title: IEC, B6J wt SPF, d1, proximal, Biol. Rep1

description:
Library name: Sample 1
prox_d1_1

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

value: epithelial cells

tag: age

tag: localization


title: IEC, B6J wt SPF, d1, medial, Biol. Rep3

status: Public on Dec 23 2024

type: SRA

city: Aachen

first: Mathias

last: Hornef

address: Pauwelstr. 30

department: Institute for Medical Microbiology

country: Germany

institute: University Hospital RWTH Aachen

description:
Library name: Sample 6
med_d1_3

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adapter/low quality reads using Cutadapt v4.4
Trimmed sequences were mapped to the murine genome GRCm38.102 using STAR v2.7.10a
Read count matrix was created using feaureCounts function from Rsubread v2.16
Assembly: GRCm38.102
Supplementary files format and content: comma-delimited Excel file including raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: small intestine

growth_protocol: Intestinal epithelial cells were isolated from murine small intestinal tissue using EDTA

extract_protocol:
Total RNA was isolated from small intestinal epithelial cells using TRIzol reagent following manufacturer's instructions
cDNA libraries were prepared using the NEBNext ultra II directional RNA library kit for Illumina in combination with the NEBNext poly(A) mRNA magnetic isolation module (New England Biolabs) following manufacturer's instructions

tag: tissue

tag: cell type

value: medial


title: 07T6

city: Bratislava

first: Evan

last: Paul

address: Ilkovičova 8

country: Slovakia

institute: MultiplexDX

description: Library name: MDX_07T6_LumA

data_processing:
The bioinformatics pipeline for RNA sequencing is outlined below. 1) FASTQC (v0.11.9) – used for initial quality check of raw sequencing data 2) Cutadapt (v3.4) – removal of adapters and filtering for sequence quality and length. 3) STAR (v2.7.7a) – alignment 4) SAMtools (v1.16.1) – indexing 5) UMI-tools (v1.0.0) – deduplicating bam files based on unique molecular identifiers introduced during library preparation. 6) FeatureCounts (v1.5.2)
Assembly: GRCh38.104
Supplementary files format and content: quantification table generated by featureCounts tool of a Subread package

organism: Homo sapiens

source_name: breast

extract_protocol:
The Macherey Nagel NucleoSpin total RNA FFPE XS kit was used for RNA isolation. After RNA isolation, RNA quantity was measured using the Qubit RNA HS (High Sensitivity) Assay Kit with a Qubit 4 Fluorometer and RNA quality using the Agilent High Sensitivity RNA ScreenTape with an Agilent 4150 TapeStation. The DV200 value of the sample (i.e., the percentage of fragments more than 200 bases in length) was calculated as recommended by Illumina. Samples with DV200 values over 15% were considered viable samples for library preparation.
We used the Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit to prepare total RNA-SEQ libraries following the manufacturer's instructions. We included a single natural positive control sample in each library preparation batch and a synthetic spike-in control in each sample to control for batch library preparation effects. Following library preparation, the quantity and fragment size range of the library was assessed using both the Qubit dsDNA HS kit (Qubit 4 Fluorometer) and the Agilent High Sensitivity DNA ScreenTape kit (Agilent 4150 TapeStation). Successfully prepared libraries contained sufficient library to pool on an Illumina NovaSeq 6000 sequencing instrument and fragment range spanning 200 - 1,000 bp, with a local maximum of 250 - 350 bp. Depending on pool size, individual sequencing libraries were pooled and sequenced on an Illumina NovaSeq 6000 using SP, S1, S2, or S4 flow cells. Pooled libraries were spiked with 10% PhiX as recommended by both Illumina and Takara for low-complexity libraries sequenced on patterned flow cells. Paired-end sequencing (2 x 100 bp) was conducted to obtain approximately 100 million reads per sample.

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

tag: Sex

value: missing

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: LSK, R396Q, replciate 3-2, scRNA-Seq

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

country: USA

institute: St Jude Children's Research Hospital

description:
R396Q 3-2
10X Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger with counts (V.7.0.0) is used for quantification and seurat in R is used for downstream analysis.
nfeatures >=200 | nfeature <=6000 with mitocondrial percentage less than 5 percent is used for quality control.
Assembly: mm10
Supplementary files format and content: Processed data is provided in cell ranger filtered matrix containing barcode, features, counts.

source_name: bone marrow

extract_protocol:
To isolate bone marrow (BM) hematopoietic cells in adult mice, tibias, femurs, and pelvic bones were removed and crushed in ice cold PBS, followed by passage through 70μm filters. Cells were then lysed, washed, and resuspended in FACS buffer followed by sorting for LSK cells.
Expression libraries were constructed according to the Chromium 10X single cell 3′ reagent v3.1 protocol.

tag: tissue

value: bone marrow

tag: cell type

value: Lineage(neg)Sca1(pos)c-Kit(pos) (LSK)

tag: genotype


title: 07T5

description: Library name: MDX_07T5_LumA

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac


title: Sdr5a2 knockdown biol rep 1

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description:
10X genomics
21225X11

data_processing:
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
MEX data were further processed and merged with Seurat (4.1)
Assembly: R_norvegicus_Mar_2012
Supplementary files format and content: csv - counts and metadata - xlsx

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Dissected prefrontal cortex was flash frozen in LN2 and preserved at -80C until processing. The specimens were gently thawed in 2 ml of ice-cold phosphate-buffered saline (PBS, devoid of Ca2+ and Mg2+). This solution was supplemented with various compounds to preserve the quality of the sample: 0.54 μM Nectostatin (Inc. #J65341, ThermoFisher Scientific Chemicals, Waltham, MA), 1 μM HPN-07 (SML2163, Sigma-Aldrich), 0.32 μM sodium hydroxybutyrate (A1161314, ThermoFisher Scientific Chemicals), 78 nM Q-VD-Oph (SML0063, Sigma-Aldrich), and 0.2 U/ml of Ribolock RNase inhibitor (EO0381, Life Technologies Corporation, Carlsbad, CA). The tissue, held over dry ice in a 60-mm Petri dish, was methodically minced into fragments smaller than 2 mm using a razor blade. Subsequently, this tissue was transitioned to a 2 ml Dounce homogenizer containing 1.5 ml of nuclei extraction buffer (130-128-024, Miltenyi Biotec, Bergisch Gladbach, Germany) along with 0.2 U/ml Ribolock RNase inhibitor.  Samples were then centrifuged at 600×g for 5 min, resuspended in 400 μL of PBS enriched with 2% BSA, passed through a 70-μm FLOWMI for clarification, and strained via a 40-μm FLOWMI. Specimens were then entrusted to the Hunstman Cancer Institute High Throughput Genomics Core for 10X Genomics library construction and sequencing.
Libraries were prepped according to the 10X Genomics scRNA-seq 3’ v3.1 Next GEM protocol, NovaSeq Reagent Kit v1.5_150x150 bp Sequencing (these six samples were sequenced on a lane of an S4 flowcell).

treatment_protocol: Stress was introduced with the forced swim test. Rats were plunged individually into a vertical plexiglass cylinder (diameter: 30 cm; height: 45.7 cm) containing 30 cm of water maintained at 25°C. After 10 min in the cylinder, they were removed and allowed to dry for 15 min in a heated enclosure (32°C) before being returned to their cages. Environmental light was kept at 300 lux. Animals were video recorded, and the latency to immobility (s) and the duration of immobility (s) during the first 5 minutes were measured. When the FST was used as an acute stress paradigm, animals were sacrificed immediately or 30 minutes after the test.

tag: tissue

value: brain

tag: brain region

value: prefrontal cortex

tag: genotype

value: Srd5a2 knockdown

tag: treatment

value: control


title: 07T4

description: Library name: MDX_07T4_TNBC

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

value: TNBC

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 5xFADTRAP_rep1

city: New York

first: Anna

last: Flury

state: NY

address: 85 St Nicholas Terrace

institute: CUNY Graduate Center

description: RNA-seq

data_processing:
Quality control was performed on raw sequencing reads with Trim Galore
Reads were aligned to the mouse genome (mm10) with HISAT2 (version 2.2.1) using default parameters
featureCounts (version 2.0.3) was used to obtain the raw read counts per gene against the mm10 GENCODE annotation
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts per gene per sample
Supplementary files format and content: tab-delimited file includes RPKM values for each gene per sample

molecule: polyA RNA

source_name: cortex

growth_protocol: not applicable

extract_protocol:
The brain tissue was thawed in an ice-cold  glass homogenizer containing 1 mL cell-lysis buffer. After manually homogenizing the samples with 3-5 gentle strokes, samples were  homogenized in a motor-driven overhead stirrer. A post-nuclear supernatant was prepared by centrifugation. Post-mitochondrial supernatant was prepared by centrifugation after NP40 and DHPC treatment. GFP-antibod-coated beads were added to each supernatant. After overnight incubation, the polysome-bound beads were washed with the high-salt buffer. RNA clean-up was performed using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
libraries were constructed using SMART-Seq® mRNA LP (Takara, 634768), multiplexed using Unique Dual Index Kit 1–96 (Takara, 634752), and size-selected using NucleoMag® NGS Clean-up and Size Select beads (Takara 744970.5) as per the manufacturer’s recommendations.

