title: V16-2

city: tsukuba

first: Ichiro

last: Chihara

state: Ibaraki

address: 1-1-1 tennodai

department: Urology

country: Japan

institute: University of TSUKUBA

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 7.5.1; Qiagen, Redwood City, CA).
Assembly: mm10
Supplementary files format and content: CSV files were generated usingCLC Genomics Workbench (Version 7.5.1; Qiagen, Redwood City, CA).

source_name: whole bladder

extract_protocol:
Total RNA from whole blood samples was isolated using a PAX gene Blood RNA kit (PreAnalytix) according to the manufacturer’s instructions. The globin RNA was removed from total RNA using a GLOBINclear-Human Kit (Thermo Fisher SCIENTIFIC).
For RNA sequencing, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) according to the manufacturer's instructions. Library preparation was performed using an NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: After bilateral adrenalectomy of the mice, corticosterone was administered at inactive timing pending recovery.

tag: operation

value: bilateral adrenalectomy

value: vehicle only

tag: time


title: C20-2

status: Public on Jun 16 2022

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: treatment

value: CORT

tag: strain


title: V08-2


title: V04-2


title: C16-2


title: sample.ginkgo.11767078

city: Austin

first: Joshua

last: Urrutia

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

country: USA

institute: University of Texas at Austin

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_IcaR_Gate/1

molecule: polyA RNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cell culture

extract_protocol:
Total RNA was extracted using Magjet RNA extraction kit (Thermo) according to manufacturer's instructions.
RNA quality was assessed using Tapestation (Agilent). KAPA RNA Hyperprep kit (Roche) was used for ribosomal RNA depletion and Illumina compatible library preparation.

tag: temperature

value: 37.0 celsius

tag: timepoint

value: 6.5 hour


title: sample.ginkgo.11767041

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pJS007_LALT__backbone/1

value: 5.0 hour


title: sample.ginkgo.11767039


title: V20-1


title: Plate 12, 96 vagal neurons

city: Berlin

first: Carmen

last: Birchmeier

address: Robert-Roessle-Str. 10

country: Germany

institute: MDC

library_source: transcriptomic single cell

data_processing:
quality filtering with Drop-seq tools
trimming with Drop-seq tools
annotation of the reads with the cell barcode and UMI
mapping with STAR
quantification with Drop seq tools
Assembly: mm10
Supplementary files format and content: tsv of the Digital Gene Expression Matrix (counts)

source_name: vagal ganglia

extract_protocol:
We dissected the vagal ganglia from 15 VGlut2Cre;R26nGFP mice of either sex at P4, removed excess nerve, muscle and vascular tissue, and placed them in a 1.5 ml Eppendorf tube with warm F12/FHS (F12 with 10% fetal horse serum). Briefly, ganglia were digested in F12/FHS solution containing 0.125% collagenase, incubated at 37Co for 1 hour, washed 3x in PBS, and then incubated in PBS with 0.25% trypsin at 37Co for 15 minutes. Ganglia were dissociated using fire-polished Pasteur pipettes of decreasing diameter. The solution was transferred on top of a 2 ml BSA cushion (F12/FHS solution with 15% bovine serum albumin) and spun for 10 minutes at 900 RPM. The cell pellet was resuspended in 500 µl of HBSS without calcium or magnesium, strained twice through a 70 µm filter (Sysmex), and DAPI (Sigma) was added to a final concentration of 300 nM to label dead cells before sorting. We sorted GFP-positive / DAPI-negative cells into 96-well plates using ARIA Sorter III (BD) and BD FACSDiva software 8.0.1.
Libraries were constructed following the CEL-Seq2 protocol (doi: 10.1186/s13059-016-0938-8).

tag: tissue

value: vagal ganglia

tag: cell type

value: neuron

tag: genotype

tag: age


title: sample.ginkgo.11767038


title: sample.ginkgo.11767075

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pTACmin/1


title: sample.ginkgo.11767021


title: sample.ginkgo.11767106

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pJS007_LALT__P3__PhlF/1


title: sample.ginkgo.11767061


title: sample.ginkgo.11767051

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pJS007_LALT__I1__IcaRA/1


title: V08-1


title: C08-1


title: V04-1


title: sample.ginkgo.11767024

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_NAND_Circuit/1


title: C20-1


title: C16-1


title: sample.ginkgo.11767089

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pBADmin/1


title: V20-2


title: sample.ginkgo.11767055


title: C04-1


title: C08-2


title: sample.ginkgo.11767072

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_empty_landing_pads/1


title: sample.ginkgo.11767028


title: C04-2


title: V16-1


title: V24-1


title: sample.ginkgo.11767080


title: sample.ginkgo.11767030


title: sample.ginkgo.11767022

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_WT/1


title: sample.ginkgo.11767029


title: V12-1


title: V12-2


title: V24-2


title: C24-2


title: C24-1


title: sample.ginkgo.11767033

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_PhlF_Gate/1


title: sample.ginkgo.11767069


title: sample.ginkgo.11767031


title: sample.ginkgo.11767098


title: C12-1


title: sample.ginkgo.11767048


title: sample.ginkgo.11767096


title: SpibWT.Pdpn-CD104-.mTEClo.rep#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: raw read counts

source_name: Thymus

extract_protocol:
500-1000 cells were cytofluorometrically sorted into 5ul TCL buffer (Qiagen) with 1% 2-mercaptoethanol (Sigma). Cells were double-sorted when cell numbers permitted. For quadriceps muscle, 2ng total RNA was added directly to TCL plus 1% 2-mercaptoethanol. Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter).
Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: mTEC subsets were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies and flow sorting subsets of interest into 5ul TCL buffer plus 1% 2-mercaptoethanol. Gut epithelial cells were isolated by incubation in PBS/20mM EDTA, mechanical disruption, trypsinization, staining, and sorting. Lung epithelial cells were isolated by digestion with Liberase TM, staining, and sorting. Quadriceps muscle was isolated by flash freezing, homogenization in Trizol, and phenol-chloroform extraction of RNA.

