title: clone6_k9me3_R2 (Cut&Run)

value: undifferentiated pleomorphic sarcoma cell line


title: Whole brain, 6m, rep 4 [Illumina]

status: Public on Mar 13 2024

type: SRA

city: Göttingen

first: Nisha

last: Hemandhar Kumar

address: Humboldtallee 23

department: Institute for Neuro and Sensory Physiology

country: Germany

institute: University Medical Center Goettingen

library_source: transcriptomic

data_processing:
Trimming for adapters using trimgalore v0.4.11
RNA-seq reads were aligned to the GRCm39.103 genome assembly using hisat2 v2.1.0
Assembly: GRCm39.103

molecule: total RNA

organism: Mus musculus

source_name: Whole brain

extract_protocol:
RNA was extracted from a total of 8 biological samples, corresponding to 4 young-adult samples (6-month, brain hemisphere, from 4 males), 4 aged (24-month, brain hemisphere, from 4 males). Raw data were procured inNovoSeq 6000 sequencing
NEBNext Ultra II directional polyA+

tag: tissue

value: Whole brain

tag: Sex

value: Male

tag: age

value: 6 months


title: Hippocampus, ID18_S8

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
Raw sequencing reads were aligned to the rat reference genome (rn6) using HISAT2 (Kim et al., 2019).
MACS was utilized to assess sites of chromatin accessibility in ATAC-seq samples
diffReps (Shen et al., 2013) was run on the processed samples to find differential sites for the comparisons to the IS control group (ID, IDch, or ISch vs IS).
The atacseq.txt and chipseq.txt files are the annotation peak lists obtained from MACS software. The fold change for each peak is computed as the ratio of the read count in the peak to the maximum of the local and global lambda values.
Local Lambda: MACS2 computes a local lambda value for each peak, which is a measure of the local background noise around the peak.
Global Lambda: MACS2 also computes a global lambda value, which is a measure of the background noise across the entire genome.
Assembly: rn6
Supplementary files format and content: tab-delimited text peaks file

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Hippocampi were bisected, flash-frozen in liquid nitrogen, and stored at -80°C. For ATAC-seq, nuclei were isolated from tissue using iodixanol gradient and DNA was transposed with Tn5 transposase followed by MinElute Reaction Cleanup kit purification. DNA was quantified using the PicoGreen dsDNA Assay Kit.
ATAC-seq library preparation was performed in accordance with the ATAC-seq protocol as described by Buenrostro et al. (2015). Libraries were assessed for quality using electrophoresis on an Agilent Bioanalyzer (Agilent) and size-selected for 200~800 bp fragments.

value: Brain

tag: tissue region

value: Hippocampus

tag: group

tag: maternal treatment

value: ID

tag: offspring age


title: P-G04

city: qingdao

first: xuechao

last: liu

address: jiangsuroad

country: China

institute: Affiliated Hospital of Qingdao University

description: HiSeq X Ten

library_source: transcriptomic single cell

data_processing:
Quality control
Cell type identification and clustering analysis were conducted using the Seurat program (v.3.0.1), an R package for scRNA-seq analysis.
The UMI count tables of each cellular barcode were loaded into R with the read.table function.
Assembly: mm10
Supplementary files format and content: expression matrix file using RNA raw count

organism: Homo sapiens

source_name: gastrointestinal stromal tumors

extract_protocol:
Single-cell suspensions with 1×105 cells/mL in concentration in PBS (HyClone) were prepared.
The scRNA-seq libraries were constructed using the GEXSCOPER Single-Cell RNA Library Kit (Singleron Biotechnologies), according to the manufacturer's protocol

value: gastrointestinal stromal tumors

tag: cell type

value: Spindle cell

tag: genotype

value: KIT exon 11

tag: treatment

value: First-line


title: SAA-/- Pooled Tumor 1, scRNAseq

city: Philadelphia

first: Jesse

last: Lee

state: PA

address: South Pavilion, Room 8-326

institute: University of Pennsylvania

description: 10X Genomics

data_processing:
Data was demultiplexed and aligned using the Cell Ranger pipeline (10x Genomics, v.6.1.2).
Datasets were processed using Seurat (v.4.3.0) in R (v.4.2.2) and filtered to include cells with a minimum of 200 genes and genes expressed in greater than 3 cells.
Assembly: mm10
Supplementary files format and content: feature count matrix exported as csv sheet with raw counts per UMI

source_name: Tumor

growth_protocol: Cell lines were cultured in DMEM (Corning) supplemented with 10% FBS (VWR), 83 μg/mL gentamicin (Thermo Fisher Scientific), and 1% GlutaMAX (Thermo Fisher Scientific) at 37°C, 5% CO2

extract_protocol:
Tumors from Saa+/+ and Saa-/- mice were processed and pooled for scRNAseq (n=4 mice pooled to n=2 per condition). Following tumor digestion, live cells were isolated using a dead cell removal kit (Miltenyi Biotec #130-090-101) according to manufacturer’s instructions.
Single cell libraries were generated using the 10x Genomics Chromium Single Cell 3’ GEM Kit per manufacturer’s instructions

value: Tumor

tag: cell line

value: KPC derived Tcelllow PDAC


title: clone6_k9me3_R1 (Cut&Run)

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Cut and run reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the SEACR software.
Assembly: hg38
Supplementary files format and content: bigwig files normalized to read depth
Supplementary files format and content: bed files generated by SEACR
Library strategy: CUT&RUN

extract_protocol:
Cells were collected by trypsin. Washed by PBS and followed the protocol from EpiCypher.
Libraries were generated using NEBNext Ultra II kits.

value: Atrx knockout

tag: chip antibody


title: CD6_O2R17

city: Waltham

first: Susan

middle: Dina

last: Ghiassian

address: 500 Totten Pond Rd, 6th Floor

institute: Scipher Medicine

description: female CD patient; aged 40 years

data_processing:
Sequence reads were aligned to GRCh38 using STAR alignment software.
Gene expression was calculated (in fragments per kilobase of transcript per million mapped reads) using the RSEM software package.
Assembly: hg38
Supplementary files format and content: Comma-delimited text file includes FPKM values for each sample.

molecule: polyA RNA

source_name: colon

growth_protocol: Biopsy tissues were cultured in triplicate in 12-well plates containing a modified Connaught Medical Research Laboratory (CMRL)–based cell-culture media at 37 °C, 5% CO2.

extract_protocol:
RNA was extracted by proprietary process by REPROCELL. Briefly, tissue lysates were treated with Proteinase K. NA was eluted with an elution solution of concentration ≥20 ng/μL. The lysates were then centrifuged, ethanol was added to the supernatant, and the solutions were loaded onto spin-columns. DNase digestion was performed on column to remove any traces of DNA and RNA.
RNA libraries for 150bp paired-end sequencing were prepared by an mRNA library prep kit for sequencing by an Illumina Novaseq 6000.

treatment_protocol: Culture plates were incubated in media with either test compounds (10 uM) or vehicle. Tissues were treated with Staphylococcus enterotoxin B (List Biological Laboratories, Campbell, CA) to stimulate inflammatory cytokine secretion.

value: colon

tag: age (years)

value: Female

tag: ethnicity

value: Unknown (not stated)

tag: blood pressure

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking

tag: drinking

tag: major reason_for_surgery

tag: medical history

value: Crohns, BMI 26.5

tag: acute medication

tag: chronic medication

value: Adalimumab, coleclaciferol, hyoscine butylbromide, omeprazole, prednisilone


title: clone6_k27ac_R3 (Cut&Run)

tag: cell type

value: undifferentiated pleomorphic sarcoma cell line

value: H3K27Ac (Active motif,39133)


title: WT Pooled Tumor 1, scRNAseq

description: 10X Genomics

tag: tissue

tag: genotype

value: WT


title: Hippocampus, ID17_S7

value: Brain

tag: tissue region

value: Hippocampus

tag: group

tag: maternal treatment

tag: offspring age


title: WT Pooled Tumor 2, scRNAseq

description: 10X Genomics

tag: cell line


title: clone6_k27ac_R2 (Cut&Run)

tag: chip antibody


title: M-P02

description: HiSeq X Ten

value: gastrointestinal stromal tumors

value: KIT exon 11 and exon 17

tag: treatment


title: Hippocampus, ID16_S6

value: ID


title: CK6

city: Hefei

first: Kan

last: He

address: 111 Jiulong Road

department: School of life sciences

institute: Anhui University

data_processing:
PE150 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 v2.0.5.
We used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Bidirectional clustering analysis was performed for all different genes in the samples using R language Pheatmap(1.0.8) software package.
Assembly: mm9
Supplementary files format and content: raw counts

source_name: breast cancer tumor

growth_protocol: Healthy BALB/c mice were 53 females, 4~6 weeks old, weighing 18~20 g, and 45 mice were randomly selected for breast cancer cell injection and modeling. Seed 200 μl of the corresponding concentration of cell suspension subcutaneously under the flank wall of 45 BALB/c mice, respectively.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra II RNA Library Prep Kit for Illumina was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Model group (CK): gavage 50 μl of drug solvent; Tamoxifen group (TAM): gavage 50 μl solution containing TAM 40 mg/kg; oleanolic acid group (OA): gavage 50 μl solution containing OA 40 mg/kg; Normal control group (Blank): gavage 50 μl of the drug solvent.