treatment_protocol:
Tamoxifen treatment: To activate Tamoxifen-inducible Cre-Ert2, all mice were gavaged at 4-6 weeks of age with six doses of 100 mg/kg of Tamoxifen (T5648, Sigma, St. Louis, MO) in corn oil (C8267, Sigma) with a separation of at least 48 hours between doses. Tamoxifen was dissolved directly in corn oil with 2 hours of incubation at 55°C.
VEGF/ASV treatment: Mice were injected with 1 μg/kg VEGF in 0.9% saline. 30 minutes after VEGF administration, we orally administered 5 mg/kg ASV in 1:9 DMSO:PEG300. This was repeated biweekly for 4 weeks. In iPKR mice, treatment started at 4-5 months of age, 5xFADTRAP mice at 5 months, and 5xFADiPKR at 5 months.
VEGF/vehicle treatment: Vehicle-treated animals received an intraperitoneal VEGF administration followed by 1:9 DMSO:PEG300 at 10ml/kg. In iPKR mice, treatment started at 4-5 months of age.

tag: tissue

value: cortex

tag: age (months)

tag: Sex

value: M

tag: batch

tag: cell type

value: microglia

tag: genotype

tag: treatment

value: tamoxifen and VEGF/ASV


title: 08T1

description: Library name: MDX_08T1_C_LumA

tag: isolate

tag: age

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

value: missing

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t


title: Control_TRAP_rep5

description: RNA-seq

tag: tissue

tag: age (months)

tag: Sex

value: F

tag: batch

tag: cell type

tag: genotype

tag: treatment

value: tamoxifen


title: 07T3

description: Library name: MDX_07T3_TNBC

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: LSK, R396Q, replicate 2, scRNA-Seq

description:
R396Q 2
10X Genomics

tag: tissue

value: bone marrow

tag: cell type

value: Lineage(neg)Sca1(pos)c-Kit(pos) (LSK)

tag: genotype


title: wt - stress biol rep 3

description:
10X genomics
21225X8

value: brain

tag: brain region

value: prefrontal cortex

value: wild type

tag: treatment

value: stress


title: 08T14

description: Library name: MDX_08T14_Her2

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t


title: LSK, R396Q, replicate 3-1, scRNA-Seq

description:
R396Q 3-1
10X Genomics

tag: tissue

tag: cell type

tag: genotype


title: wt - stress biol rep 2

description:
10X genomics
21225X7

tag: brain region

tag: treatment


title: 07T2

description: Library name: MDX_07T2_LumA

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: missing

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: LSK, R396Q, replicate 1, scRNA-Seq

description:
R396Q 1
10X Genomics

tag: tissue

tag: cell type

tag: genotype


title: LSK, WT, replicate 4, scRNA-Seq

description:
WT 4
10X Genomics

value: WT


title: Control_TRAP_rep4

description: RNA-seq

value: cortex

tag: age (months)

tag: Sex

value: M

tag: batch

value: microglia

tag: treatment

value: tamoxifen


title: 5xFADTRAP_rep3

description: RNA-seq

value: F

value: tamoxifen and VEGF/ASV


title: 07T12

description: Library name: MDX_07T12_LumA

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t


title: wt - stress biol rep 1

description:
10X genomics
21225X6

tag: tissue

value: brain

tag: brain region

value: prefrontal cortex

tag: genotype

value: wild type

tag: treatment

value: stress


title: Control_TRAP_rep2

description: RNA-seq

tag: age (months)

tag: Sex

tag: batch

tag: cell type


title: Control_TRAP_rep3

description: RNA-seq


title: 07T11

description: Library name: MDX_07T11_LumA

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

value: missing

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: LSK, WT, replicate 2, scRNA-Seq

description:
WT 2
10X Genomics

tag: tissue

value: bone marrow

tag: cell type

value: Lineage(neg)Sca1(pos)c-Kit(pos) (LSK)

tag: genotype

value: WT


title: wild type biol rep 4

description:
10X genomics
21225X5

tag: brain region

tag: treatment

value: control


title: 07T10_excluded_subtype

description: Library name: MDX_07T10_excluded_subtype

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: extra ROI - invasive

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t


title: LSK, WT, replicate 3, scRNA-Seq

description:
WT 3
10X Genomics

tag: tissue

tag: cell type

tag: genotype


title: wt - stress biol rep 4

description:
10X genomics
21225X9

value: brain

tag: brain region

value: prefrontal cortex

value: wild type

tag: treatment


title: 5xFADTRAP_rep2

description: RNA-seq

value: cortex

tag: age (months)

tag: Sex

value: M

tag: batch

value: microglia

value: tamoxifen and VEGF/ASV


title: Control_TRAP_rep1

description: RNA-seq

value: tamoxifen


title: LSK, WT, replicate 1, scRNA-Seq

description:
WT 1
10X Genomics


title: wild type biol rep 2

description:
10X genomics
21225X3


title: wild type biol rep 1

description:
10X genomics
21225X2


title: WT_CD_4

city: ATHENS

first: Paraskevas

last: Zampas

address: 4 Soranou Ephessiou St

country: Greece

institute: Biomedical Research Foundation of the Academy of Athens (BRFAA)

description:
Aorta Raw Counts.xlsx
WT_HFD_LNAME vs WT_CD.xlsx

data_processing:
Sequencing reads were trimmed for adaptor sequence and low-quality reads using the Trimmomatic tool (Galaxy Version 0.39)
The alignment of the sequenced reads was performed using the HISAT2 tool (Galaxy Version 2.2.1), choosing the “option” reverse regarding the library strandness, while the NCBI Build mouse GRCm38/mm10 was selected as the reference genome
The measurement of the reads per gene was made using the Feature Counts algorithm (Galaxy Version 2.0.3)
The determination of the differentially expressed genes by DESeq2 (Galaxy Version 2.11.40.7).
Assembly: mm10
Supplementary files format and content: Excel file including Aorta raw data counts for each sample
Supplementary files format and content: Excel files MPST KO_HFD_LNAME vs WT_HFD_LNAME.xlsx and WT_HFD_LNAME vs WT_CD.xlsx contain the results from DESeq2 analysis.

source_name: Aorta

extract_protocol:
RNA was extracted from aortas using TRIzol reagent
Libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7775) according to the manufacturer’s guidelines

treatment_protocol: Six to seven weeks old C57BL6/J Wilt type mice (WT) or Mpst knockout mice were fed a HFD (45% calories from fat) for 15 weeks to induce obesity and hyperglycemia, and followed by a nitric oxide synthase inhibitor, for the additional 5 weeks to induce hypertension. Control mice fed a chow diet (CD; 10% calories from fat) for 15 weeks.Then the whole aorta (aortic arch, thoracic and abdominal segment) was isolated and was cleared from the perivascular adipose tissue.

value: Aorta

value: Chow diet


title: PIF4v3m, rep3

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

country: China

institute: Yangzhou Univerisity

description: Library name: PIF4v3m-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100.
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9.
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: msu7.0
Supplementary files format and content: FPKM values for each Sample.

organism: Oryza sativa

source_name: leaf

growth_protocol: All the plant materials  were grown in pots under fluctuating light and drought stress

extract_protocol:
Total RNA was extracted from rice leaves using a Trelief® RNApre Pure Plant Kit (tsingke, code: TSP411) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The leaves of 3-week-old rice plants were collected.

value: leaf

value: leaf cells


title: WT_CD_3

value: WT


title: 06T1

description: Library name: MDX_06T1_LumB

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

value: missing

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: PIF4v3m, rep2

description: Library name: PIF4v3m-2

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Sorafenib-3

city: Shanghai

first: Xiaochen

last: Tang

address: 1678 Dongfang Road, Pudong New Area, Shanghai

institute: Shanghai Jiao Tong University

data_processing:
Data processing: removing connectors, removing low-quality reads
Match genomes to obtain expression profile data
Differential analysis
GO,KEGG analysis
Assembly: hg19
Supplementary files format and content: Gene_Expression_Profiling txt file for each sample; CP, FPKM, Counts

source_name: HeLa

extract_protocol:
Total RNA was extracted using Trizol reagent
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

tag: cell line

value: HeLa

value: Sorafenib


title: 07T1

description: Library name: MDX_07T1_LumA

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t


title: Sorafenib-2

tag: cell line

tag: treatment


title: wild type biol rep 3

description:
10X genomics
21225X4

tag: tissue

value: brain

tag: brain region

value: prefrontal cortex

tag: genotype

value: wild type

value: control


title: PIF4v3m, rep1

description: Library name: PIF4v3m-1

value: leaf

tag: cell type

value: leaf cells


title: wt, rep3

description: Library name: WYG7-3

value: wt


title: WT_CD_1

value: Aorta

value: WT

value: Chow diet


title: P3 primary human RPE biol rep 3

city: wenzhou

first: yu

last: chen

address: 270 West Xueyuan Road

institute: Wenzhou Medical University

description: Library name: SAMPLES 6

data_processing:
Data quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Retinal pigment epithelium

