title: CB482 Control leaf,48 hr

city: Beijing

first: Zeng

last: Hongmei

state: Beijing

address: Chinese Academy of Agricultural Sciences, 12 Zhongguancun,, Haidian district, Building 39, International Students Dorm

department: Biological Control

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Reads with adaptors, unknown bases more than 10%, and low quality reads were removed before downstream analysis was carried out.
Bowtie2 was used to map clean reads to reference genes and HISAT map reads to reference genome.
RSEM was used to compute the Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene. FPKM method is used in the calculated expression level.
NOISeq method was used to screen differentially expressed genes between two groups. The sample's gene expression in each group was computed to log2(foldchange).
All DEGs were first mapped to GO terms on http://www.geneontology.org/ by calculating the gene numbers for each term. A hypergeometric test was then performed to identify significantly enriched GO terms on the GO term finder platform (http://www.yeastgenome.org/help/analyze/goterm-finder). KEGG pathway enrichment analysis was performed using the public database for genes and genomes (https://www.kegg.jp/kegg/kegg1.html) to enhance the overall understanding of the biological functions of the DEGs.
Assembly: Os-Nipponbare-Reference-IRGP-1.0
Supplementary files format and content: *.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa Japonica Group

source_name: leaf

growth_protocol: Rice cv. Nipponbare (Oryza sativa spp. japonica) seeds were surface-sterilized in a 5% NaClO solution for 10 min and rinsed seven times with double-distilled water (ddH2O). The seeds were spread on soaked Whatman filter paper, placed in a 30 mm Petri dish, and incubated in a growth chamber to sprout. The growth chamber was set at 30 °C under light and 25 °C in the dark under a 12/12 h photoperiod. Seedlings were transplanted into nutrient-rich soil after 5 d and grown in a greenhouse under the same conditions to reach the 3-leaf stage.

extract_protocol:
Total RNA was extracted using the Easy Pure Plant RNA Kit (Transgene Biotechnology Company) by following the manufacturer's protocol. Total RNA (3 μg) was reverse transcribed into first-strand cDNA following the instructions and kit from Transcript all-in-one first-strand cDNA Synthesis SuperMix (Transgene Biotechnology Company).
RNA extracted from twenty-four samples (triplicate samples per time point) of Hrip1-treated and buffer-treated seedlings were sequenced using the RICfoiR_BGISEQ-500 RNA_Seq platform (BGI Co., Ltd., Beijing, China), following the RICfoiR_BGISEQ-500 protocol.

treatment_protocol: 30 nM Hrip1 protein was sprayed on rice seedlings at the third-leaf stage. Control plants were sprayed with 30 µM Tris-HCl buffer, pH8.0. Triplicate samples were obtained from both Hrip1-treated (HT) and control buffer-treated (CB) plants after 6, 12, 24, and 48 h for RNA-seq analysis.

tag: cultivar

value: Nipponbare

tag: tissue

value: leaf

value: Tris-HCl buffer control

tag: time

value: 48 hr


title: 13168

status: Public on Aug 21 2022

type: RNA

city: Bethesda

first: Mallikarjuna

middle: Rao

last: Gedda

state: MD

address: 6 Center Dr

country: USA

institute: NEI

hyb_protocol: Hybridisation at 65°C for 16 hours using PCR,

scan_protocol: Post hybridization steps and scanning were performed on the nCounter Prep Station and Digital Analyzer

data_processing: R (Version 4.1.1)

molecule: total RNA

organism: Homo sapiens

source_name: COVID convalenscent whole blood

extract_protocol: RNA extraction, Nanodrop, Bioanalyser .

treatment_protocol: ACK Lysis of Whole Blood

value: plate 7

tag: date

tag: generlf

tag: systemapf

tag: fovcount

tag: fovcounted

tag: scannerid

tag: stageposition

tag: bindingdensity

tag: cartridgeid

value: tcr diversity plate 7 wb 12142020


title: HT481 leaf, 48 hr

type: SRA

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: transcriptomic

tag: treatment


title: MInt2APC

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome mm10 with STAR aligner (version STAR_2.6.1c ), using Ensembl 91 gene models. TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: mm10
Supplementary_files_format_and_content: TPM gene expression in csv file

organism: Mus musculus

source_name: Intestine

extract_protocol:
1. Sort into clear RNase free tube containing 200ul of Trizol, use 27G needle to homogenize cells. 2. Filled samples up to 1ml with Trizol, and added 200µl chloroform per 1ml of Trizol to each sample. 3. Incubation 10 min and Centrafuge. 4.Transferred 400µl of the upper aqueous layer to a new tube repeat step 2-3.  5.Transferred ~400 of upper aqueous layer to the tube had 1.5µl glycogen. 6. Added 450µl Isopropanol to each sample and mix well. 7. Incubation 10 min and Centrafuge.  8.  Removed supernatant and Added 1ml 75% EtOH/DEPC H2O. 9. After centrafuge, removed supernatant and circled pellet with marker, air dried for 20 min. 10. Add adequate amount f DEPC H2O to each sample for 10min, mix well and keep at-80 ℃ until use.
Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina) and NEXTflex DNA barcodes (Perkin Elmer). The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies).  Libraries were re-quantified, normalized, pooled and sequenced on an Illumina NextSeq 500 instrument as High Output 75bp single read runs. Following sequencing, Illumina NextSeq Real Time Analysis version 2.4.11 and bcl2fastq2 version 2.20 were run to demultiplex reads and generate FASTQ files.

tag: strain/genotype

value: APCmin/+ mutant

tag: cell type

value: M-Myeloid-derived suppressor cells

value: Intestine


title: Mouse alveolar organoids, BLM48h, rep4

city: Hamamatsu

first: Yasunori

last: Enomoto

state: Shizuoka

address: 1-20-1 Handayama

department: Department of Regenerative and Infectious Pathology

country: Japan

institute: Hamamatsu University School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore ver. 0.6.5
Trimmed sequence reads were mapped to UCSC GRCm39/mm39 using HISAT2 ver. 2.2.1 with default parameters
Read count extraction was performed using StringTie ver. 2.1.4
Normalization was performed using edgeR ver. 3.32.1
Supplementary files format and content: GRCm39/mm39
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: Lung

extract_protocol:
RNA was harvested using ISOGEN (NIPPON GENE). 250 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep, Ligation following manufacturer's protocols.

value: Lung

tag: description

value: primary cells

value: Alveolar epithelial cell type 2

tag: genotype

value: Bleomycin (100μM), 48h


title: HT482 leaf, 48 hr

tag: cultivar


title: 13178_52


title: 13184_32

value: plate 6

value: tcr diversity plate 6 wb 12142020


title: 13158


title: HT483 leaf, 48 hr

tag: tissue


title: CB481 Control leaf,48 hr

tag: time


title: Mouse alveolar organoids, BLM48h, rep1


title: HT243 leaf, 24 hr

value: 24 hr


title: CB243 Control leaf,24 hr


title: GInt2APC

value: G-Myeloid-derived suppressor cells


title: CB483 Control leaf,48 hr

value: Nipponbare


title: HT242 leaf, 24 hr

value: leaf


title: Gspl2APC

source_name: Spleen

value: Spleen


title: CB242 Control leaf,24 hr

value: Tris-HCl buffer control


title: 13155_42

tag: date


title: CB241 Control leaf,24 hr


title: Mspl2APC


title: HT241 leaf, 24 hr


title: Mspl1APC


title: CB122 Control leaf,12 hr

value: 12 hr


title: 13020_21

source_name: COVID convalenscent Whole Blood

extract_protocol: RNA extraction, Nanodrop, Bioanalyser.

value: host response panel plate 5 wb 11 19 2020

tag: generlf

tag: cartridgebarcode


title: 13147

tag: systemapf

tag: fovcount


title: CB123 Control leaf,12 hr


title: CB121 Control leaf,12 hr


title: Gspl1APC

value: APCmin/+ mutant


title: RNA_11: NME2-EV2

city: Budapest

first: István

last: Likó

address: Üllői út 26.

country: Hungary

institute: Semmelweis University

data_processing:
FASTQ Generation | Version: 1.0.0  on Illumina BaseSpaceFS version: 2.0.1018 system
Sequenced reads were trimmed for adaptor and low-quality sequence with trim_galore version 0.4.1 and cutadapt version 1.14
The trimmed sequence sets were aligned to the genome with TopHat v2.1.0 (bowtie2-align-s version 2.3.4.3), using default parameters
Performed union-CDS based count with R Rsubread package version 1.34.7 , and count processing and rpkm calculation with R edgeR package version 3.26.8
Assembly: hg19
Supplementary files format and content: tab-delimited text files include union-CDS based RPKM values and annotation information for each Sample

source_name: patient-derived normal fibroblast mRNA extract

growth_protocol: MDA-MB-231T cell lines were cultured in DMEM high glucose media supple-mented with 10% FBS, 2 mM L-glutamine, 100 µI/mL penicillin–streptomycin, 7.5% NaHCO3 and 50 mg/mL geneticin at 37 °C with 5% CO2. Fibroblast 203-9 cell line were cultured in DMEM high glucose media supplemented with 10% FBS, 2 mM L-glutamine, 100 µI/mL penicillin–streptomycin and 1% sodium pyruvate at 37 °C with 5% CO2.

extract_protocol:
After a 24 h incubation, fibroblasts were lysed, and RNA isolation was performed with RNeasy Mini kit (Qiagen, Hilden, Germany) as recommended by the manufacturer. The RNA concentration and purity were measured by NanoDrop (ND-100, RNA-40).
NEB NEXT ULTRA II Directional RNA Library Preparation Kit (Illumina,San Diego, CA, USA)

treatment_protocol: Extracellular vesicles (mEVs and sEVs) were isolated from the three transfected MDA-MB-231T cell lines and fibroblast were treated with the mixture of mEVs and sEVs in 6-well plate and incubated for 24 h at 37 °C with 5% CO2. Three parallel fibroblasts cultures were treated with EVs for each treatment (NME1-EVs, NME2-EVs, CO-EVs).

tag: cell line

value: NME2_EVs:mEVs and sEVs were isolated from MYC::NME2 overexpressing MDA-MB231T cells.

value: Fibroblasts were incubated for 24h with a mixture of NME2-EVs, then mRNA was isolated and RNAseq was peformed.


title: RNA_10: NME2-EV1

value: patient-derived normal fibroblast mRNA extract


title: MInt1APC

value: M-Myeloid-derived suppressor cells

value: Intestine


title: HT121 leaf, 12 hr


title: HT122 leaf, 12 hr


title: RNA_09: NME1-EV3

value: NME1-EVs:mEVs and sEVs were isolated from FLAG::NME1 overexpressing MDA-MB231T cells.

value: Fibroblasts were incubated for 24h with a mixture of NME1-EVs, then mRNA was isolated and RNAseq was peformed.


title: 13154_31

value: plate 6

tag: fovcounted

tag: scannerid

tag: stageposition

value: tcr diversity plate 6 wb 12142020


title: Mspl3BC

value: BALB/c immune-deficiency


title: 13130_31

tag: bindingdensity

tag: cartridgeid


title: 13146


title: 13119_41


title: 13118_42


title: RNA_08: NME1-EV2

tag: treatment


title: GInt1APC

tag: strain/genotype

tag: cell type

value: G-Myeloid-derived suppressor cells


title: RNA_12: NME2-EV3


title: Mspl1BC


title: CB63 Control leaf,6 hr

tag: cultivar

value: Nipponbare

value: leaf

value: 6 hr


title: HT123 leaf, 12 hr

tag: tissue

value: 12 hr


title: RNA_07: NME1-EV1


title: 13089

value: plate 5

value: tcr diversity plate 5 wb 12142020


title: 13092


title: 13107_21


title: Gspl3BC

value: Spleen


title: Mspl2BC


title: HT63 leaf, 6 hr

tag: time


title: RNA_03: Co-EV2

value: Co-EVs:mEVs and sEVs were isolated from control vector (pCDNA) expressing MDA-MB231T cells.