value: SpibWT

value: mTEClo


title: SpibKO.Pdpn-CD104-.mTEClo.rep#1

value: SpibKO


title: sample.ginkgo.11767084


title: sample.ginkgo.11767046


title: C12-2


title: SpibWT.Pdpn-CD104-.mTEClo.rep#1


title: sample.ginkgo.11767065


title: SpibWT.Pdpn-CD104-.mTEClo.rep#2


title: SpibKO.Pdpn-CD104-.mTEClo.rep#2


title: SpibKO.Pdpn-CD104-.mTEClo.rep#3


title: sample.ginkgo.11767043


title: Sox8KO.Pdpn-CD104-.mTEClo.rep#3


title: Sox8WT.Pdpn-CD104-.mTEClo.rep#2


title: sample.ginkgo.11767093


title: sample.ginkgo.11767092


title: Sox8WT.Pdpn-CD104-.mTEClo.rep#1


title: Sox8WT.Pdpn-CD104-.mTEClo.rep#3


title: sample.ginkgo.11767019


title: sample.ginkgo.11767105


title: AireKO.microfold.mTEC.rep#1

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

value: AireKO

value: Microfold mTEC


title: sample.ginkgo.11767090


title: sample.ginkgo.11767074


title: AireKO.microfold.mTEC.rep#2


title: sample.ginkgo.11767073


title: AireKO.microfold.mTEC.rep#3


title: CkmYFP+.mTEC.rep#1

value: Ckm-Cre Rosa26-LSL-eYFP

value: Muscle mTEC


title: CkmYFP+.mTEC.rep#2


title: Sox8KO.Pdpn-CD104-.mTEClo.rep#2


title: sample.ginkgo.11767070


title: sample.ginkgo.11767087


title: AireKO.microfold.mTEC.rep#4


title: sample.ginkgo.11767097


title: Muscle.quadriceps.rep#1

source_name: Quadriceps muscle

value: WT

value: Skeletal muscle tissue


title: AT2.lung.rep#3

source_name: Lung

value: Foxj1-CreERT2-eGFP Rosa26-LSL-eYFP

value: Lung AT2 epithelial cell


title: Sox8KO.Pdpn-CD104-.mTEClo.rep#1


title: CkmYFP-.mTEC.rep#2

value: Non-muscle mTEC


title: Muscle.quadriceps.rep#2


title: sample.ginkgo.11767067

value: 37.0 celsius


title: sample.ginkgo.11767036


title: CkmYFP-.mTEC.rep#1


title: sample.ginkgo.11767047


title: sample.ginkgo.11767102

value: 6.5 hour


title: sample.ginkgo.11767088


title: Ciliated.lung.rep#2

value: Lung ciliated epithelial cell


title: Foxj1YFP-.mTEC.rep#2

value: Non-ciliated mTEC


title: AT2.lung.rep#1


title: sample.ginkgo.11767103


title: AT2.lung.rep#2


title: sample.ginkgo.11767042

value: 5.0 hour


title: sample.ginkgo.11767060


title: Foxj1YFP-.mTEC.rep#3


title: sample.ginkgo.11767032


title: sample.ginkgo.11767108


title: sample.ginkgo.11767094


title: sample.ginkgo.11767095


title: sample.ginkgo.11767027


title: Ciliated.lung.rep#1


title: sample.ginkgo.11767063


title: Ciliated.lung.rep#3


title: Foxj1YFP+.mTEC.rep#2

value: Ciliated mTEC


title: Foxj1YFP-.mTEC.rep#1


title: Foxj1YFP+.mTEC.rep#1


title: sample.ginkgo.11767077


title: sample.ginkgo.11767058


title: sample.ginkgo.11767054


title: SpibKO.mTEChi.rep#2

value: mTEChi


title: sample.ginkgo.11767081


title: SpibKO.mTEChi.rep#3

value: SpibKO


title: sample.ginkgo.11767107


title: SpibKO.mTEChi.rep#1


title: sample.ginkgo.11767083


title: sample.ginkgo.11767026


title: SpibWT.mTEChi.rep#3

value: SpibWT


title: sample.ginkgo.11767100


title: sample.ginkgo.11767071


title: Sox8KO.mTEChi.rep#2


title: Sox8KO.mTEChi.rep#1


title: Sox8KO.mTEChi.rep#3


title: sample.ginkgo.11767040


title: sample.ginkgo.11767053


title: SpibWT.mTEChi.rep#1


title: sample.ginkgo.11767099


title: Enterocyte.rep#3

source_name: Peyer's patch

value: Enterocyte


title: sample.ginkgo.11767079


title: sample.ginkgo.11767085


title: Sox8WT.mTEChi.rep#1


title: sample.ginkgo.11767062


title: sample.ginkgo.11767101


title: sample.ginkgo.11767052


title: Enterocyte.rep#1


title: Microfold.PP.rep#2

value: Intestinal microfold cell


title: Sox8WT.mTEChi.rep#3


title: Enterocyte.rep#2


title: sample.ginkgo.11767066


title: SpibWT.mTEChi.rep#2


title: sample.ginkgo.11767044


title: Sox8WT.mTEChi.rep#2


title: sample.ginkgo.11767034


title: Microfold.PP.rep#1


title: TECs IRI RIPC rep3

city: Münster

first: Jan

last: Rossaint

address: Albert-Schweitzer-Campus 1, Bldg. A1

department: Dpt. of Anesthesiology

institute: University of Münster

data_processing:
quality control was performed with FastQC and MultiQC and adapter trimming was performed with trim-galore (v0.6.4).
Read-mapping and quantification with Salmon (v1.0.0) using the Gencode mouse reference transcriptome vM23
The transcript counts where summarized to gene-level with tximport and supplementary annotation data from Ensembl
The differential expression analysis was carried out by DESeq2 on gene level counts
The reported log foldchanges where shrunk with apeglm and s-values where calculated for statistical significance filtering. For a significant differential gene we require a s-value below 0.01.
Assembly: mm10
Supplementary files format and content: Tab separated matrix of quantification counts of each gene per sample.

source_name: kidney

extract_protocol:
RNA was extracted from the sorted cells using a RNeasy Mini Kit (Qiagen).
Reverse transcription into cDNA was performed based on polyA tail. For library construction, PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The single strand circle DNA (ssCirDNA) were formatted as the final library. The library was amplified to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: IRI-induced AKI was induced in wildtype mice by temporal clamping of the renal pedicals. Cells were isolated from the blood (neutrophils) and kidney tissue (renal tubular epithelial cells) 24 hours after the procedure.

value: kidney

value: tubular epithelial cells

value: wildtype

value: cells isolated 24 hours after RIPC and induction of IRI-induced AKI


title: TECs IRI RIPC rep2


title: TECs IRI Control rep1

value: cells isolated 24 hours after control and induction of IRI-induced AKI


title: Non-microfold.mTEC.rep#4

value: WT

value: Non-microfold mTEC


title: TECs IRI Control rep2


title: TECs IRI RIPC rep1


title: TECs Sham RIPC rep3

value: cells isolated 24 hours after RIPC and sham operation


title: TECs Sham RIPC rep1


title: sample.ginkgo.11767002

value: 37.0 celsius


title: Non-microfold.mTEC.rep#3


title: Non-microfold.mTEC.rep#2


title: sample.ginkgo.11766988


title: TECs Sham Control rep1

value: cells isolated 24 hours after control and sham operation


title: TECs Sham Control rep2


title: Non-microfold.mTEC.rep#1


title: PMNs IRI RIPC rep2

source_name: blood

value: blood

value: neutrophils


title: PMNs IRI RIPC rep3


title: TECs Sham RIPC rep2


title: sample.ginkgo.11766992

value: 5.0 hour


title: PMSs IRI Control rep2


title: PMNs IRI RIPC rep1


title: sample.ginkgo.11767023


title: sample.ginkgo.11766978


title: TECs Sham Control rep3


title: PMSs IRI Control rep1


title: sample.ginkgo.11766999


title: sample.ginkgo.11766997


title: WT.mTEChi.rep#3

value: mTEChi


title: Microfold.mTEC.rep#2

value: Microfold mTEC


title: PMNs Sham Control rep1


title: Microfold.mTEC.rep#1


title: sample.ginkgo.11767015


title: PMNs Sham RIPC rep1


title: PMNs Sham RIPC rep3


title: sample.ginkgo.11767000


title: Microfold.mTEC.rep#4


title: Microfold.mTEC.rep#3


title: WT.mTEChi.rep#1


title: PMNs Sham Control rep2


title: sample.ginkgo.11766975


title: sample.ginkgo.11766976


title: WT.mTEChi.rep#2


title: SiHa,hnRNP E1,biol rep 3

city: Taiyuan City

first: JinTao

last: Wang

state: Shanxi

address: 56 Xin Jian Nan Road

department: Department of Epidemiology, School of Public Health

country: China

institute: Shanxi Medical University

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
After the completion of DNA sequencing,decontaminate the original data, remove connectors and remove low-quality data, and count the output of clean data. One order,If the column meets any of the following conditions, it will be determined as unqualified and removed:1) The sequence contains adapter connectors;2) The content of N base exceeds 10% of the sequence length;3) The low quality base content exceeds 50% of the sequence length.
ChIP-seq reads were aligned to the UCSC hg19 genome using soapaligner / soap2 version: 2.21t. Only uniquely mapping reads with at most two mismatches were retained.
Clean Parameter: soap_mm_gz -p 4 -v 2 -s 35
Peaks were called uing MACS  with the significance cut-off q-value <=le-05
Assembly: Peak Calling Parameter: macs14 -s 50 -g hs -p 1e-5 -w --space 50 -m 10,30
Supplementary files format and content: hg19
Supplementary files format and content: bigWig (except for Input sample)

molecule: genomic DNA

organism: Homo sapiens

source_name: SiHa

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, cross-linked DNA was sonicated and ranged in size from 200 to 900 bp.

tag: cell line

value: SiHa

value: Human Cervical squamous cell carcinoma cells

tag: chip antibody

value: hnRNP E1 (CST, #8536)


title: SiHa,hnRNP E1,biol rep 2

value: hnRNP E1 (CST, #8535)


title: WT.Pdpn+CD104+.mTEClo.rep#3

value: mTEClo


title: SiHa,hnRNP E1,biol rep 1

value: hnRNP E1 (CST, #8534)


title: PMNs Sham RIPC rep2

value: wildtype


title: SiHa,hnRNP E1,input


title: WT.Pdpn+CD104+.mTEClo.rep#2

value: WT


title: sample.ginkgo.11767009


title: sample.ginkgo.11766980


title: WT.Pdpn-CD104-.mTEClo.rep#2


title: sample.ginkgo.11767007


title: sample.ginkgo.11766993


title: 7dpf-FedVentral_2

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome, and counted using FeatureCounts. For normalization, differential gene expression analysis, and GO analysis, iDEP version 0.951 was utilized with default parameters. For differential gene expression, a fold-change of 2 and false-discovery rate of 0.1 was used for cut-off.
Assembly: Zebrafish GRCz11
Supplementary files format and content: Matrix with rows as genes and columns as samples

organism: Danio rerio

source_name: Liver

extract_protocol:
Livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrep RNA Miniprep Systems (Promega, Z6110).
cDNA synthesis, library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH.  Integrity and quantity of the starting mRNA was determined by appropriate methods, e.g. measurement of volume and quantity, gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology, using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation, after first strand synthesis, the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next, the sequencing adapters were ligated to the DNA fragments, and the dUTP containing second strand was removed.

value: Fed


title: WT.Pdpn-CD104-.mTEClo.rep#1


title: sample.ginkgo.11766991


title: 7dpf-FedVentral_1


title: IgG.mTEC.rep#2

description: CUT&Tag

data_processing:
Library strategy: CUT&Tag
Low quality reads were discared using Trimmomatic (v0.36)
Reads were mapped to the mouse reference genome (mm10) with bowtie2 (v2.29) using parameters --local --very-sensitive -no-mixed --no-discordant -I 10 -X 700
Bam files were generated and multimapping reads removed by samtools (v1.3.1), and duplicate reads were removed by picard (v2.8.0)
Bigwig files were generated using deeptools (v3.0.2) with counts-per-million normalization
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
mTECs were washed in wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), bound to concavalin A beads (Bangs Laboratories), permeabilized in wash buffer plus 0.05% digitonin, and incubated overnight with 1:50 primary antibody (anti-H3K27ac [Abcam], -Hnf4α [Abcam], -Grhl1 [Novus], -Pou2f3 [Sigma], or -IgG [Rockland]) at 4°C in wash buffer plus 0.05% digitonin, 2mM EDTA and 0.1% BSA. The next day, H3K27ac, Grhl1, IgG, and some Pou2f3 samples were lightly fixed with 0.1% paraformaldehyde at room temperature for 2 minutes before proceeding. (We and others have observed improved CUT&Tag signal-to-noise ratio for some TFs with light fixation.) Samples were incubated with secondary antibody (guinea pig anti-rabbit [Rockland] for H3K27ac, Grhl1, Pou2f3, and IgG; rabbit anti-mouse [Abcam] for Hnf4α) at 1:100 for 1 hour at room temperature in wash buffer plus 0.05% digitonin. Samples were washed and incubated with pA-Tn5 (Addgene #124601, gift from Steve Henikoff, purified in-house) at 1:200 for 1 hour at room temperature in 300mM NaCl wash buffer plus 0.01% digitonin. Samples were washed twice then tagmented for 1 hour at 37°C in 300mM NaCl wash buffer plus 0.01% digitonin and 10mM MgCl.
Tagmentation was halted with EDTA, sodium dodecyl sulfate and proteinase K for 1 hour at 55°C. Tagmented DNA was phenol-chloroform extracted and amplified by PCR with NEBNext 2X Master Mix (NEB) using the following program: 72°C for 2min, 98°C for 30s, 16 cycles of 98°C for 10s and 63°C for 10s, 72°C for 1min, hold. Amplified libraries were quantified by Qubit (Thermo) and Tapestation (Agilent).

treatment_protocol: mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, and flow sorting mTECs into DMEM/10%FCS.