growth_protocol: Primary human RPE (phRPE) cells were isolated from the donor’s eyes (obtained from the Eye Bank of Wenzhou Medical University & Wenzhou Eyebank). PhRPE cells were cultured in DMEM/F12 supplemented with 10 % fetal bovine serum (FBS) (Gibco, Life Technologies) at 37 °C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNAs of native RPE cells and P3 cultured phRPE cells were extracted using the RNAprep Pure Micro Kit (TIANGEN Biotech Co. Ltd., Beijing, China) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Retinal pigment epithelium

value: Retinal pigment epithelium cell


title: WT_HFD_LNAME_4

description:
Aorta Raw Counts.xlsx
MPST KO_HFD_LNAME vs WT_HFD_LNAME.xlsx
WT_HFD_LNAME vs WT_CD.xlsx

value: HFD and LNAME


title: Native primary human RPE biol rep 3

description: Library name: SAMPLES 5


title: Rhein-3

value: HeLa

value: Rhein


title: P3 primary human RPE biol rep 2

description: Library name: SAMPLES 4


title: wt, rep2

description: Library name: WYG7-2


title: Sorafenib-1

value: Sorafenib


title: WT_HFD_LNAME_3


title: wt, rep1

description: Library name: WYG7-1


title: Rhein-2


title: HEK CLN3-KO (3)

city: Hershey

first: Nuno

last: Raimundo

state: PA

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

data_processing:
Strand NGS for alignement, quantification and normalization
Assembly: ENSEMBL GRCh38.p5
Supplementary files format and content: gene expression normalized per gene

source_name: HEK cells

growth_protocol: DMEM + 10% FBS + 1% P/S

extract_protocol:
cDNA
TrueSeq RNA Sample Preparation Kit (Illumina, Netherlands) was used to prepare samples for NGS analysis. Accurate quantitation of cDNA libraries was performed by using the QuantiFluorTM dsDNA System (Promega, Germany). The size range of cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp).
cDNA libraries were amplified and sequenced by using the cBot and HiSeq 1000 from Illumina (SR, 1×50bp).

value: HEK cells


title: WT_HFD_LNAME_2


title: 07T10

description: Library name: MDX_07T10_ERPR_LumA

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

tag: Sex

value: missing

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

value: not applicable

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: Native primary human RPE biol rep 2

description: Library name: SAMPLES 3

tag: tissue

value: Retinal pigment epithelium

tag: cell type

value: Retinal pigment epithelium cell


title: P3 primary human RPE biol rep 1

description: Library name: SAMPLES 2


title: WT_CD_2

value: Aorta

tag: genotype

value: WT

tag: treatment

value: Chow diet


title: HEK CLN3-KO (2)

tag: cell line

value: HEK cells


title: WT_HFD_LNAME_1

value: HFD and LNAME


title: MA-3

value: HeLa

value: MA


title: Native primary human RPE biol rep 1

description: Library name: SAMPLES 1


title: MPST KO_HFD_LNAME_3

description:
Aorta Raw Counts.xlsx
MPST KO_HFD_LNAME vs WT_HFD_LNAME.xlsx

value: Mpst knockout


title: MA-2


title: parental HEK (3)

description: control


title: LN229-TAZ(4SA) cell, KO_Glu-, Rep1

first: Wei

last: Li

address: 500 University Drive, PO Box 850, MC H085

institute: Penn State Hershey College of Medicine

data_processing:
Sequencing data were analyzed using Galaxy (https://usegalaxy.org/). Briefly, reads were trimmed and aligned to reference human genome and annotation files (GRCh38, build 38) using HISAT2. Difference of gene expression were detected by edgeR.
Assembly: human genome and annotation files (GRCh38, build 38)
Supplementary files format and content: tsv, normalized counts

source_name: LN229-TAZ(4SA) Cell line

growth_protocol: Human GBM cell lines LN229-TAZ(4SA) were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Corning, 10-013-CV) supplemented with 10% fetal bovine serum (FBS; Gibco, 10437028) and 1% Antibiotic-Antimycotic Solution (Corning, 30-004-CI) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were lysed in TRIzol reagent (Invitrogen) and total RNA was extracted by following the protocol from the manufacture.
RNA-seq libraries were prepared using the SMART-Seq mRNA HT kit (Takara Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions.

treatment_protocol: TrxR1 knockout (KO) or control (EV) LN229-TAZ(4SA) cells cultured in the glucose-deprived condition (Glu-) or regular condition.

value: LN229-TAZ(4SA) Cell line

value: glioblastoma cell line


title: MA-1


title: MPST KO_HFD_LNAME_2


title: parental HEK (2)

description: control


title: LMB-2

value: LMB


title: LN229-TAZ(4SA) cell, EV_Glu-, Rep1


title: LN229-TAZ(4SA) cell, KO_Glu-, Rep2


title: WT2

city: Changsha

first: Mei

last: Yang

address: 139 Middle Renmin Road

institute: The Second Xiangya Hospital, Central South University

library_source: genomic

data_processing:
Trimmomatic software were used to remove adapter and low quality reads. [Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.]
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Assembly: Mus musculus mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: skeletal muscle

extract_protocol:
muscle from mice was collected and instantly frozen in liquid nitrogen for conservation and transportation, and anti-H3K9me3 antibody (#13969, Cell Signaling) was used to map its binding sites in the 384 genome.
DNA was purified, genomic fragments with adapters at both ends were amplified by PCR, sequenced and mapped to the genome for further analysis.
To amplify libraries, 21 µL DNA was mixed with 2 µL of a universal i5 and a uniquely barcoded i7 primer33, using a different barcode for each sample. A volume of 25 µL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in aThermocycler with aheated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. Post-PCR clean-up was performed by adding 1.1× volume of Ampure XP beads (Beckman Counter), and libraries were incubated with beads for 15 min at RT, washed twice gently in 80% ethanol, and eluted in 30 µL 10 mM Tris pH 8.0.

value: skeletal muscle

tag: antibody


title: MPST KO_HFD_LNAME_1


title: parental HEK (1)

description: control


title: LMB-1


title: Rhein-1

value: Rhein


title: LN229-TAZ(4SA) cell, KO_Regular culture, Rep2


title: WT3

value: anti-H3K9me3 antibody (#13969, Cell Signaling)


title: MCF7_POP-seq_rep2

city: Pittsburgh

first: Rajneesh

last: Srivastava

state: Pennsylvania

address: 450 Technology Dr

department: Surgery, University of Pittsburgh

institute: McGowan Institute for Regenerative Medicine

description: Adaptor_sequence (removed): TGGAATTCTCGGGTGCCAAGG

data_processing:
Library strategy: POP-Seq
POP-seq reads were pre-processed using FASTX toolkits for trimming adaptor sequence ("TGGAATTCTCGGGTGCCAAGG"), and low-quality read fragments. Then the sequence reads were mapped to hg38 (Homo_sapiens.GRCh38.97) reference genome using hisat2 with default parameters. Reads mapped onto Human ribosomal DNA complete repeating unit (U13369.1) were discarded.
Aligned reads were post-processed using samtools version 1.9 and formatted for peak calling using bedtools version 2.18.1
Peaks were called using Piranha version 1.2.1 with default parameters
Peaks overlapping by 25%  for the two replicates were merged. Only reads with length < 250 nt were considered for downstream data analysis
Assembly: hg38 (Homo_sapiens.GRCh38.97)
Supplementary files format and content: tsv.gz

source_name: Non-crosslinked POP-seq_Replicate_2

growth_protocol: All cell lines were obtained from the American Type Culture Collection (ATCC). Cells were cultured in Dulbecco’s minimal essential medium (DMEM, Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Atlanta Biologicals) along with 1% antibiotics (penicillin 5000 Units/ml, Streptomycin 5000 μg/ml). All cells were maintained at 37°C and 5% CO2 in a humidified incubator and fresh media was replenished every alternate day until confluent.