value: Fibroblasts were incubated for 24h with a mixture of Co-EVs, then mRNA was isolated and RNAseq was peformed.


title: Gspl1BC


title: CB62 Control leaf,6 hr

value: Tris-HCl buffer control


title: Mbm2B6

source_name: Bone marrow

value: C57BL/6 New born-P7

value: M-Myeloid-derived suppressor cells

value: Bone marrow


title: RNA_02: Co-EV1

value: patient-derived normal fibroblast mRNA extract


title: Gspl2BC


title: 13069

tag: date


title: HT62 leaf, 6 hr


title: NCI-H446_ERY974+Paclitaxel_9

city: Kajiwara

first: YUJI

last: SANO

state: Kamakura

institute: Chugai Pharmaceutical Co., Ltd

data_processing:
The RNAseq reads were mapped to human (GRCh38) and mouse (GRCm38) RefSeq transcripts  using  bowtie 1.1.2
Reads mapped to the transcripts of both organisms were excluded
The calculation of fragments per kilobase of transcript per million reads mapped (FPKM) using RSEM v1.2.31
Assembly: GRCh38 + CRCm38 with RefSeq annotations
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism:
Homo sapiens
Mus musculus

growth_protocol: NCI-H446 were expanded in vitro, and inoculated into the huNOG mice.

extract_protocol:
RNA was harvested from the tumors using RNeasy mini kit (Qiagen). Total RNA was used for RNAseq.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: When tumor was established, 20 mg/kg paclitaxel was administered one day before the administration of 5 mg/kg ERY974 in the combination group. In the monotherapy group, each agent was administered as described above. Then, tumours were collected on day 6 after ERY974 administration and used for RNA analysis.

value: Lung tumor

value: Day 6


title: Mbm3B6


title: 13068

tag: generlf


title: NCI-H446_ERY974+Paclitaxel_7


title: Mbm1B6


title: 13049_21

value: plate 26

value: tcr diversity plate 26 wb 12302020


title: NCI-H446_ERY974+Paclitaxel_6


title: 13060


title: Combine4_2

city: chapel hill

first: Jenny

middle: P

last: Ting

state: North Carolina

address: 450 West Drive

department: LCCC

institute: UNC-CH

data_processing:
samtools/1.15
Samples were processed using the samtools/1.15 program which aligned samples to the Ensembl mm10 genome using STAR(2.7.7a)
Read count extraction were performed using R package Rsubread (function featureCounts)
Assembly: mm10
Supplementary files format and content: excel file with raw counts for each gene in each sample

source_name: NK cells

extract_protocol:
Total RNA was extracted from sorted tumoral NK cells using the RNeasy Mini Kit (Qiagen, 74106). A total amount of 1 µg RNA per sample was used to generate sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit from Illumina® following manufacturer's protocols.

treatment_protocol: Tumor bearing mice were received 10µg cGAMP or PBS by intravenous (i.v.) injection, starting on day 8 post tumor cell injection, and repeated every 3 days for a total of 4 times. 200µg anti-IL-35 were intraperitoneally (i.p.) injected every 3 days for a total of 3 times starting on day 8 post tumor injection

value: NK cells

tag: genotype

value: WT

value: cGAMP, IL-35 blocking antibodies

value: Day 21


title: Combine4_3


title: 13041_31

tag: systemapf


title: Gbm3B6

value: G-Myeloid-derived suppressor cells


title: NCI-H446_ERY974+Paclitaxel_4


title: HT61 leaf, 6 hr

value: Nipponbare

value: leaf

value: 6 hr


title: NCI-H446_ERY974+Paclitaxel_5


title: NCI-H446_ERY974+Paclitaxel_8


title: CB61 Control leaf,6 hr

value: Tris-HCl buffer control


title: 13032

value: plate 5

tag: fovcount

value: tcr diversity plate 5 wb 12142020


title: Combine4

tag: cell line


title: aEb3_3

value: IL-35 blocking antibodies


title: aEb3_2


title: GMSpl2apc

value: APCmin/+ mutant

value: (G+M)-Myeloid-derived suppressor cells

value: Spleen


title: Gbm1B6

value: C57BL/6 New born-P7

value: Bone marrow


title: 13022_21

value: plate 26

tag: fovcounted

value: tcr diversity plate 26 wb 12302020


title: 13027_21

tag: scannerid


title: aEb3

value: NK cells

value: WT


title: NCI-H446_ERY974+Paclitaxel_3

value: Lung tumor

value: Day 6


title: NCI-H446_ERY974+Paclitaxel_1


title: cGAMP2_3

value: cGAMP

value: Day 21


title: GMSpl3apc


title: 12990_41

tag: stageposition


title: 13020_21

tag: bindingdensity


title: NCI-H446_Paclitaxel_9

value: Paclitaxel


title: GMSpl1apc


title: Gbm2B6

value: G-Myeloid-derived suppressor cells


title: NCI-H446_Paclitaxel_8


title: cGAMP2_2


title: cGAMP2


title: NCI-H446_Paclitaxel_6


title: GMint1apc

value: Intestine


title: GMint3apc


title: NCI-H446_Paclitaxel_7


title: NCI-H446_ERY974+Paclitaxel_2


title: GMint2apc


title: CTRL1_3

value: IgG


title: StroInt2apc

value: APCmin/+ mutant

value: Intestine single cells


title: StroInt3apc


title: NCI-H446_Paclitaxel_4


title: 12981_41

value: plate 4

tag: cartridgeid

value: tcr diversity plate 4 wb 12102020


title: 12966


title: 12967


title: 12983_21

value: plate 5

value: tcr diversity plate 5 wb 12142020


title: NCI-H446_Paclitaxel_5

tag: treatment


title: 12955_21


title: RAD21 Pds5a-KO siPds5b, Rep2

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

description:
RAD21_Pds5a-KO_siPds5b_Merge.bw
Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample. This was paired-end and only the first read of the pair was used for analysis (samples with "R1").

library_source: genomic

data_processing:
Any samples that were split scross sequencing lanes were treated as technical replicates and "L1" and "L2" were concatenated for each sample. If the sample was paired-end, only the first read of the pair was used for analysis (samples with "R1").
Alignment: reads were aligned to a hybrid mm10+hg38 genome with  bowtie v 1.2.3 with parameters -v 2 -p 24 -S -m 1 --best --strata
PCR Duplicate Removal: duplicates removed with samtools v 1.11 fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v2.2.7.1) with parameters -f BED -g mm -q 0.01
Spike-In Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = 1/(number human reads / 1,000,000)
Coverage File Generation: bigwig files were generated using bedtools (v 2.29.0) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normalization Factor) followed by ucsctools (v 320) bedGraphToBigWig
Assembly: Custom built bowtie index of Mus musculus build mm10 plus Homo sapiens build hg38
Supplementary files format and content: For each ChIP sample, a BigWig coverage track of merged replicates is provided for viewing in a genome browser.

molecule: genomic DNA

source_name: Mouse embryonic stem cells v6.5

growth_protocol: Murine embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Kagey et al. 2010).

extract_protocol:
mESCs were crosslinked in 1% formaldehyde for 5 minutes before quenching with 2.5M glycine. After chromatin extraction, 5% of HEK293T chromatin was added to the mESC samples to be later used as a spike-in normalization for the indicated experiments. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before washing and resuspension in Shearing Buffer. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 5, PIP/W 140, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1000 base pairs were generated. The antibodies were incubated with 30uL and 50uL Protein G Dynabeads for RAD21 and PDS5 IPs respectivly, for 6 hours prior to addition of chromatin. The chromatin in shearing buffer was spiked with NaCl and Triton X-100 to be in a ChIP buffer. Chromatin from 1 x 10^7 cells was added to antibody conjugated beads and incubated rotating overnight at 4C. Beads were then washed with ChIP Buffer and Wash Buffers 1, 2, and 3. Chromatin was eluted and crosslinks were reversed overnight via incubation at 65C and addition of 5ul Proteinase K. The next day, DNA was purified using a Zymo ChIP DNA Clean and Concentrate kit. Sequencing libraries were prepared using Kapa Hyper Prep Kit.
Sequencing libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems).

treatment_protocol: As indicated, cells were counted and 5 x 10^5 were plated per well in 6-well plates. Each well was treated with 50nM of siRNA or siGLO transfection control using DharmaFECT (Dharmacon) transfection reagent following manufacturer’s instructions: siGLO (D-001630-01-0) and siPds5b (M-058400-01-0005). Cell were harvested after 48 hours for crosslinking.

value: Pds5a knockout

value: mouse embryonic stem cells (mESCs)

tag: chip antibody

value: Abcam ab992


title: NCI-H446_Paclitaxel_3

tag: cell type

value: Lung tumor


title: StroInt1apc

tag: strain/genotype


title: RAD21 Pds5a-KO siPds5b, Rep1


title: 12968


title: NCI-H446_Paclitaxel_2

value: Day 6


title: GMspl3BC

value: BALB/c immune-deficiency

value: (G+M)-Myeloid-derived suppressor cells

tag: tissue

value: Spleen


title: RAD21 Pds5a-KO siGLO, Rep2

description:
RAD21_Pds5a-KO_siGLO_Merge.bw
Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample. This was paired-end and only the first read of the pair was used for analysis (samples with "R1").


title: CTRL1_2

value: NK cells

value: WT

tag: time

value: Day 21


title: NCI-H446_Paclitaxel_1

value: Paclitaxel


title: CTRL1

value: IgG


title: 12917_51

value: plate 4

tag: date


title: GMspl2BC


title: RAD21 Pds5a-KO siGLO, Rep1


title: GMspl1BC


title: NCI-H446_ERY974_10


title: RAD21 WT siPds5b, Rep2

description:
RAD21_WT_siPds5b_Merge.bw
Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample. This was paired-end and only the first read of the pair was used for analysis (samples with "R1").

value: Wildtype


title: BM3b6

value: C57BL/6 New born-P7

value: Bone marrow single cells

value: Bone marrow


title: RAD21 WT siPds5b, Rep1

value: mouse embryonic stem cells (mESCs)


title: 12929

tag: generlf

value: tcr diversity plate 4 wb 12102020


title: NCI-H446_ERY974_9

value: Lung tumor


title: BM1b6


title: 12954_21


title: NCI-H446_ERY974_8

value: Day 6


title: NCI-H446_ERY974_6


title: NCI-H446_ERY974_7


title: PDS5B Pds5a-KO, Rep1

description:
PDS5B_Pds5a-KO_Merge.bw
Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample. This was paired-end and only the first read of the pair was used for analysis (samples with "R1").

tag: genotype

value: Pds5a knockout

value: Bethyl A300-538A


title: 12915_21

value: plate 26

tag: systemapf

value: tcr diversity plate 26 wb 12302020


title: 12907

tag: fovcount


title: NCI-H446_ERY974_5

tag: cell line


title: Spleen_TRIF-KO_TNF

city: Medford

first: rebecca

last: batorsky

state: MA

address: 419 Boston Ave

institute: Tufts University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ were generated from the raw BCL files using 10x Genomics CellRanger (v3.0) mkfastq.
Paired-end reads were aligned to the mm10 Mouse reference genome using 10x Genomics CellRanger (v3.0) count with argument --expect-cells 10,000.
Putative doublet cells were removed using predictions generated from DoubletFinder (v2.0.3).
Cells were filtered using the Seurat R package (v4.1.1) to remove poor quality cells with <500 UMI and <250 genes.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single cell suspensions were generated from mouse spleens, red blood cells were lysed and dead cells were removed using MACS Dead Cell Removal Kit (130-090-101).
Librarys were prepared according to standard Illumina protocols on the NextSeq 550 platform, using the High Output 150 Cycle Kit with paired-end reads

treatment_protocol: 10-week-old wild type (B6) or TRIF-KO mice were intravenously injected with 100 ul of recombinant murine TNF (9ug) or PBS. After 4 hours mice were sacrificed and spleens were isolated.