value: mTEC


title: select_wt_replicate2_tile12

city: Copenhagen N

first: Sarah

last: Gersing

address: Ole Maaløes vej 5

country: Denmark

institute: University of Copenhagen

description: Amino acid positions 371-404

data_processing:
Library strategy: Tile-Seq
Libraries were sequenced on a NextSeq 550 instrument (Illumina) and base called using the instriment's Real Time Analysis software.
Sequencing reads were converted to fastq format and demultiplexed using BaseSpace Sequence Hub.
Reads were alligned and variants called using the TileSeq mutation count pipeline (https://github.com/RyogaLi/tileseq_mutcount) version 0.5.9
Variant calls from the TileSeq mutation count pipeline were then used for calling protein-level amino acid changes and for calculating the enrichment of variants using the TileSeqMave pipeline (https://github.com/jweile/tileseqMave) version 0.6.0.9000
reference sequence: sequence.txt on the series record contains the sequence used for read alignment.

organism: synthetic construct

source_name: Yeast cells

growth_protocol: Following transformation, yeast cells were grown in SC-URA galactose until saturation. Cells were either pelleted and stored at -20C before plasmid DNA extraction to serve as the nonselect condition or used for selection. For selection of GCK activity, cells were grown on solid SC-URA 0.2% glucose for three days at 30C. After selection, cells were pelleted and stored at -20C prior to plasmid DNA extraction to serve as the post-selection samples (select).

extract_protocol:
For each condition (select/nonselect, library/wt, replicate1/replicate2), 9 OD units of cells were used for plasmid DNA extraction using the ChargeSwitch Plasmid Yeast Mini kit (Invitrogen) according to the manufacturer's instructions.
The three regional libraries spanning the GCK sequence (aa 2-171, 172-337, 338-466) were constructed by pooled mutagenesis using NNK-degenerate oligos.

tag: host yeast strain

tag: selection

value: yes

tag: molecule subtype

value: plasmid


title: select_wt_replicate2_tile14

description: Amino acid positions 438-465


title: select_wt_replicate2_tile13

description: Amino acid positions 405-437


title: select_wt_replicate2_tile11

description: Amino acid positions 338-370


title: 7dpf-Fed_2


title: RNA seq of Oryzae sativa cv TN1 in  drought and pathogen stress

city: Faridabad

first: Ramu

last: Vemanna

address: NCR Biotech Science Cluster, Faridabad

institute: Regional Centre for Biotechnology

description: TN1-45 days old plant wrre brought down to 80%  FC,  infected with Xoo,  and maintianed at 60% FC.

data_processing:
Read alignment was carried out using Hisat2 v2.1.0
The quantification of the gene expression level in FPKM (Fragments per kilobase of the transcript sequence per million base pairs sequenced) were done by StringTie (1.3.4) by counting the number of reads mapped to each gene.
The differential expression analysis was performed using the DESeq2 R package (2.11.38).
Genome_build: RGAP 7
Supplementary_files_format_and_content: tab-delimited gene abundance files whcih include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa

source_name: Leaf

extract_protocol:
Total RNA was extracted according to the protocol described by Datta et al. (1989) with some modifications. Solutions were prepared with 0.1% (v/v) diethylpyrocarbonate (DEPC). Leaf material (1 g) was collected, flash frozen in liquid nitrogen, and finely ground. 10ml of extraction buffer [0.1 M tris HCl pH 9.0, 0.25M sucrose, 0.2 M NaCl and 10 mM MgCl2] was added and homogenized properly. To the extraction buffer, 10 ml of phenol (water saturated): chloroform mixture (1:1) v/v was added and homogenized, 1 ml of 0.5 M potassium EDTA and 1 ml of 20% (w/v) SDS were added sequentially. The extract was transferred to Oakridge tube and 144 μl of ß- mercaptoethanol was added and kept on rocking shaker in ice for 20 min. The extract was centrifuged at 16000 rpm for 30 min and the supernatant was transferred to the Oakridge tube. An equal volume of chloroform: isoamyl alcohol (49:1) was added to the aqueous phase, vortexed and spin at 15000 rpm for 15 min at 40C. The aqueous phase was transferred to a new Oakridge tube and 8 M LiCl2 was added to a final concentration of 3 M and kept in -200C for 12-18 h. After precipitation, the tubes were centrifuged at 16000 rpm for 30 min at 40C. The supernatant was discarded and the precipitate was washed with 5 ml of 2 M LiCl2 and subsequently with 5 ml of 75 % (v/v) ethanol by centrifuging at 15000 rpm for 20 min at 4oC. The pellet was air dried and dissolved in 100μl of autoclaved DEPC treated water and RNA quantity was estimated spectrophotometrically (Nanodrop®, USA). The purity was checked by analysing the 260/280 ratio and visualizing on formaldehyde denaturing agarose (1% (w/v)) gel. Three micrograms of total RNA was reverse transcribed to single stranded cDNA in a 20 μl reaction mixture consisting of 200 units MMLV reverse transcriptase (RT) (MBI Fermentas), 1X MMLV- RT buffer, 40 picomoles oligo-dT primer and 100 mM dNTP mix. Reverse transcription was performed at 42oC for 1 h.  Synthesized cDNA was confirmed by semi-quantitative Reverse Transcription PCR (RT-PCR) using actin as housekeeping gene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaf

tag: cultivar

value: Taichung Native 1 (TN1)

value: drought+pathogen treatment

value: 51 days


title: WT.Pdpn+CD104+.mTEClo.rep#1


title: RNA seq of Oryzae sativa cv TN1 in  pathogen stress

description: TN1-47 days old plant were infected with Xoo and maintained at 100% field capacity

value: pathogen treatment


title: RNA seq of Oryzae sativa cv TN1 in drought stress

description: TN1-Moisture stress was imposed to 45 days old plants and maintianed at 60% field capacity (FC)

value: drought treatment


title: IgG.mTEC.rep#1

description: CUT&Tag


title: select_wt_replicate2_tile10

description: Amino acid positions 305-337


title: H3K27ac.mTEC.rep#2

description: CUT&Tag


title: WT.Pdpn-CD104-.mTEClo.rep#3


title: DMSO-treated GM03813 fibroblasts, biological replicate 1

type: RNA

city: Philadelphia

first: Matthew

middle: E R

last: Butchbach

state: PA

address: 1020 Locust St

institute: Thomas Jefferson University

description: gene expression data from treated SMA fibroblasts

hyb_protocol: The probes were fragmented and then hybridized for 16 hours at 45C on Clariom D Human GeneChip Arrays in a GeneChip Hybridization Oven 645. The arrays were washed and stained in the GeneChip Fluidic Station 450.

scan_protocol: The arrays were scanned with the GeneChip 3000 scanner.

data_processing: Raw signal intensities were analyzed with TAC 4.0 software (Applied Biosystems)

label: biotin

label_protocol: Fragmented cDNA was end-labeled with a biotinylated dideoxynucleotide using terminal transferase.

growth_protocol: GM03813 type II SMA fibroblasts were grown in DMEM supplemented with 1% glutamine, pen/strept and 10% EqualFetal serum 24 hours prior to treatment

extract_protocol: Total RNA was isolated from cells using the Rnease Mini kit (QIAGEN) according to manufacturer's directions.

treatment_protocol: GM03813 cells were treated with either 10 microM amiloride, 10 microM EIPA or and equivalent volume of DMSO for 5 days at 37C.

value: DMSO


title: amiloride-treated GM03813 fibroblasts, biological replicate 3

value: 10 microM amiloride


title: amiloride-treated GM03813 fibroblasts, biological replicate 1


title: DMSO-treated GM03813 fibroblasts, biological replicate 3


title: DMSO-treated GM03813 fibroblasts, biological replicate 2


title: EIPA-treated GM03813 fibroblasts, biological replicate 1

value: 10 microM EIPA


title: EIPA-treated GM03813 fibroblasts, biological replicate 3


title: EIPA-treated GM03813 fibroblasts, biological replicate 2


title: RNA seq of Oryzae sativa cv TN1 control plants

description: Rice TN1 control

value: untreated


title: amiloride-treated GM03813 fibroblasts, biological replicate 2


title: 7dpf-Fast_2

value: Fast


title: 7dpf-Fast_1


title: RNA seq of Oryzae sativa cv BPT in drought stress

description: BPT5204- Moisture stress was imposed to 45 days old plants and maintianed at 60% field capacity (FC)


title: H3K27ac.mTEC.rep#1

description: CUT&Tag


title: 7dpf-Fed_1


title: select_wt_replicate2_tile7

description: Amino acid positions 207-240


title: select_wt_replicate2_tile6

description: Amino acid positions 172-206


title: RNA seq of Oryzae sativa cv BPT in pathogen stress

description: BPT5204- 47 days old plant were infected with Xoo and maintained at 100% field capacity


title: select_wt_replicate2_tile5

description: Amino acid positions 138-171


title: select_wt_replicate2_tile8

description: Amino acid positions 241-272


title: 6dpf-EtOH_2

value: Fast+EtOH


title: NGFP2 (N+/-;S+/-) 2i-3-D12-4678

city: Cambridge

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description:
NGFP2 (N+/-;S+/-)
RNA-seq

data_processing:
Tophat was used to map reads onto mm9 genome
cuffdiff2 was used to quantify gene expression using mm9 knownGene annotation from UCSC genome browser
Genome_build: mm9
Supplementary_files_format_and_content: genes FPKM tracking from cuffdiff2

growth_protocol: Pluripotent cells grown under 2i/Lif (sample intial name starts by 2i) or S/Lif conditions (sample intial name starts by ES)

extract_protocol: Total RNA from each replicate of one line was isolated from one well of 6-well plate. RNA was isolated using Qiagen kit by following the manufacturer instructions

treatment_protocol: No treatment

value: GFP replaces one allele of Nanog

value: tdTomato replaces one allele of Sall4


title: select_wt_replicate2_tile9

description: Amino acid positions 273-304


title: RNA seq of Oryzae sativa cv BPT in drought and pathogen stress

description: BPT5204- 45 days old plant wrre brought down to 80%  FC,  infected with Xoo,  and maintianed at 60% FC.