extract_protocol:
Following the trizol lysis, interphase pellet was subjected to RNase A/T1 (thermo scientific) degradation in RNase buffer (10 mM Tris-HCl, pH 7.5, 300 mM NaCl and 5 mM EDTA, pH 7.5). 2 µg of RNase A/T1 mix was added to the interphase pellet, mixed by pipetting and incubated at 37° C for 15 min. Interphase-RNase mixture was resolubilized in trizol reagent to recover the RNA-protein complexes. After addition of chloroform, tubes were incubated at room temperature for 5 min, vortexed and centrifuged at 12000 g for 10 min. This results in protein bound RNA at the interphase, unbound RNA in the aqueous phase while the unbound proteins in the organic phase. The aqueous and organic layers were discarded as described previously. Interphase pellet was precipitated in 1 ml methanol and spun down to remove the methanol. Next, the interphase was mixed with Proteinase K in appropriate buffer (0.1M NaCl, 10 mM Tris-HCl, pH 8, 1 mM EDTA, 0.5% SDS and 200 µg/ml proteinase K). Samples were incubated at 50° C for 2 hours. After proteinase K digestion, free RNA was recovered from the aqueous layer by trizol extraction as described previously.  Samples were cooled and the released RNA was purified by standard trizol extraction. The upper aqueous layer containing the free RNA fragments (previously bound to proteins) was transferred to new tube and precipitated with isopropanol as per the manufacturer instructions.   Protein bound RNA’s concentration was estimated using Nanodrop and up to 1 µg of RNA was incubated with DNase I, 1U (thermo scientific) at 37° C for 30 min to remove any traces of DNA contamination. 1 µl of 50 mM EDTA was added to the reaction mixture and incubated at 65° C for 10 min to terminate the reaction. RNA was purified using conventional trizol extraction from the aqueous layer. At this point, r-RNA depletion was performed with 1 µg input RNA using Ribo-cop kit (Lexogen) as per manufacturer instructions. Further, the ends of r-RNA depleted RNA were modified by treating with Calf intestine alkaline phosphatase (CIAP, Invitrogen) and T4 polynucleotide kinase (T4 PNK, thermo scientific) as per manufacturer protocol.  The end modification enabled the library preparation of these RNA fragments.
RNA purity and concentration were assessed at each step using Nanodrop (thermo scientific) based on the absorbance ratio 260/280 >2. RNA integrity was evaluated using Agilent 2100 bioanalyser system. At least 50 ng of r-RNA depleted POP-seq RNA was used to generate sequencing libraries using the True-seq small RNA library prep kit (Illumina). All libraries were barcoded and sequenced in parallel on a Next-seq platform for 400 million reads to obtain 75 bp single end reads.
POP-seq libraries prepared using Illumina True seq small RNA library preparation kit

treatment_protocol: Cells were cultured in T-175 flask until a maximum of 90% confluency was reached. A total of 100 million cells per replicate of each sample were used for UV and no-crosslinking control. Cell were washed twice with 1X PBS, the supernatant was removed by pipetting and cells were resuspended in 1X PBS. For UV crosslinking, cells in PBS suspension were transferred to 100 mm dishes and UV irradiated at 254 nm with 400 mJ/cm2 dosage (UV Stratalinker 1800). Immediately after crosslinking, cells were collected in 15 ml tubes and pelleted at 1500 rpm for 5 min. Supernatant was discarded and cells were lysed in 8 ml trizol reagent (Life Technologies) by pipetting up and down to obtain a homogenous cell lysate. For non-crosslinked samples, cells were pelleted down, washed in 1X PBS and subsequently lysed in trizol for phase separation.


title: MCF7_POP-seq_rep1

source_name: Non-crosslinked POP-seq_Replicate_1


title: WT1


title: LN229-TAZ(4SA) cell, EV_Glu-, Rep2


title: HEK CLN3-KO (1)


title: K562_uPOP-seq_rep2

source_name: Ultra violet crosslinked POP-seq_Replicate_2


title: LN229-TAZ(4SA) cell, KO_Regular culture, Rep1


title: KO3

value: KO


title: DOX-2

value: DOX


title: K562_uPOP-seq_rep1

source_name: Ultra violet crosslinked POP-seq_Replicate_1


title: DOX-3


title: KO2


title: DOX-1


title: LMB-3


title: K562_POP-seq_rep2


title: KO1


title: DMSO-3

value: DMSO


title: K562_POP-seq_rep1


title: DMSO-2


title: LN229-TAZ(4SA) cell, AF+Glucose deprivation 7 hour, Rep1

treatment_protocol: LN229-TAZ(4SA) cells cultured in the glucose-deprived condition with AF (1 uM) for 1 hour or 7 hours (E) compared to cells in regular conditions without AF for the same times.


title: LN229-TAZ(4SA) cell, Regular culture 7 hour, Rep1


title: LN229-TAZ(4SA) cell, AF+Glucose deprivation 7 hour, Rep2


title: DMSO-1


title: EV-Proficient HTO-multiplexed-pool tumors 4-6

city: Portland

first: Laura

last: Heiser

state: Oregon

address: 2730 S. Moody Ave

department: BME

institute: OHSU

description: 10X Genomics 3' V3

data_processing:
Libraries were sequenced on a NovaSeq 6000 (Illumina) running RTA v3.4.4. BCL files were demultiplexed using bcl2fastq v2.20.0.422 (Illumina). A custom reference genome was constructed using GRCm38 (Ensembl) and the reporter gene dLNGFR with genome annotations from GRC38.89.gtf. Briefly, the dLNGFR fasta file was added to the end of the GRCm38 fasta as a virtual chromosome using the linux cat command. The gtf file was manually edited to add dLNGFR annotation. The fasta and gtf files were then used to construct a reference genome using the STAR genomeGenerate runMode command. Cell Ranger 7.1.0 uses STAR 2.7.2a aligner for building and aligning to the reference genome.
Assembly: modified GRCm38
Supplementary files format and content: h5 count output from CellRanger v7.1.0

source_name: Oral Carcinoma

growth_protocol: Cells were cultured from frozen aliquots in EMedia, prepared by mixing Dulbecco’s Modified Eagle Medium (DMEM) with Ham’s F12 at a ratio of 3:1 and supplemented with 10% Fetal Bovine Serum (FBS). Additionally, the media was supplemented with 0.5% Penicillin/Streptomycin Solution, 10 µl of 25 µg/µl Hydrocortisone, 16.8 µl of 0.25 µg/µl Cholera toxin, 100 µl of 25 µg/µl Transferrin, 250 µl of 10 µg/µl Insulin, 3.4 µl of 0.2 µg/µl Tri-Iodo-Thyronine, and 250 µl of 10 µg/ml EGF.

extract_protocol:
Samples were dissociated by mincing them with scissors in dissociation media composed of 2% FBS, 1x penicillin/streptomycin, 1x Glutamine, 0.2 mg/ml collagenase IV, 2 mg/ml Dispase, and 5 U/ml DNase I in IMDM. The dissociated tissue was then incubated for 30 minutes at 37 degrees Celsius at 500 rpm. Following the incubation, the tissue was filtered through a 100 µm strainer in MACS buffer containing 2 mM EDTA, 0.5% BSA, and 500 ml PBS, and centrifuged at 500 g for 10 minutes. For multiplexed samples only (CEL230406FP_SEV_Deficient, CEL230406FP_SEV_Proficient): The resulting pellets were transferred to corresponding tubes and incubated with a 1:200 dilution of the appropriate Hashtag antibody (TotalSeq™-B0304 anti-mouse Hashtag 4 Antibody, barcode sequence: AAAGCATTCTTCACG; TotalSeq™-B0305 anti-mouse Hashtag 5 Antibody, barcode sequence: CTTTGTCTTTGTGAG; TotalSeq™-B0306 anti-mouse Hashtag 6 Antibody, barcode sequence: TATGCTGCCACGGTA) for 15 minutes on ice. Finally, the samples were pooled together, washed twice, and then resuspended in staining buffer.
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kit v 3.1 with dual indexes kit (10x Genomics). Cells were counted, then processed through a Chromium Controller (10x Genomics) to produce amplified cDNAs with cell-specific tags. The cDNA was enzymatically fragmented and then size selected using SPRI beads. Adapters were ligated to the cDNA and samples were indexed using indexed amplification primers. Libraries were profiled on a 4200 Tapestation (Agilent) and quantified using real time PCR with an NGS Library Quantification Kit (Roche/Kapa Biosystems) on a StepOnePlus Real Time PCR Workstation (Thermo/ABI).

treatment_protocol: After expansion, cells were induced to senescence by the addition of 600 nM paclitaxel for 48 hours. Subsequently, they were harvested from the media and injected orthotopically into mice at a concentration of 500,000 cells per mouse. Three days post-injection, the injection site was dissected and washed with PBS.

value: Oral Carcinoma

value: Paclitaxel pretreatment prior to implantation (to induce senescence)


title: LN229-TAZ(4SA) cell, Regular culture 7 hour, Rep2


title: Advillin-cre/ERT2 Control HFD

city: Bronx

first: Jeffrey

middle: E

last: Pessin

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

data_processing:
FASTQ files were analyzed and aggregated with Space Ranger Pipeline with default settings (10x Genomics https://www.10xgenomics.com/support/software/space-ranger/latest)
Expression violin plots were generated using Loupe Browser
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: aggregated cloupe file
Library strategy: Spatial transcriptomics

source_name: Liver

extract_protocol:
Liver tissue was flash-frozen in liquid nitrogen, sectioned at 10um thickiness, and mounted on the gene expression slide provided in the 10X Visium kit
Tissue sections were fixed, stained (H&E) and imaged according to 10x Genomics protocol CG000160 • Rev B.  An NGS library was produced from each section accoding to User Guide CG000239 Rev D