value: Gastric gavage drug solvent

tag: host strain

value: BALB/c


title: M-L01

description: HiSeq X Ten

value: Spindle cell

value: KIT exon 10

value: Progression after 3 lines


title: CK2


title: WT_rat

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

data_processing:
Raw data were input to STARsolo pipeline (version:2.7.8a), which performed read mapping, cell demultiplexing, UMI counting and cell filtering. WT and co-culture samples are both mapped to mixed GRCh38 and Rnor_6.0 reference genome.
Assembly: GRCh38 and Rnor_6.0
Supplementary files format and content: cell barcode and gene UMI matrix files generated by STARsolo pipeline (version:2.7.8a)

source_name: rat choroid

growth_protocol: EC differentiation protocol was described in a published study Zhang et al., Biomaterials 2021 (doi.org/10.1016/j.biomaterials.2021.120713).

extract_protocol:
Freshly dissected rat choroid and rat choroid-hPSC-EC co-cultured for 48 hours were dissociated to single-cell suspension and used for scRNA-seq library preparation.
libraries were generated according to 10X genomics's instrument instructions.

treatment_protocol: For co-culture of rat choroid and hPSC-EC: rat eyeballs were dissected. A circumferential cut along the cornea released the aqueous humour and the intraocular tension. After removal of the iris, lens, and the aqueous humour, four incisions were made to the cup-shaped retina-sclera complex, leaving a flower-shaped flattened tissue. Under the microscope, the retina was carefully removed.  The choroid-sclera complex were cut into 2mm squares, and transferred to 24-well tissue culture plates. For co-culture, 0.2 million EC suspension was added onto the choroid-sclera complex in 24-well plate. Media was changed daily. After 48 hours of co-culture, the choroid-sclera complex was washed and dissociated for scRNA-seq analysis.

value: rat choroid

value: primary cells


title: clone6_k27ac_R1 (Cut&Run)

value: Atrx knockout


title: OA7

value: Gastric gavage OA


title: PBMC, ATB, biol rep 3

city: shanghai

first: jinyi

last: zhang

address: Songhu Road No.2005

institute: fudan university

library_source: other

data_processing:
Cutadapt 1.10
tophat & HISAT 2.0
R package – Ballgown/edgeR
CIRCExlorer 1.0
Assembly: hg 38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: other

source_name: PBMC

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp).
We performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.

value: PBMC

tag: disease state

value: active tuberculosis (ATB)


title: clone6_IgG_R2 (Cut&Run)

value: undifferentiated pleomorphic sarcoma cell line

value: IgG (diagenode,C15410206)


title: PBMC, ATB, biol rep 2


title: Sublibrary 8, 11 week scRNAseq

city: Raleigh

first: Albert

last: Keung

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular

institute: North Carolina State University

description:
50,000 reads/cell
S9

data_processing:
A splici (spliced + intron) index was created using salmon (v1.7.0) using human GENCODE v39 and hg38 human reference genome.
Sequences were mapped to the splici indexed using salmon and quantified using alevin fry (v0.5.0). Seurat (v4.0.4) was used to filter, process, and analyze gene expression matrices.
The eight sequenced sublibraries were merged into a single Seurat object and reads not matching sample barcodes within a hamming distance of 1 were filtered out. QC filtering was performed removing cells that did not meet the following criteria: Count_RNA > 2000, nFeature_RNA > 1000, mitochondrial percentage < 10%, resulting in 43,844 high-quality cells for analysis.
SCTransform was then used to normalize for read depth across cells, scale the data, and find variable features. Mitochondrial mapping percentage was regressed out during normalization to remove this confounding source of variation.
Principle component analysis (PCA) was performed and an ElboxPlot was generated to determine the number of informative dimensions (50).
Assembly: GENCODE v39/hg38 spici index
Supplementary files format and content: quants_mat.mtx; Gene expression matrix
Supplementary files format and content: quants_mat_cols.txt; Gene List
Supplementary files format and content: quants_mat_rows.txt; Cell barcodes

source_name: cerebral organoids

extract_protocol:
Worthington papains dissociation system was used to obtain a single cell suspension from organoid cultures. Cell suspension were them fixed using Parse Biosciences fixation kits.
The Parse Biosciences Evercode kit was used to carry out scRNA-seq. Barcoding and library preparation of single cell suspensions was performed according to the manufacturer’s protocols.

value: cerebral organoids

value: H9 hESC cell line (NIH 0062), H9 hESC UBE3A m-/p- cells with a 66 kb deletion (chr15:25338949-25405676) ,H9 hESC UBE3A m-/p+ cells with a 66 kb deletion, Angelman Syndrome (AS) hiPSCs with a class II deletion (GRCh37/hg19 chr15:23406313-28897752),  AS point mutation hiPSC line (F583S) (chr15:25338949-25405676)

value: neural cultures

value: H9 WT hESC, H9 UBE3A m-/p- hESC, H9 UBE3A m-/p+ hESC, AS class II deletion iPSC, AS point mutation iPSC

value: 11 week


title: clone6_IgG_R1 (Cut&Run)


title: PBMC, ATB, biol rep 1


title: OA6

value: BALB/c


title: OA1


title: clone6_H3_3_R3 (Cut&Run)


title: M-P03

description: HiSeq X Ten

value: gastrointestinal stromal tumors

value: Spindle cell

value: KIT exon 11 and exon 13


title: PBMC, HC, biol rep 3

value: healthy


title: HDAC3miKO_tFCI_rep3 [RNA-seq]

city: Shanghai

first: Yue

last: Zhang

state: Shanghai

address: 131, Dong'an Road, Xuhui

department: Institute of Brain Science

institute: Fudan University

data_processing:
FastQC (v0.11.9) was first used for quality control assessment.
The low-quality reads (quality score lower than 20) were removed using Trim Galore!.
Paired-end clean data were then aligned to the reference genome (M. musculus, UCSC mm10) using HISAT2 (v2.2.1) after being sorted using Samtools.
HTseq (v1.99.2) was used to quantify the number of reads mapped to each gene annotated in the GENCODE release M25 (GRCm38.p6).
Assembly: mm10
Supplementary files format and content: An HTseq output file (.count) with two columns (Ensembl gene IDs and counts per gene)

source_name: brain

extract_protocol:
Isolated microglia were sent to Shanghai Megiddo Biological Pharmaceutical Co., Ltd. for RNA sequencing. Total RNA from flow-sorted microglia was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA quality was assessed by 2100 Bioanalyser (Agilent Technologies) and quantified by ND-2000 (NanoDrop Technologies).
The library was then prepared following Clontech-SMART-Seq™ v4 Ultra™ Low Input RNA kit for sequencing using 10ng of total RNA. Paired-end RNA sequencing was performed on Illumina NovaSeq 6000 sequencer (2 × 150bp read length).

treatment_protocol: The transient focal cerebral ischemia (tFCI) was induced by middle cerebral artery occlusion (MCAO) for 60 min. Briefly, mice were anesthetized with 1.5% isoflurane in a 30% O2/70% N2 mixture and placed on a temperature-adjustable heating pad to maintain the mouse rectal temperature at 37± 0.5°C during surgery. In MCAO mice, the left carotid artery was separated and exposed. The external carotid artery (ECA) was ligated and cut. The suture (diameter 0.10mm) wrapped with a silicone tip (0.21- 0.23mm, RWD, Shanghai, China) was inserted into the ECA and advanced along the internal carotid arteries until it meets resistance (occluding the middle cerebral artery). Sham-operated mice received the same anesthesia and arterial exposure, except that no MCAO procedure was performed.  FACS-purified microglia were applied to RNA-seq. FACS was performed using a Beckman CytoFLEX SRT cell sorter powered by Kaluza analysis software. Fluorescence compensation was performed using single-stained OneComp eBeads according to the manufacturer's instructions. The antibodies used for sorting are as follows: CD45-eFluor 450 (48-0451-82, eBioscience, 1:50), CD11b-APC cy7 (47-0112-82, eBioscience, 1:200), CD11c-PerCP cy5.5(45-0114-82, eBioscience, 1:100), Ly6G(Gr1)-PE (12-9669-82, eBioscience, 1:200). Data were analyzed using FlowJo software to quantify positively stained cells.

