi, adult, WT, cell540


title: SARO_RS10965 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS10965 protein with purified gDNA


title: mTEChi, adult, WT, cell542


title: SARO_RS02260 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS02260 protein with purified gDNA


title: mTEChi, adult, WT, cell463, G400


title: mTEChi, adult, WT, cell539


title: iCLIP_PRPF8_RPE_Y2334N_TATT_Rep2

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

description: iCLIP

data_processing:
Basecalls performed using CASAVA version 1.4.
For detail on data processing see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959.
Assembly: mm9
Supplementary files format and content: bed files containing the genomic coordinates and counts of uniquely mapped X-links for merged replicates.
Library strategy: iCLIP-seq

source_name: RPE

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and penicillin/streptomycin antibiotics at 37˚C with 5% CO2.

extract_protocol:
Cells were lysed and treated with RNase I. GFP-tagged proteins were immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transferred to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was size selected by denaturing gel electrophoresis and circularized by ssDNA circligase. A specific oligonucleotide was annealed to create a restriction site for BamHI and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplified with Solexa sequencing primers to create the final libraries. For more details see: Huppertz et al., (2014): iCLIP: protein-RNA interactions at nucleotide resolution. Methods. PMID:24184352.

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

tag: cell line

value: RPE

value: PRPF8-GFP Y2334N

value: UV

tag: antibody

value: anti-EGFP

tag: barcode sequence

value: TATT


title: mTEChi, adult, WT, cell462, G400

source_name: thymus


title: SARO_RS09330 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS09330 protein with purified gDNA


title: iCLIP_PRPF8_RPE_Y2334N_CGGA_Rep1

description: iCLIP

value: CGGA


title: mTEChi, adult, WT, cell461, G400


title: iCLIP_PRPF8_RPE_WT_TATT_Rep2

description: iCLIP

value: PRPF8-GFP WT


title: mTEChi, adult, WT, cell460, G400

value: male


title: mTEChi, adult, WT, cell459, G400

value: thymus


title: iCLIP_PRPF8_RPE_WT_noUV_CCGG_Rep1

description: iCLIP

value: PRP8-GFP WT

value: no UV control

value: CCGG


title: iCLIP_BRR2_HeLa_R1090L_TGGC_Rep3

description: iCLIP

source_name: HeLa

value: HeLa

value: SNRNP200-GFP R1090L

value: TGGC


title: iCLIP_PRPF8_RPE_WT_CGGA_Rep1

description: iCLIP


title: SARO_RS14285 DAP-seq

description: DAP-seq performed in vitro on HaloTagged SARO_RS14285 protein with purified gDNA