treatment_protocol: All mice were fed HFD (research diets #D12492) for 10 weeks

value: Liver

tag: strain

tag: Sex

value: Male

value: Advillin-cre/ERT2 Control

tag: diet

value: HFD:research diets #D12492


title: Advillin-cre/ERT2 Casp3 HFD

value: Advillin-cre/ERT2 Casp3


title: LN229-TAZ(4SA) cell, EV_Regular culture, Rep2


title: EV-Deficient HTO-multiplexed-pool tumors 4-6

description: 10X Genomics 3' V3


title: Jurkat_POP-seq_rep1

value: Jurkat


title: CDDP-3

value: HeLa

value: CDDP


title: HepG2_uPOP-seq_rep2


title: HepG2_uPOP-seq_rep1


title: EV-Deficient tumor 3

description: 10X Genomics 3' V3


title: LN229-TAZ(4SA) cell, AF+Glucose deprivation 1 hour, Rep1

value: LN229-TAZ(4SA) Cell line

value: glioblastoma cell line


title: CDDP-1


title: HepG2_POP-seq_rep2


title: LN229-TAZ(4SA) cell, EV_Regular culture, Rep1


title: LN229-TAZ(4SA) cell, AF+Glucose deprivation 1 hour, Rep2


title: patient 5 with cachexia

city: Xi'an

first: Xunliang

last: Jiang

address: No. 169, Changle West Road, Xincheng District, Xi'an, Shaanxi

institute: Air Force Military Medical University

library_source: other

data_processing:
Sequencing Data and Its Quality Control
Sequencing base mass value
Sequencing data output statistics
Compare with the reference genome. Use the designated GRCh38 as the reference genome for sequence alignment and subsequent analysis.
In terms of identification of known miRNAs, we will compare the reads sequence of the reference genome to the mature miRNA sequence in the known miRNA database miRBase (v22).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

molecule: other

source_name: plasma

growth_protocol: Peripheral venous blood was collected from the patients on the day of surgery. Within 30 min of collection, the blood samples were centrifuged at a low speed (1000 g) for 15 min at 4°C; the supernatant (plasma) was collected and labeled. All plasma samples were stored at −80°C.

extract_protocol:
Plasma exosomes were extracted from the patients using an exosome rapid extraction kit (exoRNeasy middle extraction kit, QIAGEN, Germany). The operation method is carried out according to the manufacturer’s instructions.
Use the designated GRCh38 as the reference genome for sequence alignment and subsequent analysis.

tag: disease state

value: gastric cancer

tag: condition

value: with cachexia

value: plasma

value: extract exosomes from plasma

tag: fraction

value: exosomal RNA


title: Control_iPKR_vehicle_rep1

description: RNA-seq

value: cortex

tag: age (months)

value: M

tag: batch

value: microglia

value: tamoxifen and VEGF/PEG:DMSO


title: LN229-TAZ(4SA) cell, Regular culture 1 hour, Rep2


title: EV-Deficient tumor 2

description: 10X Genomics 3' V3

value: Oral Carcinoma

value: Paclitaxel pretreatment prior to implantation (to induce senescence)


title: Jurkat_POP-seq_rep2


title: EV-Deficient tumor 1

description: 10X Genomics 3' V3


title: LN229-TAZ(4SA) cell, Regular culture 1 hour, Rep1


title: patient 4 with cachexia


title: CDDP-2


title: patient 3 with cachexia


title: Tumor, EV,  3

source_name: Tumor from LN229-EV cells

growth_protocol: Human GBM cell lines LN229-4SA or LN229-EV were injected intracranially into nude mice. Tumors were collected at the terminal stages.

extract_protocol:
Tumors were lysed in TRIzol reagent (Invitrogen) and total RNA was extracted by following the protocol from the manufacture.
RNA-seq libraries were prepared using the SMART-Seq mRNA HT kit (Takara Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions.

value: Tumor from LN229-EV cells

value: LN229-EV cells

value: Empty vector

value: Tumor


title: EV-Proficient tumor 3

description: 10X Genomics 3' V3


title: patient 2 without cachexia

value: without cachexia


title: patient 1 without cachexia


title: EV-Proficient tumor 1

description: 10X Genomics 3' V3


title: HEK293_POP-seq_rep1


title: Tumor, EV,  1

value: glioblastoma cell line


title: A549_POP-seq_rep2


title: Tumor, EV,  2


title: A549_POP-seq_rep1


title: GFP3

data_processing:
Raw reads were first filtered with minimum average read quality score=6 and minimum read length=350bp. Ribosomal RNA were discarded after mapping to rRNA database. Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads. Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish.
Consensus sequences were mapped to reference genome using minimap2. Mapped reads were further collapsed by cDNA_Cupcake package with min-coverage=85% and min-identity=90%. 5’ difference was not considered when collapsing redundant transcripts.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with a Pvalue < 0.05 and foldchange ≥ 1.5 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm38_release95
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes CPM for each Sample

extract_protocol:
total RNA was extracted from frozen tissues and checked for quality and quantity by nanodrop and 2100/GX
1ug total RNA was prepared for cDNA libraries using cDNA-PCR Sequencing Kit (SQK-LSK110+EXP-PCB096) protocol provided by Oxford Nanopore Technologies（ONT）. Briefly,the template switching activity of reverse transcriptases enrich for full-length cDNAs and add defined PCR adapters directly to both ends of the first-strand cDNA. And following cDNA PCR for 14 circles with LongAmp Tag (NEB). The PCR products were then subjected to ONT adaptor ligation using T4 DNA ligase (NEB). Agencourt XP beads was used for DNA purification according to ONT protocol.

value: skeletal muscle

value: KO

value: GFP


title: Tumor, 4SA,  6

source_name: Tumor from LN229-4SA cells

value: Tumor from LN229-4SA cells

value: LN229-4SA cells


title: MOC2-27 cells, EV-Deficient, in vitro, paclitaxel 3

data_processing:
Libraries were aligned with STAR v2.5.0a
Assembly: modified GRCm38
Supplementary files format and content: count matrix output from STAR v2.5.0a

growth_protocol: Cells were cultured from frozen aliquots in EMedia, which was prepared by mixing Dulbecco’s Modified Eagle Medium (DMEM) with Ham’s F12 at a ratio of 3:1 and supplemented with 10% Fetal Bovine Serum (FBS). Additionally, the media was supplemented with 0.5% Penicillin/Streptomycin Solution, 10 µl of 25 µg/µl Hydrocortisone, 16.8 µl of 0.25 µg/µl Cholera toxin, 100 µl of 25 µg/µl Transferrin, 250 µl of 10 µg/µl Insulin, 3.4 µl of 0.2 µg/µl Tri-Iodo-Thyronine, and 250 µl of 10 µg/ml EGF. Following expansion, cells were induced to senescence by the addition of 600 nM paclitaxel for 48 hours. Subsequently, the cells were washed with PBS and suspended in MACS buffer containing 2 mM EDTA, 0.5% BSA, and 500 ml PBS.

extract_protocol:
Total RNA was extracted from cell cultures using a column-based RNA purification kit (Qiagen RNeasy Mini kit). The eluted samples were dissolved in water, and their concentration and yield were measured.
Bulk RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina). Briefly, RNA was profiled for integrity on a 2200 Bioanalyzer (Agilent). Poly(A)+ RNA was isolated using oligo-dT magnetic beads and then fragmented using divalent cations and heat. Fragmented RNA was converted to double stranded cDNA using random hexamer priming. The second strand was synthesized with dUTP in place of dTTP to prevent priming from this strand during amplification. The cDNA was ligated to adapters with dual unique indexes and amplified by limited rounds of polymerase chain reaction. The amplified material was cleaned using AMPure XP Beads (Beckman Coulter). The final library was profiled on a 4200 Tapestation (Illumina) and quantified using real time PCR with an NGS Library Quantification Kit (Roche/Kapa Biosystems) on a StepOnePlus Real Time PCR Workstation (Thermo/ABI).

treatment_protocol: To induce senescence in MOC2, MOC2 cells were expanded in E-media and plated at 1M cells in 15-cm plates, maintained at 37°C and under 5% CO2 for 24 hours. Subsequently, 600nM of Paclitaxel was added to the cells, and they were incubated for an additional 48 hours at 37°C in 5% CO2.

value: Squamous Cell Carcinoma

value: Paclitaxel


title: GFP2


title: Tet.Rybp.Stat3.DOX+.STAT3.rep2

city: Guangzhou

first: Chao

last: Wei

address: No.74 Zhongshan Rd.2

institute: Sun Yat-Sen University

description:
Library name: Sample 18
STAT3 ChIP-seq

data_processing:
The Fastq data underwent quality checking using trim_galore
subsequent alignment of paired-end reads to the MM9 reference genome was performed using STAR
Gene-specific read counts were generated using Htseq-count
Assembly: mm9
Supplementary files format and content: narrowPeak, broadPeak

source_name: Mus musculus

growth_protocol: ESCs were cultured in ESC medium containing DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Hyclone), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1000 U/mL recombinant LIF (Millipore) in 37 C, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent
RNA library for RNA-seq was performed according the manufacture's protocol

treatment_protocol: Mouse Rybp-floxed ESCs (Rybp+/+) were cultured in ESC medium, RYBP-depleted ESCs (Rybp-/-) were generated by supplementing the medium with 5 μM 4-hydroxytamoxifen (4-OHT, Sigma) for 4 days.