value: brain

value: microglia

value: HDAC3 knockout

value: tMCAO-surgery

tag: batch


title: Sublibrary 6, 11 week scRNAseq

description:
50,000 reads/cell
S7


title: Sublibrary 5, 11 week scRNAseq

description:
50,000 reads/cell
S6


title: HDAC3miKO_tFCI_rep2 [RNA-seq]


title: clone6_IgG_R3 (Cut&Run)

value: Atrx knockout


title: clone6_H3_3_R2 (Cut&Run)

value: undifferentiated pleomorphic sarcoma cell line


title: Sublibrary 4, 11 week scRNAseq

description:
50,000 reads/cell
S5


title: CK1

value: Gastric gavage drug solvent


title: PBMC, HC, biol rep 1

value: PBMC


title: Sublibrary 3, 11 week scRNAseq

description:
50,000 reads/cell
S4

value: cerebral organoids

value: H9 hESC cell line (NIH 0062), H9 hESC UBE3A m-/p- cells with a 66 kb deletion (chr15:25338949-25405676) ,H9 hESC UBE3A m-/p+ cells with a 66 kb deletion, Angelman Syndrome (AS) hiPSCs with a class II deletion (GRCh37/hg19 chr15:23406313-28897752),  AS point mutation hiPSC line (F583S) (chr15:25338949-25405676)


title: clone6_H3_3_R1 (Cut&Run)


title: M-P01

description: HiSeq X Ten

value: KIT exon 9

value: Progression after 3 lines


title: WT_tFCI_rep3 [RNA-seq]

value: WT


title: clone4_k9me3_R2 (Cut&Run)


title: Sublibrary 7, 11 week scRNAseq

description:
50,000 reads/cell
S8

value: neural cultures

value: H9 WT hESC, H9 UBE3A m-/p- hESC, H9 UBE3A m-/p+ hESC, AS class II deletion iPSC, AS point mutation iPSC

value: 11 week


title: Sublibrary 2, 11 week scRNAseq

description:
50,000 reads/cell
S3


title: WT_tFCI_rep2 [RNA-seq]


title: clone4_k9me3_R1 (Cut&Run)


title: WT_tFCI_rep1 [RNA-seq]


title: Sublibrary 1, 11 week scRNAseq

description:
50,000 reads/cell
S2


title: clone4_k27ac_R3 (Cut&Run)

value: H3K27Ac (Active motif,39133)


title: PBMC, HC, biol rep 2

value: healthy


title: CC45_pos

city: Cape Town

first: Stuart

last: Meier

state: Western Cape

address: Groote Schuur Hospital, Anzio Road, Observatory

department: Lung Institute

country: South Africa

institute: University of Cape Town

data_processing:
The FastQC program  was used to assess read quality and trimming was performed using the Trim Galore program.
The Spliced Transcripts Alignment to a Reference software (version STAR_2.7.7a) was used to map reads to the Ensembl  human genome primary assembly (version GRCh38.99) with the quantMode and GeneCounts option selected to generate raw genewise read counts for each sample.
Filtering of lowly expressed genes, normalisation and differential expression analysis was performed the using the edgeR Bioconductor package
Assembly: Ensembl  human genome primary assembly (version GRCh38.99)
Supplementary files format and content: tab-delimited text file of raw gene counts for each sample

source_name: whole blood

extract_protocol:
Total RNA was extracted from PAXgene blood RNA tubes using the PAXgene blood RNA isolation kit (Qiagen, PreAnalytix; catalog: 762174).
Total RNA was processed with the QIAGEN QIAseq FastSelect HMR + Globin kit (for rRNA depletion) and library preparation was performed with the NEB Ultra II RNA library preparation kit.
RNAseq - 150bp pair-end reads

value: whole blood

tag: infectious

value: pos


title: Treated_3_3

city: Omaha

first: Surinder

last: Batra

email: sbatra@unmc.edu, pranitaatri@gmail.com

state: NE

address: 42nd and, Emile St, Omaha, NE

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

data_processing:
Raw reads were mapped to the hg38 human genome using bowtie based tophat followed by cufflinks and cuffdiff based differential expression
Assembly: hg38
Supplementary files format and content: Excel file (cuffdiff output)

growth_protocol: Cells were maintained in DMEM with 10% FBS supplement

extract_protocol:
Thermo fisher MirVana kit was used for RNA extraction
Library preparation was achieved using Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s protocol.

treatment_protocol: Treated samples were treated with 1 µM of ISOX for 48 hours before sample colllection

value: Pancreatic Cancer

value: 1uM ISOX 48 hours


title: Treated_3_4


title: HDAC3miKO_Sham_rep3 [RNA-seq]

value: brain

value: microglia

value: HDAC3 knockout

value: sham-surgery


title: HDAC3miKO_tFCI_rep1 [RNA-seq]

value: tMCAO-surgery


title: clone4_k9me3_R3 (Cut&Run)

value: undifferentiated pleomorphic sarcoma cell line

value: Atrx knockout


title: clone4_k27ac_R2 (Cut&Run)


title: CC44_pos


title: clone4_k27ac_R1 (Cut&Run)


title: Treated_3_1


title: HDAC3miKO_Sham_rep2 [RNA-seq]


title: CC43_neg

value: neg


title: Sublibrary 1, 6 week scRNAseq

description:
50,000 reads/cell
S1

value: cerebral organoids

value: H9 hESC cell line (NIH 0062), H9 hESC UBE3A m-/p- cells with a 66 kb deletion (chr15:25338949-25405676)

value: neural cultures

value: H9 WT hESC, H9 UBE3A m-/p- hESC

value: 6 week


title: HDAC3miKO_Sham_rep1 [RNA-seq]


title: Embryo brain, CDD, replicate 3

city: Singapore

first: Long

middle: Nam

last: Nguyen

address: 28 Medical Drive

department: Biochemistry

country: Singapore

institute: Singapore

description:
EBC3
WT_CDDvsWT_ND_deg.txt
WT_CDDvsWT_ND_deg_all.txt
WT_CDDvsWT_ND_deg_up.txt
WT_CDDvsWT_ND_deg_down.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughfastp software
In this step, clean data (clean reads) were obtained by removing readscontaining adapter, reads containing ploy-N and low quality reads from raw data.
At the same time, Q20, Q30 and GC content the clean data were calculated. All thedownstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2 v2.0.5and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to eachgene. And then FPKM of each gene was calculated based on the length of the geneand reads count mapped to this gene
Assembly: (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0)
Supplementary files format and content: file.txt excel files contain differential analysis data with FPKM and gene count

extract_protocol:
RNAs were extracted using the RNeasy Mini Plus kit from Qiagen; about 8ug was used to send to Novogene company for RNA-sequencing service
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads; The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size  distribution  detection.  Quantified  libraries  will  be  pooled  and  sequenced  on  Illumina platforms, according to effective library concentration and data amount.

tag: developmental stage

value: embryo

value: wild-type

value: choline deficient diet for pregnant mother


title: CC42_pos

value: whole blood

value: pos


title: WT_Sham_rep3 [RNA-seq]

value: brain

value: microglia

value: WT


title: Treated_2_3

value: Pancreatic Cancer

value: 1uM ISOX 48 hours


title: clone4_IgG_R2 (Cut&Run)

value: undifferentiated pleomorphic sarcoma cell line

value: Atrx knockout

value: IgG (diagenode,C15410206)


title: CC41_neg

value: neg


title: Treated_2_2


title: CC40_neg


title: clone4_IgG_R1 (Cut&Run)


title: Treated_3_2


title: CC37_pos


title: clone4_H3_3_R3 (Cut&Run)


title: Treated_2_1


title: Treated_2_4


title: clone4_H3_3_R2 (Cut&Run)


title: WT_Sham_rep1 [RNA-seq]

value: sham-surgery


title: SCC7_3

city: Nanjing

first: Chengwan

last: Xia

state: Jiangsu

address: No.30 Central Rd., Xuanwu District

institute: Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University

description: Control

data_processing: Raw data were output in a FASTQ format file, clean data were obtained by removing low-quality reads and adapters from the raw data, and quality control was performed using FastQC. Gene expression analysis was performed using HTSeq (RRIDSCR_005514)

growth_protocol: Raw 264.7 cells were cultured in DMEM (Gibco, American) supplemented with 10% fetal bovine serum (FBS, Gibco, American) and 1% penicillin/streptomycin (Sigma, American), and SCC7 cells were cultured in RPMI 1640 media (Gibco, USA) supplemented with 10% FBS (Gibco, American) and 1% penicillin/streptomycin. Fusion cells were cultured in RPMI 1640 medium (Gibco, USA) supplemented with 10% FBS (Gibco, Grand Island, NY, USA) and 1% penicillin/streptomycin

extract_protocol:
Total RNA from SCC7, Raw 264.7, and hybrid cells (n=3 per group) was isolated using TRIzol Reagent (Invitrogen Life Technologies), after which the concentration, quality, and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
RNA sequencing libraries were prepared from 2 μg of total RNA with the following modifications: Ribosomal RNA was removed using an Epicenter Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat). Fragmentation was performed using divalent cations at elevated temperatures in an Illumina proprietary fragmentation buffer. Using RNA as a template and random oligonucleotides as primers, the first strand of cDNA was synthesized and RNase H was used to degrade the RNA strand. In the DNA polymerase I system, dNTP with dUTP were used instead of dTTP as raw material to synthesize the second strand of cDNA. Double-stranded cDNA was purified. Double-end repair was then performed, the "A" base at the 3' end was introduced, and the sequencing adapter was connected. The USER enzyme (NEB, USA) was added to degrade the second strand of cDNA containing U. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with ligated adaptor molecules at both ends were selectively enriched using the Illumina PCR Primer Cocktail in a 15 cycle PCR. The products were purified (AMPure XP system) and quantified using an Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: oral cancer cell line


title: CC36_pos


title: Treated_1_3


title: Treated_1_2


title: CC35_pos


title: clone4_H3_3_R1 (Cut&Run)


title: clone4_IgG_R3 (Cut&Run)


title: SCC7_1

description: Control


title: SCC7_2

description: Control


title: WT_R3 (ATAC-seq)

data_processing:
ATACseq reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the MACS2 software.
Assembly: hg38
Supplementary files format and content: bigwig files normalized to read depth
Supplementary files format and content: narrowPeak files generated by MACS2

extract_protocol:
Cells were harvested and then washed by PBS. Lysis with ATAC resuspension buffer(TRIS-HCl-pH7.4, 10mM; NaCl,10mM;MgCl2,3mM) plus 0.1% NP40, 0.1%Twwen-20,0.01%Digitonin.
Libraries were generated using NEBNext Ultra II kits.