value: Spleen

value: TRIF-KO (C57BL/6 background)

value: mTNF

tag: age

value: 10 weeks old


title: Spleen_TRIF-KO

description: 10x Genomics

value: PBS


title: PDS5A Pds5b-KO, Rep2

description:
PDS5A_Pds5b-KO_Merge.bw
Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample. This was paired-end and only the first read of the pair was used for analysis (samples with "R1").

value: Pds5b knockout

value: Bethyl A300-089A


title: PDS5B WT, Rep2

description:
PDS5B_WT_Merge.bw
Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample. This was paired-end and only the first read of the pair was used for analysis (samples with "R1").

value: Wildtype


title: NCI-H446_ERY974_3


title: NCI-H446_ERY974_4


title: Spleen_B6

description: 10x Genomics


title: BM2b6

value: C57BL/6 New born-P7

value: Bone marrow single cells

value: Bone marrow


title: PDS5B WT, Rep1

value: mouse embryonic stem cells (mESCs)


title: Spleen_B6_TNF

description: 10x Genomics


title: PDS5B Pds5a-KO, Rep2


title: NCI-H446_ERY974_2

value: Lung tumor

value: Day 6


title: NCI-H446_ERY974_1


title: Neuroblastoma, E6R, rep2

city: Cambridge

first: Samira

last: Ibrahim

address: 400 Technology Square

institute: Ragon Institute

description: Seq-Well

data_processing:
Cell barcode and UMI tagging of transcript reads was performed using StarSolo alignment pipeline (v2.7.9a)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human neuroblastoma SK-N-BE(2)-C cells

extract_protocol:
Cells were harvested by incubating them in TryplE (Thermo Fisher)
High-throughput scRNA-seq was performed using the Seq-Well S3 platform as previously described (Gierahn et al., 2017)

value: Human neuroblastoma SK-N-BE(2)-C cells


title: 12900

value: plate 3

tag: fovcounted

tag: scannerid

value: tcr diversity plate 3 wb 12102020


title: 12792_21

tag: stageposition

tag: bindingdensity


title: 12786_21

tag: cartridgeid


title: 12862_21


title: 12889_31

value: plate 25

value: tcr diversity plate 25 wb 12302020


title: 12896_52

value: plate 4

value: tcr diversity plate 4 wb 12102020


title: PDS5A WT, Rep2

description:
PDS5A_WT_Merge.bw
Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample. This was paired-end and only the first read of the pair was used for analysis (samples with "R1").

tag: chip antibody


title: NCI-H446_vehicle_10

tag: cell type

tag: treatment

value: Vehicle


title: Neuroblastoma, E6R, rep1

description: Seq-Well


title: PDS5A WT, Rep1


title: Pds5a-KO siStag2, Rep3

data_processing:
Reads Per Gene: Reads per gene were analyzed using STAR --runThreadN 24 -c SortedByCoordinate
Differentially expressed genes were identified using DESeq2 from Bioconductor (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: For each sample, a text file with reads per gene (gene count) is given.

molecule: polyA RNA

growth_protocol: Mouse embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Kagey et al. 2010).

extract_protocol:
Cells were resuspended in Trizol (Invitrogen) and RNA was extracted and purified using the Zymo Direct-zol RNA MiniPrep kit (Zymo).
Libraries were prepared by Novogene, with poly-A transcript enrichment and sequenced by Novogene.

treatment_protocol: Cells were counted and 5 x 10^5 were plated per well in 6-well plates. Each well was treated with 50nM of siRNA or siGLO transfection control using DharmaFECT 1 (Dharmacon) transfection reagent following manufacturer’s instructions: siGLO (D-001630-01-0), siPds5b (M-058400-01-0005), siStag1 (M-041989-01-0005), and siStag2 (M-057033-01-0005). Cell were harvested after 48 hours for RNA collection.

value: Pds5a knockout


title: Neuroblastoma, TSA, rep1

description: Seq-Well

value: TSA


title: NCI-H446_vehicle_9


title: PDS5A Pds5b-KO, Rep1

value: Pds5b knockout

value: Bethyl A300-089A


title: 12812_31


title: Pds5a-KO siStag2, Rep2


title: Pds5a-KO siStag2, Rep1


title: 12781


title: Neuroblastoma, TSA, rep2

description: Seq-Well


title: 12774


title: Neuroblastoma, DMSO, rep1

description: Seq-Well

value: DMSO


title: Neuroblastoma, DMSO, rep2

description: Seq-Well


title: Pds5a-KO siStag1, Rep3


title: Pds5a-KO siStag1, Rep1


title: NCI-H446_vehicle_8


title: 12772_31


title: Pds5a-KO siPds5b, Rep3


title: 12766


title: Pds5a-KO siStag1, Rep2


title: NCI-H446_vehicle_5


title: THP-1 macrophages DFO rep3

city: Kumamoto

first: Taishi

last: Yamane

address: 1-1-1 Honjo

institute: 1.	Department of Cell Signaling and Metabolic Medicine, Faculty of Life Sciences, Kumamoto University

data_processing:
NextSeq Control Software v4 were used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence using Trim Galore, then mapped to hg38 whole genome using HISTAT2.
Differential expression analysis was performed using the DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text files for differential gene expression between FAC-treated macrophages relative to DFO-treated macrophages.

source_name: macrophages

growth_protocol: THP-1 monocytes were differentiated into macrophages using 6 ng/mL phorbol 12-myristate 13-acetate for 48 h.

extract_protocol:
Total RNA was extracted from THP1 cells using TRIzol reagent. TruSeq Stranded mRNA Library Prep kit (#RS-122-2101; Illumina) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: THP-1 macrophages were pretreated with 100 μM FAC or 100 μM DFO for 8 h, followed by treatment with F. nucleatum at a multiplicity of infection (MOI) of 10 for 3 h.

value: wild type

value: deferoxamine


title: THP-1 macrophages FAC rep3

value: ferric anmonium citrate


title: NCI-H446_vehicle_6

value: Lung tumor

value: Day 6


title: NCI-H446_vehicle_7


title: NCI-H446_vehicle_2


title: 12726_21

value: plate 2

value: tcr diversity plate 2 wb 12102020


title: 12733


title: THP-1 macrophages DFO rep2


title: 12745


title: 12751_41


title: THP-1 macrophages DFO rep1


title: 12736


title: NCI-H446_vehicle_4


title: Pds5a-KO siPds5b, Rep2

value: mouse embryonic stem cells (mESCs)


title: Pds5a-KO siPds5b, Rep1


title: NCI-H446_vehicle_3


title: 12721


title: THP-1 macrophages FAC rep1


title: NCI-H446_vehicle_1


title: THP-1 macrophages FAC rep2


title: MKN45_ERY974+capecitabine_3

growth_protocol: MKN45 were expanded in vitro, and inoculated into the huNOG mice.

treatment_protocol: When tumor was established, 359 mg/kg capecitabine orally was administered one day before the administration of 5 mg/kg ERY974 for 5 consective days in the combination group. In the monotherapy group, each agent was administered as described above. Then, tumours were collected on day 14 after ERY974 administration and used for RNA analysis.

value: Gastric tumor

value: Day 14


title: 12709_21


title: 12727


title: Pds5b-KO siGLO, Rep3

value: siGLO control


title: 12707_31

value: plate 1

value: tcr diversity plate 1 wb 12102020


title: 12708 _51


title: MKN45_ERY974+capecitabine_2


title: Pds5a-KO siGLO, Rep3

value: Pds5a knockout


title: MKN45_Capecitabine_2

value: Capecitabine


title: Pds5b-KO siGLO, Rep1

value: Pds5b knockout


title: Pds5a-KO siGLO, Rep1


title: MKN45_Capecitabine_3


title: Pds5b-KO siGLO, Rep2


title: Pds5a-KO siGLO, Rep2


title: WT siPds5b, Rep3

value: Wildtype


title: MKN45_ERY974+capecitabine_1


title: WT siPds5b, Rep2


title: CGE cells at E18.5 biological replica 2

city: LONDON

first: Nicoletta

last: Kessaris

state: LONDON

address: Gower Street

department: WIBR

country: United Kingdom

institute: University College London

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450, according to the standard Affymetrix protocol for the array (Fluidics Script FS450_0004)

scan_protocol: Subsequent washing and scanning of the genechip arrays was performed on an Affymetrix GeneChip Fluidics station 450 and GCS3000 7G Affymetrix scanner respectively according to the manufacturer’s recommendations

data_processing: Data was normalised using the MAS5 algorithm to generate .CHP files

label: biotin

source_name: Purified Migrating CGE cells from the cortex at E18.5

label_protocol: Biotinylated cRNA were prepared using the Ambion MessageAmpII Biotin Enhanced kit from 500ng total RNA (MessageAmp II-Biotin Enhanced Kit User Guide, Ambion)

growth_protocol: Transgenic mice expressing fluorescent reporters

extract_protocol: RNeasy Micro Kit (Qiagen) RNA extraction followed by cDNA amplification using the NuGEN Ovation Pico System

treatment_protocol: Fluorescence-activated Cell Sorting (FACS) of labelled cells migrating in the cortex

tag: embryonic stage


title: 12694_21


title: CGE cells at E18.5 biological replica 3


title: MKN45_ERY974_3

tag: time


title: 12700_21

tag: date


title: 12693_21

tag: generlf


title: MKN45_Capecitabine_1


title: MKN45_ERY974_2


title: MGE cells at E18.5 biological replica 2

source_name: Purified Migrating MGE cells from the cortex at E18.5


title: WT siPds5b, Rep1

tag: genotype


title: 12672

tag: systemapf


title: 12688_41

tag: fovcount


title: MKN45_ERY974_1

tag: cell line


title: CGE cells at E18.5 biological replica 1


title: MGE cells at E18.5 biological replica 1


title: MGE cells at E18.5 biological replica 3


title: MKN45_vehicle_3

value: Vehicle


title: WT siGLO, Rep 2


title: WT siGLO, Rep 3


title: CGE cells at E16.5 biological replica 2

source_name: Purified Migrating CGE cells from the cortex at E16.5


title: MKN45_vehicle_1


title: 12591_51


title: MKN45_vehicle_2


title: 12650


title: WT siGLO, Rep 1


title: 12590


title: HN3-INPUT

status: Public on Aug 20 2022

city: Glasgow

first: Rachana

middle: Ravindra

last: Patel

state: Outside the United States or Canada

address: Bearsden, Switchback Road

department: Prostate Cancer

institute: Cancer Research UK Beatson Institute

data_processing:
For analyses of ChIP-Sequencing data, the quality checks on the raw ChIPSeq data files were done using fastqc version 0.10.1 and fastq_screen version 0.4.2. ChIPSeq single-end reads were aligned to the GRCm38 version of the mouse genome using tophat2 version 2.0.10 with Bowtie version 2.1.0.0. Regions of AR occupancy were determined using USeq Version 8.6.6 and MACS Version 1.4.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: alligned and normalised data as bw files and comparative peaks in csv file.