value: Mus musculus

value: embryonic stem cell

value: DOX-induced Rybp_Stat3 integration

value: DOX


title: Tumor, 4SA,  5


title: HepG2_POP-seq_rep1


title: Tet.Rybp.Stat3.DOX+.STAT3.rep1

description:
Library name: Sample 17
STAT3 ChIP-seq


title: MOC2-27 cells, EV-Deficient, in vitro, paclitaxel 1


title: GFP1


title: Tumor, 4SA,  4


title: HEK293_POP-seq_rep2


title: Tet.Rybp.Stat3.DOX-.STAT3.rep2

description:
Library name: Sample 16
STAT3 ChIP-seq

value: control


title: EV-Proficient tumor 2

description: 10X Genomics 3' V3

value: Oral Carcinoma

value: Paclitaxel pretreatment prior to implantation (to induce senescence)


title: Tet.Rybp.Stat3.DOX-.STAT3.rep1

description:
Library name: Sample 15
STAT3 ChIP-seq


title: GFP_MEF2C3


title: Tet.Rybp.Stat3.DOX+.RING1B.rep2

description:
Library name: Sample 14
RING1B ChIP-seq


title: Tumor, 4SA,  2

value: Tumor


title: GFP_MEF2C2


title: MOC2-25 cells, EV-Proficient, in vitro, paclitaxel 2


title: Tumor, 4SA,  3


title: MOC2-27 cells, EV-Deficient, in vitro, paclitaxel 2


title: GFP_MEF2C1


title: K7 (RNA-seq)

data_processing:
Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp. Ribosomal RNA were discarded after mapping to rRNA database. Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads. Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish.
Consensus sequences were mapped to reference genome using minimap2. Mapped reads were further collapsed by cDNA_Cupcake package with min-coverage=85% and min-identity=90%. 5’ difference was not considered when collapsing redundant transcripts.
Full length reads were mapped to the reference transcriptome sequence. Reads with match quality above 5 were further used to quantify. Expression levels were estimated by reads per gene/transcript per 10,000 reads mapped.
For the samples with biological replicates:
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with a FDR < 0.01 and foldchange ≥ 2 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm38_release95
Supplementary files format and content: tab-delimited text file includes raw counts and CPM values for each Sample

extract_protocol:
Total RNA was prepared from mouse tissues using TRIzol (Invitrogen) following the manufacturer’s instructions. The purity, concentration and integrity of RNA samples were detected to ensure qualification for later analysis by Nano Photometer spectrophotometer (IMPLEN, Westlake Village, USA)
1ug total RNA was prepared for cDNA libraries using cDNA-PCR Sequencing Kit (SQK-LSK110+EXP-PCB096) protocol provided by Oxford Nanopore Technologies（ONT）. Briefly,the template switching activity of reverse transcriptases enrich for full-length cDNAs and add defined PCR adapters directly to both ends of the first-strand cDNA. And following cDNA PCR for 14 circles with LongAmp Tag (NEB). The PCR products were then subjected to ONT adaptor ligation using T4 DNA ligase (NEB). Agencourt XP beads was used for DNA purification according to ONT protocol. The final cDNA libraries were added to FLO-MIN109 flowcells and run on PromethION platform at Biomarker Technology Company (Beijing, China).

value: quadriceps femoris


title: MOC2-27 cells, EV-Deficient, in vitro, control 3

value: DMSO


title: MOC2-27 cells, EV-Deficient, in vitro, control 2


title: BT549ENL-3

city: Harbin

first: Wu

last: Hao

address: 哈尔滨市南岗区保健路6号

institute: Harbin Medical University

data_processing:
1.mRNA data quality control: FastQC software and R were used to evaluate the quality of raw sequencing data；2. mRNA reference genome alignment, using STAR software to align the filtered reads with the reference database；3.mRNA analysis, using Stringtie's analysis workflow to quantify the expression of known genes and transcripts, using Deseq2 software to analyze differential genes, and significantly differentially differentiated gene GO and KEGG enrichment analysis
Assembly: hg38
Supplementary files format and content: gene_count_matrix.txt

source_name: mammary gland epithelial tissue

extract_protocol:
The concentration of RNA samples was ≥ 100 ng/μL, the total amount was > 2 μg, the OD value was between 1.8~2.2, the OD was ≥ 2.0, and Agilent 2100 was required The Bioanalyzer assays RIN ≥ 6.5 to ensure the construction of downstream high-quality mRNA-seq libraries
Library concentration and fragment length distributions were measured using Qubit and Agilent 2100 Bioanalyzers, respectively. The concentration is required to be >5ng/μl and the fragment length is concentrated Between 300-400 bp

value: mammary gland epithelial tissue

value: breast cancer cell line

value: ENL


title: BT549ENL-2

address: 哈尔滨市南岗区保健路6号


title: Tet.Rybp.Stat3.DOX-.RING1B.rep1

description:
Library name: Sample 11
RING1B ChIP-seq


title: Tet.Rybp.Stat3.DOX-.RING1B.rep2

description:
Library name: Sample 12
RING1B ChIP-seq


title: MOC2-27 cells, EV-Deficient, in vitro, control 1


title: K4 (RNA-seq)

value: skeletal muscle


title: MOC2-25 cells, EV-Proficient, in vitro, paclitaxel 1


title: BT549ENL-1

address: 哈尔滨市南岗区保健路6号


title: Tet.Rybp.Stat3.DOX+.RING1B.rep1

description:
Library name: Sample 13
RING1B ChIP-seq


title: Tet.Rybp.Stat3.DOX+.Input

description:
Library name: Sample 10
Input


title: MOC2-25 cells, EV-Proficient, in vitro, paclitaxel 3


title: MOC2-25 cells, EV-Proficient, in vitro, control 3


title: W8 (RNA-seq)


title: BT549Control-3

address: 哈尔滨市南岗区保健路6号


title: K5 (RNA-seq)


title: Tet.Rybp.Stat3.DOX-.Input

description:
Library name: Sample 9
Input


title: MOC2-25 cells, EV-Proficient, in vitro, control 2


title: W4 (RNA-seq)


title: Tumor, 4SA,  1

value: Tumor from LN229-4SA cells

value: LN229-4SA cells

value: glioblastoma cell line


title: BT549Control-2

address: 哈尔滨市南岗区保健路6号


title: ESC, shStat3, RING1B

description:
Library name: Sample 8
RING1B ChIP-seq

value: Mus musculus

value: Stat3 knockdown


title: MOC2-25 cells, EV-Proficient, in vitro, control 1

value: Squamous Cell Carcinoma


title: BT549Control-1

address: 哈尔滨市南岗区保健路6号


title: W3 (RNA-seq)


title: ESC, shEV, RING1B

description:
Library name: Sample 7
RING1B ChIP-seq

value: embryonic stem cell

value: shEV


title: Myo7a_Cochlea_WT_P30_Rep3

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

data_processing:
nf-core/rnaseq pipline
mapped using STAR to mm10
reads were counted using salmon
differential expression testing was performed using DeSeq2
Assembly: mm10
Supplementary files format and content: Myo7a_P15_P30_counts.csv; counts from Salmon without normalization
Supplementary files format and content: DEGs_Myo7a_P15_P30.xlsx; differentially expressed genes from DeSEQ2, comparing all ages and genotypes

source_name: cochlea

extract_protocol:
Tissues were homogenized in 350ul of RLT buffer + DTT using a pestle until the tissue was no longer visible by eye. The homogenized lystate was mixed with 350 ul of 70% ethanol and then applied directly to the Qiagen RNeasy Micro Kit, according to the manufacturer's instructions and RNA was eluted into 15 ul of dH20.
RNA quantity was established using a Nanodrop spectrophotometer and RNA integrity number (RIN) was calculated using a BioAnalyzer. All samples had a RIN score greater than 9.1. Preparation of the mRNA library was performed using poly A enrichment and sequenced on the Illumina NovaSeq sequencer using paired-end 150 bp reads.

treatment_protocol: Tissue was snap frozen after dissection and then thawed on ice in preparation for RNA extraction, with several cochlear tissues combined in one tube.

value: cochlea

tag: age

value: Flox


title: ESC, shStat3, Input

description:
Library name: Sample 6
Input


title: LAD_scRNAseq_4

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description: 10x Genomics

data_processing:
Cell Ranger (10x Genomics, v7.1.0) was used to performalignment (GRCh38, Ensembl 93), filtering, barcode counting and UMI counting of sequencing reads from fastq files.
Assembly: GRCh38
Supplementary files format and content: Tab -separated values files and matrix files

source_name: coronary plaque

extract_protocol:
Left and right anterior descending arteries were washed, minced, and digested then filtered using cell strainers. Following a dead cell removal step, single-cell suspensions were counted and loaded onto a Chromium Controller (10x Genomics).
Libraries were prepared using the Chromium Single Cell 3’ Library v3 reagent, Gel Bead and Multiplex Kit and Chip Kit (10X Genomics; 1000268, 1000215 and 100127, respectively)

value: coronary plaque


title: Myo7a_Cochlea_WT_P30_Rep2


title: LAD_scRNAseq_2

description: 10x Genomics


title: ESC, shEV, Input

description:
Library name: Sample 5
Input

value: control


title: LAD_scRNAseq_1

description: 10x Genomics


title: Myo7a_Cochlea_WT_P15_Rep4


title: ESC,  Rybp-/-,STAT3

description:
Library name: Sample 4
STAT3 ChIP-seq

value: RYBP KO


title: Myo7a_Cochlea_WT_P30_Rep1


title: Myo7a_Cochlea_WT_P15_Rep3


title: 786-O_xenograft_EmptyVector_RNA_Rep3

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data
Paired-end clean reads were aligned to the reference genome (hg38) using STAR
FeatureCounts was used to count the read numbers mapped of each gene. Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed
Gene set enrichment analysis (GSEA) was performed by using the GSEA software and Hallmark signatures. KEGG pathway enrichment analysis was performed by the DAVID functional annotation bioinformatics tools (https://david.ncifcrf.gov/home.jsp) using the up- or downregulated differentially expressed genes (DEGs). Z-scores are computed on a gene-by-gene (row-by-row) basis by subtracting the mean and then dividing by the standard deviation
Assembly: hg38
Supplementary files format and content: Raw counts per gene matrix

growth_protocol: In vitro cells were cultured in traditional Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco, 11995073) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco). 6-8-week-old NOD SCID gamma (NSG) mice were used for xenografts, and mice were fed with regular diets. All animal experiments were following NIH guidelines and were approved by the Institutional Animal Care and Use Committee (IACUC) of UT Southwestern Medical Center.