title: Raw_3

description: Control

value: macrophage cell  line


title: Whole brain, 24m, rep 3 [Illumina]

value: Whole brain

tag: Sex

value: Male

tag: age

value: 24 months


title: CC33_pos

value: whole blood


title: Untreated_3_4

tag: cell type

value: none; untreated


title: WT_Sham_rep2 [RNA-seq]

tag: tissue

value: brain


title: WT_R2 (ATAC-seq)

tag: genotype


title: WT_R1 (ATAC-seq)


title: CC32_pos

value: pos


title: Treated_1_4


title: sg1_clone6_R3 (ATAC-seq)


title: Raw_1

description: Control

value: macrophage cell line


title: CC31_pos


title: Untreated_3_2

value: Pancreatic Cancer


title: Fusion_3

description: treatment

source_name: fusion

value: fusion

value: generation from the fusion between Raw 264.7 and SCC7


title: Untreated_3_1


title: Fusion_2

description: treatment


title: sg1_clone6_R1 (ATAC-seq)

value: undifferentiated pleomorphic sarcoma cell line

value: Atrx knockout


title: sg1_clone6_R2 (ATAC-seq)


title: CC30_neg

value: neg


title: CC28_neg


title: CC34_pos


title: CC27_neg


title: Untreated_2_3


title: Untreated_2_4


title: Fusion_1

description: treatment


title: sg1_clone4_R3 (ATAC-seq)


title: REST_PSD95_pd_rep_3 [Ribo-Seq]

first: Caryn

middle: R

last: Hale

address: 1230 York Avenue

description: ribosomal profiling of pulldown fraction of psd region in rest neuron, replicate 3

data_processing:
Tab-delimited text files include RPKM values and counts for each sample.
Remove ribosomal reads: The processed reads were aligned to mouse ribosomal sequences (mm10) by Rsubread. The aligned reads were removed, and the filtered reads were converted into fastq format for the following analysis.
Align to mouse genome: The filtered reads were aligned to BSgenome (mm10) with Rsubread. The alignment results were stored as BAM format.
Annotation and counting: After alignment, Plastid was applied to count expression level of each transcript in each sample. Before counting, the annotation files for U5/CDS/U3 were derived from TxDb.Mmusculus.mm10.knownGene. The annotations were based on Ensembl transcript ID. Then, the counts for U5/CDS/U3 in each sample was calculated by Plastid. The RPKM value of each transcript ID in each sample was gathered into single table for following analysis.
Assembly: Reference genome: Bsgenome.Mmusculus.UCSV.mm10; Annotation database: Txdb.Mmusculus.UCSC.mm10.knownGene.
Supplementary files format and content: Tab-delimited text files include RPKM values and counts for each sample.
Library strategy: Ribo-Seq [Ribo-Seq]

growth_protocol: Primary cortical neurons were grown in Neurobasal media supplemented with B27 and Glutamax. [Ribo-Seq]

extract_protocol:
RNA from inputs and streptavidin pulldowns (from beads directly) was extracted using the TRIzol protocol.   [Ribo-Seq]
RNA from inputs and streptavidin pulldowns was resolved by electrophoresis through a denaturing gel to isolate ribosome footprints. The expected size range fragments were extracted, and 3’ ends of these RNA fragments were treated with T4 polynucleotide ligase to ligate a pre-adenylated barcoded DNA linker to be able to pool samples. After treatment with deadenylase and RecJ, inputs and pulldowns were pooled, purified with Zymo columns, and were depleted of ribosome RNA (rRNA) using Ribo-Zero. Following rRNA removal, RNA was used as template for reverse transcription, using an oligo specifically designed to be able to sequence from the 5’end of the ribosome protected fragment. The single-stranded cDNA is then circularized using an optimized CircLigase after another gel purification step of full-length products. A double stranded DNA library is generated using the circularized cDNA fragments that are amplified with the Kapa enzyme and a fixed primer combined with an Illumina index encoding primer. The resulting products are gel purified from a non-denaturing gel and quantified on a bioanalyzer. Pooled libraries were then sequenced on the Illumina Novaseq 6000 sequencer.  [Ribo-Seq]

treatment_protocol: Primary cortical neurons were treated with cycloheximide for 2 minutes before biotinylation for 30 minutes. Depolarization was performed by incubating the cells with tetrodotoxin and DL-AP5 for 2 hours before 55 mM KCl addition for 1 hour, followed by resting for 30 minutes before harvest.   [Ribo-Seq]

value: primary neuronal culture (cortical)

tag: lentivirus

tag: fraction

value: streptavidin pulldown

value: Chx


title: CC26_pos


title: Raw_2

description: Control

value: macrophage cell  line


title: sg1_clone4_R2 (ATAC-seq)


title: Untreated_3_3


title: CC25_pos


title: REST_PSD95_in_rep_3 [Ribo-Seq]

description: ribosomal profiling of input fraction of psd region in rest neuron, replicate 3

value: input


title: Untreated_2_2


title: sg1_clone4_R1 (ATAC-seq)


title: MG24H_RNA_rep3

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
Aligned using STAR
Counts generated with featureCounts and GENCODE v27
Assembly: hg19
Supplementary files format and content: tab-delimited text: column 1 = gene, column 2 = counts

source_name: breast

extract_protocol: none provided

value: breast

value: cancer


title: Untreated_2_1

value: none; untreated


title: Treated_1_1

value: 1uM ISOX 48 hours


title: REST_Pan_pd_rep_3 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of cytosol region in rest neuron, replicate 3

value: Pan-TurboID


title: CC23_neg

value: whole blood


title: REST_Pan_in_rep_3 [Ribo-Seq]

description: ribosomal profiling of input fraction of cytosol region in rest neuron, replicate 3


title: MG24H_RNA_rep2


title: Untreated_1_4

value: Pancreatic Cancer


title: MG24H_RNA_rep1


title: Untreated_1_2


title: CC22_neg


title: MG4H_RNA_rep3


title: CC20_pos

value: pos


title: CC19_pos


title: DEP_PSD95_in_rep_3 [Ribo-Seq]

description: ribosomal profiling of input fraction of psd region in dep neuron, replicate 3

value: Chx + KCl depolarization


title: DEP_PSD95_pd_rep_3 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of psd region in dep neuron, replicate 3


title: CC18_pos


title: Untreated_1_1


title: MG4H_RNA_rep2


title: MG4H_RNA_rep1


title: DEP_Pan_in_rep_3 [Ribo-Seq]

description: ribosomal profiling of input fraction of cytosol region in dep neuron, replicate 3


title: DEP_Pan_pd_rep_3 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of cytosol region in dep neuron, replicate 3


title: CC17_neg


title: UNTR_RNA_rep3

value: Veh


title: CC15_pos


title: REST_PSD95_pd_rep_2 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of psd region in rest neuron, replicate 2


title: mesendoderm-Igf2_Igf2_dCTCFinICR-RNAseq-BS18543A

first: Matthew

middle: T

last: Maurano

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

data_processing:
Illumina libraries were sequenced in single-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences.
Illumina sequencing adapters were trimmed with Trimmomatic v0.39. Sequencing reads were aligned using STAR v2.5.2a to a genome reference (GRCm38/mm10).
Read counts estimation and normalization were performed using RSEM v1.2.31 with mouse GENCODE v23 reference.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts, TPM and FPKM values for each Sample

source_name: mesendodermal cells

growth_protocol: Differentiation to mesendodermal cells was adapted from a published protocol (Thomson et al. 2011). mESCs were seeded on plates coated with 0.1% gelatin (EMD Millipore ES006-B) in N2/B27 medium, containing a 1:1 mixture of DMEM/F12 (ThermoFisher 11330032) and Neuro-basal (ThermoFisher 21103049), supplemented with 0.5% N2 Supplement (ThermoFisher 17502048), 1% B27 Supplement (ThermoFisher 17504044), 1% glutamax (ThermoFisher 35050061), 1% Pen-Strep (ThermoFisher 15140122), 1% MEM nonessential amino acids (ThermoFisher 11140050), 100 μM sodium pyruvate (ThermoFisher 11360070), 0.1 mM 2-mercaptoethanol (Sigma M3148). The differentiation media was supplemented with 10 μM ROCK inhibitor Y-27632 (Cell Signaling 13264) the first 24 h after seeding the cells. For the next 3 days, 3 μM CHIR99021 (R&D Systems 4423) was added to the media, and replaced every 24 h. Four days after differentiation, plates were rinsed twice using PBS and cells were collected for further studies.

