title: Hepatocyte organoid, WT, treated with WNT, rep 1

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

institute: Prinses maxima centrum

data_processing:
Mapping using STAR
Read count assignment using Subread
Assembly: Hg38
Supplementary files format and content: raw read counts

source_name: Liver

extract_protocol:
Quiagen Rneasy minikit
Illumina truseq mRNA stranded

value: Liver

value: Organoid

value: WT

value: with WNT


title: Hepatocyte organoid, WT, rep 1

status: Public on Jul 30 2023

type: SRA

country: Netherlands

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: genotype

tag: treatment

value: no WNT


title: Hepatocyte organoid, WT, treated with WNT, rep 2


title: Hepatocyte organoid, WT, rep 2


title: KSQ-IVP-0027_GP1_Tumor_M3_S3

city: Lexington

first: Micah

last: Benson

state: MA

address: 4 Maguire Rd

country: USA

institute: KSQ Therapeutics

library_source: genomic

data_processing:
Read and UMI counts were tabulated using linux command line programs awk, sed, sort, uniq, zcat and paste
Sequencing-errors in guide and UMI sequences were suppressed by aggregating guides and UMIs with an edit-distance of one
UMIs that did not match the synthesized degenerate UMI-pattern were removed
UMIs potentially representing index-swapping between samples on the same sequencing run were removed
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: Pooled CRISPR Screen

molecule: genomic DNA

organism: Mus musculus

source_name: OT-I

extract_protocol:
Cas9-Tg x TCR-Tg OT1 or PMEL CD8 T cells were isolated from freshly harvested mouse spleens and dissociated using a GentleMACS (Miltenyi), and with CD8 T cells purified by negative selection (EasySep Mouse CD8+ T cell isolation kit).  CD8s were then placed in T225 flasks at a concentration of 1M CD8s/ml and activated with CD3/CD28 Dynabeads and 2ng/ml mouse rIL-2.  The following day, T cells were transduced wither either lentivirus (OT1 B16-Ova screen) or retrovirus (PMEL / MC38-gp100 screen).  Dynabeads were removed the following day, with cells resuspended on cRPMI + 32ng/ml IL-2. On Day 4, transduced T cells were harvested and selected by positive selection using either Thy1.1 for OT1s or hCD2 for PMELs. 5x106 Thy1.1+ Cas9-Tg x OT1 CD8 T cells or 7x106 hCD2+ Cas9-Tg x PMEL CD8 T cells were injected into tumor-bearing mice i.v. via tail vein in 200L PBS, with 10x106 CD8+ T cells saved to determine the sgRNA distribution of the input population of T cells.  Group sizes were 7-8 mice per library.  At the indicated time (eg 11-21 days) following adoptive transfer of cells, mice were euthanized and blood was harvested in EDTA tubes, and stored at -80C. Tumors, spleens, tumor draining and non-draining lymph nodes were harvested and processed further for extraction of CD8 T cells using CD8a Microbeads (Miltenyi, cat# 130-049-401) from the spleen and CD45 Microbeads (Miltenyi, cat# 130-052-301) from the tumor. Tumors were digested using the Miltenyi Tumor Dissociation Kit (Cat# 130-096-730) according to the manufacturer’s instructions.
Genomic DNA was isolated using the Qiamp Blood Midi and Maxi kids, according to the manufacturer’s instructions.

treatment_protocol: The ‘Lib30’ sgRNA library targets 369 genes involved in T cell function with 10sgRNAs per gene and 3089 sgRNAs total, including controls, was cloned into pKSQ044.  Lib31 sgRNA library targets 1004 predicted CSR genes with 8 sgRNAs/gene and 11,148 sgRNAs total, including controls, was also cloned into pKSQ044 (see Supplementary Methods for more information on library design and lentivirus production).

tag: cell type

value: OT-I

tag: group

value: day 14

tag: library

value: Cas9 Over-Expression


title: KSQ-IVP-0027_GP1_Tumor_M1_S1


title: KSQ-IVP-0027_GP8_Tumor_M7_S2

value: day 21


title: Hepatocyte organoid, base edited in CTNNB1 T41A, rep 2


title: Cxadr_ko mouse #1, LSK population

city: Vienna

first: Lukas

last: Kazianka

address: Währinger Gürtel 18-20

department: Medicine I, Div. of Hematology

country: Austria

institute: Medical University of Vienna

data_processing:
R/Python computing environment
Biomedical Sequencing Facility, Vienna, Austria
reads were aligned to the us musculus GRCm38/mm10 genome using STAR
aligned reads and normalized counts were analyzed using the DESeq2 package in R
Assembly: Mus musculusGRCm38/mm10 Reference Genome Assembly (December 2011)
Supplementary files format and content: normalized counts are presented in an .xlsx Excel sheet

molecule: total RNA

source_name: bone marrow

extract_protocol:
TRIzol extraction with chloroform and isopropanaol precipitation
NEBNextSingle Cell/Low Input RNA Library Prep Kit for Illumina according to manufacturer's recommendation

treatment_protocol: cells were directly sorted into TRIzol followed by downstream RNA isolation

tag: animal

value: Cxadr_ko mouse #1

value: bone marrow

value: LSK

value: Cxadr ko (Mx1-Cre+ Cxadrfl/fl)


title: KSQ_001_tumor_4_5_vdj

description: 10X Genomics VDJ

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using the Cell Ranger software version 6.0.1 (more detailed downstream data processing in Methods section).
Assembly: mm10
Supplementary files format and content: For GEX, filtered feature-barcode matrices are provided in tab separated value files. For VDJ data, clonotype and filtered contig annotations  provided in comma separated value files.

source_name: CD45+ tumor infiltrating lymphoytes

extract_protocol:
For the OT1 / B16-Ova model, female C56BL/6J mice were inoculated with 0.5x106 B16-Ova cells subcutaneously in the right flank.    After eight days for small tumor studies (~100mm3 – range of 80mm3-120mm3) or 14 days for large tumor studies (~300mm3 – range of 135mm3-550mm3) mice were randomized by tumor volume and 3x106 sgOlf, sgPD-1 or sgSocs1 OT-1 T cells were transferred in 0.2mL PBS via the lateral tail vein.  Prior to transfer into mice, OT-1s are tested via PCR for a comprehensive list of mouse pathogens by Charles River Laboratory Testing Management.  Tumor volumes were measured twice weekly using a digital caliper and tumor volume (mm3) calculated using the formula: (width2 x length)/2, where length was the longer dimension.  To assess tumor growth following re-challenge in Figure 2, mice undergoing complete tumor rejection were re-challenged with 0.5x106 B16-Ova cells subcutaneously on the left flank on Day 61 and monitored for tumor growth. For the PMEL / MC38-gp100 model: Female C56BL/6J mice were inoculated with 1x106 MC38-gp100 cells.  At the indicated tumor size, mice were randomized and received 7x106 sgOlf, sgPD-1 or sgSocs1 PMEL T cells in 0.2mL PBS intravenously via the lateral tail vein.  For the NOG / hIL-2 NOG engraftment model, female NOG or hIL-2 NOG mice were dosed with 10x106 TIL or KSQ-001 TIL intravenously in 100ml volume. For the TIL / A375-mOKT3 model, female hIL-2 NOG mice were inoculated with 5x106 A375-mOKT3 cells subcutaneously in a 50:50 mix with Matrigel (Corning Biosciences). 7 days post-inoculation, 10x106 TIL or KSQ-001 were transferred intravenously.
Droplet-base 5’ single-cell RNA sequencing (scRNA-Seq) was performed by the 10x Genomics platform and libraries were prepared by the Chromium Single Cell 5’ Reagent kit according to the manufacturer’s protocol (10x Genomics, CA, USA).

value: CD45+ tumor infiltrating lymphoytes


title: KSQ_001_tumor_1_2_GEX

description: 10X Genomics GEX


title: Olfactory_tumor_4_5_GEX

description: 10X Genomics GEX

value: SgOlfr


title: KSQ_001_tumor_1_2_vdj

description: 10X Genomics VDJ


title: Olfactory_tumor_4_5_vdj

description: 10X Genomics VDJ


title: KSQ-IVP-0027_GP8_Tumor_M6_S1


title: PD_1_tumor_1_2_vdj

description: 10X Genomics VDJ


title: Cxadr_ko mouse #1, GMP population

value: GMP


title: Hepatocyte organoid, base edited in CTNNB1 T41A, rep 1


title: Hepatocyte organoid, base edited in CTNNB1 D32G, rep 2


title: KSQ-IVP-0027_GP1_Tumor_M4_S4


title: KSQ-IVP-0027_GP6-10_INPUT2_PCR2_lib31_S14

value: input


title: Cxadr_ko mouse #1, CMP population

value: CMP


title: PD_1_tumor_1_2_GEX

description: 10X Genomics GEX


title: KSQ-IVP-0027_GP1_Tumor_M2_S2


title: KSQ-IVP-0027_GP6-10_INPUT_PCR1_lib31_S13


title: control mouse #4, MEP population

value: control mouse #4

value: MEP

value: control (Mx1-Cre- Cxadrfl/fl)


title: KSQ-IVP-0027_GP1-5_INPUT_PCR2_lib30_S12


title: Hepatocyte organoid, base edited in CTNNB1 S33F, rep 1

value: Liver

value: Organoid

value: no WNT


title: control mouse #4, LSK population


title: Hepatocyte organoid, base edited in CTNNB1 S33F, rep 2


title: Olfactory_tumor_1_2_vdj

description: 10X Genomics VDJ


title: Olfactory_tumor_1_2_GEX

description: 10X Genomics GEX


title: control mouse #4, GMP population


title: KSQ_001_tumor_4_5_GEX

description: 10X Genomics GEX


title: Hepatocyte organoid, base edited in CTNNB1 S45P, rep 2


title: MP cells 3

city: Xi'an

first: Yi

last: Zhou

state: Shaanxi

address: 277# Yanta West Road

country: China

institute: The First Affiliated Hospital of Xi'an Jiaotong university

data_processing:
Poor quality reads were trimmed using the fastq-mcf (1.05). Reads quality was checked using the fastqc (v0.11.7).
Gene read counts were in Ensembl Gene ID and converted to Entrez Gene ID.
Corresponding Symbol annotations and full gene names were added using the “org.Mm.eg.db” library. NA (Not Annotated), duplicate Entrez IDs and genes without symbols were removed.
Only the genes having CPM values above 0.5 in at least two libraries were kept. Normalization by TMM (Trimmed mean of M values) was performed by using calcNormFactors function to eliminate composition biases between libraries.
Assembly: GRCm38
Supplementary files format and content: tab-delimited excel files include RPKM values for each Sample

source_name: mouse HCC cell line

growth_protocol: Mice were humanely euthanized and rinsed in 70% ethanol. Liver tumor (2-3g) was dissected, washed in PBS and minced into ~1mm fragments using scalpel blade. All procedures were operated in the hood using autoclaved dissecting tools. The tumor fragments were digested with 0.6 mg/L collagenase (Sigma-Aldrich, C5138) in 37°C for 15~30min, then filtered through 100 μm nylon mesh cell strainer (BD, 352360) and spined (700-1000rpm, 5 min). The cell pellet were resuspended and cultured in 5 ml DMEM with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin at 37 °C and 5 % CO2 for~4 weeks. The primary liver tumor cells were generated. In order to obtain a stablely passaged cell line, 1×107 primary tumor cells were injected into flanks of 6~8 week-old FVB/N mice. When the subcutaneous tumor developed, tumor tissue was dissected into small pieces and digested with trypsin (Sigma-Aldrich, T4049). The new generation of liver tumor cells (P0) were cultured and passaged in vitro for 3 times. Then 1×107 “P0” cells were implanted into the flanks of a new recipient FVB/N mouse. These procedures were repeated for three rounds. The stably passaged cell line from c-MET/sgp53 HCC (MP cell) was finally generated.

extract_protocol:
Total RNA was extracted from MP cells (n=3) and FVB/N normal livers (n=3) using Quick-RNA Miniprep Kit (Zymo Research, CA, USA).
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA.

value: mouse HCC cell line

tag: disease state

value: HCC cell line

tag: strain

value: FVB/N

tag: Sex

value: male


title: KSQ-IVP-0027_GP1-5_INPUT_PCR1_lib30_S11

value: OT-I

value: Cas9 Over-Expression


title: control mouse #3, MEP population

value: control mouse #3

value: bone marrow


title: Hepatocyte organoid, base edited in CTNNB1 S45P, rep 1


title: KSQ-IVP-0027_GP8_Tumor_M5_S20

value: day 21


title: KSQ-IVP-0027_GP1_Tumor_M7_S21

value: day 14


title: MP cells 1


title: control mouse #4, CMP population

value: CMP


title: NR,replicate 3, scRNAseq

city: lanzhou

first: xiao

middle: dong

last: xie

state: Gansu

address: 1 wujiayuan west street, qilihe district, lanzhou city

department: clinical laboratory

institute: The first people's hospital of Lan Zhou

description: Free from any disease,HBsAb<10mIU/ml and peripheral blood was collected one month after vaccination, followed by immediate isolation of peripheral blood mononuclear cells.