source_name: prostate tumour from 9 months old Ctnnb1pcex3(Δ)/+Ptenpc-/+ mouse 3

extract_protocol:
Minced frozen prostate tissue was fixed using 1% formaldehyde for 15 mins and quenched with Glycine (125mM) at room temperature for 5 mins.  Tissues were homogenised, nuclei isolated and lysed.  Nuclear lysates were sonicated using the Bioruptor sonicator on high setting 30s on/30s off for 25 minutes (2x 10 minutes + 1x 5 minutes). Pre-cleared chromatin samples using IgG were used for ChIP assay with AR antibody with protein G-agarose suspension. 10% input control was stored separated at -20°C. After ChIP at 4°C with rotation overnight, the pellet was washed and DNA isolated and dissolved for sequencing which was carried out at BGI
Libraries were prepared according to Illumina's instructions

tag: tissue type

value: prostate tumour

tag: strain


title: HN3-AR

treatment_protocol: Minced frozen prostate tissue was fixed using 1% formaldehyde for 15 mins and quenched with Glycine (125mM) at room temperature for 5 mins.  Tissues were homogenised, nuclei isolated and lysed.  Nuclear lysates were sonicated using the Bioruptor sonicator on high setting 30s on/30s off for 25 minutes (2x 10 minutes + 1x 5 minutes). Pre-cleared chromatin samples using IgG were used for ChIP assay with AR antibody with protein G-agarose suspension. 10% input control was stored separated at -20°C. After ChIP at 4°C with rotation overnight, the pellet was washed and DNA isolated and dissolved for sequencing which was carried out at BGI


title: HN1-AR

source_name: prostate tumour from 9 months old Ctnnb1pcex3(Δ)/+Ptenpc-/+ mouse 1


title: HN1-INPUT


title: 12645_21

tag: fovcounted

tag: scannerid


title: CGE cells at E16.5 biological replica 1


title: HN2-AR

source_name: prostate tumour from 9 months old Ctnnb1pcex3(Δ)/+Ptenpc-/+ mouse 2


title: HN2-INPUT


title: MGE cells at E14.5 biological replica 1

source_name: Purified Migrating MGE cells from the cortex at E14.5


title: WT3-INPUT

source_name: prostate tissue from 9 months old wildtype mouse 3

value: wild type

value: prostate tissue


title: MGE cells at E14.5 biological replica 2


title: WT2-INPUT

source_name: prostate tissue from 9 months old wildtype mouse 2


title: WT1-AR

source_name: prostate tissue from 9 months old wildtype mouse 1


title: WT1-INPUT


title: WT3-AR


title: WT2-AR


title: MGE cells at E14.5 biological replica 3


title: MV049G_Dneg7

first: Robert

last: Morrison

address: 29 Lincoln Drive

department: NIAID

institute: NIH

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to human genome GRC38.p2 using bowtie2 v2.3.4.3 with parameters  " -q --phred33-quals  --trim5 6  --trim3 4  --very-sensitive   -k 10  "
TPM values for each gene (Transcripts Per Million mapped reads) were calculated using R package DuffyNGS v1.9.1, using only reads landing within exon boundaries.
Assembly: GRCh38.p2
Supplementary files format and content: TPM

source_name: Whole blood

extract_protocol:
Whole blood was collected in PAXgene tubes from vaccinees and controls and stored at -80C. Total RNA was extracted using the PAXgene miRNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Whole blood

tag: day

tag: outcome

value: Infected

value: PreVaccination

value: 3 doses of 1.8M PfSPZ sporozoites


title: Hepatocyte (other donors)

city: Kyoto

first: Yoshiki

last: Nakashima

state: Kyoto

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChip array was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChip array was scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Hepatocyte

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit Thermo Fisher Scientific) from 100 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield was checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: The frozen hepatocytes were dissolved using KLC-TM medium (KaLy-Cell, Plobsheim, France). Hepatocytes were then seeded on two collagen-coated 100 mm dishes using KLC-SM medium (KaLy-Cell, Plobsheim, France). The medium was replaced after 6 and 24 hours. After 48 hours, the medium was changed using hepatocyte basal medium (CC-3199) (Lonza, Basel, Switzerland). Thereafter, the medium was changed every two days.

tag: cell type

value: Hepatocyte


title: iTS-L cells (No. 33)

source_name: iTS-L cells

value: iTS-L cells


title: iPSCs (201B7)

source_name: iPSCs

value: iPSCs


title: MV049G_D116

value: PostVaccination

tag: treatment


title: MV047K_Dneg7


title: MV047K_D116


title: MV048D_Dneg7

value: Uninfected


title: MV045S_Dneg7


title: MV048D_D116


title: Hepatocyte


title: MV045S_D116


title: MV040D_D116


title: MV039B_Dneg7


title: MV039B_D116


title: MV036K_Dneg7


title: MV037M_Dneg7


title: MV037M_D116


title: MV036K_D116


title: MV034Z_Dneg7


title: CGE cells at E16.5 biological replica 3

tag: embryonic stage


title: MV032K_D116

tag: time


title: MV032K_Dneg7


title: MV029K_Dneg7


title: MV033T_Dneg7


title: MV040D_Dneg7


title: MV031W_Dneg7


title: MV033T_D116


title: MV031W_D116


title: MV023P_Dneg7


title: MV023P_D116


title: MV028F_D116


title: MV021D_D116


title: hEnSC,GSK591,2

city: Nanjing

first: Xinyu

last: Cai

address: No.321 Zhongshan Road

department: Reproductive Medicine Center

institute: Drum Tower Hospital，Nanjing University Medical School

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default
Assembly: mm10
Supplementary files format and content: Rawcount values for each Sample

source_name: Endometrium

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

extract_protocol:
Total RNA was isolated from the mice oviducts following the standard TRIzol extraction protocol
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: The primary endometrial stromal cells were treated with 5μM GSK591 (#HY-100235, MCE) or solvent for 24h, then were incubated in DMEM/F12 medium without phenol red containing 2.5% carbon adsorbed serum. l μM MPA (Sigma) and 0.5 mM 8-Br-cAMP (Sigma) was added to the cellular supernatant for 48h.

value: Endometrium

value: stromal cells


title: hEnSC,GSK591,Decidual1


title: MV034Z_D116


title: MV029K_D116


title: hEnSC,GSK591,Decidual2


title: hEnSC,GSK591,1


title: hEnSC,Control,Decidual2

value: solvent


title: MV028F_Dneg7


title: hEnSC,Control,2


title: hEnSC,Control,1


title: GAT1-siRNA-2,  dorsal striatum, day 28

city: Shanghai

first: Yanjiao

last: WU

state: Shanghai

address: 280 South Chongqing Road

department: Discipline of Neuroscience and Department of Anatomy and Physiology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz.
Assembly: GRCm38
Supplementary files format and content: File include Count and  FPKM values for each sample

source_name: dorsal striatum

growth_protocol: Dorsal striatum of GAT1+/+ and GAT1–/– mice were maintained in -80 ℃.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Briefly, a 1.57 kb DNA fragment that contains the exon 2 and exon 3 of the mouse GAT1 gene was replaced by a 1.37 kb neomycin-resistant gene cassette (neo) to eliminate the GAT1 gene activity.

value: dorsal striatum

value: Day 28


title: GAT1-siRNA-3,  dorsal striatum, day 28


title: Control-2, dorsal striatum, day 28

value: GAT1+/+ mice


title: GAT1-siRNA-1,  dorsal striatum, day 28


title: MV021D_Dneg7


title: Control-1, dorsal striatum, day 28


title: Ex vivo gastric units (A3)

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description: mRNA

data_processing:
Data were analyzed using Cell Ranger™ pipelines which is available in 10x Genomics website.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix.

source_name: stomach

growth_protocol: Generation and culture of stomach gastric organoids was performed as described before (Bartfeld et al. 2015, Kayisoglu et al. 2020). Monolayers were allowed to grow using the culture media described above (ENRWFGTi_) and differentiate for 14 days to reach 90-100% confluency. Six days prior infection, primocin was exchange for H. pylori compatible antibiotics.

extract_protocol:
Ex vivo gastric units were isolated from gastric biopsies as described before (Bartfeld et al. 2015). Ex vivo gastric units, 3D organoids and 2D organoid-derived monolayers were made single cells by incubation with TripLE Express. Ex vivo units were stained for EpCam before sorting. Cells were then subjected to FACS sorting. Total RNA was isolated using 10x Chromium kit.
Cells were loaded in the 10X Genomics Chromium at a concentration of 200 cells/µl with the aim of recovering 3000 cells. Libraries were generated with the Chromium Single Cell 3’ Reagents Kit v2 Chemistry.
Chromium single cell 3'v2 (10X Genomics).

treatment_protocol: Infection: Organoid-derived monolayers were infected with Helicobacter pylori by adding the bacteria apically onto monolayers with a MOI of 1 for 6 h.

value: Ex vivo gastric unit

value: Epithelial gastric cells

value: untreated

tag: disease state

value: Healthy


title: hEnSC,Control,Decidual1


title: sur_batch2_rep382

city: Palo Alto

first: Xue

last: Feng

state: CA

address: 1651 Page Mill road

institute: Stanford

data_processing:
Illumina's bcl2fastq 2.17 software used for basecalling.
Raw data were trimmed by trim-galore (version 0.6.7) to remove adaptor sequences and aligned with Hisat2 (version 2.2.1) to the mouse reference genome (mm10). Transcripts per million reads (TPMs) per gene was calculated by StringTie (version 2.1.7), and genes with TPM > 0 were defined as detected genes.
All the downstream analysis was performed by R, using Seurat (version 4.1.0) with modifications.
Assembly: mm10
Supplementary files format and content: Matrix table with gene TPM for every gene and every sample

source_name: retina

extract_protocol:
The fresh isolated retinas at one day post retrograde labeling were dissociated with AMES solution. FACS purification with BD Influx System cell sorter was gated as: Alexa Fluor 488 positive but Texas Red negative RGCs were collected as surRGCs; Texas Red positive RGCs were collected as regRGCs. Individual cell was directly sorted into individual well of 96 well plate with 4ul pre-filled cell lysis buffer, containing 1 U/µl of Recombinant RNase inhibitor (Clontech), 0.1% Triton X-100 (Thermo), 2.5mM dNTP (Thermo), 2.5 µM oligodT30VN (5'AAGCAGTGGTATCAACGCAGAGTACT30VN-3', IDT). Cells were immediately spun down after sorting and frozen at -80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For AAV intravitreal injection, a pulled and polished microcapillary was inserted into the peripheral retina of around 4-week-old mice just behind the ora serrata. Approximately 2 µl of the vitreous was removed to allow injection of 2 µl AAV into the vitreous chamber. ONC was performed 2 weeks following AAV injection at about 7-8 weeks of age and crushed with a jeweler’s forceps (Dumont #5; Fine Science Tools, Foster City, California) for 5 seconds approximately 0.5 mm behind the eyeball. For retrograde labeling regenerating RGCs, the ON was exposed intraorbitally ~1.5-2 mm distal to the eyeball. A piece of tissue paper was placed in between the ON trunk and surrounding soft tissue to keep it from moving. A 33g needle was used to pock a hole on the dura at the injection site first, ~1 mm distal to ONC site. Then a glass micropipette connected with 50μL microsyringe (80900, Hamilton) that attached to a Micro4 controller was used to delivery ~60nL dextran into the ON through the pre-made hole, at a speed of 100nL/min. The leaking dye at injection site were removed by the tissue paper.