title: NGFP2 (N+/-;U+/-) 2i-5-D12-4680

description:
NGFP2 (N+/-;U+/-)
RNA-seq

value: tdTomato replaces one allele of Utf1


title: NGFP2 (N+/-;E+/-) 2i-4-D12-4679

description:
NGFP2 (N+/-;E+/-)
RNA-seq

value: tdTomato replaces one allele of Esrrb


title: 6dpf-EtOH_1

value: WT


title: RNA seq of Oryzae sativa cv BPT control plants

description: Rice BPT5204 control

value: Leaf


title: 6dpf-GcaMP_2


title: NGFP2 (N+/-) 2i-2-D12-4677

description:
NGFP2 (N+/-)
RNA-seq


title: CLDC18

city: Illkirch

first: Manuel

last: Mendoza

address: 1 rue Laurent Fries

country: France

institute: INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Alignment : Reads were mapped onto S288C assembly of Saccharomyces cerevisiae genome using STAR v.2.5.3a
Quantification : Gene expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 94 annotations.
Assembly: S288C
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

organism: Saccharomyces cerevisiae

source_name: RNA of asynchronic yeast culture

growth_protocol: Freshly defrozen cells were grown over night in YP+2%glucose+adenine media; in the morning saturated cell culture was diluted to 0.1 OD and grown at 25C with constant shaking to reach 0.6-0.7 OD.

extract_protocol:
RiboPure-Yeast (Invitrogen) kit was used to isolate total RNA and remove DNA contamination (according to the manufacturer’s protocol)
P2665 : RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 8 minutes.
The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H.
Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library.
Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Once the cells reached target OD, they were pelleted by centrifugation, supernatant was removed and cell pellets were snap frozen in liquid nitrogen.

value: nup60-K467R-GFP::HIS3MX6  S288C


title: select_wt_replicate2_tile4

description: Amino acid positions 104-137

value: yes

value: plasmid


title: WT ESCs 2i-1-D12-4676

description:
WT ESCs
RNA-seq


title: CLDC17


title: 6dpf-GcaMP_1


title: NGFP2 (N+/-;U+/-) ES-5-D12-4675

description:
NGFP2 (N+/-;U+/-)
RNA-seq


title: select_wt_replicate2_tile2

description: Amino acid positions 38-69


title: CLDC16


title: NGFP2 (N+/-;S+/-) ES-4-D12-4674

description:
NGFP2 (N+/-;S+/-)
RNA-seq


title: 6dpf-Fast_2


title: 6dpf-Fast_1


title: select_wt_replicate2_tile1

description: Amino acid positions 2-37


title: CLDC14


title: select_wt_replicate1_tile14

description: Amino acid positions 438-465


title: 5dpf_2

value: Normal


title: select_wt_replicate1_tile13

description: Amino acid positions 405-437


title: CLDC12


title: CLDC15


title: WT ESCs ES-1-D12-4671

description:
WT ESCs
RNA-seq


title: 5dpf_1


title: select_wt_replicate1_tile12

description: Amino acid positions 371-404


title: CLDC13


title: NGFP2 (N+/-) ES-2-D12-4672

description:
NGFP2 (N+/-)
RNA-seq


title: 4dpf_2


title: CLDC11


title: select_wt_replicate1_tile11

description: Amino acid positions 338-370


title: 4dpf_1


title: select_wt_replicate2_tile3

description: Amino acid positions 70-103


title: CLDC10


title: Sample_IL13R1KO-DKO_EC-MM-4573_F_DKO_ABC_Rep4

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

description:
Def6tr/trSwap-70-/- (DKO)
ABC_DKO replicate 3

data_processing:
Sequencing libraries were pair-end sequenced by the Weill Cornell Epigenomics Core using HiSeq2500 at the depth of ~30–50 million fragments per sample. Sequencing performance was evaluated using FASTQC.
50-bp paired reads were mapped to mouse genome (mm10) with CLC Bio Genomic Workbench 7.5 software (Qiagen).
Duplicated reads with more than 5 copies were discarded. Read count tables were created using unique exon read counts and the differential expression was analyzed using EDGER (Bioconductor). Genes with the expression levels less than 1 count per million (cpm) in at least three conditions were considered non-expressing and removed from further analysis. A negative binomial generalized log-linear model was fit to read counts for each gene. A likelihood ratio tests with the null hypothesis that the pairwise contrasts of the coefficients are equal to zero was used to evaluate the significance of differences in expression between analyzed groups. Benjamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with a FDR-corrected P-value > 0.01 and less than 2-fold change were filtered out. Genes that passed the filtering were considered to be differentially expressed.
Assembly: mm10
Supplementary files format and content: tab separated values, containing raw expression values of the gene expression of the knockout mice  Xlsx file contains log transformed cpms via edgeR

source_name: mouse spleen

growth_protocol: Female C57BL/6 were obtained from Jackson Laboratory. DEF6-deficient (Def6tr/tr) mice were generated by Lexicon Pharmaceuticals by a gene-trapping strategy as previously described. Swap-70-deficient mice (Swap-70-/-) were generated as previously described. Def6tr/trSwap-70-/- (DKO) mice were generated by crossing Def6tr/tr mice with Swap-70-/- mice and have been backcrossed into C57BL/6 background for over 10 generations. Il13rα1-/- and Il13rα1-GFP mice were previously generated and were crossed with DKO mice to generate Il13rα1-/-DKO mice and Il13rα1-GFP-DKO, respectively. YaaDKO mice were generated as recently reported and then crossed with Il13rα1-/- mice to generate YaaIl13rα1-/-DKO mice.

extract_protocol:
Total RNA was extracted from mouse spleen using RNeasy Plus Mini kit (Qiagen).
SMART-Seq v3 Ultra Low Input RNA Kit (Clontech) followed by Nextera library preparation were used to prepare Illumina-compatible sequencing libraries. Quality of all RNA and library preparations were evaluated with BioAnalyser 2100 (Agilent).

value: DKO

value: spleen

tag: Sex

value: female


title: Sample_IL13R1KO-DKO_EC-MM-4573_F_DKO_ABC_Rep5

description:
Def6tr/trSwap-70-/- (DKO)
ABC_DKO replicate 4


title: select_wt_replicate1_tile10

description: Amino acid positions 305-337


title: 57KO_VA24_#4

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Libraries were sequenced on HiSeq3000/4000 using pair-end sequencing with 150 nt read length (2x150 cycle mode).
Reads were trimmed using CutAdapt v1.18
Trimmed reads were then aligned to the reference genomeGRCh38 (hg38)+KSHV Bac36 (HQ404500) chimeric genome using STAR 2.7.0f using the following option (--runThreadN 32   --genomeDir KSHV_HG38   --readFilesIn R1.trim.fastq.gz   R2.trim.fastq.gz      --readFilesCommand zcat      --limitSjdbInsertNsj 4000000  --outSAMtype BAM   SortedByCoordinate      --outSAMstrandField None   --outSAMunmapped Within      --outWigType None      --outWigStrand Stranded      --outFilterType BySJout   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --outFilterMismatchNoverLmax 0.3   --outFilterIntronMotifs RemoveNoncanonicalUnannotated   --clip3pAdapterSeq -      --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1   --sjdbFileChrStartEnd uniq.filtered.SJ.out.tab      --sjdbGTFfile KSHV_HG38.gtf   --quantMode TranscriptomeSAM   GeneCounts ).
Extraction of spliced reads was performed as a part of alignment process by STAR
Genome_build: GRCh38 (hg38)/HQ404500 (KSHV) chimera
Supplementary_files_format_and_content: TAB-delimited text file containing junction information as reported by STAR

source_name: BCBL-1 57KO (clone #6)

growth_protocol: BCBL-1 cells were maintained at exponential growth in RPMI1640 medium supplemented with 10% FBS and 1x penicillin, streptomycin, glutamine (Thermo Fisher Scientific) at 37C in the presence of 5% CO2.

extract_protocol:
The cells were harvested in TRIpure reagent (Roche, cat. no. 11667165001) for total RNA isolation followed by on-column Dnase I treatment with miRNeasy Mini kit (Qiagen, cat. No. , 217004).
Total RNA-seq libraries were prepared with Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero ribosomal RNA reduction chemistry.

treatment_protocol: To induce viral lytic replication the cells diluted to 0.5 x 10e6 cells/ml were treated with sodium salt of VA (Sigma-Aldrich) at final concentration of 1 mM for 24h. The paired untreated cells represent latently infected cell samples.

value: 1 mM VA/24 h

tag: agent

value: Kaposi's sarcoma-associated virus (KSHV)

tag: infection stage

value: lytic

tag: gender

value: male

tag: cancer type

value: primary effusion lymphoma


title: Sample_IL13R1KO-DKO_EC-MM-3717_F_DKO_ABC_Rep3

description:
Def6tr/trSwap-70-/- (DKO)
ABC_DKO replicate 2


title: CLDC9


title: select_wt_replicate1_tile9

description: Amino acid positions 273-304


title: NGFP2 (N+/-;E+/-) ES-3-D12-4673

description:
NGFP2 (N+/-;E+/-)
RNA-seq

value: GFP replaces one allele of Nanog


title: Sample_IL13R1KO-DKO_EC-MM-3234_F_DKO_ABC_Rep2

description:
Def6tr/trSwap-70-/- (DKO)
ABC_DKO replicate 1


title: 57KO_VA24_#3

tag: treatment


title: CLDC8


title: select_wt_replicate1_tile8

description: Amino acid positions 241-272


title: select_wt_replicate1_tile7

description: Amino acid positions 207-240


title: Sample_IL13R1KO-DKO_EC-ZC-5726_F_IL13R1KO-DKO_Rep2

description:
Def6tr/trSwap-70-/- (DKO)+Il13rα1--
IL13KO + DKO, replicate 2


title: 57KO_VA24_#1


title: CLDC7


title: Sample_IL13R1KO-DKO_EC-ZC-5726_F_IL13R1KO-DKO_Rep3

description:
Def6tr/trSwap-70-/- (DKO)+Il13rα1--
IL13KO + DKO, replicate 3


title: Sample_IL13R1KO-DKO_EC-ZC-5726_F_IL13R1KO-DKO_Rep1

description:
Def6tr/trSwap-70-/- (DKO)+Il13rα1--
IL13KO + DKO, replicate 1


title: CLDC6

value: NUP60-GFP::HIS3(S.kluyveri)  S288C


title: select_wt_replicate1_tile5

description: Amino acid positions 138-171


title: CLDC5


title: WT_VA24_#4

source_name: BCBL-1 WT (clone B4)


title: select_wt_replicate1_tile6

description: Amino acid positions 172-206


title: Adult_and_Pernatal.Pdpn-CD104-.mTEClo.rep1-3_HASH

description: 6 samples (3 adult and 3 perinate) were hashed together into a single 10X scRNA-seq run