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger (v.4.0.0) Pipeline coupled with human reference version GRCh38-2020-A.
Assembly: GRCH38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
Fresh whole blood was diluted with equal volume PBS (Tianjin Hao Yang Biological Manufacture Co., Ltd.) and then added to a centrifuge tube containing Human Lymphocyte Separation Medium (Dakewe Biotech Co., Ltd.) and centrifuged at 700×g for 20 min. Peripheral blood mononuclear cell (PBMC) was between the plasma layer and the separation fluid layer, then it was carefully drain into another centrifuge tube and washed twice with PBS (Phosphate buffered saline).  1mL medium that contained 10% Foetal Bovine Serum (FBS) and 90% Iscove’s Modified Dulbecco Medium (IMDM) were added to suspend the PBMC again. After the PBMC was prepared into single cell suspension, Luna-FL automatic cell counting apparatus was used to measure the cell count and cell survival rate. The cell activity was higher than 85% and the dead cells were removed with dead cell removal kit. Finally, the cell concentration was adjusted to the ideal concentration of 700-1200 cells /μL.
scRNA-seq libraries were constructed Using a Single Cell 3′v3.1 Library and Gel Bead kit (10X Genomics, 1000121) and Chromium Single Cell A Chip kit (10X Genomics, 1000120) according to the manufacturer’s introduction.

value: Blood

tag: age

value: Peripheral Blood Mononuclear

value: recombinant hepatitis B vaccine

value: NR(no immune response to hepatitis B vaccine group)


title: MP cells 2


title: control mouse #3, LSK population

value: LSK

value: control (Mx1-Cre- Cxadrfl/fl)


title: NR,replicate 2, scRNAseq


title: FVB/N normal liver 3

source_name: normal mouse liver

value: normal mouse liver

value: WT


title: KSQ-IVP-0027_GP8_Tumor_M3_S18


title: KSQ-IVP-0027_GP8_Tumor_M4_S19


title: FVB/N normal liver 2

value: FVB/N


title: Hepatocyte organoid, base edited in CTNNB1 D32G, rep 1

value: Liver

value: Organoid

value: no WNT


title: control mouse #3, GMP population

value: control mouse #3

value: GMP


title: NR,replicate 1, scRNAseq

value: male


title: KSQ-IVP-0027_GP8_Tumor_M2_S17

value: OT-I

value: day 21

value: Cas9 Over-Expression


title: FVB/N normal liver 1


title: KSQ-IVP-0027_GP8_Tumor_M1_S16


title: control mouse #3, CMP population

value: bone marrow

value: CMP


title: control mouse #2, MEP population

value: control mouse #2

value: MEP


title: MeVa2.2.dOVA cell line

city: Amsterdam

first: PETROS

last: DIMITRIADIS

email: p.dimitriadis@nki.nl, d.rao@nki.nl

state: Noord-Holland

address: Plesmanlaan 121

institute: NETHERLANDS CANCER INSTITUTE - NKI

description: tumor

data_processing:
The quality of FASTQC files were analyzed with FastQC (v0.11.5-cegat).
The exome sequencing data were first mapped to Mus_musculus.GRCm38 sequence reference genome using the Burrows-Wheeler Aligner BWA MEM (v0.7.17-r1188)
After alignment, the data were sorted and indexed by samtools (v 1.10) followed by marking duplicates with Picard-tools (v1.140) (Broad Institute) and base quality recalibration with GATK BaseRecalibrator (v4.2.3.0)
Assembly: Mus_musculus.GRCm38
Library strategy: Exome sequencing

source_name: MeVa2.2.dOVA cell line

extract_protocol:
DNA was isolated from snap frozen cell line pellets using DNeasy Blood and Tissue kit (Qiagen) according to manufacturer’s protocol.
Library preparation was performed using Twist Mouse Exome Panel (Twist Bioscience) and sequencing was performed using 2x100 p on Novaseq 6000. Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq 2.20. Adapters were trimmed with Skewer (v0.2.2).

treatment_protocol: cells were untreated

value: MeVa2.2.dOVA cell line

value: murine melanoma cell line

value: untreated


title: HR,replicate 3, scRNAseq

description: Free from any disease,HBsAb>1000mIU/ml and peripheral blood was collected one month after vaccination, followed by immediate isolation of peripheral blood mononuclear cells.

value: Blood

value: Peripheral Blood Mononuclear

value: recombinant hepatitis B vaccine

value: HR(High immune response to hepatitis B vaccine group)


title: HR,replicate 2, scRNAseq


title: control mouse #2, LSK population

value: LSK

value: control (Mx1-Cre- Cxadrfl/fl)


title: KSQ-IVP-0027_GP3_Tumor_M7_S7


title: KSQ-IVP-0027_GP3_Tumor_M6_S6


title: MeVa2.2 cell line

description: tumor

source_name: MeVa2.2 cell line

value: MeVa2.2 cell line

value: WT


title: HuH-7_meRIP_Input

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

data_processing:
library strategy: meRIP-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 (for RIP-seq) or Bowtie (for MeRIP-seq)
Gene annotated in NCBI were quantified using featureCounts
Peaks were identified using the MACS2 peak caller
Assembly: hg38
Supplementary files format and content: txt, counts for each RIP-seq sample
Supplementary files format and content: txt, MeRIP-seq peak (except for Input sample)

growth_protocol: HuH-7 was cultured in Dulbecco’s modified Eagle’s medium (DMEM) (BasalMedia, Shanghai, China) containing 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) and antibiotics (penicillin and streptomycin, Invitrogen) at 37 °C in 5% CO2.

extract_protocol:
Total RNA from HuH-7 cells were extracted using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's instructions.
For the RIP-seq, the sequencing library was prepared deploying NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs, USA) and sequenced on the Illumina HiSeq 3000 platform.  For the MeRIP-seq, the library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

value: HCC

tag: ip antibody


title: MeVa2.1 cell line

description: tumor

source_name: MeVa2.1 cell line

value: MeVa2.1 cell line


title: MeVa2.1.dOVA cell line

description: tumor

source_name: MeVa2.1.dOVA cell line

value: MeVa2.1.dOVA cell line


title: D4M.3A.dOVA cell line

description: tumor

source_name: D4M.3A.dOVA cell line

value: D4M.3A.dOVA cell line


title: control mouse #2, CMP population

value: control mouse #2

value: bone marrow

value: CMP


title: KSQ-IVP-0027_GP3_Tumor_M5_S5

value: OT-I

value: day 21

value: Cas9 Over-Expression


title: control mouse #1, MEP population

value: control mouse #1

value: MEP


title: D4M.3A cell line

description: tumor

source_name: D4M.3A cell line

value: D4M.3A cell line

value: murine melanoma cell line

value: untreated


title: HuH-7_m6A_meRIP

value: m6A, RiboBio, C11051-1


title: control mouse #1, LSK population

value: LSK

value: control (Mx1-Cre- Cxadrfl/fl)


title: H-MAT1,Homo sapiens,Normal mesenteric adipose tissue in Non-IBD control

city: Guangzhou

first: Fengfei

last: Wu

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District, Guangzhou, Guangdong, China

department: Department of Gastroenterology

institute: Nanfang   Hospital, Southern Medical University

description: 10x Genomics

data_processing:
Raw reads of mouse were aligned to the human genome (hg38), cells were called and gene expression matrices were generated for each sample by the cellranger (v5.0.1) count function with default parameters.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Adipose tissue

extract_protocol:
Fresh tissues were immediately used to prepare their single cell suspension. Briefly, the collected fresh tissue was washed by DPBS (PBS without calcium and magnesium) and carefully chopped into small pieces. Enzymatic digestion was performed with collagenase II (2 mg/mL), collagenase IV (2 mg/mL) and dispase (0.2 mg/mL) under 37 °C for 15-25 minutes. The digested solution was transferred to a centrifuge tube through a 40 μm stainless nylon mesh (Greiner Bio-OneGmbH, Germany). The filtrate was immediately centrifuged at 500 g for 5 min, and discarded the supernatant slowly. The cell sediment was resuspended and lysis with RBC Lysis buffer on ice for 5 min to remove red blood cells, and then washed with DPBS at 500 g for 5 min twice. Cell concentration and viability were determined on a Cellometer Auto 2000 (nexcelom, USA) after AO/PI staining, and cells with viability of greater than 80% were subjected to 10 × Genomics single-cell RNA-seq (scRNA-seq).
The library synthesis was conducted in accordance with the instructions of Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× GENOMICS). In brief, the cells of each sample was adjusted to 1000 cell/μL. Cell suspensions were loaded on the Chromium Controller instrument to generate single-cell Gel Beads-In-Emulsions (GEMs), and individual cells were isolated into droplets together with gel beads that coated with unique primers bearing 10× cell barcodes, unique molecular identifiers (UMI), and poly (dT) sequences. In GEMs, individual cells were barcode-labeled and mixed with reverse transcriptase, and the GEM-reverse transcriptions were performed on a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA). Then the cDNA libraries were amplified, fragmented, end repaired, and A-tailed after reverse transcription; then adaptor was ligated after size selection; finally, sample index PCR was performed and SPRI select beads were used for final purification. At last, the barcoded sequencing libraries were 150 bp paired-end sequenced on an Illumina Novaseq 6000 platform.