value: retinal ganglion cell (RGC)

value: retina

value: Pten knock out

tag: cell subtype

value: surviving RGCs (surRGCs)


title: sur_batch2_rep383

tag: genotype


title: sur_batch2_rep378


title: sur_batch2_rep381


title: sur_batch2_rep384


title: sur_batch2_rep376


title: sur_batch2_rep379


title: sur_batch2_rep380


title: sur_batch2_rep375


title: sur_batch2_rep369


title: sur_batch2_rep368


title: sur_batch2_rep374


title: sur_batch2_rep371


title: sur_batch2_rep372


title: Control-3, dorsal striatum, day 28


title: sur_batch2_rep377


title: sur_batch2_rep373


title: sur_batch2_rep364


title: sur_batch2_rep362


title: sur_batch2_rep365


title: sur_batch2_rep363


title: sur_batch2_rep361


title: sur_batch2_rep360


title: sur_batch2_rep370


title: sur_batch2_rep356


title: sur_batch2_rep352


title: sur_batch2_rep351


title: sur_batch2_rep347


title: sur_batch2_rep345


title: sur_batch2_rep357


title: sur_batch2_rep339


title: sur_batch2_rep367


title: sur_batch2_rep336


title: sur_batch2_rep359


title: sur_batch2_rep343


title: sur_batch2_rep344


title: sur_batch2_rep338


title: sur_batch2_rep340


title: sur_batch2_rep342


title: sur_batch2_rep366


title: sur_batch2_rep335


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title: sur_batch2_rep315


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title: sur_batch2_rep291


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title: sur_batch2_rep280


title: sur_batch2_rep284


title: sur_batch2_rep281


title: sur_batch2_rep283


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title: sur_batch2_rep276


title: sur_batch2_rep275


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title: sur_batch2_rep278


title: sur_batch2_rep274


title: sur_batch2_rep272


title: sur_batch2_rep273


title: sur_batch2_rep271


title: sur_batch2_rep268


title: sur_batch2_rep269


title: sur_batch2_rep270


title: sur_batch2_rep265


title: sur_batch2_rep267


title: sur_batch2_rep282


title: sur_batch2_rep263


title: sur_batch2_rep264


title: sur_batch2_rep262


title: sur_batch2_rep261


title: sur_batch2_rep260


title: sur_batch2_rep259


title: sur_batch2_rep257


title: sur_batch2_rep256


title: sur_batch2_rep252


title: sur_batch2_rep254


title: sur_batch2_rep255


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title: sur_batch2_rep251


title: sur_batch2_rep250


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title: sur_batch2_rep249


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title: sur_batch2_rep234


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title: sur_batch2_rep212


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title: sur_batch2_rep199


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title: sur_batch2_rep194


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title: sur_batch2_rep181


title: sur_batch2_rep180


title: sur_batch2_rep191


title: sur_batch2_rep192


title: sur_batch2_rep188


title: sur_batch2_rep173


title: sur_batch2_rep172


title: sur_batch2_rep169


title: sur_batch2_rep178


title: sur_batch2_rep166


title: sur_batch2_rep167


title: sur_batch2_rep176


title: sur_batch2_rep163


title: sur_batch2_rep161


title: sur_batch2_rep174


title: sur_batch2_rep155


title: sur_batch2_rep150


title: sur_batch2_rep152


title: sur_batch2_rep170


title: sur_batch2_rep171


title: sur_batch2_rep160


title: sur_batch2_rep164


title: sur_batch2_rep175


title: sur_batch2_rep165


title: sur_batch2_rep144


title: sur_batch2_rep142


title: sur_batch2_rep154


title: sur_batch2_rep141


title: sur_batch2_rep151


title: sur_batch2_rep156


title: sur_batch2_rep162


title: sur_batch2_rep140


title: sur_batch2_rep147


title: sur_batch2_rep159


title: sur_batch2_rep143


title: sur_batch2_rep146


title: sur_batch2_rep193


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title: sur_batch2_rep149


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title: sur_batch2_rep145


title: sur_batch2_rep158


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title: sur_batch2_rep136


title: sur_batch2_rep168


title: sur_batch2_rep137


title: sur_batch2_rep132


title: sur_batch2_rep130


title: sur_batch2_rep129


title: sur_batch2_rep133


title: sur_batch2_rep128


title: sur_batch2_rep127


title: sur_batch2_rep123


title: sur_batch2_rep122


title: sur_batch2_rep124


title: sur_batch2_rep126


title: sur_batch2_rep118


title: sur_batch2_rep121


title: sur_batch2_rep120


title: sur_batch2_rep119


title: sur_batch2_rep117


title: sur_batch2_rep115


title: sur_batch2_rep134


title: sur_batch2_rep116


title: sur_batch2_rep114


title: sur_batch2_rep112


title: sur_batch2_rep111


title: sur_batch2_rep110


title: sur_batch2_rep113


title: sur_batch2_rep108


title: sur_batch2_rep105


title: sur_batch2_rep109


title: sur_batch2_rep104


title: sur_batch2_rep125


title: sur_batch2_rep107


title: sur_batch2_rep106


title: sur_batch2_rep103


title: sur_batch2_rep101


title: sur_batch2_rep102


title: sur_batch2_rep100


title: sur_batch2_rep96


title: sur_batch2_rep99


title: sur_batch2_rep94


title: sur_batch2_rep91


title: sur_batch2_rep95


title: sur_batch2_rep89


title: sur_batch2_rep98


title: sur_batch2_rep93


title: sur_batch2_rep88


title: sur_batch2_rep97


title: sur_batch2_rep131


title: sur_batch2_rep87


title: sur_batch2_rep78


title: sur_batch2_rep79


title: sur_batch2_rep80


title: sur_batch2_rep84


title: sur_batch2_rep86


title: sur_batch2_rep81


title: sur_batch2_rep83


title: sur_batch2_rep75


title: sur_batch2_rep90


title: sur_batch2_rep74


title: sur_batch2_rep76


title: sur_batch2_rep69


title: sur_batch2_rep68


title: sur_batch2_rep70


title: sur_batch2_rep92


title: sur_batch2_rep85


title: sur_batch2_rep71


title: sur_batch2_rep72


title: sur_batch2_rep77


title: sur_batch2_rep60


title: sur_batch2_rep65


title: sur_batch2_rep64


title: sur_batch2_rep66


title: sur_batch2_rep63


title: sur_batch2_rep55


title: sur_batch2_rep61


title: sur_batch2_rep52


title: sur_batch2_rep49


title: sur_batch2_rep62


title: sur_batch2_rep51


title: sur_batch2_rep67


title: sur_batch2_rep73


title: sur_batch2_rep47


title: sur_batch2_rep45


title: sur_batch2_rep44


title: sur_batch2_rep41


title: sur_batch2_rep82


title: sur_batch2_rep54


title: sur_batch2_rep57


title: sur_batch2_rep59


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title: sur_batch2_rep46


title: sur_batch2_rep30


title: sur_batch2_rep31


title: sur_batch2_rep56


title: sur_batch2_rep53


title: sur_batch2_rep42


title: sur_batch2_rep29


title: sur_batch2_rep27


title: sur_batch2_rep43


title: sur_batch2_rep39


title: sur_batch2_rep50


title: sur_batch2_rep48


title: sur_batch2_rep24


title: sur_batch2_rep23


title: sur_batch2_rep22


title: sur_batch2_rep36


title: sur_batch2_rep40


title: sur_batch2_rep37


title: sur_batch2_rep33


title: sur_batch2_rep38


title: sur_batch2_rep34


title: sur_batch2_rep32


title: sur_batch2_rep16


title: sur_batch2_rep14


title: sur_batch2_rep26


title: sur_batch2_rep25


title: sur_batch2_rep11


title: sur_batch2_rep28


title: sur_batch2_rep7


title: sur_batch2_rep8


title: sur_batch2_rep21


title: sur_batch2_rep4


title: sur_batch2_rep35


title: sur_batch2_rep20


title: sur_batch2_rep18


title: sur_batch2_rep2


title: sur_batch2_rep17


title: sur_batch2_rep19


title: sur_batch2_rep6


title: sur_batch2_rep12


title: sur_batch2_rep138


title: sur_batch2_rep15


title: sur_batch2_rep5


title: sur_batch2_rep13


title: reg_batch2_rep381

value: regenerating RGCs (regRGCs)