value: Bacterial gDNA

value: WT


title: iCLIP_BRR2_HeLa_R1090L_GGTT_Rep1

description: iCLIP

value: GGTT


title: mTEChi, adult, WT, cell456, G400

value: epitherial cells

value: mTEChi


title: mTEChi, adult, WT, cell457, G400


title: mTEChi, adult, WT, cell455, G400


title: mTEChi, adult, WT, cell454, G400


title: iCLIP_BRR2_HeLa_S1087L_TTGT_Rep2

description: iCLIP

value: SNRNP200-GFP S1087L

value: UV

value: anti-EGFP

value: TTGT


title: iCLIP_BRR2_HeLa_S1087L_GGTT_Rep1

description: iCLIP


title: iCLIP_BRR2_HeLa_S1087L_noUV_CCGG_Rep1

description: iCLIP

value: SNRNP200 S1087L


title: iCLIP_BRR2_HeLa_WT_TGGC_Rep3

description: iCLIP

value: SNRNP200-GFP WT


title: mTEChi, adult, WT, cell451, G400

value: thymus

value: male


title: mTEChi, adult, WT, cell453, G400


title: mTEChi, adult, WT, cell452, G400


title: mTEChi, adult, WT, cell450, G400


title: mTEChi, adult, WT, cell449, G400


title: mTEChi, adult, WT, cell448, G400


title: iCLIP_BRR2_HeLa_WT_GGTT_Rep1

description: iCLIP


title: iCLIP_BRR2_HeLa_WT_noUV_CCGG_Rep1

description: iCLIP

value: SNRNP200 WT

value: no UV control

value: CCGG


title: mTEChi, adult, WT, cell447, G400


title: mTEChi, adult, WT, cell458, G400


title: mTEChi, adult, WT, cell446, G400


title: mTEChi, adult, WT, cell445, G400


title: iCLIP_PRPF8_HeLa_Y2334N_GGTT_Rep1

description: iCLIP

value: HeLa

value: PRPF8-GFP Y2334N


title: iCLIP_PRPF8_HeLa_Y2334N_noUV_CCGG_Rep1

description: iCLIP

value: PRP8-GFP Y2334N


title: mTEChi, adult, WT, cell443, G400

value: WT


title: iCLIP_PRPF8_HeLa_Y2334N_TGGC_Rep3

description: iCLIP

value: TGGC


title: iCLIP_PRPF8_HeLa_F2314L_GGTC_Rep1

description: iCLIP

value: PRPF8-GFP F2314L

value: GGTC


title: iCLIP_BRR2_HeLa_S1087L_TGGC_Rep3

description: iCLIP

value: SNRNP200-GFP S1087L

value: UV


title: iCLIP_PRPF8_HeLa_Y2334N_TTGT_Rep2

description: iCLIP

value: anti-EGFP

value: TTGT


title: iCLIP_BRR2_HeLa_R1090L_TTGT_Rep2

description: iCLIP

value: SNRNP200-GFP R1090L


title: mTEChi, adult, WT, cell442, G400

value: thymus

value: epitherial cells

value: mTEChi


title: mTEChi, adult, WT, cell441, G400

value: male


title: iCLIP_PRPF8_HeLa_F2314L_noUV_CCAC_Rep1

description: iCLIP

value: PRP8-GFP F2314L

value: no UV control

value: CCAC


title: mTEChi, adult, WT, cell440, G400


title: iCLIP_PRPF8_HeLa_WT_TGGC_Rep3

description: iCLIP

value: HeLa

value: PRPF8-GFP WT


title: iCLIP_BRR2_HeLa_WT_TTGT_Rep2

description: iCLIP

value: SNRNP200-GFP WT


title: iCLIP_PRPF8_HeLa_WT_TTGT_Rep2

description: iCLIP


title: mTEChi, adult, WT, cell438, G400

value: WT


title: mTEChi, adult, WT, cell437, G400


title: iCLIP_PRPF8_HeLa_WT_GGTT_Rep1

description: iCLIP

value: GGTT


title: iCLIP_PRPF8_HeLa_WT_noUV_CCGG_Rep1

description: iCLIP

value: PRP8-GFP WT

value: CCGG


title: mTEChi, adult, WT, cell436, G400


title: A549_shNT

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: shRNA control

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (hg19) by TopHat (version 2.0.10).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on June 02, 2014) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.18.0).
Assembly: hg19
Supplementary files format and content: The first column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.

growth_protocol: All cells were cultured in RPMI with 10% FBS.

extract_protocol:
RNA was prepared using the RNeasy Plus kit (Qiagen)
Samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions.

tag: shRNAs

value: non-targeting shRNA

value: puro select 4 days


title: A549_shAHL1L_2

description: ASH1L shRNA knockdown

value: ASH1L shRNA2


title: mTEChi, adult, WT, cell434, G400

value: thymus


title: A549_shASH1L_1

description: ASH1L shRNA knockdown

value: ASH1L shRNA1


title: mTEChi, adult, WT, cell433, G400

value: epitherial cells

value: mTEChi


title: mTEChi, adult, WT, cell444, G400

value: male


title: HMC3 cells, SLO 1, replicate 3

city: Montreal

first: Janelle

last: Drouin-Ouellet

state: Quebec

address: 2940, chemin de Polytechnique Pavillon Jean Coutu

department: Pharmacy

country: Canada

institute: University of Montreal

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.38
Read count extraction and normalization were performed using STAR to obtain normalized gene and transcript level expression in TPM values.
Assembly: Trimmed sequences were aligned to the reference human genome version GRCh38 (gene annotation from Gencode version 40, based on Ensembl 106) using STAR version 2.7.1a
Supplementary files format and content: tab-separated text file includes raw read counts for each sample (summary_star_genes_readcount.stranded.annotated)
Supplementary files format and content: tab-separated text file includes TPM values for each sample (summary_star_genes_tpm.stranded.annotated)

growth_protocol: Immortalized human microglial HMC3 cells were cultured in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% fetal bovine serum (FBS) and 100U/mL of penicillin/streptomycin solution (P/S) at 37oC and in 5% CO2. When cells reached 80-90% confluence, they were trypsinized by incubation with Trypsin-EDTA for 5 min, then collected in fresh complete medium. After centrifuging the cell suspension at 400G for 5 min at room temperature (RT), the supernatant was discarded, and the remaining pellet resuspended in culture medium. Viable cell number was assessed using a Hausser Scientific™ Bright Line™ Counting Chamber and cells were seeded on plastic multi-well culture plates coated with Gelatin 0.1% for 1h at 37oC.