value: Adipose tissue

value: Primary cells

value: Stromal vascular fraction

tag: condition

value: Non-IBD control

tag: tissue type

value: Normal mesenteric adipose tissue


title: control mouse #1, GMP population

value: bone marrow

value: GMP


title: normal tissue_spleen from healthy C57BL/6 mouse

description: normal

source_name: spleen

value: spleen

value: murine splenocytes

value: WT


title: HR ,replicate 1, scRNAseq

value: Blood

value: male

value: Peripheral Blood Mononuclear

value: recombinant hepatitis B vaccine

value: HR(High immune response to hepatitis B vaccine group)


title: CD-MAT5,Homo sapiens,Normal mesenteric adipose tissue in Crohn's disease

description: 10x Genomics

value: Crohn's disease


title: control mouse #2, GMP population

value: control mouse #2

value: control (Mx1-Cre- Cxadrfl/fl)


title: Cis_DXZ_3

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were build index by hisat2, and masked for low-complexity or low-quality sequence
Mapped to mm9 whole genome using hisat2 and  exported StringTie readable format files
Expression values for all genes in each sample (FPKM) were calculated by StringTie
Differentially expressed gene between the paired groups were analyzed by using DEGseq
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from each tissue sample using Trizol method
RNA libraries were prepared for sequencing using standard illumina protocls

value: kidneys

value: 6~8 weeks

value: DXZ


title: CD-MAT4,Homo sapiens,Normal mesenteric adipose tissue in Crohn's disease

description: 10x Genomics

value: Adipose tissue

value: Primary cells

value: Stromal vascular fraction

value: Normal mesenteric adipose tissue


title: control mouse #1, CMP population

value: control mouse #1

value: bone marrow

value: CMP


title: KSQ-IVP-0027_GP3_Tumor_M1_S1

value: OT-I

value: day 21

value: Cas9 Over-Expression


title: KSQ-IVP-0027_GP3_Tumor_M4_S4


title: PlasmidLib-SE23-lib31_S7

source_name: plasmid

value: plasmid


title: H-MAT2,Homo sapiens,Normal mesenteric adipose tissue in Non-IBD control

description: 10x Genomics

value: Non-IBD control


title: KSQ-IVP-0027_GP3_Tumor_M3_S3


title: SARSCoV2_Ext_5P_Mock_GEX

city: New York

first: Brad

middle: R

last: Rosenberg

state: NY

address: 1 Gustave L Levy Place, Box 1124

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Fastq files from bcl files for standard 10X 3' and 10X 5' libraries were generated using cellranger (v3.1.0, 10X Genomics) mkfastq. Fastqs for 5' libraries sequenced with the Extended R1 protocol were generated using bcl2fastq (v2.20.0, Illumina, Inc).Extended R1 fastqs were then separated into pseudo R1 fastqs, containing the cell barcode and UMI, and pseudo read 2 (R2) fastqs, containing cDNA sequence, using a customized Python/3.7.3 script (available at github link pending) as follows. The cell barcode and UMI are selected from the first 26 bp of R1. The subsequent 13 bp derive from the template switch oligonucleotide and are ignored. The remaining nucleotides (and corresponding quality scores) are reverse complemented and stored as pseudo R2. The read header of the pseudo R2 fastqs are modified to reflect the format for standard R2 fastqs.
To control for differences in sequencing depth per library, read depth per library was downsampled to approximately 50,000 reads multiplied by the number of cells in the library using seqtk (version 1.2). We do this by generating a whitelist of cell barcodes using a preliminary gene cell matrix generated using cellranger (v3.1.0, 10X Genomics) count with a combined African Green Monkey reference (ChlSab1.1) combined with SARS-CoV-2 transcripts  (NC_045512.2) with modifications for the USA/WA01 strain. This output was analyzed in R (v4.0.4) with the Seurat package (version 4.0.1) to filter out putative multiplets, empty droplets, and dead cells based on total UMIs/cell, number of genes/cell, and percent of mitochondrial gene expression per cell.
Downsampled fastq files were mapped and quantified using cellranger (v3.1.0, 10X Genomics) count to a combined African Green Monkey (ChlSab1.1) and SARS-CoV-2 reference derived from empirically defined RNAs sequenced with long-read direct RNA Nanopore sequencing published by Kim et al, Cell 2020. These were downloaded from the UCSC Genome Table Browser after filtering for TRS-dependent transcripts and score > 900 and exporting to gtf format. Transcripts for previously unknown ORFs were excluded and an additional annotation for genomic RNA covering the entire length of the SARS-CoV-2 genome was added. Modifications the reference were made to match the USA/WA01 SARS-CoV-2 strain.
To quantify SARS-CoV-2 RNAs, we developed single cell coronavirus sequencing (scCoVseq), which quantifies only unambiguous genomic RNA (gRNA)-derived reads and reads from subgenomic mRNAs (sgmRNAs) containing junctions between the 5' leader of the genome and sgmRNA. We did this using samtools (v1.11) to filter SARS-CoV-2 aligned reads to contiguous reads aligning upstream of sgmRNA-containing regions of the genome or to SARS-CoV-2 reads aligning in part the the 5' leader (defined as the 5' proximal 80 nt of the genome) and in part to the regions of the genome used by sgmRNAs with any gap length. Reads not matching these filters were excluded. Filtered SARS-CoV-2 reads were then merged with host reads and quantified using umi_tools (v1.0.0) and converted to a sparse matrix using a custom R (v3.5.3) script with the Matrix package (v1.2-18) and the readr package (v1.3.1). UMIs assigned to multiple genes were removed from the resulting matrix during downstream analysis.
Genome_build: custom build described above
Supplementary_files_format_and_content: h5: gene x cell matrix output by cellranger in h5 format; rds: gene x cell matrix output by scCoVseq as R data file, rds;

organism: Chlorocebus aethiops

source_name: Vero E6 African Green Monkey kidney cell line

growth_protocol: Vero E6 cells were cultured with Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (PSN) at 37°C and 5% CO2.

extract_protocol:
Cultures were washed with calcium/magnesium-PBS and disassociated with TrypLE (Gibco # 12605010) for 5 minutes at 37°C. Cells were then centrifuged (200 x g for 5 minutes), resuspended in calcium/magnesium free PBS supplemented with 1% BSA and counted. Cells were then filtered through a 40μm FlowMi strainer (ScienceWare # H13680-0040) and counted again. Mock and infected samples were loaded on separate lanes of a 10X Genomics Chromium Controller, according to manufacturer's protocol, for either NextGem Single Cell 3' v3.1 (10X 3') or NextGEM Single Cell V(D)J v1.1 (10X 5').
Single cell RNA sequencing of mock and SARS-CoV-2 infected Vero E6 cells performed with either 10X Genomics Chromium Next GEM Single Cell 3' (10X 3') or 10X Genomics Chromium Next GEM Single Cell V(D)J (10X 5'). Final 10X 3' mock and infected gene expression libraries and 10X 5' infected gene expression libraries were PCR amplified for 16 cycles, while the 10X 5' mock gene expression library was amplified for 14 cycles. 10X 3' libraries were pooled and sequenced according with the following read lengths: read1 28 nt, i7 index 8 nt, read2 130 nt. 10X 5' libraries were also pooled and sequenced with the following read lengths: read 1 26 nt, i7 index 8nt, read 2 132 nt. 10X 5' were also sequenced with our custom extended R1 protocol (read 1 158 nt, i7 index 8 nt, no read 2).

treatment_protocol: In 6 well plates, cells were infected with SARS-CoV-2 (USA-WA1/2020) at an MOI of 0.1 or mock infected with equivalent control media in reduced serum media (2% FBS, 1% PSN) for 24 hours.

tag: infection

value: Mock

tag: scrnaseq method

value: 10X Genomics Chromium Next GEM Single Cell V(D)J v1.1

tag: sequencing method

value: Extended R1 Protocol (Read 1 158 nt, i7 index 8 nt, no read 2)


title: PlasmidLib-SE23-lib30_S6


title: Cis_Saline_4

tag: tissue

value: kidneys

value: 6~8 weeks

value: saline


title: CF6,Homo sapiens,Creeping fat of Mesenteric adipose tissue in Crohn's disease

description: 10x Genomics

value: Adipose tissue

tag: cell line

value: Primary cells

value: Crohn's disease

value: Creeping fat


title: Cis_DXZ_1

value: DXZ


title: Cis_DXZ_2


title: SARSCoV2_5P_Mock_GEX

value: Vero E6 African Green Monkey kidney cell line

value: Read 1 26 nt, i7 index 8 nt, read 2 132 nt


title: HepG2, sh_KIF11_2

city: Hefei

first: Pengfei

last: Zhang

address: 443 Huang-Shan Road

department: School of Life Sciences

institute: University of Science and Technology of China

description:
counts_anno.xls
FPKM_anno.xls

data_processing:
Bcl2fastq(v1.8.4) was used for base-calling for output.
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome (Human GRCh38/hg38) using hisat2 (HISAT2 2.1.0).
FPKM value of each gene was calculated using cufflinks (2.2.1), and the read counts of each gene were obtained by htseq-count (0.9.1).
DEGs were identified using the DESeq (2012, 1.18.0) R package functions estimate SizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: Excel file includes raw counts for each sample.
Supplementary files format and content: Excel file includes FPKM values for each sample.

extract_protocol:
RNA was isolated by mirVana™ miRNA ISOlation Kit (Ambion-1561). 4 μg total RNA was used for purification and sequencing library construction.
Library was prepared using TruSeq Stranded mRNA LTSample Prep Kit (RS-122-2101).

value: hepatoma cell

tag: treatment


title: CF5,Homo sapiens,Creeping fat of Mesenteric adipose tissue in Crohn's disease

description: 10x Genomics

tag: cell type

value: Stromal vascular fraction


title: CD-MAT1, Homo sapiens,Normal mesenteric adipose tissue in Crohn's disease

description: 10x Genomics

value: Normal mesenteric adipose tissue


title: Cis_Saline_3

tag: group


title: HepG2, sh_KIF11_3

description:
counts_anno.xls
FPKM_anno.xls


title: SARSCoV2_5P_Inf_GEX

value: SARS-CoV-2, MOI 0.1, 24 hours


title: KSQ-IVP-0027_GP3_Tumor_M2_S2

source_name: OT-I

value: OT-I

value: day 21

tag: library

tag: genotype

value: Cas9 Over-Expression


title: CF4,Homo sapiens,Creeping fat of Mesenteric adipose tissue in Crohn's disease

description: 10x Genomics


title: HepG2, sh_KIF11_1

description:
counts_anno.xls
FPKM_anno.xls


title: SARSCoV2_3P_Mock_GEX

value: Mock

value: 10X Genomics Chromium Next GEM Single Cell 3' v3.1

value: Read 1 28 nt, i7 index 8 nt, read 2 130 nt


title: CF3,Homo sapiens,Creeping fat of Mesenteric adipose tissue in Crohn's disease

description: 10x Genomics

value: Adipose tissue


title: HepG2, sh_ctrl_3

description:
counts_anno.xls
FPKM_anno.xls

value: shctrl


title: Cis_Saline_2

value: kidneys

value: 6~8 weeks

value: saline


title: Cis_Saline_1


title: SARSCoV2_Ext_5P_Inf_GEX

value: Vero E6 African Green Monkey kidney cell line

value: 10X Genomics Chromium Next GEM Single Cell V(D)J v1.1

value: Extended R1 Protocol (Read 1 158 nt, i7 index 8 nt, no read 2)


title: CF2,Homo sapiens,Creeping fat of Mesenteric adipose tissue in Crohn's disease

description: 10x Genomics

value: Primary cells

value: Stromal vascular fraction

value: Crohn's disease

value: Creeping fat


title: HepG2, sh_ctrl_2

description:
counts_anno.xls
FPKM_anno.xls

value: hepatoma cell


title: SARSCoV2_3P_Inf_GEX

value: SARS-CoV-2, MOI 0.1, 24 hours


title: HepG2, sh_ctrl_1

description:
counts_anno.xls
FPKM_anno.xls


title: S2_G11_M_R1

status: Public on Jul 29 2023

city: Bethesda

first: Susan

middle: T

last: Harbison

state: MD

address: 10 Center Drive, Bldg. 10, Rm. 7D13

department: Center for Systems Biology

institute: National Heart Lung and Blood Institute

description:
Short population 2, Generation 11, Male, Replicate 1
STH_447

data_processing:
Base calls and quality were assessed  using RTA version 1.18.64 and CASAVA 1.8.2.
We used fastqc to evaluate the quality of each sequence (Babraham Institute, Cambridge, UK).
We used STAR to align reads to the genome (Dobin et al., 2013, PMID: 23104886) with the default parameters except that minimum and maximum intron sizes were coded as 2 and 268,107 based on the Flybase FB2015_04 release 6 version 07 genome.
We used HTSeq to count only the uniquely mapped reads (Anders et al., 2015, PMID: 25260700).
Read counts were normalized using the method described by Love et al., 2014 (PMID: 25516281)
Assembly: FlyBase FB2015_04 release 6 version 07
Supplementary files format and content: There are two supplemental tables. The first, 'Raw_read_counts.csv', contains the raw read counts per gene as evaluated using HTSeq. The second file, 'Normalized_read_counts.csv', are the DESeq-normalized read counts for each gene. Both files are comma-separated values.

organism: Drosophila melanogaster

source_name: Whole body

growth_protocol: All flies were kept in the following controlled environmental conditions.  They were reared in an incubator on standard Drosophila food (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/bloomfood.htm) at 25°C, 60% humidity, and a 12:12-hour light:dark  cycle.  Prior to making sleep measurements, we collected and maintained male and female virgins at 20 flies to a same-sex vial for four days to control for social exposure.  We assayed night sleep duration as well as other sleep and activity measures using the Drosophila Activity Monitoring System (DAMS) (Trikinetics, Waltham, MA).  Night and day sleep duration, average sleep bout length, and bout number as well as sleep latency and waking activity were computed from the DAMS activity data using an in-house C# program (R. Sean Barnes, personal communication).