title: sur_batch2_rep9


title: sur_batch2_rep1


title: reg_batch2_rep382


title: sur_batch2_rep10


title: reg_batch2_rep378


title: reg_batch2_rep380


title: reg_batch2_rep376


title: reg_batch2_rep383


title: sur_batch2_rep3


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title: reg_batch2_rep373


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title: reg_batch2_rep369


title: reg_batch2_rep371


title: reg_batch2_rep379


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title: reg_batch2_rep366


title: reg_batch2_rep364


title: reg_batch2_rep362


title: reg_batch2_rep363


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title: reg_batch2_rep361


title: reg_batch2_rep359


title: reg_batch2_rep355


title: reg_batch2_rep348


title: reg_batch2_rep351


title: reg_batch2_rep353


title: reg_batch2_rep354


title: reg_batch2_rep356


title: reg_batch2_rep350


title: reg_batch2_rep352


title: reg_batch2_rep358


title: reg_batch2_rep347


title: reg_batch2_rep365


title: reg_batch2_rep343


title: reg_batch2_rep345


title: reg_batch2_rep344


title: reg_batch2_rep342


title: reg_batch2_rep341


title: reg_batch2_rep338


title: reg_batch2_rep337


title: reg_batch2_rep349


title: reg_batch2_rep360


title: reg_batch2_rep339


title: reg_batch2_rep336


title: reg_batch2_rep334


title: reg_batch2_rep346


title: reg_batch2_rep331


title: reg_batch2_rep333


title: reg_batch2_rep329


title: reg_batch2_rep325


title: reg_batch2_rep322


title: reg_batch2_rep335


title: reg_batch2_rep326


title: reg_batch2_rep330


title: reg_batch2_rep327


title: reg_batch2_rep332


title: reg_batch2_rep318


title: reg_batch2_rep328


title: reg_batch2_rep324


title: reg_batch2_rep320


title: reg_batch2_rep323


title: reg_batch2_rep316


title: reg_batch2_rep315


title: reg_batch2_rep321


title: reg_batch2_rep313


title: reg_batch2_rep314


title: reg_batch2_rep319


title: reg_batch2_rep312


title: reg_batch2_rep311


title: reg_batch2_rep310


title: reg_batch2_rep340


title: reg_batch2_rep309


title: reg_batch2_rep308


title: reg_batch2_rep307


title: reg_batch2_rep306


title: reg_batch2_rep304


title: reg_batch2_rep305


title: reg_batch2_rep317


title: reg_batch2_rep303


title: reg_batch2_rep301


title: reg_batch2_rep298


title: reg_batch2_rep297


title: reg_batch2_rep300


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title: reg_batch2_rep295


title: reg_batch2_rep292


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title: reg_batch2_rep287


title: reg_batch2_rep288


title: reg_batch2_rep289


title: reg_batch2_rep286


title: reg_batch2_rep290


title: reg_batch2_rep291


title: reg_batch2_rep280


title: reg_batch2_rep279


title: reg_batch2_rep285


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title: reg_batch2_rep283


title: reg_batch2_rep302


title: reg_batch2_rep282


title: reg_batch2_rep281


title: reg_batch2_rep277


title: reg_batch2_rep274


title: reg_batch2_rep275


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title: reg_batch2_rep269


title: reg_batch2_rep272


title: reg_batch2_rep267


title: reg_batch2_rep268


title: reg_batch2_rep271


title: reg_batch2_rep266


title: reg_batch2_rep263


title: reg_batch2_rep264


title: reg_batch2_rep265


title: reg_batch2_rep262


title: reg_batch2_rep278


title: reg_batch2_rep276


title: reg_batch2_rep259


title: reg_batch2_rep250


title: reg_batch2_rep257


title: reg_batch2_rep248


title: reg_batch2_rep256


title: reg_batch2_rep254


title: reg_batch2_rep253


title: reg_batch2_rep251


title: reg_batch2_rep249


title: reg_batch2_rep260


title: reg_batch2_rep270


title: reg_batch2_rep246


title: reg_batch2_rep247


title: reg_batch2_rep261


title: reg_batch2_rep241


title: reg_batch2_rep238


title: reg_batch2_rep255


title: reg_batch2_rep258


title: reg_batch2_rep236


title: reg_batch2_rep237


title: reg_batch2_rep242


title: reg_batch2_rep252


title: reg_batch2_rep235


title: reg_batch2_rep239


title: reg_batch2_rep243


title: reg_batch2_rep233


title: reg_batch2_rep232


title: reg_batch2_rep240


title: reg_batch2_rep223


title: reg_batch2_rep234


title: reg_batch2_rep220


title: reg_batch2_rep227


title: reg_batch2_rep245


title: reg_batch2_rep230


title: reg_batch2_rep219


title: reg_batch2_rep218


title: reg_batch2_rep215


title: reg_batch2_rep228


title: reg_batch2_rep214


title: reg_batch2_rep221


title: reg_batch2_rep212


title: reg_batch2_rep224


title: reg_batch2_rep229


title: reg_batch2_rep231


title: reg_batch2_rep209


title: reg_batch2_rep213


title: reg_batch2_rep225


title: reg_batch2_rep244


title: reg_batch2_rep226


title: reg_batch2_rep205


title: reg_batch2_rep203


title: reg_batch2_rep200


title: reg_batch2_rep204


title: reg_batch2_rep201


title: reg_batch2_rep211


title: reg_batch2_rep207


title: reg_batch2_rep198


title: reg_batch2_rep217


title: reg_batch2_rep197


title: reg_batch2_rep222


title: reg_batch2_rep194


title: reg_batch2_rep210


title: reg_batch2_rep216


title: reg_batch2_rep195


title: reg_batch2_rep193


title: reg_batch2_rep196


title: reg_batch2_rep192


title: reg_batch2_rep191


title: reg_batch2_rep206


title: reg_batch2_rep188


title: reg_batch2_rep186


title: reg_batch2_rep199


title: reg_batch2_rep202


title: reg_batch2_rep184


title: reg_batch2_rep180


title: reg_batch2_rep208


title: reg_batch2_rep189


title: reg_batch2_rep178


title: reg_batch2_rep177


title: reg_batch2_rep190


title: reg_batch2_rep185


title: reg_batch2_rep182


title: reg_batch2_rep183


title: reg_batch2_rep174


title: reg_batch2_rep176


title: reg_batch2_rep187


title: reg_batch2_rep175


title: reg_batch2_rep169


title: reg_batch2_rep173


title: reg_batch2_rep168


title: reg_batch2_rep170


title: reg_batch2_rep167


title: reg_batch2_rep161


title: reg_batch2_rep164


title: reg_batch2_rep181


title: reg_batch2_rep165


title: reg_batch2_rep160


title: reg_batch2_rep162


title: reg_batch2_rep179


title: reg_batch2_rep171


title: reg_batch2_rep158


title: reg_batch2_rep156


title: reg_batch2_rep155


title: reg_batch2_rep154


title: reg_batch2_rep151


title: reg_batch2_rep157


title: reg_batch2_rep153


title: reg_batch2_rep159


title: reg_batch2_rep172


title: reg_batch2_rep150


title: reg_batch2_rep152


title: reg_batch2_rep149


title: reg_batch2_rep166


title: reg_batch2_rep147


title: reg_batch2_rep148


title: reg_batch2_rep163


title: reg_batch2_rep145


title: reg_batch2_rep146


title: reg_batch2_rep144


title: reg_batch2_rep142


title: reg_batch2_rep141


title: reg_batch2_rep138


title: reg_batch2_rep137


title: reg_batch2_rep139


title: reg_batch2_rep136


title: reg_batch2_rep134


title: reg_batch2_rep133


title: reg_batch2_rep130


title: reg_batch2_rep128


title: reg_batch2_rep143


title: reg_batch2_rep124


title: reg_batch2_rep125


title: reg_batch2_rep121


title: reg_batch2_rep120


title: reg_batch2_rep135


title: reg_batch2_rep140


title: reg_batch2_rep115


title: reg_batch2_rep126


title: reg_batch2_rep127


title: reg_batch2_rep112


title: reg_batch2_rep122


title: reg_batch2_rep131


title: reg_batch2_rep132


title: reg_batch2_rep109


title: reg_batch2_rep117


title: reg_batch2_rep119


title: reg_batch2_rep123


title: reg_batch2_rep113


title: reg_batch2_rep105


title: reg_batch2_rep104


title: reg_batch2_rep129


title: reg_batch2_rep118


title: reg_batch2_rep114


title: reg_batch2_rep102


title: reg_batch2_rep111


title: reg_batch2_rep116


title: reg_batch2_rep98


title: reg_batch2_rep99


title: reg_batch2_rep94


title: reg_batch2_rep93


title: reg_batch2_rep108


title: reg_batch2_rep107


title: reg_batch2_rep90


title: reg_batch2_rep106


title: reg_batch2_rep88


title: reg_batch2_rep84


title: reg_batch2_rep100


title: reg_batch2_rep103


title: reg_batch2_rep96


title: reg_batch2_rep97


title: reg_batch2_rep91


title: reg_batch2_rep75


title: reg_batch2_rep77


title: reg_batch2_rep81


title: reg_batch2_rep74


title: reg_batch2_rep79


title: reg_batch2_rep92


title: reg_batch2_rep95


title: reg_batch2_rep110


title: reg_batch2_rep86


title: reg_batch2_rep101


title: reg_batch2_rep89


title: reg_batch2_rep80


title: reg_batch2_rep78


title: reg_batch2_rep85


title: reg_batch2_rep72


title: reg_batch2_rep70


title: reg_batch2_rep69


title: reg_batch2_rep76


title: reg_batch2_rep68


title: reg_batch2_rep66


title: reg_batch2_rep65


title: reg_batch2_rep82


title: reg_batch2_rep83


title: reg_batch2_rep73


title: reg_batch2_rep57


title: reg_batch2_rep58


title: reg_batch2_rep64


title: reg_batch2_rep48


title: reg_batch2_rep52


title: reg_batch2_rep50


title: reg_batch2_rep46


title: reg_batch2_rep63


title: reg_batch2_rep87


title: reg_batch2_rep71


title: reg_batch2_rep67


title: reg_batch2_rep60


title: reg_batch2_rep41


title: reg_batch2_rep61


title: reg_batch2_rep62


title: reg_batch2_rep54


title: reg_batch2_rep49


title: reg_batch2_rep56


title: reg_batch2_rep36


title: reg_batch2_rep35


title: reg_batch2_rep44


title: reg_batch2_rep34


title: reg_batch2_rep51


title: reg_batch2_rep33


title: reg_batch2_rep53


title: reg_batch2_rep30


title: reg_batch2_rep55


title: reg_batch2_rep45


title: reg_batch2_rep32


title: reg_batch2_rep40


title: reg_batch2_rep28


title: reg_batch2_rep47


title: reg_batch2_rep59


title: reg_batch2_rep39


title: reg_batch2_rep43


title: reg_batch2_rep42


title: reg_batch2_rep37


title: reg_batch2_rep38


title: reg_batch2_rep25


title: reg_batch2_rep23


title: reg_batch2_rep29


title: reg_batch2_rep31


title: reg_batch2_rep26


title: reg_batch2_rep20


title: reg_batch2_rep22


title: reg_batch2_rep27


title: reg_batch2_rep16


title: reg_batch2_rep24


title: reg_batch2_rep18


title: reg_batch2_rep14


title: reg_batch2_rep13


title: reg_batch2_rep21


title: reg_batch2_rep15


title: reg_batch2_rep9


title: reg_batch2_rep19


title: reg_batch2_rep10


title: reg_batch2_rep5


title: reg_batch2_rep8


title: reg_batch2_rep17


title: reg_batch2_rep11


title: reg_batch2_rep6


title: reg_batch2_rep12


title: reg_batch2_rep2


title: reg_batch2_rep3


title: reg_batch2_rep7


title: reg_batch2_rep1


title: sur_batch1_rep384


title: sur_batch1_rep378


title: sur_batch1_rep383


title: sur_batch1_rep380


title: sur_batch1_rep379


title: sur_batch1_rep373


title: sur_batch1_rep370