extract_protocol:
Total RNA from triplicates was extracted from homogenized xenograft tumors or in vitro cells grown in 6-well plates by using RNeasy® Mini Kit (QIAGEN, 74106) with on column DNase digestion (QIAGEN, 79256).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Library preparation, sequencing, and data processing were performed by Novogene as paired end 100bp reads.

treatment_protocol: HEK293T cells were used for generating lentivirus particles. Virus packaging plasmids were transfected with lipofectamine 3000 (Invitrogen). 8-12hr post transfection, fresh medium was added to replace old medium. Then, viruses were collected twice after 24hr and 48hr. After passing through 0.45μm filters, an appropriate amount of viruses was used to infect target cells in the presence of 8 μg/mL polybrene (Santa Cruz). Subsequently, target cell lines were cultured in the presence of puromycin (2 μg/ml) or neomycin (0.8mg/ml) depending on the vector.

tag: sample type

value: Xenograft

value: Empty vector control


title: bulk Dip-C like 293T 50cell

city: Shenzhen

first: Chong

address: BGI Center, No.9 Yunhua Road, Yantian District

institute: BGI Genomics

description: Library name: bulkPCR_50

data_processing:
The raw reads of snHiChew or other benchmarked single-cell chromatin conformation capture technologies were demultiplexed to each cell using an in-house script. This script utilizes multi-thread functions adapted from [scHicDemultiplex.py](http://schicdemultiplex.py/) in scHiCExplorer. Single-cell or bulk sample Hi-C paired-end reads were then aligned to the hg19 or mm10 reference genome using HiC-Pro {Servant, 2015 #1611} (v.3.1.0, default settings). The nomenclature for HiC-Pro metrics, including terms such as valid pairs and reported pairs, adheres to the conventions established in the HiC-Pro publication. This data was used to generate HiC-Pro filtering and alignment metrics, valid pairs, and contact matrices, which were then corrected with ice_norm. For each chromosome, contact matrices at resolution levels ranging from 5 kb to 2.5 Mb were created for further analysis. To estimate the number of valid cells in the snHiChew data, we employed a barcode rank plot to identify the steep drop-off pattern that distinguishes valid cells from background noise. Specifically, all detected snHiChew barcodes were plotted in descending order based on the number of nonduplicated valid pairs associated with each barcode. The R package kneedle (v1.0.0) was utilized to identify two critical knee points in the data{Satopaa, 2011 #1614}.. The first knee point (knee1) was used to differentiate doublet-enriched cells from valid cells, while the second knee point (knee2) was used to distinguish background noise from valid cells. Barcodes with ranks above knee1 were classified as doublet-enriched cells, and those with ranks below knee2 were classified as background noise. Only the data associated with valid cells, which fall between knee1 and knee2, were retained for further analysis.
Assembly: hg19
Supplementary files format and content: Contact matrices for bulkHiChew and pseudo bulk of snHiChew data

growth_protocol: **Cell Type and Cell Culture**  Mouse embryonic fibroblasts cell line NIH/3T3 was obtained from ATCC.  Human embryonic kidney cell line HEK293T and CTCF Knockdown (*CTCF*+/-) 293T Cell Line were obtained from Abclonal Technology Co.,Ltd. NIH/3T3, HEK293T and CTCF Knockdown 293T were cultured in DMEM (Gibco, Cat. No. 11965092) medium supplemented with 10%FBS (Gibco, Cat. No. 10099141) and 1%penicillin–streptomycin (Gibco Cat. No. 15140122), under the conditions of 37°C, 5%CO$_2$. For transcript inhibition experiment, HEK293T cells were treated with 1 μM triptolide for 2 hours.

extract_protocol:
Cell Lysis. Cells were lysed in 500 μL of  permeabilization buffer (10 mM Tris-HCl [pH 8.0], 10 mM NaCl, 0.2% CA-630, 1× protease inhibitors cocktail) per 2 × 10$^6$ cells and incubated on ice for 10 minutes. After centrifugation at 800 × g at 4°C for 3 minutes, the supernatant was discarded, and the pellet was washed once with 1.2×NEBuffer r3.1. The pellet was resuspended in 199 μL of 1.2× NEBuffer r3.1, supplemented with 1 μL of 20% SDS (final concentration 0.1%), and incubated at 65°C for 10 minutes. After cooling on ice for 2 minutes, 10 μL of 20% Triton X-100 was added to neutralize SDS, followed by incubation at 37°C for 15 minutes.
The HiChew protocol consists of four essential steps prior to PCR amplification. Initially, we employ formaldehyde to crosslink DNA strands and proteins. Subsequently, we utilize DpnII to cleave the DNA at GATC motifs. Following this, we implement proximal ligation to join nearby digested DNA ends, resulting in a GATC ligation scar. After cellular lysis, we proceed with DNA library construction, selecting either an adapter ligation-based or Tn5-based method, contingent upon DNA quantity and experimental requirements.  Following PCR amplification, we employ dam methyltransferase to label the ligation scar with m6A methylation on the GATC motif. Subsequently, we implement an immunoprecipitation (IP) protocol to selectively enrich the ligation scars using m6A antibody pull-down. This post-PCR enrichment strategy enhances the efficiency of our chromatin conformation capture process.

value: wild type


title: ESC,  Rybp+/+,STAT3

description:
Library name: Sample 3
STAT3 ChIP-seq

value: WT


title: bulk Dip-C like 293T 500cell

description: Library name: bulkPCR_500


title: 786-O_xenograft_EmptyVector_RNA_Rep2


title: 786-O_xenograft_EmptyVector_RNA_Rep1


title: Myo7a_Cochlea_WT_P15_Rep2


title: Myo7a_Cochlea_WT_P15_Rep1


title: bulk Dip-C like 293T 5000cell

description: Library name: bulkPCR_5000


title: ESC,  Rybp+/+,Input for STAT3

description:
Library name: Sample 1
Input


title: ESC,  Rybp-/-,Input for STAT3

description:
Library name: Sample 2
Input


title: 786-O_xenograft_BBOX1_RNA_Rep3

value: BBOX1 re-expression


title: 786-O_xenograft_BBOX1_RNA_Rep2


title: CRS 3, BLA

first: Carla

last: Nasca

address: 1 Park Avenue

institute: NYU Grossman School of Medicine

data_processing:
FastQC v.0.12.1
STAR v2.7.7a
HTSEQ 0.13.5
EdgeR 3.42.4
Assembly: mm39
Supplementary files format and content: count

source_name: Basolateral Amygdala

extract_protocol:
Basolateral amygdala tissues were dissected and weighed before homogenization and tissue was lysed. Total RNA was extracted using Qiazol reagent and RNeasy mini Kit (Qiagen, US), according to the manufacturer’s instructions. RNA quality was checked using the 2100 Bioanalyzer (Agilent Technologies, US) and quantified spectrophotometrically. The acceptance criteria for RNA quality were a 260/280 ratio ≥ 1.80 and ≤ 2.20.
After checking RNA for quality, Total RNA was extracted according to the manufacturer’s instructions (TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat).

value: Basolateral Amygdala


title: Myo7a_Cochlea_CRE_P30_Rep3

value: Cre


title: CRS 2, BLA


title: Myo7a_Cochlea_CRE_P30_Rep2


title: bulkHiChew 293T 500cell

description: Library name: bulkHiChew_500


title: CRS 1, BLA


title: 786-O_xenograft_BBOX1_RNA_Rep1


title: Myo7a_Cochlea_CRE_P30_Rep1


title: Ctrl 3, BLA


title: 786-O_cells_EmptyVector_RNA_Rep3

value: Cells


title: bulkHiChew 293T 5000cell

description: Library name: bulkHiChew_5000


title: Ctrl 2, BLA


title: 786-O_cells_EmptyVector_RNA_Rep1


title: snHiChew 200cell 293T

description: Library name: snHiChew_200cell293T


title: Ctrl 1, BLA


title: Myo7a_Cochlea_CRE_P15_Rep3


title: 786-O_cells_BBOX1_RNA_Rep3


title: BLM+aPD-1 3

city: 广州

first: maolin

last: zhou

address: 广东省越秀区东风西路195号

institute: 广州医科大学

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles

source_name: Lung tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: The BLM group underwent a single intratracheal instillation of bleomycin. the BLM+aPD-1 group, the mice received both a single intratracheal instillation of bleomycin and an intraperitoneal injection of an anti-mouse PD-1 mAb.