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, Hilden, Germany), followed with phenol-chloroform extraction, isopropanol precipitation, and DNase digestion (Qiagen, Hilden, Germany).  Qiagen RNeasy MinElute Cleanup kits (Qiagen, Hilden, Germany) were used to purify RNA according to the manufacturer’s instructions.  Total RNA yield was measured using a Nanodrop 8000 (Thermo Scientific, Waltham, MA).  We used Agilent Bioanalyzer RNA chips on the 2100 Bioanalyzer system (Agilent, Santa Clara, CA) according to the manufacturer instructions to visually inspect electrophoregrams for RNA degradation.
PolyA-selected stranded mRNA libraries were constructed from 1 µg total RNA using Illumina TruSeq Stranded mRNA Sample Prep Kits (Illumina, San Diego, CA).  We followed the manufacturer’s protocol with the exception of the PCR amplification. The PCR amplification was performed for 10 cycles rather than 15 in order to reduce potential over-amplification.  We applied unique barcode adapters to each library. Libraries were pooled for sequencing.  To achieve a minimum of 38 million 126-base read pairs, the pooled libraries were sequenced on multiple lanes of an Illumina HiSeq2500 (Illumina, San Diego, CA) using version 4 chemistry.

treatment_protocol: We created four populations selected for long and short night sleep and two control populations in two stages.  In the first stage, we created an outbred population (the Sleep Advanced Intercross Population, SAIP) using the five longest- and five shortest-sleeping lines of the Drosophila Genetic Reference Panel (DGRP) (Mackay et al., Nature, 2012, PMID 22318601; Huang et al., Genome Res, 2014, PMID 24714809).  We crossed the following DGRP lines in a full diallel cross: DGRP_38, DGRP_235, DGRP_310, DGRP_313, DGRP_335, DGRP_338, DGRP_365, DGRP_379, DGRP_808, and DGRP_832.  Two virgin males and two virgin females from each of the 100 F1 crosses were mixed together, and 10 males and 10 females were placed into 20 bottles.  The progeny from the bottles were mixed for 21 generations, with 20 males and 20 females placed in each bottle for the subsequent generations.  After generation 21, the bottles were maintained by bottle-to-bottle tipping.  In the second stage, we established six populations at generation 47 of the outbred population by randomly choosing 25 males and 25 virgin females from the SAIP for each bottle.  We assayed night sleep duration as well as other sleep and activity measures in 100 males and 100 females in each population.   In two of the populations, the 25 longest-sleeping males and females were chosen from each bottle as parents to establish replicate long-sleeping populations.  We followed a similar procedure to establish two replicate short-sleeper populations, choosing the 25 shortest-sleeping males and 25 shortest-sleeping females in each population as parents for the next generation.  The remaining two populations served as replicated unselected controls; the parents for these populations were chosen by randomly selecting 25 males and 25 females from each of these populations.  We repeated this procedure for 13 generations, and flies were not mixed across replicate populations.  For generation 0 and generations 2-13, we randomly froze virgin male and virgin female flies from the sleep assays for RNA extraction.  Ten males and ten females were frozen in two same-sex replicates from each of the six populations to generate 24 RNA sequence profiles per generation.  All flies were frozen for RNA extraction at the same circadian time (12:00 pm).

tag: developmental stage

value: Adult

value: Male

tag: selection treatment

value: short

tag: selection generation

tag: population replicate

tag: sample replicate


title: S2_G13_F_R2

description:
Short population 2, Generation 13, Female, Replicate 2
STH_505

tag: Sex

value: Female


title: S2_G12_F_R2

description:
Short population 2, Generation 12, Female, Replicate 2
STH_481


title: S2_G13_M_R1

description:
Short population 2, Generation 13, Male, Replicate 1
STH_506


title: S2_G11_F_R2

description:
Short population 2, Generation 11, Female, Replicate 2
STH_446


title: S2_G11_M_R2

description:
Short population 2, Generation 11, Male, Replicate 2
STH_448


title: S2_G13_M_R2

description: Short population 2, Generation 13, Male, Replicate 2


title: S2_G10_F_R2

description:
Short population 2, Generation 10, Female, Replicate 2
STH_422


title: S2_G10_F_R1

description:
Short population 2, Generation 10, Female, Replicate 1
STH_421


title: S2_G12_F_R1

description:
Short population 2, Generation 12, Female, Replicate 1
STH_469


title: S2_G10_M_R1

description:
Short population 2, Generation 10, Male, Replicate 1
STH_423


title: HSCs, WT naïve

city: Houston

first: Bailee

last: Kain

state: Texas

address: 1102 Bates Avenue

institute: Baylor College of Medicine

description: Single cell library

data_processing:
quality control on the samples to remove low-quality cells based on number of genes, number of UMIs, and mitochondrial ratio
cell cycle scaling on each sample group individually by predicting the cell cycle phase of each cell and regressing out the predicted score
integrated the datasets for each of the sample groups using the 4000 most variable features.
Uniform Manifold Approximation and Projection (UMAP) using the first 30 principal components of a Principal Components Analysis (PCA)
clustered the cells using the FindNeighbors and FindClusters functions in the Seurat R package
Using self-curated gene lists, as well as the scCATCH R package, we determined the cell types of each of the clusters
differential expression and pseudotime analyses on the resulting cell type groupings. All analyses were performed in R (v3.2.3) using the Seurat R package (v3.6.1) except for the pseudotime analysis which used the slingshot R package (v1.4.0)
Genome_build: m38
Supplementary_files_format_and_content: Cell Ranger and Seurat output files

source_name: purified and sorted murine WBM

growth_protocol: in vivo growth

extract_protocol:
Cells were FACS sorted, counted, and combined. Depending on the rarity of the isolated population, 20,000-50,000 sorted cells were combined to a concentration of ~7200 cells/uL. Samples were loaded into the Chromium controller system and generated 3’ 10x scRNAseq barcoded libraries for each sample.
10x Genomics Chromium controller system
scRNAseq barcoded libraries

treatment_protocol: control vs. M.avium treatment

value: whole bone marrow (WBM)

value: hematopoietic cells

value: control - no treatment


title: HSCs, WT M. avium-infected

description: Single cell library

value: Mycobacterium avium (1 month)


title: S2_G13_F_R1

description:
Short population 2, Generation 13, Female, Replicate 1
STH_504


title: S2_G12_M_R1

description:
Short population 2, Generation 12, Male, Replicate 1
STH_482


title: S2_G11_F_R1

description:
Short population 2, Generation 11, Female, Replicate 1
STH_445


title: S2_G10_M_R2

description:
Short population 2, Generation 10, Male, Replicate 2
STH_424


title: S2_G9_M_R2

description:
Short population 2, Generation 9, Male, Replicate 2
STH_395


title: S2_G8_M_R2

description:
Short population 2, Generation 8, Male, Replicate 2
STH_371


title: S2_G8_F_R2

description:
Short population 2, Generation 8, Female, Replicate 2
STH_369


title: S2_G9_F_R1

description:
Short population 2, Generation 9, Female, Replicate 1
STH_392


title: S2_G9_F_R2

description:
Short population 2, Generation 9, Female, Replicate 2
STH_393


title: Ets1 binding levels

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to desired concentrations in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices).

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the fluorescence signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. For each unique sequence represented on the array, we then calculated the median over replicate spots and then normalized the signal for direct comparison between experiments.

label: Alexa 488

molecule: protein

organism: synthetic construct

source_name: Human Ets1

label_protocol: Proteins were tagged with N-terminal GST by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen).

growth_protocol: Gateway-compatible clones containing the full-length gene for Ets1 was  transferred into pDEST15 vector using the LR Clonase reaction (Life Technologies). pDEST15 vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged protein was purified from the soluble portion of the lysate using GST resin (GE Healthcare) according to manufacturer’s instructions.

tag: transcription factor

tag: protein concentration


title: S2_G12_M_R2

description:
Short population 2, Generation 12, Male, Replicate 2
STH_483


title: CF1,Homo sapiens,Creeping fat of Mesenteric adipose tissue in Crohn's disease

description: 10x Genomics

value: Adipose tissue

tag: condition

tag: tissue type


title: S2_G7_M_R2

description:
Short population 2, Generation 7, Male, Replicate 2
STH_347


title: Sup-B15 cell line

type: genomic

city: Fortaleza

first: Caio

middle: Bezerra

last: Machado

state: Ceará

address: St. Coronel Nunes de Melo, 1000

department: Drug Research and Development Center (NPDM)

country: Brazil

institute: Federal University of Ceará (UFC)

description: SUP-B15 cell line harvested after multiple passages and before cell confluence

hyb_protocol: Incubation in Hybridization Master Mix for 3 minutes, at 95 ºC, followed by 30 minutes at 37 ºC and a 1 minute spin at 6000x g. 100 ul of solution added to hybridization slide and incubated during 24h at 67 ºC and 20 rpm, followed by sequential washes with aCGH/ChIP-on-Chip Wash Buffer 1 and Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2

scan_protocol: Slides scanned with DNA Microarray Scanner with SureScan High-Resolution (G2505C, Agilent Technologies, Santa Clara, CA, USA). Images analysed with Agilent Feature Extraction v.12.5.

data_processing:
Data analysed through CytoGenomics 5.0.2.5 (Agilent Technologies, Santa Clara, CA). Only regions > 1kb were used to build the reference mapping archive using intersetBed and multiIntersectBed functions of R package BEDtools. All statistical analysis made with software GX 14.5 (Agilent Technologies, Santa Clara, CA) and R v.3.6.2.
CNVs calculated using Aberration Detection Method 2 (ADM-2) algorithm with sensibility threshold = 6, aberration filter = 3 and minimum AvgAbsLogRatio = 0.25.