title: sur_batch1_rep374


title: sur_batch1_rep371


title: sur_batch1_rep377


title: sur_batch1_rep372


title: sur_batch1_rep375


title: sur_batch1_rep369


title: reg_batch2_rep4


title: sur_batch1_rep368


title: sur_batch1_rep367


title: sur_batch1_rep359


title: sur_batch1_rep363


title: sur_batch1_rep365


title: sur_batch1_rep357


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title: sur_batch1_rep356


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title: sur_batch1_rep354


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title: sur_batch1_rep364


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title: sur_batch1_rep352


title: sur_batch1_rep346


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title: sur_batch1_rep355


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title: sur_batch1_rep362


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title: sur_batch1_rep361


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title: sur_batch1_rep333


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title: sur_batch1_rep322


title: sur_batch1_rep315


title: sur_batch1_rep324


title: sur_batch1_rep316


title: sur_batch1_rep317


title: sur_batch1_rep312


title: sur_batch1_rep314


title: sur_batch1_rep311


title: sur_batch1_rep319


title: sur_batch1_rep308


title: sur_batch1_rep325


title: sur_batch1_rep310


title: sur_batch1_rep326


title: sur_batch1_rep309


title: sur_batch1_rep305


title: sur_batch1_rep313


title: sur_batch1_rep307


title: sur_batch1_rep302


title: sur_batch1_rep301


title: sur_batch1_rep303


title: sur_batch1_rep306


title: sur_batch1_rep300


title: sur_batch1_rep297


title: sur_batch1_rep287


title: sur_batch1_rep298


title: sur_batch1_rep299


title: sur_batch1_rep286


title: sur_batch1_rep292


title: sur_batch1_rep296


title: sur_batch1_rep288


title: sur_batch1_rep291


title: sur_batch1_rep285


title: sur_batch1_rep289


title: sur_batch1_rep293


title: sur_batch1_rep294


title: sur_batch1_rep282


title: sur_batch1_rep283


title: sur_batch1_rep290


title: sur_batch1_rep280


title: sur_batch1_rep279


title: sur_batch1_rep284


title: sur_batch1_rep277


title: sur_batch1_rep278


title: sur_batch1_rep295


title: sur_batch1_rep275


title: sur_batch1_rep273


title: sur_batch1_rep274


title: sur_batch1_rep281


title: sur_batch1_rep276


title: sur_batch1_rep270


title: sur_batch1_rep266


title: sur_batch1_rep267


title: sur_batch1_rep256


title: sur_batch1_rep269


title: sur_batch1_rep264


title: sur_batch1_rep271


title: sur_batch1_rep265


title: sur_batch1_rep261


title: sur_batch1_rep255


title: sur_batch1_rep257


title: sur_batch1_rep253


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title: sur_batch1_rep268


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title: sur_batch1_rep250


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title: sur_batch1_rep240


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title: sur_batch1_rep237


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title: sur_batch1_rep304


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title: sur_batch1_rep226


title: sur_batch1_rep222


title: sur_batch1_rep220


title: sur_batch1_rep219


title: sur_batch1_rep239


title: sur_batch1_rep218


title: sur_batch1_rep213


title: sur_batch1_rep227


title: sur_batch1_rep215


title: sur_batch1_rep214


title: sur_batch1_rep216


title: sur_batch1_rep217


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title: sur_batch1_rep209


title: sur_batch1_rep202


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title: sur_batch1_rep193


title: sur_batch1_rep192


title: sur_batch1_rep212


title: sur_batch1_rep191


title: sur_batch1_rep188


title: sur_batch1_rep190


title: sur_batch1_rep187


title: sur_batch1_rep208


title: sur_batch1_rep189


title: sur_batch1_rep185


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title: sur_batch1_rep204


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title: sur_batch1_rep112


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title: sur_batch1_rep121


title: sur_batch1_rep117


title: sur_batch1_rep127


title: sur_batch1_rep138


title: sur_batch1_rep105


title: sur_batch1_rep119


title: sur_batch1_rep131


title: sur_batch1_rep102


title: sur_batch1_rep130


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title: sur_batch1_rep114


title: sur_batch1_rep108


title: sur_batch1_rep88


title: sur_batch1_rep134


title: sur_batch1_rep123


title: sur_batch1_rep86


title: sur_batch1_rep107


title: sur_batch1_rep103


title: sur_batch1_rep133


title: sur_batch1_rep83


title: sur_batch1_rep82


title: sur_batch1_rep101


title: sur_batch1_rep104


title: sur_batch1_rep81


title: sur_batch1_rep99


title: sur_batch1_rep106


title: sur_batch1_rep95


title: sur_batch1_rep93


title: sur_batch1_rep87


title: sur_batch1_rep109


title: sur_batch1_rep92


title: sur_batch1_rep80


title: sur_batch1_rep97


title: sur_batch1_rep96


title: sur_batch1_rep90


title: sur_batch1_rep91


title: sur_batch1_rep94


title: sur_batch1_rep78


title: sur_batch1_rep89


title: sur_batch1_rep84


title: sur_batch1_rep75


title: sur_batch1_rep74


title: sur_batch1_rep85


title: sur_batch1_rep71


title: sur_batch1_rep70


title: sur_batch1_rep72


title: sur_batch1_rep76


title: sur_batch1_rep79


title: sur_batch1_rep66


title: sur_batch1_rep73


title: sur_batch1_rep77


title: sur_batch1_rep65


title: sur_batch1_rep68


title: sur_batch1_rep64


title: sur_batch1_rep63


title: sur_batch1_rep62


title: sur_batch1_rep67


title: sur_batch1_rep69


title: sur_batch1_rep61


title: sur_batch1_rep60


title: sur_batch1_rep113


title: sur_batch1_rep58


title: sur_batch1_rep57


title: sur_batch1_rep59


title: sur_batch1_rep56


title: sur_batch1_rep55


title: reference male mouse13/ 0.05mGyLM

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

source_name: reference male mouse13

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail


title: reference male mouse13/ 0.05mGyL2

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: sur_batch1_rep54


title: 0.05mGyLM/ reference male mouse13


title: 0.05mGyL1/ reference male mouse13


title: reference male mouse13/ 0.05mGyLF


title: 0.05mGyK6/ reference male mouse13


title: sur_batch1_rep52


title: reference male mouse13/ 0.05mGyL1


title: reference male mouse13/ 0.05mGyK3


title: reference male mouse13/ 0.05mGyK5


title: sur_batch1_rep51


title: sur_batch1_rep53


title: 0.05mGyK2/ reference male mouse13


title: 0.05mGyLF/ reference male mouse13


title: 0.05mGyK7/ reference male mouse13


title: reference male mouse13/ 0.05mGyK6


title: sur_batch1_rep49


title: 0.05mGyK4/ reference male mouse13


title: 0.05mGyK3/ reference male mouse13


title: reference male mouse13/ 0.05mGyK7


title: sur_batch1_rep47


title: sur_batch1_rep46


title: sur_batch1_rep45


title: reference male mouse13/ 0.05mGyK4


title: 0.05mGyKF/ reference male mouse13


title: reference male mouse13/ 0.05mGyKM


title: 0.05mGyK1/ reference male mouse13


title: sur_batch1_rep44


title: reference male mouse6/ 0.05mGyJ6

source_name: reference male mouse6


title: reference male mouse13/ 0.05mGyK1


title: reference male mouse13/ 0.05mGyKF


title: sur_batch1_rep43


title: sur_batch1_rep42


title: sur_batch1_rep41


title: 0.05mGyK5/ reference male mouse13


title: 0.05mGyJ5/ reference male mouse6


title: sur_batch1_rep39


title: sur_batch1_rep37


title: sur_batch1_rep36


title: sur_batch1_rep40


title: sur_batch1_rep38


title: sur_batch1_rep34


title: sur_batch1_rep35


title: reference male mouse6/ 0.05mGyJ3


title: reference male mouse6/ 0.05mGyJ5


title: sur_batch1_rep48


title: reference male mouse13/ 0.05mGyK2


title: sur_batch1_rep50


title: sur_batch1_rep33


title: sur_batch1_rep32


title: sur_batch1_rep29


title: sur_batch1_rep31


title: 0.05mGyJ3/ reference male mouse6


title: 0.05mGyJ6/ reference male mouse6


title: 0.05mGyKM/ reference male mouse13


title: sur_batch1_rep28


title: reference male mouse6/ 0.05mGyJ4


title: 0.05mGyJ4/ reference male mouse6


title: 0.05mGyJ2/ reference male mouse6


title: sur_batch1_rep27


title: reference male mouse6/ 0.05mGyJ1


title: sur_batch1_rep30


title: sur_batch1_rep25


title: reference male mouse6/ 0.05mGyJ2


title: 0.05mGyJ1/ reference male mouse6


title: sur_batch1_rep26


title: sur_batch1_rep24


title: 0.05mGyI5/ reference male mouse6


title: sur_batch1_rep22


title: reference male mouse6/ 0.05mGyJF


title: sur_batch1_rep23


title: sur_batch1_rep21


title: reference male mouse6/ 0.05mGyI7


title: 0.05mGyJM/ reference male mouse6


title: sur_batch1_rep20


title: 0.05mGyI7/ reference male mouse6


title: reference male mouse6/ 0.05mGyI5


title: 0.05mGyI6/ reference male mouse6


title: reference male mouse6/ 0.05mGyI6


title: 0.05mGyJF/ reference male mouse6


title: sur_batch1_rep16


title: reference male mouse6/ 0.05mGyJM


title: sur_batch1_rep18


title: sur_batch1_rep19


title: sur_batch1_rep15


title: sur_batch1_rep14


title: 0.05mGyI1/ reference male mouse6


title: sur_batch1_rep13


title: sur_batch1_rep12


title: sur_batch1_rep17


title: sur_batch1_rep11


title: sur_batch1_rep10


title: reference male mouse6/ 0.05mGyI4


title: 0.05mGyI2/ reference male mouse6


title: reference male mouse6/ 0.05mGyI2


title: 0.05mGyI3/ reference male mouse6


title: sur_batch1_rep9


title: 0.05mGyI4/ reference male mouse6


title: sur_batch1_rep8


title: reference male mouse6/ 0.05mGyIM


title: sur_batch1_rep7


title: sur_batch1_rep6


title: reference male mouse6/ 0.05mGyI3


title: sur_batch1_rep5


title: 0.05mGyH5/ reference male mouse6


title: sur_batch1_rep4


title: sur_batch1_rep3


title: sur_batch1_rep2


title: reg_batch1_rep384

data_processing:
Illumina's bcl2fastq 2.17 software used for basecalling.
Raw data were trimmed by trim-galore (version 0.6.7) to remove adaptor sequences and aligned with Hisat2 (version 2.2.1) to the mouse reference genome (mm10). Transcripts per million reads (TPMs) per gene was calculated by StringTie (version 2.1.7), and genes with TPM > 0 were defined as detected genes.
All the downstream analysis was performed by R, using Seurat (version 4.1.0)5 with modifications.
Assembly: mm10
Supplementary files format and content: Matrix table with gene TPM for every gene and every sample