value: Lung tissue


title: Δpcr1 cells over-expressing pREP41-Atf1 set1

city: Kolkata

first: Geetanjali

last: Sundaram

state: West Bengal

address: 35, Ballygunge Circular Road

department: Biochemistry

country: India

institute: University of Calcutta

description: Library name: 90-A1

data_processing:
Raw sequence data generation was done using Fastq file followed by data quality check.
Mapping is done to the reference genome using Hisat2 to evaluate sample quality
Differential expression analysis using Cuffdiff.
Gene Ontology Annotations were assigned using Uniprot and pombase
Assembly: ASM294v2
Supplementary files format and content: Gene_Exp_Annotated.xlsx
Supplementary files format and content: Gene-FPKM_Matrix_Annotated.xlsx

organism: Schizosaccharomyces pombe

source_name: yeast cell

growth_protocol: All cells were grown at 30°C. For overexpression experiments, cells were grown overnight in Edinburgh minimal medium (EMM)-Leu supplemented with 20uM thiamine, harvested, washed, resuspended in EMM-Leu-thiamine, and incubated for another 24 h at 30°C.

extract_protocol:
RNA was harvested using Trizol Reagent
TruSeqstranded mRNA sample preparation protocol was used for library preparation

value: yeast cell

value: h90 ade6leu1 ura4 pcr1::ura4+ +pREP41-Atf1


title: Myo7a_Cochlea_CRE_P15_Rep1


title: 786-O_cells_BBOX1_RNA_Rep2


title: Δpcr1 cells over-expressing pREP41-Atf1 set2

description: Library name: 90-A2


title: BLM+aPD-1 2

address: 广东省越秀区东风西路195号


title: bulkHiChew 293T 50cell

last: Tang

description: Library name: bulkHiChew_50


title: K7 (ATAC-seq)

data_processing:
Raw reads were filtered and trimmed by Trimmomatic
The clean reads were then aligned to reference genome sequences using the bwa program
callpeak with cutoff qvalue<0.05 was performed with macs2 software
reads distributions across gene were analyzed by deeptools, and bedtools were employed to annotate peaks
Differential peak analysis of two conditions/groups was performed using the DESeq2 R package (1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with a FDR < 0.01 and foldchange ≥ 2 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm38_release95
Supplementary files format and content: tab-delimited text file includes raw counts and normalized values for each Sample
Supplementary files format and content: merged bigwig file for WT and KO respectively

source_name: skeletal muscle

extract_protocol:
Instantly frozen muscle from mice were used to collect nuclei for transposition by Tn5 Transposase. The samples were then purified using a Qiagen MinElute PCR Purification Kit (Qiagen)
Purified DNA were amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA) for library construction, which were again purified using the Qiagen MinElute PCR Purification Kit (Qiagen)

value: skeletal muscle

value: quadriceps femoris


title: BLM+aPD-1 1

address: 广东省越秀区东风西路195号


title: 786-O_cells_BBOX1_RNA_Rep1


title: K5 (ATAC-seq)


title: snHiChew 400cell gm12878

description: Library name: snHiChew_400cellgm12878


title: Δpcr1 cells over-expressing pREP41 set 2

description: Library name: 90-F2

value: h90 ade6leu1 ura4 pcr1::ura4+ +pREP41


title: Myo7a_Cochlea_CRE_P15_Rep2

value: cochlea


title: Δpcr1 cells over-expressing pREP41 set 1

description: Library name: 90-F1


title: BLM 3

address: 广东省越秀区东风西路195号

value: BLM


title: K4 (ATAC-seq)


title: Myo7a_Cochlea_CRE_P15_Rep4


title: 786-O_cells_EmptyVector_RNA_Rep2


title: W8 (ATAC-seq)


title: Tumor 2 PG1lo

city: Kyoto

first: Yoshifumi

last: Ueda

address: Katsura, Kyoto-daigaku

department: Department of Synthetic Chemistry and Biological Chemistry

country: Japan

institute: Graduate School of Engineering, Kyoto University

data_processing:
Each obtained read was mapped to the human genome version GRCh37/hg19 with STAR (v2.6.0c) using default parameters.
To normalize the expression data, trimmed mean of M values (TMM) were calculated based on edgeR R package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: NCI-N87 subcutaneous tumor (day 21)

growth_protocol: 2 x 10^6 NCI-N87 tumor cells in PBS containing 50 % Growth Factor Reduced Matrigel (BD Biosciences) were injected subcutaneously into the flank of each nude mouse.

extract_protocol:
Freshly isolated NCI-N87 tumors were enzymatically digested and the dissociated cells were sorted according to the fluorescence of PG1 and AF647. Total RNA isolation was performed with the Qiagen RNeasy micro kit.
A cDNA library was prepared using a SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio) and a Nextera XT Index Kit v2 SetA/B/C/D (Illumina).

treatment_protocol: 21 days after the inoculation, mice were injected with PTA through tail vein.

tag: pg1 fluorescence

tag: sample number

value: Tumor 2


title: BLM 1

address: 广东省越秀区东风西路195号

tag: tissue


title: Tumor 1 PG1lo

value: Tumor 1


title: C268A_37_A

city: College Park

first: Jiqiang

last: Ling

state: MD

address: 2202 Microbiology Bldg., 4062 Campus Dr.

department: Cell Biology and Molecular Genetics

institute: The University of Maryland, College Park

description: Library name: Sample 4

data_processing:
Raw counts of sequence reads (FKPM) were analyzed by Novogene according to standard protocol using HISAT2 software.
Assembly: Reads were mapped to the reference genome (Saccharomyces cerevisiae S288c GCA_000146045.2) using HISAT2 software by Novogene.
Supplementary files format and content: Excel sheet. FKPM.

organism: Saccharomyces cerevisiae

source_name: Cell pellet

extract_protocol:
Total RNA extraction using QiaGen RNAeasy kit according to manufacture's protocol
Constructed by Novogene according to standard protocol

value: Cell pellet

tag: cell type

value: Yeast


title: C268A_37_C

description: Library name: Sample 6


title: C268A_37_B

description: Library name: Sample 5


title: Tumor 3 PG1hi

value: Tumor 3


title: control 3

address: 广东省越秀区东风西路195号

tag: treatment

value: No


title: W3 (ATAC-seq)

tag: genotype


title: control 2

address: 广东省越秀区东风西路195号


title: WT_37_C

description: Library name: Sample 3

tag: cell line


title: Tumor 2 PG1hi


title: WT_37_B

description: Library name: Sample 2


title: Huh-7 cells, shSLC3A2

city: Xiamen

first: Yipeng

last: Rao

address: Xiangan Campus, Xiamen University, Xiangan Road, Xiangan District, Xiamen City, Fujian Province, China

institute: national insititute of diagnostics and vaccine development in infectious diseases（xiamen university）

description: Library name: HUH7_shSLC3A2

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment:  Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis  In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis  Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis  GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG.  KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Assembly: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: liver

growth_protocol: Freshly purified mouse T cells were grown in RPMI 1640 medium supplemented with 10% FBS, 100 µg/ml penicillin-streptomycin, 1 mM sodium pyruvate, 50 µM 2-mercaptoethanol, and 50 U/ml recombinant IL-2. Huh-7 cells were cultured in DMEM medium supplemented with 10% FBS and 100 µg/ml penicillin-streptomycin.

extract_protocol:
RNA samples were extracted using the Trizol method. 1 μg total RNA was used for following library preparation
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: T cells were activated with anti-CD3/CD28-coated beads (Thermo Fisher Scientific, 11452D) and cultured with fresh medium or tumor supernatants for 72 hours. The Huh-7 cells were infected with a control and SLC3A2 knockdown lentivirus.

value: liver

value: hepatocellular carcinoma cells

value: Huh-7 cells treated with lentivirus for SLC3A2 knockdown


title: control 1

address: 广东省越秀区东风西路195号

value: Lung tissue


title: Huh-7 cells, shNC

description: Library name: HUH7_shNC

value: shNC

value: control lentivirus-treated Huh-7 cells


title: Tumor 1 PG1hi


title: Using IRBP peptide and CFA for an additional 2 weeks, followed with CSD for  4 week rep3

status: Public on Dec 22 2024

city: Wu Han

first: Zhen

last: Chen

state: Hu bei

address: Zhangzhidong Road

institute: Renmin Hospital of Wuhan University

description: Library name: CSD-EAU3

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include gene count values for each Sample

source_name: Retina

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Retina

value: CSD-EAU


title: BLM 2

address: 广东省越秀区东风西路195号


title: Using IRBP peptide and CFA for an additional 2 weeks, followed with CSD for  4 week rep2

description: Library name: CSD-EAU2