source_name: SUP-B15 cell line

label_protocol: Labeling with either Cy5-dUTP, for SUP-B15 DNA, or Cy3-dUTP, for reference DNA, in Labeling Master Mix composed of 5x reactivation buffer, 10x dNTPs, Exo-Klenow (DNA polymerase), and either Cy5-dUTP or Cy3-dUTP

growth_protocol: Cells grown in RPMI medium supplemented with 10% of fetal bovine serum and with regular passages 2 to 3 times a week

extract_protocol: DNA extracted with Illustra – Tissue&Cells, GenomicPrep Mini Spin Kit according to manufacturer's instructions

tag: tissue

value: Bone marrow

tag: morphology

value: B lymphoblast

tag: gender

source_name: Reference DNA


title: S2_G7_M_R1

description:
Short population 2, Generation 7, Male, Replicate 1
STH_346


title: S2_G8_M_R1

description:
Short population 2, Generation 8, Male, Replicate 1
STH_370


title: S2_G9_M_R1

description:
Short population 2, Generation 9, Male, Replicate 1
STH_394


title: S2_G6_F_R1

description:
Short population 2, Generation 6, Female, Replicate 1
STH_320


title: S2_G5_F_R1

description:
Short population 2, Generation 5, Female, Replicate 1
STH_296


title: S2_G5_M_R1

description:
Short population 2, Generation 5, Male, Replicate 1
STH_298


title: S2_G8_F_R1

description:
Short population 2, Generation 8, Female, Replicate 1
STH_368


title: S2_G6_F_R2

description:
Short population 2, Generation 6, Female, Replicate 2
STH_321


title: S2_G7_F_R1

description:
Short population 2, Generation 7, Female, Replicate 1
STH_344


title: S2_G6_M_R2

description:
Short population 2, Generation 6, Male, Replicate 2
STH_323


title: S2_G4_F_R2

description:
Short population 2, Generation 4, Female, Replicate 2
STH_273


title: S2_G5_M_R2

description:
Short population 2, Generation 5, Male, Replicate 2
STH_299


title: S2_G4_M_R1

description:
Short population 2, Generation 4, Male, Replicate 1
STH_274


title: S2_G3_M_R2

description:
Short population 2, Generation 3, Male, Replicate 2
STH_250


title: S2_G4_F_R1

description:
Short population 2, Generation 4, Female, Replicate 1
STH_272


title: S2_G4_M_R2

description:
Short population 2, Generation 4, Male, Replicate 2
STH_275


title: S2_G3_M_R1

description:
Short population 2, Generation 3, Male, Replicate 1
STH_249


title: S2_G3_F_R2

description:
Short population 2, Generation 3, Female, Replicate 2
STH_248


title: S2_G2_M_R2

description:
Short population 2, Generation 2, Male, Replicate 2
STH_226


title: S2_G6_M_R1

description:
Short population 2, Generation 6, Male, Replicate 1
STH_322


title: S2_G2_M_R1

description:
Short population 2, Generation 2, Male, Replicate 1
STH_219


title: S2_G2_F_R1

description:
Short population 2, Generation 2, Female, Replicate 1
STH_217


title: S2_G3_F_R1

description:
Short population 2, Generation 3, Female, Replicate 1
STH_247


title: S2_G0_F_R1

description:
Short population 2, Generation 0, Female, Replicate 1
STH_143


title: S2_G2_F_R2

description:
Short population 2, Generation 2, Female, Replicate 2
STH_218


title: S2_G0_M_R2

description:
Short population 2, Generation 0, Male, Replicate 2
STH_159


title: S2_G7_F_R2

description:
Short population 2, Generation 7, Female, Replicate 2
STH_345


title: S2_G0_M_R1

description:
Short population 2, Generation 0, Male, Replicate 1
STH_158


title: S2_G0_F_R2

description:
Short population 2, Generation 0, Female, Replicate 2
STH_144


title: S2_G5_F_R2

description:
Short population 2, Generation 5, Female, Replicate 2
STH_297


title: S1_G13_M_R2

description:
Short population 1, Generation 13, Male, Replicate 2
STH_495


title: S1_G12_M_R2

description:
Short population 1, Generation 12, Male, Replicate 2
STH_477


title: S1_G13_F_R2

description:
Short population 1, Generation 13, Female, Replicate 2
STH_493


title: S1_G13_M_R1

description:
Short population 1, Generation 13, Male, Replicate 1
STH_494


title: S1_G12_F_R2

description:
Short population 1, Generation 12, Female, Replicate 2
STH_458


title: S1_G12_M_R1

description:
Short population 1, Generation 12, Male, Replicate 1
STH_476


title: S1_G11_F_R1

description:
Short population 1, Generation 11, Female, Replicate 1
STH_433


title: S1_G11_F_R2

description:
Short population 1, Generation 11, Female, Replicate 2
STH_434


title: S1_G9_M_R2

description:
Short population 1, Generation 9, Male, Replicate 2
STH_383


title: S1_G10_F_R1

description:
Short population 1, Generation 10, Female, Replicate 1
STH_409


title: S1_G11_M_R2

description:
Short population 1, Generation 11, Male, Replicate 2
STH_436


title: S1_G11_M_R1

description:
Short population 1, Generation 11, Male, Replicate 1
STH_435


title: S1_G9_F_R1

description:
Short population 1, Generation 9, Female, Replicate 1
STH_380


title: S1_G9_M_R1

description:
Short population 1, Generation 9, Male, Replicate 1
STH_382


title: S1_G9_F_R2

description:
Short population 1, Generation 9, Female, Replicate 2
STH_399


title: S1_G10_F_R2

description:
Short population 1, Generation 10, Female, Replicate 2
STH_410


title: S1_G8_F_R2

description:
Short population 1, Generation 8, Female, Replicate 2
STH_357


title: S1_G8_M_R1

description:
Short population 1, Generation 8, Male, Replicate 1
STH_358


title: S1_G8_M_R2

description:
Short population 1, Generation 8, Male, Replicate 2
STH_359


title: S1_G7_M_R2

description:
Short population 1, Generation 7, Male, Replicate 2
STH_335


title: S1_G13_F_R1

description:
Short population 1, Generation 13, Female, Replicate 1
STH_492


title: S1_G12_F_R1

description:
Short population 1, Generation 12, Female, Replicate 1
STH_457


title: S1_G8_F_R1

description:
Short population 1, Generation 8, Female, Replicate 1
STH_356


title: S1_G7_M_R1

description:
Short population 1, Generation 7, Male, Replicate 1
STH_334


title: S1_G10_M_R2

description:
Short population 1, Generation 10, Male, Replicate 2
STH_412


title: S1_G7_F_R2

description:
Short population 1, Generation 7, Female, Replicate 2
STH_333


title: S1_G10_M_R1

description:
Short population 1, Generation 10, Male, Replicate 1
STH_411


title: S1_G6_M_R2

description:
Short population 1, Generation 6, Male, Replicate 2
STH_311


title: S1_G7_F_R1

description:
Short population 1, Generation 7, Female, Replicate 1
STH_332


title: S1_G6_M_R1

description:
Short population 1, Generation 6, Male, Replicate 1
STH_310


title: S1_G6_F_R2

description:
Short population 1, Generation 6, Female, Replicate 2
STH_309


title: S1_G5_F_R2

description:
Short population 1, Generation 5, Female, Replicate 2
STH_285


title: S1_G5_M_R1

description:
Short population 1, Generation 5, Male, Replicate 1
STH_286


title: S1_G5_F_R1

description:
Short population 1, Generation 5, Female, Replicate 1
STH_284


title: S1_G4_M_R2

description:
Short population 1, Generation 4, Male, Replicate 2
STH_263


title: S1_G6_F_R1

description:
Short population 1, Generation 6, Female, Replicate 1
STH_308


title: S1_G5_M_R2

description:
Short population 1, Generation 5, Male, Replicate 2
STH_287


title: S1_G3_M_R2

description:
Short population 1, Generation 3, Male, Replicate 2
STH_238


title: S1_G4_F_R2

description:
Short population 1, Generation 4, Female, Replicate 2
STH_261


title: S1_G4_M_R1

description:
Short population 1, Generation 4, Male, Replicate 1
STH_262


title: S1_G3_M_R1

description:
Short population 1, Generation 3, Male, Replicate 1
STH_237


title: S1_G3_F_R2

description:
Short population 1, Generation 3, Female, Replicate 2
STH_236


title: S1_G4_F_R1

description:
Short population 1, Generation 4, Female, Replicate 1
STH_260


title: S1_G3_F_R1

description:
Short population 1, Generation 3, Female, Replicate 1
STH_235


title: S1_G2_M_R2

description:
Short population 1, Generation 2, Male, Replicate 2
STH_225


title: S1_G2_F_R1

description:
Short population 1, Generation 2, Female, Replicate 1
STH_205


title: S1_G2_M_R1

description:
Short population 1, Generation 2, Male, Replicate 1
STH_224


title: S1_G2_F_R2

description:
Short population 1, Generation 2, Female, Replicate 2
STH_206


title: S1_G0_M_R2

description:
Short population 1, Generation 0, Male, Replicate 2
STH_134


title: S1_G0_F_R2

description:
Short population 1, Generation 0, Female, Replicate 2
STH_132


title: S1_G0_M_R1

description:
Short population 1, Generation 0, Male, Replicate 1
STH_133


title: L2_G13_M_R2

description:
Long population 2, Generation 13, Male, Replicate 2
STH_499

value: long


title: L2_G13_F_R2

description:
Long population 2, Generation 13, Female, Replicate 2
STH_497


title: S1_G0_F_R1

description:
Short population 1, Generation 0, Female, Replicate 1
STH_131


title: L2_G12_M_R2

description:
Long population 2, Generation 12, Male, Replicate 2
STH_478


title: L2_G12_F_R2

description:
Long population 2, Generation 12, Female, Replicate 2
STH_462


title: L2_G13_F_R1

description:
Long population 2, Generation 13, Female, Replicate 1
STH_496


title: L2_G12_M_R1

description:
Long population 2, Generation 12, Male, Replicate 1
STH_464


title: L2_G12_F_R1

description:
Long population 2, Generation 12, Female, Replicate 1
STH_461


title: L2_G11_M_R2

description:
Long population 2, Generation 11, Male, Replicate 2
STH_440


title: L2_G13_M_R1

description:
Long population 2, Generation 13, Male, Replicate 1
STH_498


title: L2_G10_M_R1

description:
Long population 2, Generation 10, Male, Replicate 1
STH_415


title: L2_G11_M_R1

description:
Long population 2, Generation 11, Male, Replicate 1
STH_439


title: L2_G11_F_R2

description:
Long population 2, Generation 11, Female, Replicate 2
STH_438


title: L2_G10_M_R2

description:
Long population 2, Generation 10, Male, Replicate 2
STH_416


title: L2_G11_F_R1

description:
Long population 2, Generation 11, Female, Replicate 1
STH_437


title: L2_G10_F_R1

description:
Long population 2, Generation 10, Female, Replicate 1
STH_413


title: L2_G9_M_R2

description:
Long population 2, Generation 9, Male, Replicate 2
STH_387


title: L2_G9_M_R1

description:
Long population 2, Generation 9, Male, Replicate 1
STH_386


title: L2_G10_F_R2

description:
Long population 2, Generation 10, Female, Replicate 2
STH_414


title: L2_G8_M_R2

description:
Long population 2, Generation 8, Male, Replicate 2
STH_363


title: L2_G9_F_R1

description:
Long population 2, Generation 9, Female, Replicate 1
STH_384


title: L2_G8_F_R2

description:
Long population 2, Generation 8, Female, Replicate 2
STH_361


title: L2_G8_F_R1

description:
Long population 2, Generation 8, Female, Replicate 1
STH_360


title: L2_G8_M_R1

description:
Long population 2, Generation 8, Male, Replicate 1
STH_362


title: L2_G7_M_R1

description:
Long population 2, Generation 7, Male, Replicate 1
STH_338


title: L2_G7_F_R2

description:
Long population 2, Generation 7, Female, Replicate 2
STH_337


title: L2_G6_M_R1

description:
Long population 2, Generation 6, Male, Replicate 1
STH_314


title: L2_G7_F_R1

description:
Long population 2, Generation 7, Female, Replicate 1
STH_336


title: L2_G6_M_R2

description:
Long population 2, Generation 6, Male, Replicate 2
STH_315


title: L2_G6_F_R1

description:
Long population 2, Generation 6, Female, Replicate 1
STH_312


title: L2_G6_F_R2

description:
Long population 2, Generation 6, Female, Replicate 2
STH_313


title: L2_G5_M_R2

description:
Long population 2, Generation 5, Male, Replicate 2
STH_291


title: L2_G5_M_R1

description:
Long population 2, Generation 5, Male, Replicate 1
STH_290


title: L2_G5_F_R1

description:
Long population 2, Generation 5, Female, Replicate 1
STH_288


title: L2_G5_F_R2

description:
Long population 2, Generation 5, Female, Replicate 2
STH_289


title: L2_G4_M_R2

description:
Long population 2, Generation 4, Male, Replicate 2
STH_267


title: L2_G9_F_R2

description:
Long population 2, Generation 9, Female, Replicate 2
STH_385


title: L2_G4_F_R2

description:
Long population 2, Generation 4, Female, Replicate 2
STH_265


title: L2_G3_M_R2

description:
Long population 2, Generation 3, Male, Replicate 2
STH_242


title: L2_G3_F_R2

description:
Long population 2, Generation 3, Female, Replicate 2
STH_240


title: L2_G7_M_R2

description:
Long population 2, Generation 7, Male, Replicate 2
STH_339


title: L2_G3_F_R1

description:
Long population 2, Generation 3, Female, Replicate 1
STH_239


title: L2_G3_M_R1

description:
Long population 2, Generation 3, Male, Replicate 1
STH_241


title: L2_G2_M_R2

description:
Long population 2, Generation 2, Male, Replicate 2
STH_212


title: L2_G2_M_R1

description:
Long population 2, Generation 2, Male, Replicate 1
STH_211


title: L2_G0_M_R1

description:
Long population 2, Generation 0, Male, Replicate 1
STH_155


title: L1_G13_M_R1

description:
Long population 1, Generation 13, Male, Replicate 1
STH_486


title: L1_G13_M_R2

description:
Long population 1, Generation 13, Male, Replicate 2
STH_487


title: L1_G13_F_R2

description:
Long population 1, Generation 13, Female, Replicate 2
STH_485


title: L2_G0_M_R2

description:
Long population 2, Generation 0, Male, Replicate 2
STH_156


title: L1_G12_M_R2

description:
Long population 1, Generation 12, Male, Replicate 2
STH_473


title: L1_G13_F_R1

description:
Long population 1, Generation 13, Female, Replicate 1
STH_484


title: L2_G2_F_R1

description:
Long population 2, Generation 2, Female, Replicate 1
STH_209


title: L1_G12_F_R2

description:
Long population 1, Generation 12, Female, Replicate 2
STH_450


title: L2_G0_F_R1

description:
Long population 2, Generation 0, Female, Replicate 1
STH_135


title: L2_G0_F_R2

description:
Long population 2, Generation 0, Female, Replicate 2
STH_136


title: L1_G12_F_R1

description:
Long population 1, Generation 12, Female, Replicate 1
STH_449


title: L1_G11_M_R2

description:
Long population 1, Generation 11, Male, Replicate 2
STH_428


title: L1_G11_M_R1

description:
Long population 1, Generation 11, Male, Replicate 1
STH_427


title: L2_G4_M_R1

description:
Long population 2, Generation 4, Male, Replicate 1
STH_266


title: L1_G11_F_R2

description:
Long population 1, Generation 11, Female, Replicate 2
STH_426


title: L1_G11_F_R1

description:
Long population 1, Generation 11, Female, Replicate 1
STH_425


title: L1_G10_M_R2

description:
Long population 1, Generation 10, Male, Replicate 2
STH_404


title: L2_G4_F_R1

description:
Long population 2, Generation 4, Female, Replicate 1
STH_264


title: L1_G10_M_R1

description:
Long population 1, Generation 10, Male, Replicate 1
STH_403


title: L1_G10_F_R2

description:
Long population 1, Generation 10, Female, Replicate 2
STH_402


title: L2_G2_F_R2

description:
Long population 2, Generation 2, Female, Replicate 2
STH_210


title: L1_G10_F_R1

description:
Long population 1, Generation 10, Female, Replicate 1
STH_401


title: L1_G9_F_R2

description:
Long population 1, Generation 9, Female, Replicate 2
STH_373


title: L1_G9_M_R2

description:
Long population 1, Generation 9, Male, Replicate 2
STH_375


title: L1_G9_M_R1

description:
Long population 1, Generation 9, Male, Replicate 1
STH_374


title: L1_G12_M_R1

description:
Long population 1, Generation 12, Male, Replicate 1
STH_451


title: L1_G9_F_R1

description:
Long population 1, Generation 9, Female, Replicate 1
STH_372


title: L1_G8_M_R2

description:
Long population 1, Generation 8, Male, Replicate 2
STH_400


title: L1_G8_M_R1

description:
Long population 1, Generation 8, Male, Replicate 1
STH_350


title: L1_G8_F_R1

description:
Long population 1, Generation 8, Female, Replicate 1
STH_348


title: L1_G5_M_R2

description:
Long population 1, Generation 5, Male, Replicate 2
STH_279


title: L1_G7_M_R2

description:
Long population 1, Generation 7, Male, Replicate 2
STH_327


title: L1_G8_F_R2

description:
Long population 1, Generation 8, Female, Replicate 2
STH_349


title: L1_G7_F_R1

description:
Long population 1, Generation 7, Female, Replicate 1
STH_324


title: L1_G7_F_R2

description:
Long population 1, Generation 7, Female, Replicate 2
STH_325


title: L1_G6_F_R1

description:
Long population 1, Generation 6, Female, Replicate 1
STH_300


title: L1_G6_M_R1

description:
Long population 1, Generation 6, Male, Replicate 1
STH_302


title: L1_G6_F_R2

description:
Long population 1, Generation 6, Female, Replicate 2
STH_301


title: L1_G5_M_R1

description:
Long population 1, Generation 5, Male, Replicate 1
STH_278


title: L1_G7_M_R1

description:
Long population 1, Generation 7, Male, Replicate 1
STH_326


title: L1_G5_F_R2

description:
Long population 1, Generation 5, Female, Replicate 2
STH_277


title: L1_G4_M_R2

description:
Long population 1, Generation 4, Male, Replicate 2
STH_255


title: L1_G5_F_R1

description:
Long population 1, Generation 5, Female, Replicate 1
STH_276


title: L1_G4_F_R2

description:
Long population 1, Generation 4, Female, Replicate 2
STH_253


title: L1_G3_M_R2

description:
Long population 1, Generation 3, Male, Replicate 2
STH_251


title: L1_G4_F_R1

description:
Long population 1, Generation 4, Female, Replicate 1
STH_252


title: Golden Promise, Control, Replicate 2

city: Dublin

first: Ailbhe

middle: Jane

last: Brazel

address: School of Natural Sciences

department: Botany Discipline

country: Ireland

institute: Trinity College Dublin

data_processing:
Raw RNA-sequencing reads were aligned to Morex V3 (from e!DAL - Plant Genomics and Phenomics Research Data Repository (PGP) (https://edal-pgp.ipk-gatersleben.de/)) using bowtie2 (v2.4.5)
Files were converted from .sam to .bam files and indexed using samtools (v1.15.1)
Gene abundance was estimated using stringtie (v2.1.7)
Differential gene expression analysis was performed using the Bioconductor package DeSeq2 in R using a design in which the factors Variety and Treatment were combined into a single factor to model multiple condition effects.
Assembly: Morex V3
Supplementary files format and content: Comma-delimited file including gene counts for each sample

organism: Hordeum vulgare

source_name: Root

growth_protocol: Commercial John Innes No2 (Vitax; UK) soil was soaked in water after filling round pots of 9-cm diameter and 9-cm height without compressing the soil. Untreated seeds were sown directly in soil at a depth of 2 cm. The sown seeds were stratified in the dark for 14 days at 4°C to ensure homogenous germination. After cold treatment, the pots were transferred to the plant room for germination and growth. Plants were grown in a custom-made plant growth room under long-day conditions (16 hours light/8 hours dark) at 15°C (constant temperature), approximately 45% relative humidity. Light intensity was determined to be ~138 µmol/m2/s and was provided by LED bulbs (Philipps LED tubes High Output, T8 20W/865). Plants were grown for 10 days before treatment.

extract_protocol:
Roots of plants grown under control conditions or subjected to partial submergence for 24 hours were rinsed under running tap water, and frozen in liquid nitrogen. The roots of 3 plants were pooled prior to grinding for RNA extraction for each sample. The tissue was ground in liquid nitrogen and total RNA was extracted using Spectrum™ Plant Total RNA kit (Sigma-Aldrich). Following RNA extraction, RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent). All RNA samples had RIN values > 7.0.
Libraries were prepared by BGI Genomics (Hong Kong)

treatment_protocol: For waterlogging treatment, pots were transferred to a large tub, which was subsequently filled with tap water up to 1 cm above soil level. The water level was kept constant throughout the duration of the experiment. The plants were kept in the same growth conditions and were treated for 24 hours. Control plants were left in the same growth conditions but received normal watering (watering every two days, avoiding any standing water in the trays).

value: Root

tag: treatment age

value: 10 day

tag: cultivar

value: Golden Promise

tag: row number

value: Two

tag: season

value: Spring

tag: treatment

value: Control


title: Golden Promise, Control, Replicate 1


title: L1_G4_M_R1

description:
Long population 1, Generation 4, Male, Replicate 1
STH_254

tag: developmental stage

value: Adult

value: Male

tag: selection treatment


title: Regina, Waterlogged, Replicate 2

value: Regina

value: Winter

value: Waterlogged


title: L1_G3_F_R1

description:
Long population 1, Generation 3, Female, Replicate 1
STH_227

value: Female

tag: selection generation

tag: population replicate


title: L1_G2_M_R2

description:
Long population 1, Generation 2, Male, Replicate 2
STH_222

tag: Sex

tag: sample replicate


title: L1_G2_M_R1

description:
Long population 1, Generation 2, Male, Replicate 1
STH_221


title: L1_G3_M_R1

description:
Long population 1, Generation 3, Male, Replicate 1
STH_230


title: L1_G2_F_R1

description:
Long population 1, Generation 2, Female, Replicate 1
STH_197


title: L1_G6_M_R2

description:
Long population 1, Generation 6, Male, Replicate 2
STH_303


title: Golden Promise, Control, Replicate 3


title: Regina, Waterlogged, Replicate 3


title: Pilastro, Waterlogged, Replicate 1

value: Pilastro

value: Six


title: Pilastro, Control, Replicate 3


title: L1_G0_F_R1

description:
Long population 1, Generation 0, Female, Replicate 1
STH_123


title: L1_G0_F_R2

description:
Long population 1, Generation 0, Female, Replicate 2
STH_124


title: Pilastro, Waterlogged, Replicate 3


title: Pilastro, Control, Replicate 1


title: L1_G0_M_R1

description:
Long population 1, Generation 0, Male, Replicate 1
STH_125


title: Regina, Control, Replicate 2


title: Pilastro, Waterlogged, Replicate 2


title: Pilastro, Control, Replicate 2


title: C2_G13_M_R2

description:
Control population 2, Generation 13, Male, Replicate 2
STH_503

value: control


title: Regina, Control, Replicate 3


title: L1_G0_M_R2

description:
Long population 1, Generation 0, Male, Replicate 2
STH_126


title: C2_G13_M_R1

description:
Control population 2, Generation 13, Male, Replicate 1
STH_502


title: C2_G13_F_R2

description:
Control population 2, Generation 13, Female, Replicate 2
STH_501


title: Regina, Control, Replicate 1


title: C2_G13_F_R1

description:
Control population 2, Generation 13, Female, Replicate 1
STH_500


title: Passport, Waterlogged, Replicate 3

value: Passport


title: Regina, Waterlogged, Replicate 1


title: L1_G3_F_R2

description:
Long population 1, Generation 3, Female, Replicate 2
STH_228

value: long


title: C2_G12_M_R2

description:
Control population 2, Generation 12, Male, Replicate 2
STH_480


title: Passport, Waterlogged, Replicate 2

value: Root


title: C2_G12_M_R1

description:
Control population 2, Generation 12, Male, Replicate 1
STH_479


title: L1_G2_F_R2

description:
Long population 1, Generation 2, Female, Replicate 2
STH_198


title: Passport, Waterlogged, Replicate 1

value: 10 day


title: C2_G12_F_R2

description:
Control population 2, Generation 12, Female, Replicate 2
STH_466


title: SGC_TAM+GFP+

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Read were aligned with HISAT2.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2.
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: Mouse leukemai cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum and 10 ng/mL rmIL-3. MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Setd1afl/fl;CreER;MLL-AF9 leukemia cells were infected with retrovirus vector containing GFP or hSETD1A-GFP-CDT expression construct and then treated with tamoxifen (or EtOH as control) for 72h. Doxycycline-inducible Cas9 expression vector was introduced with lentivirus and stable expressing single cell clone was established. sgRNA vector was introduced with lentivirus and GFP-positive cells were collected by cell sorter. 1 µg / mL of Doxycycline was treated for 6 days.