extract_protocol:
HMC3 cells were collected and centrifuged at 400G for 5 min at RT. The supernatant was discarded, and RNA extraction was carried out with the RNeasy MicroKit (QIAGEN), following manifacturer instructions.
RNA was quantified using Qubit (Thermo Scientific) and quality was assessed with the 2100 Bioanalyzer (Agilent Technologies). Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific).

treatment_protocol: The chemical compounds SBI-0206965, O-151 and Lopinavir (37) were prepared in dimethyl sulfoxide (DMSO) to obtain a stock concentration of 10 mM, 1 mM and 1 mM, respectively and stored at -80o C. HMC3 cells were seeded at a density of 2,630 cells/cm2 on 6, 12, or 24-well plates. After 24h from seeding, cells were treated for 6 consecutive days with a cocktail of SBI-0206965 10 μM, O-151 1 μM, Lopinavir 1 μM, or with an equivalent concentration of DMSO in standard HMC3 medium for the full dose treatment, and 5 μM 0,5 μM and 0,5 μM respectively, for the half dose.

value: immortalized microglia

value: SBI-0206965 10 uM, O-151 1 uM, Lopinavir 1 uM


title: mTEChi, adult, WT, cell432, G400


title: iCLIP_PRPF8_HeLa_F2314L_GGCA_Rep2

description: iCLIP

value: HeLa

value: PRPF8-GFP F2314L

value: UV

value: anti-EGFP

value: GGCA


title: HMC3 cells, SLO 1, replicate 2

value: WT


title: mTEChi, adult, WT, cell431, G400


title: mTEChi, adult, WT, cell429, G400


title: HMC3 cells, SLO 1/2, replicate 2


title: mTEChi, adult, WT, cell439, G400


title: mTEChi, adult, WT, cell428, G400


title: HMC3 cells, SLO 1/2, replicate 1


title: HMC3 cells, SLO 1, replicate 1


title: mTEChi, adult, WT, cell430, G400


title: mTEChi, adult, WT, cell426, G400


title: HMC3 cells, VEH control, replicate 3

value: DMSO (vehicle)


title: HMC3 cells, VEH control, replicate 2


title: HMC3 cells, SLO 1/2, replicate 3


title: mTEChi, adult, WT, cell427, G400


title: mTEChi, adult, WT, cell435, G400


title: HMC3 cells, VEH control, replicate 1


title: mTEChi, adult, WT, cell424, G400


title: mTEChi, adult, WT, cell425, G400


title: mTEChi, adult, WT, cell423, G400


title: Control intestinal organoid, TNFa+serotonin hydrochloride treated, rep 4

city: Brno

first: Ioanna

last: Papatheodorou

address: Studentska

department: Center for Translational Medicine

country: Czech Republic

institute: International Clinical Research Center (ICRC), St.Anne’s Hospital

data_processing:
Sequences were trimmed for adaptors/low quality sequences using Trim galore with default parameters.
Trimmed sequences were mapped to GRCh38-p10 (human genome) with HISAT2 using the default parameteres.
Read counts were determined with Htseq -count.
Raw gene counts were normalized following VST transformation by use of the package DESeq2 in the R v4.3.3. environment.
Differentially expressed genes were determined with DESeq2 in the R v4.3.3. enviroment.
Assembly: GRCh38-p10
Supplementary files format and content: The txt delimited file named SER_TNF_raw_counts.txt contains all the raw HTseq derived counts.
Supplementary files format and content: The txt delimited file named SER_TNF_normalized_counts.txt contains all the normalized counts following rlog transformation.

source_name: Intestine

growth_protocol: IOs were differentiated from human induced pluripotent cells (hiPSCs) using an adapted protocol (Jose SS et al., 2020; McCracken KW et al., 2011). In brief, hiPSCs were differentiated to definitive endoderm (DE) using Activin A (100 ng/mL, R&D) in RPMI-1640 (Gibco) with increasing concentration of HyClone-defined fetal bovine serum (HC FBS) (GE Healthcare Bio-Sciences) (first day 0%, second day 0.2% and third and fourth day 2%). Next, the DE was differentiated to mid- and hindgut using RPMI-1640 supplemented with 15 mM HEPES, 2% HC FBS, FGF-4 (500 ng/mL, R&D), and WNT-3a (500 ng/mL, R&D) until 3D spheroids were observed. Spheroids were collected and seeded in Cultrex Membrane Extract, Type 2 (R&D). The spheroids were fed with IOs medium (Advanced DMEM F12 (Gibco) supplemented with 15 mM HEPES, B27 supplement (Thermo Fisher Scientific), GlutaMAX supplement (Thermo Fisher Scientific), P/S (500 U/mL), R-Spondin 1 (500 ng/mL, R&D), Noggin (100 ng/mL, R&D), and EGF (100 ng/mL, R&D)). The medium was changed twice a week. IOs that were at least 50 days old were used for the experiments.