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. RNA was isolated using the RNeasy-mini (QIAGEN 74106) protocol followed by DNase treatment using the Turbo DNA-free kit (ThermoFisher AM1907).
RNA-seq libraries were prepared from 500 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S), and performing PolyA selection for ribosomal depletion using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) according to the manufacturer’s protocol.

treatment_protocol: Cells were engineered with different landing pads and payloads as described and were selected combinatorially with puromycin, blasticidin, proaerolysin and ganciclovir as described in the manuscript.

value: mesendodermal cells

tag: strain

value: C57BL6/6J x CAST/EiJ F1 hybrid

tag: payload id

tag: clone id

value: Mesendoderm differentiation


title: mesendoderm-Igf2_Igf2_dCTCFinICR-RNAseq-BS18544A


title: mesendoderm-Igf2_Igf2_dCTCFinICR-RNAseq-BS18542A


title: CC14_pos


title: REST_PSD95_in_rep_2 [Ribo-Seq]

description: ribosomal profiling of input fraction of psd region in rest neuron, replicate 2

tag: cell line

value: primary neuronal culture (cortical)


title: UNTR_RNA_rep2

tag: treatment


title: Untreated_1_3


title: CC12_pos


title: REST_Pan_pd_rep_2 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of cytosol region in rest neuron, replicate 2

value: streptavidin pulldown

value: Chx


title: mesendoderm-Igf2_Igf2_miICR~Igf2SV-RNAseq-BS18540A


title: mesendoderm-Igf2_Igf2_miICR~Igf2SV-RNAseq-BS18539A


title: MG24H_startRNA

data_processing:
Aligned using bowtie with parameters: -v 2 -m 1 --best --strata --trim3 1 -S
Read hits use the aligned position of the first base of mate 1 reads only
Assembly: hg19
Supplementary files format and content: bigWig: read hits, separated by strand

molecule: nuclear RNA


title: CC10_pos


title: DEP_PSD95_pd_rep_2 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of psd region in dep neuron, replicate 2


title: MG4H_startRNA


title: MG24H_ATAC_rep3

data_processing:
Aligned using bowtie with parameters: -v 2 -m 1 --best --strata
Open chromatin coverage uses first 9 bases of aligned reads
Assembly: hg19
Supplementary files format and content: bigWig: open chromatin coverage

value: Female


title: mESC-Igf2_Igf2_inverted~dEnh~dCTCFinICR-BS24928A

description: Capture-seq

data_processing:
library strategy: Capture-seq
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences.
All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39. Sequencing reads were aligned using BWA v0.7.17 to a genome reference (GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: mm10
Supplementary files format and content: coverage bigwig files for captured genomic DNA libraries to genome reference (GRCm38/mm10)

source_name: mESC

growth_protocol: mESCs were cultured on gelatin-coated plates coated in 80/20 medium comprising 80% 2i medium and 20% mESC medium and with 1% Pen-strep.

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Payload and Targeted sequencing (Capture-seq); Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.

value: mESC

tag: paylod id


title: CC04_neg

value: neg


title: mESC-Igf2_Igf2_inverted~dEnh~dCTCFinICR-BS24926A

description: Capture-seq


title: mESC-Igf2_Igf2_inverted~dEnh~dCTCFinICR-BS24929A

description: Capture-seq


title: UNTR_startRNA

value: breast

value: cancer


title: DEP_Pan_pd_rep_2 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of cytosol region in dep neuron, replicate 2

value: Pan-TurboID


title: DEP_PSD95_in_rep_2 [Ribo-Seq]

description: ribosomal profiling of input fraction of psd region in dep neuron, replicate 2

value: input


title: DEP_Pan_in_rep_2 [Ribo-Seq]

description: ribosomal profiling of input fraction of cytosol region in dep neuron, replicate 2


title: mesendoderm-Igf2_Igf2_miICR~Igf2SV-RNAseq-BS18541A


title: CC02_pos

value: whole blood


title: CC01_neg


title: mESC-Igf2_Igf2_inverted~dEnh~dCTCFinICR-BS24924A

description: Capture-seq


title: REST_PSD95_pd_rep_1 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of psd region in rest neuron, replicate 1


title: UNTR_RNA_rep1


title: mESC-Igf2_Igf2_inverted~dEnh~miICR-BS24313A

description: Capture-seq


title: MG24H_ATAC_rep1


title: MG24H_ATAC_rep2


title: REST_PSD95_in_rep_1 [Ribo-Seq]

description: ribosomal profiling of input fraction of psd region in rest neuron, replicate 1


title: MG4H_ATAC_rep3


title: REST_Pan_in_rep_2 [Ribo-Seq]

description: ribosomal profiling of input fraction of cytosol region in rest neuron, replicate 2


title: nerve2, N2, scRNAseq

first: Luo

middle: Hua

last: hong

address: 639 Manufacturing Bureau Road, Shanghai

institute: Shanghai Ninth People’s Hospital, Shanghai Jiaotong  University School of Medicine

description: 10x Genomics

data_processing:
The CellRanger (10X Genomics, v3.1) analysis pipeline was utilized for sample demultiplexing, barcode processing, and gene counting to generate gene-barcode matrices.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Great auricular nerve

extract_protocol:
Freshly collected vestibular schwannomas and great auricular nerve were resected and washed twice with 1x PBS (Gibco). Fresh samples were cut into 1 mm3 pieces and enzymatically digested with 10 mL digestion medium containing 1 mg/mL collagenase IV (Gibco) and 1 U/mL DNase I (Sigma). The samples were subsequently incubated at 37°C for 45 min and triturated by pipette for 15 min. The suspended cells were subsequently washed with 20% fetal bovine serum (FBS) in Dulbecco’s Modified Eagle Medium (DMEM) sieved through a 50-µm Cell-Strainer nylon mesh (BD) and centrifuged at 300 × g for 5 min. The supernatant was removed, and the pelleted cells were washed twice with MACS buffer (PBS containing 1% FBS, 0.5% EDTA, and 0.05% gentamycin) and resuspended in PBS with 0.04% BSA.
The cell suspension of each sample was processed through the Gel Bead Kit V3 (10x Genomics) for library preparation according to the manufacturer’s protocol. scRNA-seq libraries were constructed using a Chromium Single Cell 30 V2 or V3 Reagent Kit. The single cell libraries were then pooled and sequenced on Illumina Novaseq 6000 Systems using 150-base-pair paired-end reads. Raw data were converted to FASTQ files using Illumina bcl2fastq (version 2.19.1) and aligned to GRCh38 human reference genome.

treatment_protocol: surgery

tag: tumor size_(mm)

value: Great auricular nerve

value: 55 years old

tag: growth pattern


title: CC08_pos

tag: infectious

value: pos


title: MG4H_ATAC_rep2


title: REST_Pan_pd_rep_1 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of cytosol region in rest neuron, replicate 1


title: mESC-Igf2_Igf2_inverted~dCTCFinICR-BS24308A

description: Capture-seq


title: nerve1, N1, scRNAseq

description: 10x Genomics

value: 71 years old


title: REST_Pan_in_rep_1 [Ribo-Seq]

description: ribosomal profiling of input fraction of cytosol region in rest neuron, replicate 1


title: CC05_neg


title: mESC-Igf2_Igf2_inverted~dEnh~miICR-BS24310A

description: Capture-seq

value: C57BL6/6J x CAST/EiJ F1 hybrid


title: DEP_PSD95_pd_rep_1 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of psd region in dep neuron, replicate 1

value: Chx + KCl depolarization


title: MG4H_ATAC_rep1


title: VS, T7, scRNAseq

description: 10x Genomics

source_name: Vestibular schwannoma

value: Vestibular schwannoma

value: Male

value: 22 years old

value: fast


title: UNTR_ATAC_rep3

value: Female

value: Veh


title: VS, T6, scRNAseq

description: 10x Genomics

value: 60 years old

value: slow


title: mESC-Igf2_Igf2_inverted~dCTCFinICR-BS24305A

description: Capture-seq

value: mESC


title: DEP_PSD95_in_rep_1 [Ribo-Seq]

description: ribosomal profiling of input fraction of psd region in dep neuron, replicate 1

value: primary neuronal culture (cortical)

value: input


title: mESC-Igf2_Igf2_dCTCFinICR-BS24304A

description: Capture-seq


title: mesendoderm-DNase-BS03687A

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences.
Illumina sequencing adapters were trimmed with Trimmomatic v0.39. Sequencing reads were aligned using BWA v0.7.17 to a genome reference (GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: GRCm38/mm10
Supplementary files format and content: bw
Library strategy: DNAse-seq

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. DNase digestion was performed as described previously (John et al. 2013; Georgolopoulos et al. 2021) and adapted to 200 µL thermocycler tubes. Briefly, nuclei were extracted from cells and incubated with limiting concentrations of the DNA endonuclease DNase I (Sigma D4527-20KU) supplemented with Ca2+ and Mg2+ for 3 min at 37 °C. Digestion was stopped by the addition of EDTA, and the samples were treated with proteinase K and RNase A. Short double-hit fragments were isolated from DNaseI digestion using magnetic bead polyethylene glycol (PEG) fractionation.
DNA fragments were end-repaired with T4 DNA polymerase (NEB M0203L), Klenow DNA polymerase (NEB M0210L), and T4 polynucleotide kinase (NEB M0201L), and A-tailed using Klenow (3′-5′ exo-; NEB M0212L). Illumina sequencing adapters were then ligated to DNA ends using Quick Ligase (NEB M2200L). The post-ligation product was purified using 18% Sera-Mag Magnetic Beads (Cytiva 65152105050250) in polyethylene glycol. DNA libraries were amplified with KAPA 2× Hi-Fi Hotstart Readymix (Roche 07958935001) and purified with 18% Sera-Mag Magnetic Beads in polyethylene glycol.