tag: stimulation

tag: time

tag: cell line

value: mouse MLL-AF9 leukemia


title: C2_G11_M_R2

description:
Control population 2, Generation 11, Male, Replicate 2
STH_444


title: C2_G12_F_R1

description:
Control population 2, Generation 12, Female, Replicate 1
STH_465


title: SGC_TAM+GFP-


title: C2_G11_M_R1

description:
Control population 2, Generation 11, Male, Replicate 1
STH_443


title: Passport, Control, Replicate 2

tag: tissue


title: Passport, Control, Replicate 1


title: G_TAM-GFP+

source_name: Mouse Setd1afl/fl;CreER:MLL-AF9;GFP

value: EtOH


title: C2_G11_F_R2

description:
Control population 2, Generation 11, Female, Replicate 2
STH_442


title: C2_G11_F_R1

description:
Control population 2, Generation 11, Female, Replicate 1
STH_441


title: C2_G10_M_R1

description:
Control population 2, Generation 10, Male, Replicate 1
STH_419


title: G_TAM+GFP+


title: Infinity, Waterlogged, Replicate 3

value: Infinity

value: Two


title: Infinity, Waterlogged, Replicate 2


title: Infinity, Waterlogged, Replicate 1


title: C2_G10_F_R2

description:
Control population 2, Generation 10, Female, Replicate 2
STH_418

value: Adult


title: C2_G10_F_R1

description:
Control population 2, Generation 10, Female, Replicate 1
STH_417


title: C2_G10_M_R2

description:
Control population 2, Generation 10, Male, Replicate 2
STH_420

value: Male


title: C2_G9_F_R2

description:
Control population 2, Generation 9, Female, Replicate 2
STH_389


title: C2_G9_M_R1

description:
Control population 2, Generation 9, Male, Replicate 1
STH_390


title: C2_G9_M_R2

description:
Control population 2, Generation 9, Male, Replicate 2
STH_391


title: C2_G9_F_R1

description:
Control population 2, Generation 9, Female, Replicate 1
STH_388


title: Infinity, Control, Replicate 3

value: Control


title: Passport, Control, Replicate 3

value: Winter


title: KD 3

city: Wuhan

first: xinhe

last: XinheHuang

state: Hubei

address: Hust

country: Singapore

institute: Huazhong University of Science and Technology

data_processing:
Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters;
Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome
Use StringTie v1.3.4d for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster.
Supplementary files format and content: xlsx file includes raw counts for each Sample

source_name: mouse liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext®UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's protocols.

value: mouse liver

value: ketogenic diet


title: KD 5


title: C2_G8_M_R2

description:
Control population 2, Generation 8, Male, Replicate 2
STH_367


title: KD 2


title: KD 4


title: C2_G8_M_R1

description:
Control population 2, Generation 8, Male, Replicate 1
STH_366


title: KD 1


title: Infinity, Control, Replicate 1


title: C2_G8_F_R2

description:
Control population 2, Generation 8, Female, Replicate 2
STH_365

value: Female


title: C2_G8_F_R1

description:
Control population 2, Generation 8, Female, Replicate 1
STH_364


title: Control 6

value: control diet


title: Golden Promise, Waterlogged, Replicate 3

value: Golden Promise

value: Spring

value: Waterlogged


title: C2_G7_F_R2

description:
Control population 2, Generation 7, Female, Replicate 2
STH_341

value: control


title: Control 5


title: C2_G7_M_R1

description:
Control population 2, Generation 7, Male, Replicate 1
STH_342


title: C2_G6_M_R2

description:
Control population 2, Generation 6, Male, Replicate 2
STH_319


title: C2_G7_F_R1

description:
Control population 2, Generation 7, Female, Replicate 1
STH_340


title: Golden Promise, Waterlogged, Replicate 2

value: Root

value: 10 day


title: Control 4


title: Golden Promise, Waterlogged, Replicate 1


title: Control 3


title: C2_G6_M_R1

description:
Control population 2, Generation 6, Male, Replicate 1
STH_318


title: C2_G6_F_R2

description:
Control population 2, Generation 6, Female, Replicate 2
STH_317


title: Control 2


title: C2_G5_M_R2

description:
Control population 2, Generation 5, Male, Replicate 2
STH_295


title: Infinity, Control, Replicate 2


title: C2_G5_M_R1

description:
Control population 2, Generation 5, Male, Replicate 1
STH_294


title: Control 1


title: FKBP-SETD1A_BuGZ

data_processing:
CUT&Tag library were sequenced with paired-end, but analyzed from read R1 fastq files.
BCL2FASTQ version1.8.4 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie. CUT&Tag reads were aligned to hg19 and mm10.
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format or converted to bigwig format using HOMER software. Wig files were converted to bigwig files using UCSC wigToBigWig program.
Assembly: hg19, mm10

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP-seq, cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated. For CUT&Tag, human MOLM-13 cells were mixed with 1/10 number of mouse MLL-AF9 transduced cells for spike-in control, and fixed with 0.1% formaldehyde. Cells were mixed with conA beads, and then incubated with SETD1A antibody.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol. For CUT&Tag, tagmentation was performed using pA-Tn5 with adaptor complex.

treatment_protocol: HA-FKBP-hSETD1A expression vector were introduced with lentivirus and stable expressing cell was established. Doxycycline-inducible Cas9 expression vector was introduced with lentivirus and stable expressing single cell clone was established. sgRNA-GFP vector was introduced with lentivirus and GFP-positive cells were sorted. GFP sorted cells were treated with doxycycline for 4 days.

value: MOLM-13 leukemia cell line

tag: vector

tag: chip antibody


title: C2_G7_M_R2

description:
Control population 2, Generation 7, Male, Replicate 2
STH_343


title: FKBP-SETD1A_HA

value: HA (#3724 Cell Signaling)


title: C2_G5_F_R2

description:
Control population 2, Generation 5, Female, Replicate 2
STH_293


title: C2_G5_F_R1

description:
Control population 2, Generation 5, Female, Replicate 1
STH_292


title: C2_G4_M_R2

description:
Control population 2, Generation 4, Male, Replicate 2
STH_271


title: C2_G4_M_R1

description:
Control population 2, Generation 4, Male, Replicate 1
STH_270


title: C2_G4_F_R2

description:
Control population 2, Generation 4, Female, Replicate 2
STH_269


title: C2_G4_F_R1

description:
Control population 2, Generation 4, Female, Replicate 1
STH_268


title: C2_G6_F_R1

description:
Control population 2, Generation 6, Female, Replicate 1
STH_316


title: FKBP-SETD1A_BUB3

value: BUB3 (#ab133699 Abcam)


title: RA, biological rep 3 (miRNA-seq)

last: Zou

address: West Huangpu Avenue

institute: Jinan University

data_processing:
Quality control of paired-end FASTQ files (raw data) that came from sequencing pipelines were performed using FastQC.
Used fastx (version 0.0.13) to trimmed off the barcodes and adapters, and removed sequences that are of low quality or too short.
The reads of miRNA-seq data were aligned to the miRNAs in miRbase20.0 using Bowtie2 software (version 2.4.4) .
Assembly: miRbase20.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: craniofacial prominences

extract_protocol:
Total RNA including miRNAs was extracted using the mirVana miRNA Isolation Kit (Cat. No. AM1561, Ambion, Austin, TX, USA) according to the manufacturer's instructions. 10 ng total RNA was used to construct the sequencing library.
The standard miRNA sequencing libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (Cat.No. E7580S, New England Biolabs, Ipswich, Massachusetts, USA).

value: craniofacial prominences

tag: strain

tag: genotype

value: Wild type

value: with atRA treatment


title: RA, biological rep 1 (miRNA-seq)


title: RA, biological rep 4 (miRNA-seq)


title: RA, biological rep 2 (miRNA-seq)


title: C2_G2_M_R2

description:
Control population 2, Generation 2, Male, Replicate 2
STH_216

value: Adult

value: Male


title: Con, biological rep 3 (miRNA-seq)

value: without atRA treatment


title: C2_G2_F_R2

description:
Control population 2, Generation 2, Female, Replicate 2
STH_214

value: Female


title: C2_G2_M_R1

description:
Control population 2, Generation 2, Male, Replicate 1
STH_215


title: Con, biological rep 4 (miRNA-seq)


title: C2_G3_F_R1

description:
Control population 2, Generation 3, Female, Replicate 1
STH_243


title: C2_G0_M_R2

description:
Control population 2, Generation 0, Male, Replicate 2
STH_157


title: Con, biological rep 2 (miRNA-seq)


title: C2_G0_M_R1

description:
Control population 2, Generation 0, Male, Replicate 1
STH_142


title: C2_G0_F_R2

description:
Control population 2, Generation 0, Female, Replicate 2
STH_140


title: C2_G3_M_R2

description:
Control population 2, Generation 3, Male, Replicate 2
STH_246


title: Con, biological rep 1 (miRNA-seq)


title: C2_G2_F_R1

description:
Control population 2, Generation 2, Female, Replicate 1
STH_213


title: C2_G3_M_R1

description:
Control population 2, Generation 3, Male, Replicate 1
STH_245


title: C2_G3_F_R2

description:
Control population 2, Generation 3, Female, Replicate 2
STH_244


title: ACT + MS-275 rep3

type: RNA

city: Hamilton

first: Yonghong

last: Wan

state: Ontario

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

description: Gene expression of adoptively transferred T cells purified 4.5 days post-treatment

hyb_protocol: Sample preparation for microarray hybridization was conducted with a GeneChip WT Pico Reagent Kit according to manufacturer instructions.

scan_protocol: Samples were run on a GeneChip Scanner 3000.

data_processing: Probe set signals were SST-RMA-normalized prior to further analysis.

label: biotin

source_name: Thy1.1+ T cells flow-sorted from spleens

growth_protocol: MC38-gp33 cells were maintained in MEM/F11 medium containing 10% FBS, 2 mM l-glutamine, 5 ml sodium pyruvate, 5 mL nonessential amino acids, 5 mL vitamin solution, 55 μM 2-mercaptoethanol, 100 U/mL penicillin, and 100 ng/ml streptomycin before challenging C57BL/6 mice for 14 days.

extract_protocol: Re-suspended cells were stained for CD8, Thy1.1, and viability. Cell sorting was performed and RNA was extracted and purified using an RNeasy Mini Kit. mRNA was enriched using the NEBNext Poly(A) mRNA Isolation Module where each sample had an RNA integrity number (RIN) score of >7

treatment_protocol: In vitro-differentiated TCR transgenic CD8+ Tcm cells were injected intravenously into mice. After 24h, the mice were treated i.v. with VSVΔM51-gp33. Concomitantly, MS-275 was injected i.p. daily for five days.