extract_protocol:
Cells were lysed in of TRI Reagent®. The RNA was isolated using the RNeasy mini kit (Qiagen).
Libraries were constructed with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD using 250 ng of RNA
bulk RNAseq

treatment_protocol: IOs stimulated with serotonin hydrochloride (10 µM), TNFα (10 ng/mL), or TNFα+serotonin hydrochloride and nonstimulated controls were washed with cold PBS and the Cultrex was removed using Corning® Cell Recovery Solution (Corning) for 20 minutes at 4 °C.

value: Intestine

value: iPSC-derived organoids

value: TNFa+serotonin hydrochloride


title: Control intestinal organoid, TNFa+serotonin hydrochloride treated, rep 3


title: mTEChi, adult, WT, cell422, G400

value: thymus


title: Control intestinal organoid, serotonin hydrochloride treated, rep 4

value: serotonin hydrochloride


title: mTEChi, adult, WT, cell420, G400

value: epitherial cells


title: Control intestinal organoid, TNFa+serotonin hydrochloride treated, rep 2


title: mTEChi, adult, WT, cell419, G400

value: mTEChi


title: Control intestinal organoid, serotonin hydrochloride treated, rep 3


title: Control intestinal organoid, serotonin hydrochloride treated, rep 2


title: mTEChi, adult, WT, cell421, G400

value: male


title: mTEChi, adult, WT, cell418, G400


title: Control intestinal organoid, TNFa treated, rep 4

value: TNFa


title: mTEChi, adult, WT, cell417, G400


title: Control intestinal organoid, TNFa treated, rep 3


title: mTEChi, adult, WT, cell416, G400


title: Control intestinal organoid, TNFa treated, rep 1


title: Control intestinal organoid, TNFa treated, rep 2


title: Control intestinal organoid, untreated, rep 3

value: Untreated


title: Control intestinal organoid, untreated, rep 4


title: mTEChi, adult, WT, cell414, G400


title: mTEChi, adult, WT, cell413, G400


title: mTEChi, adult, WT, cell412, G400


title: mTEChi, adult, WT, cell415, G400


title: Control intestinal organoid, untreated, rep 1


title: CapSTARR-seq_GM12878_WT_rep2

city: Marseille

first: Salvatore

last: Spicuglia

state: France

address: Luminy

country: France

institute: Aix-Marseille University, INSERM, TAGC, UMR 1090

data_processing:
The fastq files were trimmed using sickle with -q 20 option and mapped to the hg19 reference genome using Bowtie2 with default parameters. Sam files were converted using SamTools and bed files were generated with bedtools “BamToBed” command. Fragment reads were extended to 314 nt, corresponding to the average size of the captured fragments. Coverage of captured regions was computed using bedtools “coverage” command for both transfected and non-transfected libraries. The coverage was normalized by Fragments per kilobase per million reads mapped (FPKM). Promoter regions with an FPKM < 1 in the input library were removed. The ratio of the Capstarr-seq coverage over the input (fold-change) was computed for each sample. Promoter regions with enhancer activity were defined using the inflection point of the ranked fold-change as a threshold.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CapSTARR-seq

extract_protocol:
Phenol-chloroform
Library preparation was carried out as per manufacturer’s instructions (Illumina) using 10ng material. Samples were subsequently size-selected via gel migration and extraction, with average cut sizes at about 230 bp, including adapters. Sequencing was carried out on an Illumina NextSeq 500. The quality of libraries was checked with the Bioanalyser DNA High sensitivity and by Q-PCR.