value: mesendodermal cells

value: WT

value: Mesendoderm differentiation


title: UNTR_ATAC_rep1

value: breast

value: cancer


title: VS, T4, scRNAseq

description: 10x Genomics

value: 49 years old


title: VS, T5, scRNAseq

description: 10x Genomics

value: Vestibular schwannoma

value: 48 years old


title: DEP_Pan_in_rep_1 [Ribo-Seq]

description: ribosomal profiling of input fraction of cytosol region in dep neuron, replicate 1

value: Pan-TurboID

value: Chx + KCl depolarization


title: 44D_AF_3_TGFB+AR

city: rochester

first: Roman

last: Thaler

state: MINNESOTA

address: 200 First street SW

institute: Mayo Clinic

data_processing:
Libraries were sequenced on an Illumina NextSeqP2 instrument and Fastq file quality was checked with FastQC (version 0.74).
Quality and adapter trimming was performed with Trim Galore! (version 0.6.7)
Trimmed Fastq files were mapped to the human genome (hg38) with RNA STAR (version 2.7.10b)
Gene expression was qantified with featureCounts (version 2.0.3)
Differentially expressed genes were defined with DESeq2 (version 2.11.40.8)
Assembly: hg38
Supplementary files format and content: merged_gene_count_fpkm_by_gene_annotated

source_name: Knee derived fibroblasts

growth_protocol: Cells were cultured in Advanced MEM supplemented with 5% human PLTMax (Mill Creek Life Sciences, Rochester, MN, USA), a clinical grade commercial platelet lysate product, 2 U/mL heparin (hospital pharmacy), GlutaMAXTM (Thermo Fisher Scientific), and antibiotic/antimycotic (Thermo Fisher Scientific) at 37°C, 95% humidity, 21% O2, and 5% CO2. At approximately 100% cell confluency, passage 0 cells were detached using TrypLE Express (Thermo Fisher Scientific) and banked using CryoStorR (Sigma-Aldrich, St. Louis, MO, USA). For experimental purposes, cells were retrieved from frozen stocks, expanded in growth medium (same as above), and passage 3-5 cells were used for all experiments.

extract_protocol:
RNA was extraced with a commercially available extraction kit (Zymo).
RNA libraries were prepared for sequencing using standard Illumina protocols and deep-sequncing runs were perfomed using the Illumina NextSeqP2 platform at the Mayo Clinic Medical Genome Facility Sequencing Core.

treatment_protocol: For experimental purposes, cells were retrieved from frozen stocks, expanded in growth medium (same as above), and passage 3-5 cells were used for all experiments. In this regard, at Day 0, cells were treated with 5 µM AdipoRon or its vehicle (DMSO) in the presence of 10 ng/ml TGFβ1 or its vehicle in growth medium. Additional 5 µM final concentration of AdipoRon and equal volume of its vehicle were added on Day 1 and Day 2 without media change. On Day 3, cells were processed and RNA was extracted for downstream analyses.

tag: tissue/cell type

value: Fibrotic

tag: passages

tag: agent

value: TGFB+AR


title: VS, T3, scRNAseq

description: 10x Genomics

tag: Sex

value: Male

tag: age

value: 22 years old

value: fast


title: DEP_Pan_pd_rep_1 [Ribo-Seq]

description: ribosomal profiling of pulldown fraction of cytosol region in dep neuron, replicate 1

tag: tissue

tag: cell type

value: primary neuronal culture (cortical)

value: streptavidin pulldown


title: DEP_PSD95_pd_rep_4

description: RNA-seq of dendritic (PSD95-proximal) protein-bound RNAs in depolarized neurons, replicate 5

data_processing:
Prepare transcriptome indices: The transcripts sequences were built based on Txdb.Mmusculus.Ucsc.mm10.knownGene. Then the transcripts were indexed with index function of Salmon.
Alignment and counting: The fastq files were mapped to transcriptome indices and counted by using Salmon quant.
Differential gene expression: The count results of all samples were loaded into DESeq object by using tximport. Then, the differential gene expression between groups were analyzed using limma.
Assembly: Genome version: mm10; reference genome: BSgenome.Mmusculus.UCSC.mm10; annotation database: Txdb.Mmusculus.Ucsc.Mm10.Knowngene.
Supplementary files format and content: Tab-delimited text files include raw counts values for each sample.

growth_protocol: Primary cortical neurons were grown in Neurobasal media supplemented with B27 and Glutamax.

extract_protocol:
RNA from inputs and streptavidin pulldowns was extracted using the TRIzol protocol.
RNA (input and pulldown, ~100 ng) was used as the starting material and first treated with DNAse on columns. TruSeq stranded RNA sample protocol was followed using RiboZero to get rid of ribosomal RNAs. For unique adapters, IDT Illumina Truseq RNA UD Indexes were used. The samples were then pooled and sequenced on the Illumina NovaSeq 6000 sequencer.

treatment_protocol: Primary cortical neurons were treated with cycloheximide for 2 minutes before biotinylation for 30 minutes. Depolarization was performed by incubating the cells with tetrodotoxin and DL-AP5 for 2 hours before 55 mM KCl addition for 1 hour, followed by resting for 30 minutes before harvest.

tag: lentivirus

tag: fraction

value: pulldown

tag: genotype


title: 43D_AF_2_TGFB+AR


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh~inverted-BS18988A

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences.
All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39. Sequencing reads were aligned using BWA v0.7.17 to a genome reference (GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: mm10
Supplementary files format and content: coverage bigwig files for captured genomic DNA libraries to genome reference (GRCm38/mm10)

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.
Payload and Targeted sequencing (Capture-seq)

value: mESC

tag: strain

value: C57BL6/6J x CAST/EiJ F1 hybrid

tag: payload id

tag: clone id

tag: seq method

value: Capture-seq


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh~inverted-BS18987A


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh~inverted-BS18986A


title: VS, T2, scRNAseq

description: 10x Genomics

tag: tumor size_(mm)

value: 63 years old

value: slow


title: 42D_AF_1_TGFB+AR


title: DEP_PSD95_in_rep_4

description: RNA-seq of all protein-bound RNAs in depolarized neurons transduced with PSD95-TurboID, replicate 5

tag: cell line

value: input

tag: treatment


title: 44D_AF_3_TGFB

tag: tissue/cell type

value: TGFB


title: MG24H_Input_rep3

data_processing:
Aligned using bowtie with parameters: -v 2 -m 1 --best --strata
Assembly: hg19
Supplementary files format and content: bigWig: read coverage

value: breast

value: cancer

tag: chip antibody

value: INPUT


title: VS, T1, scRNAseq

description: 10x Genomics

value: Vestibular schwannoma

value: 73 years old

tag: growth pattern


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh~inverted-BS18985A


title: MG24H_Input_rep2


title: DEP_PAN _pd_rep_4

description: RNA-seq of all Pan-TurboID proximal protein-bound RNAs in depolarized neurons, replicate 5

value: Pan-TurboID

value: Chx + KCl depolarization


title: 43D_AF_2_TGFB

value: Fibrotic

tag: passages

tag: agent


title: REST_PSD95_pd_rep_4

description: RNA-seq of dendritic (PSD95-proximal) protein-bound RNAs in resting neurons, replicate 5

tag: tissue

value: primary neuronal culture (cortical)

value: Chx


title: UNTR_ATAC_rep2

tag: cell type

tag: Sex

value: Female

value: Veh


title: DEP_PAN _in_rep_4

description: RNA-seq of all protein-bound RNAs in depolarized neurons transduced with Pan-TurboID, replicate 5

tag: lentivirus

tag: fraction


title: 42D_AF_1_TGFB


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh~inverted-BS18980A

value: mESC

tag: strain

value: C57BL6/6J x CAST/EiJ F1 hybrid

tag: genotype

value: Capture-seq


title: MG4H_Input_rep2


title: 44D_AF_3_Veh


title: MG24H_Input_rep1


title: MG4H_Input_rep3


title: mESC-Igf2_Igf2_Sox2DistalLCR~inverted~dCTCFinICR-BS18466A

tag: payload id

tag: clone id


title: REST_PSD95_in_rep_4

description: RNA-seq of all protein-bound RNAs in resting neurons transduced with PSD95-TurboID, replicate 5

value: input


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh~inverted-BS18984A

tag: seq method


title: REST_PAN _pd_rep_4

description: RNA-seq of all Pan-TurboID proximal protein-bound RNAs in resting neurons, replicate 5

tag: cell line

value: pulldown


title: REST_PAN _in_rep_4

description: RNA-seq of all protein-bound RNAs in resting neurons transduced with Pan-TurboID, replicate 5