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as transcript-by-cell matrices using Cell Ranger (v6.1.0, 10X Genomics).
Hash-by-cell matrices were computed using CITE-seq-count (v1.4.3).
Cells with no or multiple hashes, high mitochondrial content, or lineage markers of contaminants (i.e., T, endothelial cells) were filtered out in Seurat (v4.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: tsv files for barcodes, features and counts for gene expression and hash matrices, and txt files indicating retained cells with their hash assignment

extract_protocol:
mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, hashing with TotalSeq antibodies against H2-Kb and CD29 (adult/perinate expt) or just H2-Kb (WT/Spib/Sox8/Aire expt), and flow sorting mTECs into DMEM/10%FCS.
Purified cells were sent to the Broad Institute Genomics Platform, which performed encapsulation and RNA and hash library preparation following 10X Genomics protocols (3' v3 chemistry)

tag: strain

value: mTEClo

tag: condition

value: multiplexed sample (adult and perinatal CD104-.mTEClo)


title: WT_VA24_#2


title: CLDC4


title: CLDC3


title: select_wt_replicate1_tile4

description: Amino acid positions 104-137


title: Adult_and_Pernatal.Pdpn-CD104-.mTEClo.rep1-3_GEX

value: WT

tag: cell type


title: select_wt_replicate1_tile3

description: Amino acid positions 70-103


title: 57KO_VA24_#2


title: WT_UNINDUCED_#4

value: untreated

value: latent


title: CLDC2

tag: genotype


title: attIL12-PBMC, replicate 3, scRNAseq

city: Houston

first: Jiemiao

last: Hu

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Cener

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: OS tumor

extract_protocol:
Fresh tumor lesions were stored in RPMI medium and processed on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) three times and minced into 1–2 mm pieces. Then, added mixed Enzyme according to Tumor Dissociation Kit protocol (Miltenyi Biotec:130-095-929) and performed the association process in gentleMACS™ Dissociator (Miltenyi Biotec:130-093-235). After digestion, the samples were filtered through 40-µm sterile strainers and centrifuged at 800 × g for 5min. Subsequently, the supernatants were discarded, and the cell pellets were suspended in 1 mL phosphate buffered saline (PBS; HyClone, United States). To remove red blood cells, 2 mL of red blood cell lysis buffer (eBioscience™00-4333-57) was added, and cells were incubated at 25 °C for 10 min. The solution was then centrifuged at 500 × g for 5 min and resuspended in PBS. The samples were stained with trypan blue (Sigma, United States) and the cellular viability was evaluated under the phase contrast light microscope (Nikon, Japan).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: OS tumor

value: tumor dissociated cells


title: attIL12-PBMC, replicate 2, scRNAseq

description: 10x Genomics


title: select_wt_replicate1_tile2

description: Amino acid positions 38-69

value: yes

value: plasmid


title: WT_UNINDUCED_#3


title: CLDC1


title: KO 15 (4LL)

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

data_processing:
alignment using STAR
quantification using RSEM
Genome_build: hg38, ensembl version 79
Supplementary_files_format_and_content: output from RSEM

source_name: EP300 HPAF-II orthotopic cells - treatment with ETC-159 15m/k

growth_protocol: HPAF-II cells were injected into mice to form tumors

extract_protocol:
Illumina TruSeq
polyA enrichment

treatment_protocol: Treatment with Veh or various doses of PORCN inhibitor, ETC-159

value: EP300 KO

tag: drug

value: pancreas


title: WT_VA24_#3

value: 1 mM VA/24 h

value: Kaposi's sarcoma-associated virus (KSHV)


title: WT_UNINDUCED_#2

value: male


title: attIL12-PBMC, replicate 1, scRNAseq

description: 10x Genomics


title: nonselect_wt_replicate2_tile14

description: Amino acid positions 438-465

value: no


title: WT_VA24_#1

value: lytic

value: primary effusion lymphoma


title: control-PBMC, replicate 2, scRNAseq

description: 10x Genomics

value: control-PBMC


title: KO 5 (4R)

source_name: EP300 HPAF-II orthotopic cells - treatment with ETC-159 5m/k


title: nonselect_wt_replicate2_tile13

description: Amino acid positions 405-437


title: nonselect_wt_replicate2_tile12

description: Amino acid positions 371-404


title: Neuro2A cells, 1 mM xyloside, 48 h [HCX3]

city: Bethesda

first: Herbert

middle: M

last: Geller

state: MD

address: 9000 Rockville Pike

department: Cell and Developmental Biology

institute: NHLBI

data_processing:
Filter Contamininants - Bowtie
Generate aligned reads - TopHat2
Quantify to annotation model - Partek E/M
Filter Features/Normalize Counts - Partek Normalize
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

growth_protocol: DMEM + 10% FBS with Pen/Strep

extract_protocol:
Direct-zol RNA miniprep kit (Zymogen)
Illumina TruSeq Stranded mRNA library prep.

treatment_protocol: DMSO or xyloside applied 48h prior to harvest

tag: cell line

value: neuroblastoma


title: Neuro2A cells, 1 mM xyloside, 48 h [HCX2]

value: WT


title: KO Veh (4L)

source_name: EP300 KO HPAF-II orthotopic cells - no drug treatment

value: Veh


title: nonselect_wt_replicate2_tile11

description: Amino acid positions 338-370

tag: host yeast strain


title: Neuro2A cells, 1 mM xyloside, 48 h [HCX1]


title: KO 5 (3N)


title: Neuro2A cells, 500 nM xyloside, 48 h [LCX3]


title: nonselect_wt_replicate2_tile10

description: Amino acid positions 305-337

tag: selection


title: KO Veh (3LL)


title: KO 5 (3LR)


title: select_wt_replicate1_tile1

description: Amino acid positions 2-37

tag: molecule subtype


title: nonselect_wt_replicate2_tile9

description: Amino acid positions 273-304


title: nonselect_wt_replicate2_tile8

description: Amino acid positions 241-272


title: Neuro2A cells, 500 nM xyloside, 48 h [LCX2]


title: ChIPseq.AC7.SMARCE1.KO.SMARCE1.WT.SMARCE1

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq and ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut and Tag libraries, the CutRunTools pipeline was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million and gene count tables give raw read counts mapped to exons of given genes.

source_name: cancer cell line

growth_protocol: AC7 cells were grown in DMEM (Gibco, 11960-44), supplemented with 15% FBS, 1X GlutaMAX (Gibco, 35050-061), and 100 U/mL penicillin-streptomycin (Gibco, 15140-122). BT549 cells were grown in RPMI (Gibco, 21870-076), supplemented with 10% FBS, 1X GlutaMAX (Gibco, 35050-061), and 100 U/mL penicillin-streptomycin (Gibco, 15140-122).

extract_protocol:
ChIP-seq protocol: Cells were trypsonized, washed with room temperature PBS twice to remove trypsin, and divided into 40 million-cell aliquots.  Cells were fixed using 1% formaldehyde (Sigma Aldrich) for 10 min at 37 °C with constant stirring to keep cells in solution, and finally quenched with 125 mM glycine for 5 min at 37 °C. Quenched cells were washed with cold PBS, and stored in 10-million aliquots at −80 °C until they were used. 10 millions cells were used per epitope in subsequent chromatin immunoprecipitations. Following nuclei extraction, chromatin was sonicated using a Covaris E220 Focused-Ultrasonicator system. Sonicated chromatin was cleared by centrifugation for 10 min at 10,000 r.p.m. (15,000 g). Soluble fractions were incubated with the indicated antibodies (see antibody list) overnight at 4°C, and captured using Protein G Dynabeads (Thermo Fisher). All ChIP-seq samples received 20 ng of spike-in Drosophila chromatin (Active Motif), and 2 µg spike-in antibody (Active Motif) for normalization post sequencing. Antibody-chromatin complexes were captured with Protein G Dynabeads (Thermo Fisher), washed extensivley, eluted, and treated with RNAse A (Roche) for 30 min at 37 °C and Proteinase K (Life Technologies) for 3 h at 65 °C. ChIP DNA samples were extracted using SPRI beads (Beckman Coulter Agencourt AMP Xpure), washed with 80% Ethanol, and eluted using 0.1X TE. ChIP DNA samples were stored at -20C before library prep were initiated. All ChIP seq libraries were processed with Illumina’s NEBNext Ultra II DNA library Prep Kit (Followed standard protocols). All ChIP seq libraries were sequenced on the Illumina Next-seq 500 with 75 bp read single-end sequencing.
ATAC-seq protocol: ATAC-seq protocol was adapted from following protocol [cit] with slight modifications covered below. 50,000 - 100,000 cells were trypsonized, and washed with cold PBS to remove trypsin. When appropriate, lysing steps were carried out in 10X bulk. Cell pellets were resuspended in 50μl cold ATAC-seq resuspension buffer (RSB) containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2, supplemented with fresh NP40 (final 0.1% v/v), Tween-20 (final 0.1% v/v), Digitonin (final 0.01% v/v). Resuspended cells were incubated in lysis buffer for 3-5 min on ice. Lysis step was quenched with 1 mL of RSB supplemented with Tween-20 (final 0.1% v/v) and pelleted at 500 g for 10 min at 4°C. Cell pellets were resuspended in 50μl transposition reaction mix containing 25 μl 2X TD buffer, 2.5 μl transposase, 16.5 μl 1X PBS, 0.5 μl 1% digitonin (final 0.01% v/v), 0.5 μl 10% Tween-20 (final 0.1% v/v), and 5 μl water nuclease-free water. Transposition reaction was assembled, mixed, and incubated at 37°C for 30 min with constant shaking of 1,000 RPM on a thermomixer. To purify the tagmented DNA, Qiagen MinElute Reaction Cleanup Kit was used. Standard protocol (Buenrostro et al., 2015) [cit] with 10-12 cycles of amplification was used to amplify tagmented library. ATAC-seq libraries were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing.
RNA-seq protocol: 1,000,000 cells were trypsonized, and washed with cold PBS to remove trypsin. RNA was purified using the Qiagen RNeasy kit, and further processed in the Illumina TruSeq Stranded mRNA library prep kit with appropriate RNA spike-in to mitigate experimental errors. All RNA-seq samples were analyzed by Tapestation to assess quality, and a Qubit Fluorometer to measure concentration. All ChIP seq libraries were sequenced on the Illumina Next-seq 500 with 75 bp read single-end sequencing. For fresh frozen primary samples, 15-25 mg fresh frozen tissue samples were harvested on ice, and washed with cold PBS. Samples were immediately resuspended in cold Qiagen proprietary RLT buffer. The tissue was initially grinded with in a 1.5mL eppendorf tube with a small pestle, and further homogenized using a QiaShredder.  Remaining protocol was followed as done with RNA-seq for the cell cultures.
Cut&Tag protocol: CUT&Tag was carried out according to Epicypher’s protocol in 8-strip PCR tube with slight modifications. Concanavalin A coated magnetic beads were activated with Bead Activation Buffer containing 20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were kept at room temperature until used. 100,000 cells were trypsonized, washed with cold PBS to remove trypsin. Cells were lysed sing cold Nuclear Extraction Buffer containing 20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor (Roche). Nuclei samples were incubated with activated Concanavalin A beads at room temperature for  10 min. The nuclei-Concanavalin A bead complex was resuspended in Antibody 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), 0.01% Digitonin, and 500 ng of primary antibody. Following overnight incubation at 4°C, primary antibody was removed, and beads were washed once with Digitonin 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. Secondary antibody were added, and incubated with nuclei-Concanavalin A bead complex for 1 hr at room temperature. Nuclei-Concanavalin A bead complex were washed with Digitonin 150 Buffer twice before resuspensinon in 50uL cold Digitonin300 Buffer containing 20 mM HEPES, pH 7.5, 300 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. 2.0 µL CUTANA pAG-Tn5 (Epicypher) was added to each sample, and in incubated on a nutator for 1 hr at room temperature. Following incubation, beads were washed with cold Digitonin300 Buffer. Targeted chromatin tagmentation and library amplification were carried out exactly according to Epicypher’s protocol.
ChIP-sequencing libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). BT549 cells were lentivirally infected with either Empty vector, GFP, or full length SMARCE1 for 24h and then selected with blasticidin for 5-7 days. Cells were harvested 7 days post-infection. For compound treatments, cells were seeded in 6 well-plate or 10cm dishes depending on the experimental setup. Cells were treated at indicated concentrations over 5-7 days with DMSO controls. Media containing fresh compounds was added on day 3. Cells were harvested for genomics experiments using standard protocol.