value: control


title: CapSTARR-seq_GM12878_input


title: mTEChi, adult, WT, cell409, G400


title: CapSTARR-seq_GM12878_WT_rep3


title: mTEChi, adult, WT, cell411, G400


title: CapSTARR-seq_GM12878_WT_rep1


title: mTEChi, adult, WT, cell410, G400


title: mTEChi, adult, WT, cell406, G400


title: CapSTARR-seq_CEM_input

source_name: CEM

value: CEM


title: mTEChi, adult, WT, cell404, G400


title: Control intestinal organoid, serotonin hydrochloride treated, rep 1


title: CapSTARR-seq_CEM_IFNa_rep2

value: IFNa


title: CapSTARR-seq_CEM_IFNa_rep1


title: mTEChi, adult, WT, cell403, G400


title: CapSTARR-seq_CEM_WT_rep2


title: mTEChi, adult, WT, cell402, G400


title: CapSTARR-seq_CEM_WT_rep1


title: mTEChi, adult, WT, cell401, G400


title: CapSTARR-seq_RPMI_input

source_name: RPMI

value: RPMI


title: CapSTARR-seq_RPMI_WT_rep2


title: mTEChi, adult, WT, cell400, G400


title: mTEChi, adult, WT, cell408, G400


title: CapSTARR-seq_RPMI_WT_rep1


title: mTEChi, adult, WT, cell398, G400


title: mTEChi, adult, WT, cell396, G400


title: mTEChi, adult, WT, cell397, G400


title: GFP_w.o_Cys_rep2

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

data_processing:
Fastq files quality check was performed using FastQC
The fastq files were mapped to the hg19 genome using TopHat v2.1.0 with the following parameters –bowtie1 –no-coverage-search -a 5
The number of reads covered by each gene was calculated by HTSeq-Count 0.11.2 with -s no -a 0 -t exon -m intersection-nonempty parameters.
Assembly: hg19
Supplementary files format and content: HTSeq-Count txt files

source_name: epithelial Tumor cell line

growth_protocol: Cell were cultured in DMEM + 10%FBS + 2mM L-Glu + 0.01 mg/ml human insulin

extract_protocol:
Total RNA of GFP or NRF2 expressing Hs 578T cells was purified using EuroGOLD TriFast™ (Euroclone, Milan, Italy). RNA quantity and quality were evaluated by Nanodrop 8000 (Thermo Fisher Scientific, Waltham, MA, USA) and Fragment Analyzer (Advanced Analytical Technologies, Heidelberg, Germany) using the DNF-471 Standard Sensitivity RNA Analysis Kit (15nt) (Agilent Technologies, Santa Clara, CA, USA).
RNA samples were further processed for mRNA-seq library preparation according to the manufacturer’s instructions (TruSeq RNA Sample preparation v2, Illumina, San Diego, CA, USA).

treatment_protocol: For Cys depletion, cells were washed with phosphate-buffered saline solution (PBS), pH 7.4, and incubated for the indicated times in DMEM, high glucose, no glutamine, no methionine, no cystine (#21013024, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% (v/v) fetal bovine serum (FBS), 0.2 mM L-Methionine, 100 μg/ml streptomycin, 100 U/ml penicillin, and 2 mM L-glutamine. 0.8 mM L-Cystine was added in control cells

value: epithelial Tumor cell line

value: Hs 578T

value: over-expressing GFP (control)

value: medium without Cys


title: mTEChi, adult, WT, cell407, G400

value: WT


title: GFP_w.o_Cys_rep3


title: mTEChi, adult, WT, cell395, G400


title: GFP_Ctrl_rep3

value: Control medium


title: mTEChi, adult, WT, cell394, G400

value: thymus


title: mTEChi, adult, WT, cell393, G400


title: GFP_Ctrl_rep1


title: mTEChi, adult, WT, cell392, G400


title: mTEChi, adult, WT, cell405, G400


title: GFP_Ctrl_rep2


title: mTEChi, adult, WT, cell391, G400


title: NRF_w.o_Cys_rep3

value: over-expressing NRF2


title: NRF_w.o_Cys_rep2


title: mTEChi, adult, WT, cell390, G400

value: epitherial cells


title: NRF_w.o_Cys_rep1


title: mTEChi, adult, WT, cell389, G400

value: mTEChi


title: NRF_Ctrl_rep3


title: mTEChi, adult, WT, cell388, G400

value: male


title: mTEChi, adult, WT, cell399, G400


title: mTEChi, adult, WT, cell386, G400


title: NRF_Ctrl_rep2


title: NRF_Ctrl_rep1


title: mTEChi, adult, WT, cell387, G400


title: GFP_w.o_Cys_rep1


title: mTEChi, adult, WT, cell385, G400


title: RNA-seq_RPE_Y2334N_rep2

description: ribodepletion

data_processing:
RNA-seq reads were mapped against the human genome (version hg38) with GENCODE gene annotation using STAR (version 2.7.8a) with the following parameters: STAR --runMode alignReads --outSAMattributes All --outSAMtype BAM SortedByCoordinate --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04.
Reads were counted into exons of genes using htseq-count (version 0.13.5) with default parameters and the count tables used as input for differential gene expression analyses with DESeq2 (version 1.30.1).
Assembly: hg38
Supplementary files format and content: Count tables in .txt format.