tag: tumor stage

value: 14d MC38-gp33 tumor-bearing mice


title: C1_G13_M_R2

description:
Control population 1, Generation 13, Male, Replicate 2
STH_491


title: ACT - MS-275 rep5

label_protocol: Sample preparation for microarray hybridization was conducted with a GeneChip WT Pico Reagent Kit according to manufacturer instructions.


title: ACT + MS-275 rep2


title: ACT + MS-275 rep5


title: ACT + MS-275 rep4


title: C1_G13_M_R1

description:
Control population 1, Generation 13, Male, Replicate 1
STH_490


title: ACT + MS-275 rep1


title: ACT - MS-275 rep4


title: C1_G13_F_R2

description:
Control population 1, Generation 13, Female, Replicate 2
STH_489


title: RA, biological rep 3 (mRNA-seq)

data_processing:
Quality control of paired-end FASTQ files (raw data) that came from sequencing pipelines were performed using FastQC.
Trimmed off the barcodes and adapters, and removed sequences that are of low quality or too short using Seqtk.
Reads were mapped to the mouse reference genome mm (10) (GRCm38.p4) using Hisat2(version 2.0.4) for genome annotation annotations
The gene expression levels were quantified with Stringtie (version 1.3.0) using only uniquely mapped reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total mRNA was extracted using the miRNeasy Mini Kit (Cat. No. 217004, Qiagen, GmBH, Germany) according to the manufacturer's instructions. 1 µg of total RNA was used to construct the sequencing library.
RNA libraries for RNA-seq were prepared using the TruSeq RNA Library Prep Kit v2 (Catalog # RS-122-2001, Illumina, San Diego, CA, USA) following the manufacturer's protocol.


title: RA, biological rep 2 (mRNA-seq)


title: RA, biological rep 4 (mRNA-seq)


title: C1_G12_F_R2

description:
Control population 1, Generation 12, Female, Replicate 2
STH_454


title: C2_G0_F_R1

description:
Control population 2, Generation 0, Female, Replicate 1
STH_139


title: Con, biological rep 4 (mRNA-seq)


title: C1_G12_F_R1

description:
Control population 1, Generation 12, Female, Replicate 1
STH_453


title: C1_G12_M_R1

description:
Control population 1, Generation 12, Male, Replicate 1
STH_474


title: C1_G12_M_R2

description:
Control population 1, Generation 12, Male, Replicate 2
STH_475


title: ACT - MS-275 rep3


title: C1_G11_M_R1

description:
Control population 1, Generation 11, Male, Replicate 1
STH_431


title: LB4646T

city: Los Angeles

first: Lu

last: Sun

state: California

address: 10833 Le Conte Avenue

institute: University of California, LA

description:
BrainMets.ICBtreated
10x Genomics single cell barcoded mRNA from CD45+ fraction

data_processing:
The reads are first mapped to GRCh38 using cellranger software from 10x Genomics
Single-cell, gene-level raw read counts are read from cellranger output and analyzed using Seurat 3.2.2
Assembly: GRCh38
Supplementary files format and content: Combined matrix of raw counts

source_name: brain metastases

extract_protocol:
Dissociated CD45+ single cells were processed using Chromium Single Cell GEM, Library & Gel Bead Kit through the Chromium controller from 10x Genomics.
The resulting single cell barcoded mRNA were reverse transcribed and cleaned as per 10x Genomic's protocol.
10x Genomics single cell RNA-Seq

value: brain metastases

tag: cell type

value: Immune cells

value: ICB treated


title: LB4508T

tag: treatment


title: ACT - MS-275 rep2


title: C1_G13_F_R1

description:
Control population 1, Generation 13, Female, Replicate 1
STH_488

tag: developmental stage

value: control


title: Con, biological rep 3 (mRNA-seq)

first: Yi


title: LB4808T


title: C1_G11_F_R2

description:
Control population 1, Generation 11, Female, Replicate 2
STH_430

tag: selection treatment


title: Con, biological rep 2 (mRNA-seq)


title: RA, biological rep 1 (mRNA-seq)


title: C1_G11_M_R2

description:
Control population 1, Generation 11, Male, Replicate 2
STH_432

tag: selection generation


title: Con, biological rep 1 (mRNA-seq)


title: C1_G10_M_R2

description:
Control population 1, Generation 10, Male, Replicate 2
STH_408

tag: population replicate


title: C1_G11_F_R1

description:
Control population 1, Generation 11, Female, Replicate 1
STH_429

tag: Sex


title: NC484-2

city: Yinchuan

first: Mengli

last: Yang

address: No. 489, Helan Mountain West Road, Xixia District, Yinchuan City, Ningxia

institute: Ningxia University

data_processing:
clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. softrare: fastp; version: 0.21.0.
Hisat2 tools soft were used to map with reference genome. sofeware：HISAT2， version：2.0.4, parameter: --dta -p 6 --max-intronlen 5000000.
The mapped reads were assembled and quantified by StringTie. Software: StringTie; version: 1.3.4d; parameter: --merge -F 0.1 -T 0.1.
Assembly: ARS_UCD1.2

organism: Bos taurus

source_name: adipocyte

growth_protocol: adipocytes were cultured were maintained in DMEM/high glucose medium with  supplemented with 10% fetal bovine serum  (FBS) and 1% Pen-strep in an incubator containing 5% CO2 and 37℃

extract_protocol:
Total RNA was harvested from adipocytes using the Trizol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libranes were prepared for sequencing using slandard lllumina protocols

treatment_protocol: Adipocytes were transfected with bta-miR-484 agomir and agomir NC for 48h

value: adipocyte

value: agomir NC


title: NC484-3


title: BCG_Cystitis_Case12

city: Tokyo

first: Yoshiyuki

last: AKIYAMA

state: Please select...

department: Urology

institute: The University of Tokyo

data_processing:
Adaptor and low-quality portions, defined as sequences with an average Phred score < 10 in a 10-bp window, were removed from the raw reads. All remaining reads ≥ 36 bp in length were regarded as high-quality, clean data and used in downstream analyses.
The clean PE reads were aligned to the University of California Santa Cruz (UCSC) human reference genome (hg19) using Genedata Profiler Genome ver. 11.0.8 (Genedata, Basel, Switzerland).
To quantify gene expression, fragments per kilobase of exon per million mapped fragments (FPKM) values for each gene model were calculated using the Genedata Profiler Genome.
Assembly: Mapped reads were assembled using STAR ver. 2.5.3a by referring to gene structures described in the National Center for Biotechnology Information RefSeq.
Supplementary files format and content: tab-delimited text file includes FPKM value for each sample.

source_name: Bladder

extract_protocol:
Total RNA was extracted from frozen samples using NucleoSpin RNA (Macherey-Nagel, Düren, Germany). RNA was quantified on a NanoDrop 2000c Spectrophotometer (Thermo Fisher Scientific, San Jose, CA, USA), and the purity was measured using an RNA ScreenTape assay on a 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Quality assessment was performed using 2200 TapeStation Software (Agilent Technologies).
Purified total RNA (10 ng) was resuspended in Clontech buffers for mRNA amplification using 5′ template switching PCR with a Clontech SMART-Seq v4 Ultra Low Input RNA kit (Clontech, Palo Alto, CA, USA) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using Illumina Nextera XT DNA Library Prep kits (Illumina, San Diego, CA, USA).

value: Bladder

tag: disease

value: Mycobacterium bovis bacillus Calmette–Guérin (BCG)-related cystitis

tag: biopsied site

value: reddened mucosal flat lesion

tag: gender

value: M

tag: age


title: BCG_Cystitis_Case11

tag: tissue

value: F


title: BCG_Cystitis_Case10


title: ACT - MS-275 rep1


title: C1_G10_M_R1

description:
Control population 1, Generation 10, Male, Replicate 1
STH_407

tag: sample replicate


title: C1_G10_F_R2

description:
Control population 1, Generation 10, Female, Replicate 2
STH_406


title: A484-3

value: bta-miR-484 agomir


title: C1_G10_F_R1

description:
Control population 1, Generation 10, Female, Replicate 1
STH_405

value: Adult


title: BCG_Cystitis_Case9


title: Silc1–/– hippocampus snRNA-seq 1

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

description: Single-nucleus RNA sequencing

data_processing:
snRNA-seq data were processed with Cell Ranger 7.1.0 with default parameters, ‘ --expect-cells 60000’ option, and mm10-2020-A transcritome build.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix table
Library strategy: snRNA-Seq

source_name: Hippocampus

extract_protocol:
Mice were sacrificed and the hippocampus of each mouse was dissected and placed in a lysis buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40 and 1:1000 RNasIN),  according to 10x genomics Nuclei isolation for single cell sequencing protocol.
The pellet containing the nuclei was resuspended in a wash buffer (PBS, 1%BSA and 1:1000 RNasIN). 1000/ul nuclei from each sample were taken for library preparation using 10x Genomics Chromium Single Cell Kit Version 3.1 according to manufacturer protocol.
All libraries were pooled and sequenced on NovaSeq 6000 to an average depth of approximately 200,000,000 reads per sample.

value: Hippocampus


title: Silc1–/– hippocampus snRNA-seq 2

description: Single-nucleus RNA sequencing


title: BCG_Cystitis_Case13


title: A484-2


title: C1_G9_M_R2

description:
Control population 1, Generation 9, Male, Replicate 2
STH_398

value: Male


title: BCG_Cystitis_Case8


title: A484-1


title: WT hippocampus snRNA-seq 2

description: Single-nucleus RNA sequencing

value: WT


title: WT hippocampus snRNA-seq 1

description: Single-nucleus RNA sequencing


title: BCG_Cystitis_Case7


title: C1_G9_M_R1

description:
Control population 1, Generation 9, Male, Replicate 1
STH_378


title: Aortic Endothelial Cells (AoECs) from stressed (S) mice rep5

city: Munich

first: Hendrik

last: Sager

address: Lazarettstr. 36

department: Klinik für Herz- und Kreislauferkrankungen

country: Germany

institute: Deutsches Herzzentrum München

data_processing:
Raw data was generated and processed using the Real Time Analysis 2.4.11 Software (RTA) and Illumina Sequence Analysis Viewer (SVA) 2.4.7.
Raw reads were quality and adapter trimmed with Trimmomatic, mapped to mm10 using the STAR aligner and de-convoluted into gene abundances using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Aortic Endothelial Cells (AoECs)

extract_protocol:
Messenger RNA (mRNA) was extracted from FACS-sorted endothelial cells using the Arcturus PicoPure RNA Isolation Kit (KIT0204, Applied Biosystems) according to the manufacturer’s protocol.
Sequencing libraries were constructed using the TruSeq Stranded kit (Illumina).

value: Aortic Endothelial Cells (AoECs)

value: acute mental stress (S)

value: ApoE


title: BCG_Cystitis_Case6


title: NC484-1


title: RNA-seq from Silc1{+/+} hippocampus in novel environment, replicate 2

data_processing:
RNA-seq: RNA-seq reads were mapped to the mouse genome (mm10 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) with RefSeq annotations was used to call differential expression between samples
ATAC-seq: ATAC-seq reads were mapped to the mouse genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008).
Assembly: mm10
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM quantification is provided for the RNA-seq samples, and MACS2-called peaks are provided for the ATAC-seq data.

source_name: hippocampus

extract_protocol:
Total RNA was extracted from the hippocampus using the TRIREAGENT (MRC) according to the manufacturer’s protocol.
Strand-specific mRNA-seq libraries were prepared from 1 ug total RNA using the SENSE-mRNA-Seq-V2 (Lexogen), according to the manufacturers’ protocol

value: hippocampus

tag: genetic background

tag: aav

tag: environment

value: Novel environment


title: RNA-seq from Silc1{+/+} hippocampus in novel environment, replicate 3