tag: treatment


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh-BS18195A


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh-BS18194A


title: MG4H_Input_rep1

value: breast


title: 42D_AF_1_Veh

tag: tissue/cell type


title: UNTR_Input_rep3

value: cancer

tag: chip antibody


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh-BS18190A


title: 38E_SP_3_TGFB+AR

value: non-fibrotic

value: TGFB+AR


title: DEP_PSD95_pd_rep_3

description: RNA-seq of dendritic (PSD95-proximal) protein-bound RNAs in depolarized neurons, replicate 4


title: DEP_PAN_pd_rep_3

description: RNA-seq of all Pan-TurboID proximal protein-bound RNAs in depolarized neurons, replicate 4


title: 34G_SP_2_TGFB+AR


title: mESC-Sox2_Sox2_dDistalLCR~H19Enh~inverted-BS18983A


title: UNTR_Input_rep2

value: INPUT


title: 30G_SP_1_TGFB+AR


title: DEP_PSD95_in_rep_3

description: RNA-seq of all protein-bound RNAs in depolarized neurons transduced with PSD95-TurboID, replicate 4


title: mESC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS17492A


title: UNTR_Input_rep1


title: 38E_SP_3_TGFB

value: TGFB


title: DEP_PAN_in_rep_3

description: RNA-seq of all protein-bound RNAs in depolarized neurons transduced with Pan-TurboID, replicate 4

value: Pan-TurboID

value: Chx + KCl depolarization


title: mESC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS17493A


title: 43D_AF_2_Veh

value: Fibrotic


title: REST_PSD95_pd_rep_3

description: RNA-seq of dendritic (PSD95-proximal) protein-bound RNAs in resting neurons, replicate 4

value: primary neuronal culture (cortical)

value: Chx


title: REST_PAN_pd_rep_3

description: RNA-seq of all Pan-TurboID proximal protein-bound RNAs in resting neurons, replicate 4


title: mESC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS17489A


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS17482A


title: MG24H_H3K4me1_rep3


title: REST_PSD95_in_rep_3

description: RNA-seq of all protein-bound RNAs in resting neurons transduced with PSD95-TurboID, replicate 4


title: MG24H_H3K4me1_rep1


title: MG24H_H3K4me1_rep2


title: 38E_SP_3_Veh

value: Veh


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS17480A

value: mESC


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS17481A

value: C57BL6/6J x CAST/EiJ F1 hybrid


title: 34G_SP_2_Veh


title: 30G_SP_1_TGFB


title: REST_PAN_in_rep_3

description: RNA-seq of all protein-bound RNAs in resting neurons transduced with Pan-TurboID, replicate 4


title: MG4H_H3K4me1_rep2


title: 30G_SP_1_Veh


title: MG4H_H3K4me1_rep1


title: MG4H_H3K4me1_rep3


title: DEP_PSD95_pd_rep_2

description: RNA-seq of dendritic (PSD95-proximal) protein-bound RNAs in resting neurons, replicate 3


title: mESC-Igf2_Igf2_dCTCFinICR-BS17463A

value: Capture-seq


title: DEP_PAN_pd_rep_2

description: RNA-seq of all Pan-TurboID proximal protein-bound RNAs in resting neurons, replicate 3


title: HCC827 cells, TET2 KO, 3

city: Chengdu

first: Jian

state: Sichuan

address: Guoxuexiang Road

department: Westchina Hospital

institute: Sichuan University

data_processing:
Trimmed sequence reads were mapped to GRCh38/hg38 using bwa-mem
Duplicate reads were identified and removed by Picard.
5hmC-enriched regions were obtained byusing macs2
Assembly: hg38
Supplementary files format and content: file containing all 5hmC signal enriched regions
Library strategy: 5hmC-seq

source_name: lung

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were divided when they reached a high confluence, usually 3 days as an interval period.

extract_protocol:
We extract genomic DNA from the cultured cells following the manufacture's protocol (The QIAamp DNA Mini Kit (cat. nos. 51304 and 51306) ).
For each sample, two libraries were generated: a library derived from 5hmC-enriched reads and a library derived from input-unenriched DNA. Fragmented DNA was normalized to 20 ng total input for each assay and ligated to sequencing adapters. Adapter ligated products were either prepared for whole-genome sequencing using the KAPA Hyper Prep kit (Roche, Switzerland) according to the manufacturer’s instructions or 5hmC bases were biotinylated via a two-step chemistry and subsequently enriched by binding to Dynabeads M270 Streptavidin (Thermo Fisher Scientific). All libraries were quantified using a Qubit dsDNA High-Sensitivity Assay (Thermo Fisher Scientific) and normalized in preparation for sequencing. Fragment size profiles of sequencing libraries were verified with the Bioanalyzer dsDNA High-Sensitivity assay (Agilent Technologies) prior to sequencing.

treatment_protocol: TET2 sgRNA containing lentivirus were added in HCC827 cells, cells were selected by puromycin. The TET2-KO single clones were then selected.

value: lung

value: non-small cell lung cancer (NSCLC) cell line

value: TET2 KO


title: mESC-Igf2_Igf2_dCTCFinICR-BS17462A


title: UNTR_H3K4me1_rep3

value: breast

value: cancer


title: DEP_PSD95_in_rep_2

description: RNA-seq of all protein-bound RNAs in resting neurons transduced with PSD95-TurboID, replicate 3

value: input


title: mESC-Igf2_Igf2_dCTCFinICR-BS17461A


title: UNTR_H3K4me1_rep2


title: HCC827 cells, TET2 KO, 2


title: 34G_SP_2_TGFB

value: non-fibrotic


title: DEP_PAN_in_rep_2

description: RNA-seq of all protein-bound RNAs in resting neurons transduced with Pan-TurboID, replicate 3


title: UNTR_H3K4me1_rep1


title: HCC827 cells, TET2 KO, 1


title: REST_PSD95_pd_rep_2

description: RNA-seq of dendritic (PSD95-proximal) protein-bound RNAs in depolarized neurons, replicate 3

value: pulldown


title: mESC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS16856A


title: HCC827 cells, 3

value: WT


title: mESC-Igf2_Igf2_dCTCFinICR-BS17464A


title: REST_PAN_pd_rep_2

description: RNA-seq of all Pan-TurboID proximal protein-bound RNAs in depolarized neurons, replicate 3

value: Pan-TurboID


title: F_UC-MSCs_P6

first: Li

last: Wu

state: Yangpu District

address: No. 1239, Siping Road

department: School of Life and Science

institute: Tongji University

description: 10X Genomics

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10× Genomics Cell Ranger V6.0mpipeline using default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: umbilical cord

extract_protocol:
The 6th passage UC-MSCs was collected and washed by 10 ml 1 x PBS+0.04 % BSA at 300 x g for 10 min. After cell counting, the cells were resuscitated to a concentration of 700-1200 cells/ul (viability was equal or greater than 85%) in a final solution of 1 x PBS + 0.04 % BSA prior to loading on the 10× Genomics Chromium platform.
Chromium Single cell 3’ Library and Gel Bead Kit V3.1 (10× Genomics, PN1000268) was used to generate single cell gel beads in emulsion (GEM). The captured cells were lysed, and the released RNA was reverse-transcribed with primers containing poly-T, barcode, unique molecular identifiers (UMIs) and read 1 primer sequence in GEMs. Barcoded cDNA was purified and amplified by PCR. The adapter ligation reaction was performed to add sample index and read 2 primer sequence. After quality control, the libraries were sequenced on Illumina Novaseq 6000 platform in 150 bp pair-ended manner.

value: umbilical cord

value: mesenchymal stem cells

tag: gender

value: female


title: HCC827 cells, 2


title: mESC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS16855A


title: [RNA-Seq] Case9 TET-5

city: Shiyan

first: Yan

last: Ding

address: People's Road

institute: Hubei university of medicine

description: Case9 TET-5

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level tab-delimited text file includes as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM
Assembly: UCSC hg19
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: cervical cancer

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

treatment_protocol: wild type or Cas9 TET1 SiHa cells were mainteined in DMEM supplemented with 10% fetqal bowineserum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

value: cervical cancer

value: SiHa cells

value: TET1 cas9

value: normal culture


title: M_UC-MSCs_P6

description: 10X Genomics

value: male


title: HCC827 cells, 1

value: lung

value: non-small cell lung cancer (NSCLC) cell line


title: mESC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS16854A

city: New York

value: mESC

value: C57BL6/6J x CAST/EiJ F1 hybrid

value: Capture-seq


title: REST_PAN_in_rep_2

institute: Rockefeller University

description: RNA-seq of all protein-bound RNAs in depolarized neurons transduced with Pan-TurboID, replicate 3

value: primary neuronal culture (cortical)

value: input

value: Chx


title: REST_PSD95_in_rep_2

description: RNA-seq of all protein-bound RNAs in depolarized neurons transduced with PSD95-TurboID, replicate 3


title: SA_2D

city: Cambridge

first: Conner

middle: Samuel

last: Kummerlowe

state: MA

address: 77 Massachusetts Avenue

institute: MIT

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastq files from bcl files
STAR was used to align the scRNA-seq data
Genome_build: hg19 ucsc genome studio

source_name: Distal duodenum

growth_protocol: Biopsies were obtained via endoscopy and dissociated into single-cells

extract_protocol: none provided by the submitter

value: Distal duodenum

tag: condition

value: dysphagia


title: mESC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS16851A


title: DEP_PSD95_pd_rep_1

description: RNA-seq of dendritic (PSD95-proximal) protein-bound RNAs in depolarized neurons, replicate 2

value: pulldown

value: Chx + KCl depolarization


title: [RNA-Seq] Case9 TET-3

description: Case9 TET-3

value: cervical cancer


title: [RNA-Seq] Case9 TET-4

description: Case9 TET-4

value: SiHa cells


title: Knockout_Alkb_and_NaBH4_Treated_TRAC-Seq

city: Guangzhou

first: Shuibin

last: Lin

state: China

address: Zhongshan 2nd road, Guangzhou

department: Clincial for Translational Medicine

institute: The First Affliliated Hospital, Sun Yat-sen University

description:
small RNA
TRAC-seq_expression.txt

data_processing:
Library strategy: TRAC-seq
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Fragments per kilo base per million mapped reads (FPKM) using edgeR.
For Ribo-Seq data analysis, adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases, respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Polyribosome_mRNA_expression.txt: Text file of RNA-seq includes the FPKM values for every gene.
Supplementary_files_format_and_content: Ribo-seq_reads.txt: Text file of Ribo-seq includes the FPKM values for every gene.
Supplementary_files_format_and_content: TRAC-seq_expression.txt: Text file of TRAC-seq represents the ratio and cleavage score for every tRNA in each sample.