extract_protocol:
Total RNA was isolated using the Trizol method.
For RNA-seq, total RNA was subjected to ribodepletion and libraries were generated using the KAPA RNA HyperPrep Kit with RiboErase (Roche). RNA-seq libraries were sequenced on an Illumina NEXTSeq500 instrument (paired-end 75-nt reads; 35 million reads per replicate).

treatment_protocol: No treatment.

value: RPE


title: RNA-seq_RPE_Y2334N_rep1

description: ribodepletion


title: RNA-seq_RPE_WT_rep2

description: ribodepletion


title: RNA-seq_RPE_WT_rep1

description: ribodepletion


title: mTEChi, adult, WT, cell383, G400


title: mTEChi, adult, WT, cell382, G400


title: mTEChi, adult, WT, cell381, G400


title: mTEChi, adult, WT, cell384, G400


title: cTEC, adult, WT, cell77

value: cTEC


title: mTEChi, adult, WT, cell380, G400


title: cTEC, adult, WT, cell76


title: mTEChi, adult, WT, cell379, G400


title: cTEC, adult, WT, cell74


title: mTEChi, adult, WT, cell378, G400


title: cTEC, adult, WT, cell73


title: cTEC, adult, WT, cell75


title: mTEChi, adult, WT, cell377, G400


title: cTEC, adult, WT, cell72


title: cTEC, adult, WT, cell70


title: mTEChi, adult, WT, cell374, G400


title: mTEChi, adult, WT, cell375, G400


title: cTEC, adult, WT, cell69


title: mTEChi, adult, WT, cell373, G400


title: mTEChi, adult, WT, cell372, G400


title: cTEC, adult, WT, cell66


title: mTEChi, adult, WT, cell371, G400


title: mTEChi, adult, WT, cell370, G400


title: cTEC, adult, WT, cell65


title: cTEC, adult, WT, cell67


title: cTEC, adult, WT, cell64


title: mTEChi, adult, WT, cell369


title: mTEChi, adult, WT, cell368


title: mTEChi, adult, WT, cell367


title: mTEChi, adult, WT, cell366


title: mTEChi, adult, WT, cell365


title: cTEC, adult, WT, cell63


title: cTEC, adult, WT, cell62


title: cTEC, adult, WT, cell61


title: mTEChi, adult, WT, cell364


title: mTEChi, adult, WT, cell376, G400


title: mTEChi, adult, WT, cell363


title: cTEC, adult, WT, cell57


title: cTEC, adult, WT, cell59


title: mTEChi, adult, WT, cell362


title: cTEC, adult, WT, cell71


title: mTEChi, adult, WT, cell361


title: cTEC, adult, WT, cell56


title: cTEC, adult, WT, cell55


title: cTEC, adult, WT, cell53


title: cTEC, adult, WT, cell54


title: mTEChi, adult, WT, cell357


title: cTEC, adult, WT, cell51


title: mTEChi, adult, WT, cell355


title: cTEC, adult, WT, cell50


title: mTEChi, adult, WT, cell354


title: cTEC, adult, WT, cell68


title: cTEC, adult, WT, cell60


title: cTEC, adult, WT, cell49


title: mTEChi, adult, WT, cell353


title: mTEChi, adult, WT, cell352


title: cTEC, adult, WT, cell47


title: cTEC, adult, WT, cell58


title: cTEC, adult, WT, cell48


title: mTEChi, adult, WT, cell351


title: mTEChi, adult, WT, cell350


title: mTEChi, adult, WT, cell349


title: mTEChi, adult, WT, cell360


title: mTEChi, adult, WT, cell348


title: mTEChi, adult, WT, cell347


title: mTEChi, adult, WT, cell359


title: mTEChi, adult, WT, cell358


title: cTEC, adult, WT, cell42


title: mTEChi, adult, WT, cell346


title: mTEChi, adult, WT, cell345


title: cTEC, adult, WT, cell52


title: cTEC, adult, WT, cell40


title: cTEC, adult, WT, cell43


title: cTEC, adult, WT, cell41


title: cTEC, adult, WT, cell39


title: mTEChi, adult, WT, cell343


title: cTEC, adult, WT, cell38


title: cTEC, adult, WT, cell37


title: mTEChi, adult, WT, cell356


title: mTEChi, adult, WT, cell341


title: cTEC, adult, WT, cell35


title: cTEC, adult, WT, cell34


title: mTEChi, adult, WT, cell339


title: cTEC, adult, WT, cell45