tag: experimental condition

value: lentivirus:full length SMARCE1

tag: chip antibody

value: Rabbit anti-BAF57/SMARCE1 ; ab70540


title: ChIPseq.AC7.SMARCE1.KO.SMARCE1.WT.SMARCA4

value: Rabbit anti-SMARCA4 (EPNCIR111A); ab110641


title: control-PBMC replicate 3, scRNAseq

description: 10x Genomics

value: OS tumor

value: tumor dissociated cells


title: Neuro2A cells, 500 nM xyloside, 48 h [LCX1]


title: WT_UNINDUCED_#1

value: untreated

value: latent


title: nonselect_wt_replicate2_tile7

description: Amino acid positions 207-240

value: plasmid


title: WT 15 (2N)

source_name: WT HPAF-II orthotopic cells - treatment with ETC-159 15m/k

value: pancreas


title: KO 15 (3L)

value: EP300 KO


title: ChIPseq.AC7.SMARCE1.KO.SMARCE1.WT.Input


title: Neuro2A cells, DMSO control [DMSO3]

value: DMSO


title: KO Veh (4LR)


title: nonselect_wt_replicate2_tile6

description: Amino acid positions 172-206

value: no


title: WT 5 (2LR)

source_name: WT HPAF-II orthotopic cells - treatment with ETC-159 5m/k


title: nonselect_wt_replicate2_tile5

description: Amino acid positions 138-171


title: control-PBMC, replicate 1, scRNAseq

description: 10x Genomics


title: WT Veh (2R)

source_name: WT HPAF-II orthotopic cells - no drug treatment


title: Neuro2A cells, DMSO control [DMSO2]


title: ChIPseq.AC7.SMARCE1.KO.SMARCE1.WT.H3K27ac

value: Rabbit anti-Histone H3 (acetyl K27); ab4729


title: Neuro2A cells, DMSO control [DMSO1]


title: nonselect_wt_replicate2_tile4

description: Amino acid positions 104-137


title: ChIPseq.AC7.SMARCE1.KO.GFP.SMARCE1

value: lentivirus:full lengh GFP


title: WT 5 (2L)


title: nonselect_wt_replicate2_tile3

description: Amino acid positions 70-103


title: ChIPseq.AC7.SMARCE1.KO.GFP.SMARCA4


title: HFD_WTE-rep3

city: Tianjin

first: Jiayuan

last: Chen

state: State...

address: Heping

institute: Tianjin Medical University

data_processing:
Trim_galore!-0.6.6 was used to trim adaptors. Salmon-1.4.0 was used to align transcript sequences obtained from RNA-seq to the gencode M25 transcript sequences and calculate the read count aligned to the genes.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count and TPM

source_name: liver

extract_protocol: Total RNA isolation was performed using TRIzol (Invitrogen) from whole liver. Total RNAs from kidney tissues were subjected to Oligo dT selection and adaptor ligation.

value: high fatty diet + white tea extract

value: liver


title: ChIPseq.AC7.SMARCE1.KO.GFP.Input


title: nonselect_wt_replicate2_tile2

description: Amino acid positions 38-69


title: WT Veh (1N)

value: WT

value: Veh


title: HFD_WTE-rep2


title: nonselect_wt_replicate2_tile1

description: Amino acid positions 2-37


title: WT 5 (1LL)


title: HFD_WTE-rep1


title: HFD-rep3

value: high fatty diet


title: ATACseq.AC7.SMARCE1.KO.ATAC.SMARCE1.WT.Rep2

value: lentivirus:full length SMARCE1


title: nonselect_wt_replicate1_tile14

description: Amino acid positions 438-465


title: WT 15 (1LR)


title: nonselect_wt_replicate1_tile13

description: Amino acid positions 405-437


title: ATACseq.AC7.SMARCE1.KO.ATAC.GFP.Rep2


title: HFD-rep2


title: nonselect_wt_replicate1_tile12

description: Amino acid positions 371-404


title: Colon_KO3 [Bisulfite-seq]

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

data_processing:
Basecalling with: bcl2fastq 2.20.0.422
Preprocessing, read trimming: Trimmomatic 0.39
Preprocessing, quality filtering: Trimmomatic 0.39
BS-mapping: BSMAP 2.5
Computation of methylation ratios: methratio.py (part of bsmap package)
Assembly: mm9
Supplementary files format and content: bedGraph-format containing the genomic methylation ratios and coverage values of the respective sample

source_name: Colon

extract_protocol:
We followed a previously published protocol to isolate intestinal crypts [PMID: 23097115]. Briefly, the small intestine (Jejunum) was flushed with ice-cold PBS then cut open longitudinally. The Jejunum was minced into small pieces in cold PBS (2-5 mm) and then incubated for 30 min at 4 °C in PBS containing 2 mM EDTA. Intestinal fragments were then transferred into cold PBS and the villi fraction was mechanically isolated by shaking. Then the intestinal fragments were transferred into fresh cold PBS and the crypts fraction was mechanically isolated by vigorously shaking. This step was repeated further two times to recover the crypts. Crypts fractions were then combined and passed through a 70 µm cell strainer. The combined fractions of crypts were then washed in PBS, centrifuged at 300g for 3 min, and stored at -80°C for DNA extraction. Genomic DNA was extracted from intestinal epithelial crypts using DNA blood and tissue kit (cat. no. 69504, Qiagen), according to the manufacturer's instructions.
Accel-NGS Methyl-Seq DNA

value: Colon epithelial cells

tag: age

value: 11 weeks


title: HFD-rep1


title: nonselect_wt_replicate1_tile11

description: Amino acid positions 338-370


title: WT Veh (1L)


title: Colon_KO2 [Bisulfite-seq]


title: ATACseq.AC7.SMARCE1.KO.ATAC.GFP.Rep1


title: Bulk RNA-Seq_P3 lung peripheral_Pdgfra+ cells

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

description: Control lungs

data_processing:
Remove adaptor with 'trim_galore';
align the reading to genome with 'Hisat2';
sort the SAM file and convert it to BAM file;
create table counts with 'featurecounts';
generate DEG table with DeSeq2 in R;
Genome_build: mm10.

source_name: Postnatal lung

extract_protocol: Cells were sorted from PdgfraH2BGFP lung directly into Trizol buffer, and the RNAs were extracted with the RNeasy Mini Kit (Qiagen).

value: Sorted peripheral lung PDGFRa+ cells

tag: Stage

value: Postnatal day 3


title: ChIPseq.AC7.SMARCE1.KO.GFP.H3K27ac

city: Boston


title: WT 15 (1RR)


title: nonselect_wt_replicate1_tile10

description: Amino acid positions 305-337

source_name: Yeast cells

value: plasmid


title: ND-rep1

value: normal diet


title: RNAseq.CCM.RNA.SMARCE1.Null.Tumor.Sample3

description: genotype: SMARCE1 loss

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq and ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut and Tag libraries, the CutRunTools pipeline was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.bw: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million.
Supplementary_files_format_and_content: *.ReadsPerGene.txt: Gene count tables give raw read counts mapped to exons of given genes.