title: 0.05mGyH6/ reference male mouse6


title: reference male mouse6/ 0.05mGyI1


title: reference male mouse6/ 0.05mGyIF


title: reference male mouse6/ 0.05mGyH6


title: 0.05mGyH7/ reference male mouse6


title: reg_batch1_rep383


title: reference male mouse6/ 0.05mGyH7


title: 0.05mGyH4/ reference male mouse6


title: 0.05mGyIF/ reference male mouse6


title: reg_batch1_rep382


title: reg_batch1_rep381


title: 0.05mGyIM/ reference male mouse6


title: 0.05mGyH2/ reference male mouse6


title: reg_batch1_rep380


title: reg_batch1_rep379


title: reference male mouse6/ 0.05mGyH3


title: 0.05mGyH1/ reference male mouse6


title: reference male mouse6/ 0.05mGyH4


title: 0.05mGyH3/ reference male mouse6


title: reg_batch1_rep378


title: reg_batch1_rep376


title: reference male mouse6/ 0.05mGyH5


title: reference male mouse6/ 0.05mGyHM


title: reg_batch1_rep375


title: reg_batch1_rep374


title: sur_batch1_rep1


title: reference male mouse6/ 0.05mGyHF


title: reg_batch1_rep373


title: reference male mouse6/ 0.05mGyH2


title: 0.05mGyHM/ reference male mouse6


title: 0.05mGyHF/ reference male mouse6


title: reg_batch1_rep377


title: reg_batch1_rep371


title: reference male mouse5/ 0.05mGyG6

source_name: reference male mouse5


title: 0.05mGyG6/ reference male mouse5


title: reg_batch1_rep372


title: reg_batch1_rep370


title: reg_batch1_rep368


title: reference male mouse5/ 0.05mGyG4


title: reference male mouse5/ 0.05mGyG3


title: reg_batch1_rep367


title: 0.05mGyG3/ reference male mouse5


title: reg_batch1_rep369


title: 0.05mGyG2/ reference male mouse5


title: 0.05mGyG5/ reference male mouse5


title: reg_batch1_rep364


title: reg_batch1_rep366


title: 0.05mGyG4/ reference male mouse5


title: 0.05mGyG1/ reference male mouse5


title: reg_batch1_rep362


title: reference male mouse5/ 0.05mGyG5


title: reg_batch1_rep361


title: reference male mouse6/ 0.05mGyH1


title: reg_batch1_rep365


title: reference male mouse5/ 0.05mGyGM


title: reference male mouse5/ 0.05mGyG2


title: reg_batch1_rep357


title: reg_batch1_rep360


title: reg_batch1_rep359


title: reference male mouse5/ 0.05mGyGF


title: 0.05mGyGM/ reference male mouse5


title: reference male mouse5/ 0.05mGyF6


title: reg_batch1_rep358


title: 0.05mGyF4/ reference male mouse5


title: reg_batch1_rep356


title: 0.05mGyF6/ reference male mouse5


title: reference male mouse5/ 0.05mGyG1


title: 0.05mGyGF/ reference male mouse5


title: reg_batch1_rep363


title: reg_batch1_rep355


title: reg_batch1_rep354


title: reg_batch1_rep353


title: 0.05mGyF5/ reference male mouse5


title: reg_batch1_rep352


title: reg_batch1_rep349


title: reg_batch1_rep351


title: reg_batch1_rep350


title: reg_batch1_rep347


title: reg_batch1_rep348


title: reg_batch1_rep346


title: 0.05mGyF1/ reference male mouse5


title: reg_batch1_rep345


title: reference male mouse5/ 0.05mGyF1


title: 0.05mGyFF/ reference male mouse5


title: reference male mouse5/ 0.05mGyF2


title: reg_batch1_rep342


title: reference male mouse5/ 0.05mGyF3


title: reference male mouse5/ 0.05mGyE4


title: reference male mouse5/ 0.05mGyF5


title: reference male mouse5/ 0.05mGyF4


title: reg_batch1_rep343


title: reg_batch1_rep344


title: 0.05mGyF3/ reference male mouse5


title: reg_batch1_rep338


title: reg_batch1_rep339


title: reg_batch1_rep341


title: reference male mouse5/ 0.05mGyFF


title: reg_batch1_rep337


title: 0.05mGyF2/ reference male mouse5


title: reg_batch1_rep340


title: 0.05mGyFM/ reference male mouse5


title: 0.05mGyE6/ reference male mouse5


title: 0.05mGyE4/ reference male mouse5


title: 0.05mGyE3/ reference male mouse5


title: reg_batch1_rep336


title: reference male mouse5/ 0.05mGyEF


title: reference male mouse5/ 0.05mGyE5


title: 0.05mGyE5/ reference male mouse5


title: reg_batch1_rep334


title: reg_batch1_rep335


title: 0.05mGyE2/ reference male mouse5


title: reference male mouse5/ 0.05mGyE6


title: reg_batch1_rep332


title: reg_batch1_rep330


title: reg_batch1_rep329


title: reg_batch1_rep331


title: reg_batch1_rep328


title: reference male mouse5/ 0.05mGyEM


title: 0.05mGyD7/ reference male mouse5


title: reference male mouse5/ 0.05mGyE2


title: reg_batch1_rep326


title: reg_batch1_rep325


title: 0.05mGyD8/ reference male mouse5


title: reg_batch1_rep324


title: reference male mouse5/ 0.05mGyE3


title: reference male mouse5/ 0.05mGyE1


title: reference male mouse5/ 0.05mGyD6


title: reg_batch1_rep322


title: reg_batch1_rep333


title: 0.05mGyEF/ reference male mouse5


title: reg_batch1_rep321


title: reg_batch1_rep319


title: reference male mouse5/ 0.05mGyD7


title: reference male mouse5/ 0.05mGyD8


title: 0.05mGyD6/ reference male mouse5


title: reg_batch1_rep320


title: reg_batch1_rep318


title: 0.05mGyD5/ reference male mouse5


title: reg_batch1_rep316


title: reference male mouse5/ 0.05mGyFM


title: reg_batch1_rep317


title: reg_batch1_rep315


title: 0.05mGyD4/ reference male mouse5


title: reg_batch1_rep314


title: 0.05mGyD2/ reference male mouse5


title: reference male mouse5/ 0.05mGyD4


title: reference male mouse5/ 0.05mGyD3


title: reg_batch1_rep313


title: 0.05mGyE1/ reference male mouse5


title: 0.05mGyD3/ reference male mouse5


title: reference male mouse5/ 0.05mGyD2


title: reg_batch1_rep312


title: 0.05mGyDF/ reference male mouse5


title: reference male mouse5/ 0.05mGyD1


title: reg_batch1_rep310


title: reg_batch1_rep311


title: reg_batch1_rep327


title: reg_batch1_rep309


title: reg_batch1_rep308


title: reg_batch1_rep307


title: reg_batch1_rep305


title: 0.05mGyD1/ reference male mouse5


title: reg_batch1_rep304


title: reg_batch1_rep306


title: reference male mouse5/ 0.05mGyDF


title: 0.05mGyC5/ reference male mouse5


title: reference male mouse5/ 0.05mGyD5


title: reg_batch1_rep302


title: 0.05mGyDM/ reference male mouse5


title: 0.05mGyEM/ reference male mouse5


title: reg_batch1_rep301


title: reference male mouse5/ 0.05mGyDM


title: reg_batch1_rep303


title: reg_batch1_rep300


title: reg_batch1_rep299


title: reg_batch1_rep298


title: reference male mouse5/ 0.05mGyC5


title: reference male mouse5/ 0.05mGyC6


title: reg_batch1_rep323


title: 0.05mGyC3/ reference male mouse5


title: reg_batch1_rep296


title: reg_batch1_rep297


title: reg_batch1_rep295


title: 0.05mGyC4/ reference male mouse5


title: reg_batch1_rep293


title: reg_batch1_rep292


title: reference male mouse5/ 0.05mGyC3


title: reference male mouse5/ 0.05mGyC2


title: reg_batch1_rep291


title: reg_batch1_rep290


title: reference male mouse5/ 0.05mGyC1


title: 0.05mGyC2/ reference male mouse5


title: 0.05mGyCM/ reference male mouse5


title: reg_batch1_rep289


title: reg_batch1_rep288


title: 0.05mGyC1/ reference male mouse5


title: reg_batch1_rep287


title: reg_batch1_rep286


title: reference male mouse5/ 0.05mGyCF


title: reg_batch1_rep285


title: reference male mouse5/ 0.05mGyCM


title: 0.05mGyB8/ reference male mouse5


title: reference male mouse5/ 0.05mGyB7


title: 0.05mGyCF/ reference male mouse5


title: 0.05mGyB7/ reference male mouse5


title: reg_batch1_rep283


title: reg_batch1_rep284


title: reference male mouse5/ 0.05mGyB4


title: reference male mouse5/ 0.05mGyB8


title: reg_batch1_rep282


title: reference male mouse5/ 0.05mGyB5


title: 0.05mGyB6/ reference male mouse5


title: reference male mouse5/ 0.05mGyB6


title: 0.05mGyB5/ reference male mouse5


title: reference male mouse5/ 0.05mGyB3


title: 0.05mGyB4/ reference male mouse5


title: reg_batch1_rep277


title: 0.05mGyB3/ reference male mouse5


title: reg_batch1_rep276


title: reg_batch1_rep281


title: reg_batch1_rep275


title: reg_batch1_rep294


title: reg_batch1_rep274


title: reference male mouse5/ 0.05mGyB2


title: reg_batch1_rep278


title: reg_batch1_rep273


title: 0.05mGyB1/ reference male mouse5


title: 0.05mGyB2/ reference male mouse5


title: 0.05mGyBF/ reference male mouse5


title: reg_batch1_rep279


title: reg_batch1_rep272


title: reg_batch1_rep280


title: reg_batch1_rep271


title: reg_batch1_rep269


title: reg_batch1_rep270


title: reference male mouse5/ 0.05mGyB1


title: 0.05mGyBM/ reference male mouse5


title: reg_batch1_rep268


title: reg_batch1_rep267


title: reference male mouse5/ 0.05mGyBM


title: reg_batch1_rep266


title: reference male mouse5/ 0.05mGyA5


title: reg_batch1_rep265


title: reg_batch1_rep263


title: reg_batch1_rep264


title: 0.05mGyA6/ reference male mouse5


title: 0.05mGyC6/ reference male mouse5


title: reference male mouse5/ 0.05mGyBF


title: reg_batch1_rep261


title: reg_batch1_rep260


title: reference male mouse5/ 0.05mGyA6


title: reg_batch1_rep259


title: 0.05mGyA2/ reference male mouse5


title: reg_batch1_rep258


title: 0.05mGyA3/ reference male mouse5


title: reference male mouse5/ 0.05mGyA3


title: 0.05mGyA1/ reference male mouse5


title: 0.05mGyAF/ reference male mouse5


title: reference male mouse5/ 0.05mGyA4


title: reg_batch1_rep256


title: reference male mouse5/ 0.05mGyAF


title: reference male mouse5/ 0.05mGyA1


title: reg_batch1_rep257


title: reg_batch1_rep254


title: 0.05mGyA4/ reference male mouse5


title: reference male mouse5/ 0.05mGyA2


title: reg_batch1_rep253


title: reg_batch1_rep252


title: reg_batch1_rep251


title: reg_batch1_rep262


title: reg_batch1_rep250


title: reference male mouse12/ 1mGyO8

source_name: reference male mouse12


title: reg_batch1_rep249


title: reg_batch1_rep248


title: 1mGyO8/ reference male mouse12


title: reference male mouse12/ 1mGyO6


title: reference male mouse5/ 0.05mGyC4


title: reg_batch1_rep247


title: reg_batch1_rep245


title: 1mGyO7/ reference male mouse12


title: 1mGyO5/ reference male mouse12


title: reference male mouse12/ 1mGyO5


title: 1mGyO4/ reference male mouse12


title: reg_batch1_rep243


title: 1mGyO3/ reference male mouse12


title: 1mGyO2/ reference male mouse12


title: reference male mouse12/ 1mGyO2


title: reg_batch1_rep241


title: reference male mouse12/ 1mGyO3


title: 0.05mGyA5/ reference male mouse5


title: reg_batch1_rep255


title: reg_batch1_rep239


title: reg_batch1_rep240


title: 1mGyOF/ reference male mouse12


title: 1mGyO1/ reference male mouse12


title: 1mGyO6/ reference male mouse12


title: reference male mouse12/ 1mGyO4


title: reg_batch1_rep242


title: reg_batch1_rep237


title: reference male mouse12/ 1mGyO7


title: reg_batch1_rep236


title: reference male mouse5/ 0.05mGyAM


title: reg_batch1_rep246


title: 1mGyN6/ reference male mouse12


title: reference male mouse12/ 1mGyOM


title: reference male mouse12/ 1mGyN5


title: reference male mouse12/ 1mGyN6


title: reg_batch1_rep233


title: reg_batch1_rep232


title: reg_batch1_rep238


title: 1mGyOM/ reference male mouse12


title: reference male mouse12/ 1mGyOF


title: reg_batch1_rep231


title: 1mGyN5/ reference male mouse12


title: reference male mouse12/ 1mGyN4


title: reg_batch1_rep230


title: reg_batch1_rep235


title: reg_batch1_rep228


title: reg_batch1_rep227


title: 1mGyN4/ reference male mouse12


title: reg_batch1_rep226


title: reg_batch1_rep225


title: reg_batch1_rep224


title: reference male mouse12/ 1mGyN2


title: reg_batch1_rep222


title: reg_batch1_rep223


title: reg_batch1_rep234


title: 1mGyN1/ reference male mouse12


title: reg_batch1_rep244


title: reg_batch1_rep220


title: reference male mouse12/ 1mGyN1


title: reg_batch1_rep229


title: 1mGyN2/ reference male mouse12


title: reg_batch1_rep219


title: 0.05mGyAM/ reference male mouse5


title: reg_batch1_rep221


title: reg_batch1_rep217


title: 1mGyM7/ reference male mouse12


title: 1mGyN3/ reference male mouse12


title: reg_batch1_rep215


title: reference male mouse12/ 1mGyO1


title: reg_batch1_rep214


title: reg_batch1_rep213


title: 1mGyM5/ reference male mouse12


title: reference male mouse12/ 1mGyM5


title: reg_batch1_rep216


title: reg_batch1_rep212


title: 1mGyM3/ reference male mouse12


title: reg_batch1_rep211


title: reference male mouse12/ 1mGyM3


title: 1mGyM4/ reference male mouse12


title: 1mGyM6/ reference male mouse12


title: reference male mouse12/ 1mGyNM


title: reference male mouse12/ 1mGyM4


title: reg_batch1_rep209


title: reference male mouse12/ 1mGyNF


title: reference male mouse12/ 1mGyN3


title: reg_batch1_rep210


title: reg_batch1_rep208


title: 1mGyNM/ reference male mouse12


title: reference male mouse12/ 1mGyM6


title: reg_batch1_rep206


title: reg_batch1_rep205


title: reg_batch1_rep204


title: reg_batch1_rep218


title: reg_batch1_rep203


title: reg_batch1_rep202


title: 1mGyM2/ reference male mouse12


title: reference male mouse12/ 1mGyM2


title: reg_batch1_rep207


title: reference male mouse12/ 1mGyM7


title: 1mGyM1/ reference male mouse12


title: reg_batch1_rep201


title: reference male mouse12/ 1mGyMM


title: reg_batch1_rep199