title: mTEChi, adult, WT, cell338


title: cTEC, adult, WT, cell33


title: cTEC, adult, WT, cell44


title: mTEChi, adult, WT, cell337


title: cTEC, adult, WT, cell32


title: mTEChi, adult, WT, cell336


title: cTEC, adult, WT, cell31


title: mTEChi, adult, WT, cell335


title: cTEC, adult, WT, cell30


title: mTEChi, adult, WT, cell334


title: cTEC, adult, WT, cell29


title: mTEChi, adult, WT, cell344


title: mTEChi, adult, WT, cell333


title: mTEChi, adult, WT, cell332


title: cTEC, adult, WT, cell28


title: cTEC, adult, WT, cell27


title: mTEChi, adult, WT, cell331


title: mTEChi, adult, WT, cell340


title: cTEC, adult, WT, cell36


title: mTEChi, adult, WT, cell342


title: cTEC, adult, WT, cell46


title: mTEChi, adult, WT, cell330


title: cTEC, adult, WT, cell24


title: mTEChi, adult, WT, cell328


title: mTEChi, adult, WT, cell329


title: cTEC, adult, WT, cell22


title: cTEC, adult, WT, cell23


title: mTEChi, adult, WT, cell327


title: mTEChi, adult, WT, cell326


title: mTEChi, adult, WT, cell325


title: cTEC, adult, WT, cell20


title: cTEC, adult, WT, cell21


title: mTEChi, adult, WT, cell324


title: cTEC, adult, WT, cell19


title: mTEChi, adult, WT, cell323


title: cTEC, adult, WT, cell18


title: mTEChi, adult, WT, cell322


title: cTEC, adult, WT, cell17


title: mTEChi, adult, WT, cell321


title: cTEC, adult, WT, cell16


title: mTEChi, adult, WT, cell320


title: cTEC, adult, WT, cell26


title: cTEC, adult, WT, cell25


title: mTEChi, adult, WT, cell319


title: cTEC, adult, WT, cell15


title: cTEC, adult, WT, cell14


title: mTEChi, adult, WT, cell317


title: mTEChi, adult, WT, cell316


title: cTEC, adult, WT, cell10


title: mTEChi, adult, WT, cell314


title: mTEChi, adult, WT, cell318


title: cTEC, adult, WT, cell13


title: cTEC, adult, WT, cell12


title: cTEC, adult, WT, cell9


title: cTEC, adult, WT, cell8


title: mTEChi, adult, WT, cell313


title: cTEC, adult, WT, cell7


title: cTEC, adult, WT, cell11


title: mTEChi, adult, WT, cell312


title: mTEChi, adult, WT, cell310


title: mTEChi, adult, WT, cell309


title: mTEChi, adult, WT, cell308


title: mTEChi, adult, WT, cell311


title: cTEC, adult, WT, cell3


title: cTEC, adult, WT, cell6


title: cTEC, adult, WT, cell5


title: mTEChi, adult, WT, cell307


title: mTEChi, adult, WT, cell306


title: cTEC, adult, WT, cell4


title: cTEC, adult, WT, cell2


title: mTEChi, adult, WT, cell305


title: cTEC, adult, WT, cell1


title: mTEChi, adult, AireKO, cell338

value: AireKO


title: mTEChi, adult, AireKO, cell337


title: mTEChi, adult, WT, cell315


title: mTEChi, adult, WT, cell303


title: mTEChi, adult, WT, cell302


title: mTEChi, adult, AireKO, cell335


title: mTEChi, adult, AireKO, cell336


title: mTEChi, adult, AireKO, cell333


title: mTEChi, adult, WT, cell300


title: mTEChi, adult, AireKO, cell334


title: mTEChi, adult, WT, cell299


title: mTEChi, adult, AireKO, cell332


title: mTEChi, adult, WT, cell301


title: mTEChi, adult, WT, cell298


title: mTEChi, adult, AireKO, cell331


title: mTEChi, adult, WT, cell297


title: mTEChi, adult, AireKO, cell330


title: mTEChi, adult, WT, cell295


title: mTEChi, adult, WT, cell304


title: mTEChi, adult, WT, cell296


title: mTEChi, adult, AireKO, cell329


title: mTEChi, adult, AireKO, cell327


title: mTEChi, adult, AireKO, cell328


title: mTEChi, adult, AireKO, cell326


title: mTEChi, adult, WT, cell293


title: mTEChi, adult, WT, cell292


title: mTEChi, adult, WT, cell291


title: mTEChi, adult, AireKO, cell325


title: mTEChi, adult, AireKO, cell324