source_name: Primary meningioma tumor sample

extract_protocol:
ChIP-seq protocol: Cells were trypsinized, washed with room temperature PBS twice to remove trypsin, and divided into 40 million-cell aliquots. Cells were fixed using 1% formaldehyde (Sigma Aldrich) for 10 min at 37 °C with constant stirring to keep cells in solution, and finally quenched with 125 mM glycine for 5 min at 37 °C. Quenched cells were washed with cold PBS, and stored in 10-million aliquots at −80 °C until they were used. 10 millions cells were used per epitope in subsequent chromatin immunoprecipitations. Following nuclei extraction, chromatin was sonicated using a Covaris E220 Focused-Ultrasonicator system. Sonicated chromatin was cleared by centrifugation for 10 min at 10,000 r.p.m. (15,000 g). Soluble fractions were incubated with the indicated antibodies (see antibody list) overnight at 4°C, and captured using Protein G Dynabeads (Thermo Fisher). All ChIP-seq samples received 20 ng of spike-in Drosophila chromatin (Active Motif), and 2 µg spike-in antibody (Active Motif) for normalization post sequencing. Antibody-chromatin complexes were captured with Protein G Dynabeads (Thermo Fisher), washed extensively, eluted, and treated with RNase A (Roche) for 30 min at 37 °C and Proteinase K (Life Technologies) for 3 h at 65 °C. ChIP DNA samples were extracted using SPRI beads (Beckman Coulter Agencourt AMP Xpure), washed with 80% Ethanol, and eluted using 0.1X TE. ChIP DNA samples were stored at -20C before library prep were initiated. All ChIP seq libraries were processed with Illumina’s NEBNext Ultra II DNA library Prep Kit (Followed standard protocols). All ChIP seq libraries were sequenced on the Illumina Next-seq 500 with 75 bp read single-end sequencing.
ChIP-sequencing libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols.
ATAC-seq protocol: ATAC-seq protocol was adapted from following protocol [cit] with slight modifications covered below. 50,000 - 100,000 cells were trypsinized, and washed with cold PBS to remove trypsin. When appropriate, lysing steps were carried out in 10X bulk. Cell pellets were resuspended in 50μl cold ATAC-seq resuspension buffer (RSB) containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2, supplemented with fresh NP40 (final 0.1% v/v), Tween-20 (final 0.1% v/v), Digitonin (final 0.01% v/v). Resuspended cells were incubated in lysis buffer for 3-5 min on ice. Lysis step was quenched with 1 mL of RSB supplemented with Tween-20 (final 0.1% v/v) and pelleted at 500 g for 10 min at 4°C. Cell pellets were resuspended in 50μl transposition reaction mix containing 25 μl 2X TD buffer, 2.5 μl transposase, 16.5 μl 1X PBS, 0.5 μl 1% digitonin (final 0.01% v/v), 0.5 μl 10% Tween-20 (final 0.1% v/v), and 5 μl water nuclease-free water. Transposition reaction was assembled, mixed, and incubated at 37°C for 30 min with constant shaking of 1,000 RPM on a thermomixer. To purify the tagmented DNA, Qiagen MinElute Reaction Cleanup Kit was used. Standard protocol (Buenrostro et al., 2015) [cit] with 10-12 cycles of amplification was used to amplify tagmented library. ATAC-seq libraries were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing.
ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).
RNA-seq protocol: 1,000,000 cells were trypsinized, and washed with cold PBS to remove trypsin. RNA was purified using the Qiagen RNeasy kit, and further processed in the Illumina TruSeq Stranded mRNA library prep kit with appropriate RNA spike-in to mitigate experimental errors. All RNA-seq samples were analyzed by Tapestation to assess quality, and a Qubit Fluorometer to measure concentration. All RNA seq libraries were sequenced on the Illumina Next-seq 500 with 75 bp read single-end sequencing. For fresh frozen primary samples, 15-25 mg fresh frozen tissue samples were harvested on ice, and washed with cold PBS. Samples were immediately resuspended in cold Qiagen proprietary RLT buffer. The tissue was initially grinded with in a 1.5mL eppendorf tube with a small pestle, and further homogenized using a QiaShredder. Remaining protocol was followed as done with RNA-seq for the cell cultures.
RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols.
Cut&Tag protocol: CUT&Tag was carried out according to Epicypher’s protocol in 8-strip PCR tube with slight modifications. Concanavalin A coated magnetic beads were activated with Bead Activation Buffer containing 20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were kept at room temperature until used. 100,000 cells were trypsinized, washed with cold PBS to remove trypsin. Cells were lysed sing cold Nuclear Extraction Buffer containing 20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor (Roche). Nuclei samples were incubated with activated Concanavalin A beads at room temperature for 10 min. The nuclei-Concanavalin A bead complex was resuspended in Antibody 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), 0.01% Digitonin, and 500 ng of primary antibody. Following overnight incubation at 4°C, primary antibody was removed, and beads were washed once with Digitonin 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. Secondary antibody were added, and incubated with nuclei-Concanavalin A bead complex for 1 hr at room temperature. Nuclei-Concanavalin A bead complex were washed with Digitonin 150 Buffer twice before resuspension in 50uL cold Digitonin300 Buffer containing 20 mM HEPES, pH 7.5, 300 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. 2.0 µL CUTANA pAG-Tn5 (Epicypher) was added to each sample, and in incubated on a nutator for 1 hr at room temperature. Following incubation, beads were washed with cold Digitonin300 Buffer. Targeted chromatin tagmentation and library amplification were carried out exactly according to Epicypher’s protocol.

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al. 2012). BT549 cells were lentivirally infected with either Empty vector, GFP, or full-length SMARCE1 for 24h and then selected with blasticidin for 5-7 days. Cells were harvested 7 days post-infection. For compound treatments, cells were seeded in 6 well-plate or 10cm dishes depending on the experimental setup. Cells were treated at indicated concentrations over 5-7 days with DMSO controls. Media containing fresh compounds was added on day 3. Cells were harvested for genomics experiments using standard protocol.

value: Primary meningioma tumor

value: SMARCE1 loss

tag: ngs approach

value: RNA-seq


title: ND-rep2


title: nonselect_wt_replicate1_tile9

description: Amino acid positions 273-304

value: no


title: RNAseq.CCM.RNA.SMARCE1.Null.Tumor.Sample2

description: genotype: SMARCE1 loss


title: ATACseq.AC7.SMARCE1.KO.ATAC.SMARCE1.WT.Rep1


title: Colon_KO1 [Bisulfite-seq]


title: Colon_WT3 [Bisulfite-seq]

value: wild type


title: Colon_WT1 [Bisulfite-seq]


title: nonselect_wt_replicate1_tile8

description: Amino acid positions 241-272


title: RNAseq.CCM.RNA.Normal.Brain.Tissue.Sample1

description: genotype: wild type


title: nonselect_wt_replicate1_tile7

description: Amino acid positions 207-240


title: nonselect_wt_replicate1_tile5

description: Amino acid positions 138-171


title: nonselect_wt_replicate1_tile6

description: Amino acid positions 172-206


title: Colon_WT2 [Bisulfite-seq]


title: nonselect_wt_replicate1_tile4

description: Amino acid positions 104-137


title: RNAseq.CCM.RNA.SMARCE1.Null.Tumor.Sample4

description: genotype: SMARCE1 loss


title: SC of  cKO mouse, biol rep 2

city: Beijing

first: Feng

address: 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

data_processing:
The sequencing quality were assessed with FastQC  and then low quality data were filtered using NGSQC   (v2.3.3)(v0.11.5)
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters
The clean reads were then aligned to mouse genome using HISAT2 (v2.1.0) with default parameters.
The processed reads from each sample were aligned using HISAT2 against the mouse genome.
The gene expression analyses were performed with String Tie (v1.3.3b). DE Seq (v1.28.0) was used to analyze the DEGs
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary Sertoli cells

growth_protocol: The primary Sertoli cells were maintained in DMEM/F12 containing 10% FBS, 100 U/ml penicillin, 100 ug/ml streptomycin and 0.25 μg/ml EGF in humidified atmosphere with 5% CO2 at 34℃

extract_protocol:
RNA were harvested using TRIzol (T9424; Sigma-Aldrich). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Library Quantification kit (KAPA Biosystems; South Africa)

treatment_protocol: The Sertoli cells of cKO mice are conditional deletion of Arhgef15 gene

value: primary Sertoli cells

value: Arhgef15 cKO

value: knockout Arhgef15


title: RNAseq.CCM.RNA.Normal.Brain.Tissue.Sample2

description: genotype: wild type


title: L3_XX_DsxM_gof/lof_gonad_rep4

first: Brian

last: Oliver

address: 50 South Drive

department: LCDB

institute: NIDDK, NIH

description:
Pool of 25 ovaries transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
C12_XX_DsxD_4

data_processing:
We processed the data by using a RNA-Seq work flow that is developed by LCDB core (https://github.com/lcdb/lcdb-wf). Briefly we de-multiplexd and convert BCL to FASTQ format. We removed the adaptors using Cutadapt. We created a reference using Flybase 6.32 and aligned reads with Hisat2 using default setting. We generated both transcript level counts and featureCounts using Salmon and featureCounts.
Assembly: Flybase 6.32
Supplementary files format and content: FeatureCount

organism: Drosophila melanogaster

source_name: ovary transformed into testes

growth_protocol: We followed the Growth protocol as published in GSE115478. Briefly, we grew all the flies on Fly food A (LabExpress Ann Arbor, MI) in constant light at 25°C and 60% relative humidity. We collected eggs every 8-16 hr. from six mated females and allowed larvae to develop until the late third instar larval stage. For precise larval staging, we fed second and third instar larvae with water/yeast paste containing 0.5 mg/ml Sulforhodamine B sodium salt (Sigma-Aldrich, Cat. No. S1402-25G. St. Louis, MO). We selected larvae with mostly cleared foreguts that were immobilized, but that had no extended anterior spiracles.

extract_protocol:
We followed the Extraction Protocol from GSE115478. Briefly, we dissected larvae in 1XPBS at 22°C (Gibco Life Technologies, Carlsbad, CA) and separated the fatbody from the gonads. In order to separate the fatbody, we treated the gonads with 0.075 mg/ml Papain (Sigma-Aldrich, St. Louis, MO) and 0.075 mg/ml Collagenase enzyme (Sigma-Aldrich, St. Louis, MO) mixed in PBS in a 1.5ml Eppendorf tube for 3 min with gentle vertexing by flicking the tube with a forefinger. We washed the gonads twice with 1X PBS after decanting the floating fatbody cells. We collected each sample in a 350 μl RLT buffer (Qiagen, Cat. No. 79216. Valencia, CA), vortexed two times for 30 sec with a 30 sec interval and quickly frozen in a dry ice ethanol bath and stored at -80°C until RNA extraction. Using the RNeasy 96 kit, we extracted total RNA (Qiagen, Cat. No. 1019545. Valencia, CA) by following the manufacturer’s protocol. We used Quant-iT RiboGreen quantification kit (Life Technologies, Cat. No. R11490. Carlsbad, CA) quantified the RNA and stored it at -80°C until the library preparation.
We used 200 ng of total RNA and performed RNA-seq library preparation following Lee et al (doi:10.1101/032920 and Gene Expression Omnibus GSE73920). Briefly, PolyA+ selection was done using Dynabeads Oligo(dT)25 (Life technologies, Grand Island, NY), mRNA was fragmented, and RT was performed with the second strand synthesis by incorporating dUTPs. We used External RNA control consortium spike-ins pools 78A and 78B (SRM2374, Zook et al., 2012. PMID: 22859977) transcribed from standard reference. We used barcoded adaptors for indexing the libraries (Qiagen, 98 TruSeq v2 kit barcoded adaptors, Valencia, CA). We sequenced eight multiplexed libraries using a single-ended 50 bp strategy on one lane using a HiSeq Illumina 2500 (Illumina, San Diego, CA).