title: mTEChi, adult, WT, cell288


title: mTEChi, adult, WT, cell290


title: mTEChi, adult, AireKO, cell322


title: mTEChi, adult, WT, cell289


title: mTEChi, adult, AireKO, cell321


title: mTEChi, adult, AireKO, cell319


title: mTEChi, adult, WT, cell287


title: mTEChi, adult, WT, cell284


title: mTEChi, adult, AireKO, cell318


title: mTEChi, adult, AireKO, cell320


title: mTEChi, adult, AireKO, cell316


title: mTEChi, adult, WT, cell282


title: mTEChi, adult, WT, cell286


title: mTEChi, adult, AireKO, cell315


title: mTEChi, adult, WT, cell294


title: mTEChi, adult, WT, cell283


title: mTEChi, adult, AireKO, cell317


title: mTEChi, adult, WT, cell281


title: mTEChi, adult, AireKO, cell314


title: mTEChi, adult, AireKO, cell312


title: mTEChi, adult, WT, cell279


title: mTEChi, adult, WT, cell278


title: mTEChi, adult, WT, cell280


title: mTEChi, adult, AireKO, cell310


title: mTEChi, adult, AireKO, cell311


title: mTEChi, adult, AireKO, cell323


title: mTEChi, adult, WT, cell276


title: mTEChi, adult, AireKO, cell309


title: mTEChi, adult, WT, cell275


title: mTEChi, adult, WT, cell277


title: mTEChi, adult, WT, cell285


title: mTEChi, adult, WT, cell274


title: mTEChi, adult, AireKO, cell308


title: mTEChi, adult, WT, cell273


title: mTEChi, adult, AireKO, cell307


title: mTEChi, adult, AireKO, cell306


title: mTEChi, adult, WT, cell271


title: mTEChi, adult, AireKO, cell305


title: mTEChi, adult, AireKO, cell304


title: mTEChi, adult, AireKO, cell313


title: mTEChi, adult, AireKO, cell303


title: mTEChi, adult, WT, cell269


title: mTEChi, adult, AireKO, cell302


title: mTEChi, adult, WT, cell267


title: mTEChi, adult, AireKO, cell301


title: mTEChi, adult, AireKO, cell300


title: mTEChi, adult, WT, cell266


title: mTEChi, adult, AireKO, cell299


title: mTEChi, adult, WT, cell265


title: mTEChi, adult, AireKO, cell298


title: mTEChi, adult, AireKO, cell297


title: mTEChi, adult, AireKO, cell296


title: mTEChi, adult, WT, cell264


title: mTEChi, adult, WT, cell263


title: mTEChi, adult, WT, cell262


title: mTEChi, adult, AireKO, cell295


title: mTEChi, adult, WT, cell261


title: mTEChi, adult, AireKO, cell294


title: mTEChi, adult, WT, cell260


title: mTEChi, adult, WT, cell272


title: mTEChi, adult, AireKO, cell293


title: mTEChi, adult, WT, cell259


title: mTEChi, adult, AireKO, cell292


title: mTEChi, adult, WT, cell270


title: mTEChi, adult, AireKO, cell291


title: mTEChi, adult, WT, cell258


title: mTEChi, adult, WT, cell268


title: mTEChi, adult, WT, cell256


title: mTEChi, adult, WT, cell257


title: mTEChi, adult, AireKO, cell289


title: mTEChi, adult, WT, cell254


title: mTEChi, adult, WT, cell253


title: mTEChi, adult, AireKO, cell287


title: mTEChi, adult, AireKO, cell288


title: mTEChi, adult, AireKO, cell286


title: mTEChi, adult, WT, cell252


title: mTEChi, adult, WT, cell255


title: mTEChi, adult, WT, cell249


title: mTEChi, adult, WT, cell250


title: mTEChi, adult, WT, cell251


title: mTEChi, adult, AireKO, cell284


title: mTEChi, adult, AireKO, cell282


title: mTEChi, adult, AireKO, cell283


title: mTEChi, adult, WT, cell247


title: mTEChi, adult, AireKO, cell280


title: mTEChi, adult, WT, cell246


title: mTEChi, adult, AireKO, cell279


title: mTEChi, adult, AireKO, cell278


title: mTEChi, adult, AireKO, cell281


title: mTEChi, adult, AireKO, cell290


title: mTEChi, adult, AireKO, cell277


title: mTEChi, adult, WT, cell245


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title: mTEChi, adult, WT, cell163