value: female transformed into male

value: Late third instar larval stage:immobilized, partial gut clearance as dyed yeast paste exist partly in midgut and hindgut, prior to anterior spiracle eversion.


title: L3_XY_tra_gof_gonad_rep4

description:
Pool of 25 ovaries sex transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
D8_XY_U2af_4

source_name: testes transformed into ovaries

value: male transformed into female


title: L3_XX_DsxM_gof/lof_gonad_rep2

description:
Pool of 25 ovaries transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
C10_XX_DsxD_2


title: nonselect_wt_replicate1_tile2

description: Amino acid positions 38-69

data_processing:
Library strategy: Tile-Seq
Libraries were sequenced on a NextSeq 550 instrument (Illumina) and base called using the instriment's Real Time Analysis software.
Sequencing reads were converted to fastq format and demultiplexed using BaseSpace Sequence Hub.
Reads were alligned and variants called using the TileSeq mutation count pipeline (https://github.com/RyogaLi/tileseq_mutcount) version 0.5.9
Variant calls from the TileSeq mutation count pipeline were then used for calling protein-level amino acid changes and for calculating the enrichment of variants using the TileSeqMave pipeline (https://github.com/jweile/tileseqMave) version 0.6.0.9000
reference sequence: sequence.txt on the series record contains the sequence used for read alignment.

extract_protocol:
For each condition (select/nonselect, library/wt, replicate1/replicate2), 9 OD units of cells were used for plasmid DNA extraction using the ChargeSwitch Plasmid Yeast Mini kit (Invitrogen) according to the manufacturer's instructions.
The three regional libraries spanning the GCK sequence (aa 2-171, 172-337, 338-466) were constructed by pooled mutagenesis using NNK-degenerate oligos.


title: RNAseq.CCM.RNA.NF2.Null.Tumor.Sample4

description: genotype: NF2 loss

value: NF2 loss


title: L3_XX_DsxM_gof/lof_gonad_rep3

description:
Pool of 25 ovaries transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
C11_XX_DsxD_3


title: SC of  WT mouse, biol rep 2

value: WT

value: untreated


title: L3_XY_tra_gof_gonad_rep1

description:
Pool of 25 ovaries sex transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
D5_XY_U2af_1


title: SC of  cKO mouse, biol rep 1


title: RNAseq.CCM.RNA.SMARCE1.Null.Tumor.Sample1

description: genotype: SMARCE1 loss


title: SC of  cKO mouse, biol rep 3


title: L3_XY_tra_gof_gonad_rep3

description:
Pool of 25 ovaries sex transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
D7_XY_U2af_3


title: RNAseq.CCM.RNA.NF2.Null.Tumor.Sample3

description: genotype: NF2 loss


title: SC of  WT mouse, biol rep 3


title: RNAseq.CCM.RNA.NF2.Null.Tumor.Sample6

description: genotype: NF2 loss


title: nonselect_wt_replicate1_tile3

description: Amino acid positions 70-103


title: SC of  WT mouse, biol rep 1


title: L3_XX_tra_lof_gonad_rep4

description:
Pool of 25 ovaries transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
C4_XX_tra_4


title: select_library_replicate2_tile14

description: Amino acid positions 438-465

value: yes


title: nonselect_wt_replicate1_tile1

description: Amino acid positions 2-37

value: plasmid


title: L3_XX_tra_lof_gonad_rep3

description:
Pool of 25 ovaries transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
C3_XX_tra_3


title: MS1, Pspc1 kd

city: Taipei

first: Yuh-Shan

last: Jou

state: --- Select a state ---

address: No.128,Sec. 2, Academia Rd. Nankang

department: Institute of biomedical science

country: Taiwan

institute: Academia Sinica

data_processing:
Trimmomatic,version:0.39
Hisat2, version: 2.1.0
Featurecount, version:2.0.0
DESeq,version:1.39.0
Assembly: mm10
Supplementary files format and content: Normalized counts from DESeq with ENSEMBL gene ID

extract_protocol:
Total RNA isolated from MS1 cells was extracted by Trizol reagent and recommened protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) was applied to construct library and follow manufacturer’s recommendations. Poly-A RNA were be enriched by oligo-dT beads, fragmentated and produced first strand cDNA.

value: endothelial cells

value: Pspc1 knockdown

value: Lentivirus with shRNA targeting to Pspc1


title: RNAseq.CCM.RNA.NF2.Null.Tumor.Sample2

description: genotype: NF2 loss

value: Primary meningioma tumor

value: RNA-seq


title: RNAseq.CCM.RNA.NF2.Null.Tumor.Sample7

description: genotype: NF2 loss


title: select_library_replicate2_tile13

first: Sarah

institute: University of Copenhagen

description: Amino acid positions 405-437


title: L3_XY_tra_gof_gonad_rep2

description:
Pool of 25 ovaries sex transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
D6_XY_U2af_2


title: MS1, LacZ

value: wt

value: Lentivirus with shRNA targeting to LacZ


title: RNAseq.CCM.RNA.NF2.Null.Tumor.Sample5

description: genotype: NF2 loss


title: select_library_replicate2_tile12

description: Amino acid positions 371-404


title: RNAseq.CCM.RNA.KLF4.TRAF7.Null.Tumor.Sample2

description: KLF4_TRAF7 missense mutation

value: KLF4_TRAF7 missense mutation


title: L3_XX_DsxM_gof/lof_gonad_rep1

description:
Pool of 25 ovaries transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
C9_XX_DsxD_1


title: RNAseq.CCM.RNA.KLF4.TRAF7.Null.Tumor.Sample1

description: KLF4_TRAF7 missense mutation


title: select_library_replicate2_tile11

description: Amino acid positions 338-370


title: L3_XX_tra_lof_gonad_rep2

description:
Pool of 25 ovaries transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
C2_XX_tra_2


title: L3_control_testes_rep4

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
A8_TCP_4

source_name: testes

value: male


title: Liver, Experimental Group, HGPP1

city: Shanghai

first: Siran

last: Yue

address: CaiLun Road 1200,

institute: Shanghai University of traditional Chinese medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by fastp v0.20.1 for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm38 whole genome using STAR v2.7.7a with default parameters.Annotation file of Ensembl release 102  transcriptome gff file was provided to STAR as gene model.
raw reads count aligned to each gene were calculated by FeatureCount v2.0.0
Assembly: mm38
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Liver

extract_protocol:
RNA was isolated from 1-2x10^6 cells stored in TRIzol reagent following manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HGPP treatment

value: Liver

value: MCD + HGPP


title: Liver, Experimental Group, HGPP3


title: select_library_replicate2_tile10

city: Copenhagen N

last: Gersing

address: Ole Maaløes vej 5

description: Amino acid positions 305-337


title: L3_XX_tra_lof_gonad_rep1

description:
Pool of 25 ovaries transformed into testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
C1_XX_tra_1

value: female transformed into male

value: Late third instar larval stage:immobilized, partial gut clearance as dyed yeast paste exist partly in midgut and hindgut, prior to anterior spiracle eversion.


title: L3_control_testes_rep3

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
A7_TCP_3


title: Liver, Experimental Group, HGPP2

value: WT


title: RNAseq.BT549.RNA.SMARCE1.WT.Rep2

description: lentivirus: full length SMARCE1

tag: lentivirus

value: full-length SMARCE1


title: select_library_replicate2_tile9

description: Amino acid positions 273-304

value: yes


title: Liver, Model Group, MCD3

tag: treatment

value: MCD + CMC-Na


title: L3_control_testes_rep2

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
A6_TCP_2


title: select_library_replicate2_tile8

description: Amino acid positions 241-272

value: plasmid


title: Liver, Model Group, MCD2

tag: strain


title: RNAseq.CCM.RNA.NF2.Null.Tumor.Sample1

description: genotype: NF2 loss

value: NF2 loss


title: L3_control_testes_rep1

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
A5_TCP_1

tag: condition


title: select_library_replicate2_tile7

description: Amino acid positions 207-240


title: RNAseq.BT549.RNA.GFP.Rep2

description: genotype: wild type

value: wild type


title: select_library_replicate2_tile6

description: Amino acid positions 172-206


title: Liver, Model Group, MCD1


title: RNAseq.BT549.RNA.SMARCE1.WT.Rep1

description: lentivirus: full length SMARCE1


title: L3_control_ovaries_rep4

description:
Pool of 25 ovaries with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
A4_OCP_4

source_name: ovaries

value: female


title: RNAseq.BT549.RNA.GFP.Rep1

description: genotype: wild type

value: RNA-seq


title: select_library_replicate2_tile5

description: Amino acid positions 138-171


title: Liver, Normal Control, MCS3

value: MCS + CMC-Na


title: RNAseq.AC7.RNA.WT.DMSO.Rep2b

description: genotype: wild type_treatment: DMSO

value: DMSO


title: RNAseq.AC7.RNA.WT.DMSO.Rep2

description: genotype: wild type_treatment: DMSO


title: L3_control_ovaries_rep3

description:
Pool of 25 ovaries with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
A3_OCP_3


title: L3_control_ovaries_rep2

description:
Pool of 25 ovaries with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
A2_OCP_2


title: Liver, Normal Control, MCS1


title: select_library_replicate2_tile3

description: Amino acid positions 70-103


title: RNAseq.AC7.RNA.WT.DMSO.Rep1b

description: genotype: wild type_treatment: DMSO