source_name: Nasopharyngeal carcinoma 5-8F cells

growth_protocol: Human 5-8F cells were maintained in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco, USA). Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: METTL1 was knocked out by sgRNA.

value: Nasopharyngeal carcinoma cell line

value: METTL1 knockout

tag: sample type

value: TRAC-seq


title: SA_1D

tag: tissue


title: mESC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS16850A

tag: cell type


title: DEP_PSD95_in_rep_1

description: RNA-seq of all protein-bound RNAs in depolarized neurons transduced with PSD95-TurboID, replicate 2


title: mESC-Igf2_Igf2_dCTCFinICR~dIgf2~Sox2-BS16849A


title: [RNA-Seq] Wild-3

value: WT

value: normal culture


title: DEP_PAN_pd_rep_1

description: RNA-seq of all Pan-TurboID proximal protein-bound RNAs in depolarized neurons, replicate 2

value: Pan-TurboID


title: mESC-Igf2_Igf2_dCTCFinICR-BS17459A

value: mESC

value: C57BL6/6J x CAST/EiJ F1 hybrid


title: [RNA-Seq] Wild-2


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS16847A

value: Capture-seq


title: DEP_PAN_in_rep_1

description: RNA-seq of all protein-bound RNAs in depolarized neurons transduced with Pan-TurboID, replicate 2

value: primary neuronal culture (cortical)

value: input


title: Knockout_Alkb_Treated_Input_for_TRAC-Seq

description:
small RNA
TRAC-seq_expression.txt


title: Vector_Alkb_and_NaBH4_Treated_TRAC-Seq

description:
small RNA
TRAC-seq_expression.txt

value: Wild type


title: REST_PSD95_pd_rep_1

description: RNA-seq of dendritic (PSD95-proximal) protein-bound RNAs in resting neurons, replicate 2

value: Chx


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS16845A


title: Vector_Alkb_Treated_Input_for_TRAC-Seq

description:
small RNA
TRAC-seq_expression.txt


title: EoE_3D

growth_protocol: Biopsies were obtained via endoscopy and dissoicated into single-cells

value: eosinophilic esophagitis


title: REST_PAN_pd_rep_1

description: RNA-seq of all Pan-TurboID proximal protein-bound RNAs in resting neurons, replicate 2

value: pulldown


title: Wild-input

description: Wild-input

data_processing:
Raw data were generated after sequencing,  image analysis, base calling and quality filtering on Illumina HiSeq4000 sequencer.
Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.3) software, high quality clean reads were generated.
Then these clean reads were aligned to human reference genome  (UCSC hg19) using bowtie2  software  (v2.2.4) with default parameters. Peak calling was performed with MACS software (v1.4.3). Differentially methylated regions were identified by diffReps software (v1.55.4).
The methylated regions were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Assembly: UCSC hg19
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

extract_protocol:
Genomic DNA was isolated using phenol–chloroform and precipitated with ethanol.
MeDIP DNA libraries were quantified using Quant-iT PicoGreen dsDNA Kits (Life Technologies)

value: cervical cancer

value: cancer


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS16844A


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS16843A


title: EoE_2D


title: REST_PSD95_in_rep_1

description: RNA-seq of all protein-bound RNAs in resting neurons transduced with PSD95-TurboID, replicate 2


title: Wild-2

value: SiHa cells


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS16842A


title: REST_PAN_in_rep_1

description: RNA-seq of all protein-bound RNAs in resting neurons transduced with Pan-TurboID, replicate 2


title: Wild-1


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS16841A


title: EE_HIV_3D

value: environmental enteropathy


title: Case9 TET input

description: Case9 TET input

value: TET1 cas9


title: Harr

description: ribosomal profiling of pulldown fraction of cytosol region in dep neuron, replicate 1

data_processing:
Tab-delimited text files include RPKM values and counts for each sample.
Remove ribosomal reads: The processed reads were aligned to mouse ribosomal sequences (mm10) by Rsubread. The aligned reads were removed, and the filtered reads were converted into fastq format for the following analysis.
Align to mouse genome: The filtered reads were aligned to BSgnome (mm10) with Rsubread. The alignment results were stored as BAM format.
Annotation and counting: After alignment, Plastid was applied to count expression level of each transcript in each sample. Before counting, the annotation files for U5/CDS/U3 were derived from TxDb.Mmusculus.mm10.knownGene. The annotations were based on Ensembl transcript ID. Then, the counts for U5/CDS/U3 in each sample was calculated by Plastid. The RPKM value of each transcript id in each sample was gathered into single table for following analysis.
Assembly: Reference genome: Bsgenome.Mmusculus.UCSV.mm10; Annotation database: Txdb.Mmusculus.UCSC.mm10.knownGene.
Supplementary files format and content: Tab-delimited text files include RPKM values and counts for each sample.

extract_protocol:
RNA was extracted using the TRIzol protocol.
RNA was resolved by electrophoresis through a denaturing gel to isolate ribosome footprints. The expected size range fragments were extracted, and 3’ ends of these RNA fragments were treated with T4 polynucleotide ligase to ligate a pre-adenylated barcoded DNA linker to be able to pool samples. After treatment with deadenylase and RecJ, inputs and pulldowns were pooled, purified with Zymo columns, and were depleted of ribosome RNA (rRNA) using Ribo-Zero. Following rRNA removal, RNA was used as template for reverse transcription, using an oligo specifically designed to be able to sequence from the 5’end of the ribosome protected fragment. The single-stranded cDNA is then circularized using an optimized CircLigase after another gel purification step of full-length products. A double stranded DNA library is generated using the circularized cDNA fragments that are amplified with the Kapa enzyme and a fixed primer combined with an Illumina index encoding primer. The resulting products are gel purified from a non-denaturing gel and quantified on a bioanalyzer. Pooled libraries were then sequenced on the Illumina Novaseq 6000 sequencer.

treatment_protocol: Primary cortical neurons were either treated with nothing (WT), cycloheximide for 2 minutes (Chx), or harringtonine for 2 minutes followed by a Chx pulse (Harr).

value: Harringtonine


title: Case9 TET-5

description: Case9 TET-5

value: normal culture


title: [RNA-Seq] Wild-1

value: WT


title: EE_HIV_3J

source_name: Jejunum


title: WT

description: ribosomal profiling of input fraction of psd region in dep neuron, replicate 1

value: No treatment


title: Case9 TET-4

description: Case9 TET-4


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS16836A

value: mESC

value: C57BL6/6J x CAST/EiJ F1 hybrid


title: EE_HIV_3B

source_name: Duodenal bulb


title: EE_HIV_2D


title: Wild-3


title: DM13

first: Michelle

middle: E

last: Ehrlich

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Paired-end reads were aligned to the reference genome using STAR
FeatureCounts was used to count the read numbers mapped per gene
Readcounts were adjusted by TMM normalisation
DESeq2 R package was used to perform differential expression analysis.
P-values were adjusted using Benjamini Hochberg method
Genome_build: Mus musculus Grch38
Supplementary_files_format_and_content: .txt file containing a matrix of genes with readcounts against samples

source_name: striatal microglia

extract_protocol:
The striatal microglia from two striata were purified using MACS.  After purification, microglia was flash frozen on dry ice, and RNA was harvested using miRNA Micro Kit
RNA sequencing was performed by Genomics Technology Facility, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai using SMART-Seq v4 Ultra Low Input kit

tag: Sex

value: male


title: DM16

value: female


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS16837A

value: Capture-seq


title: siUBA52-3

last: Tong

state: Anhui

address: 218 Jixi Road

department: Department of General Surgery

institute: The First Affiliated Hospital of Anhui Medical University

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool,BMKCloud(www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome
The StringTie Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from Hisat2 alignment results
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)； Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Assembly: Differential expression analysis of two conditions/groups was performed using the DESeq2. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.01 & Fold Change≥2 found by DESeq2 were assigned as differentially expressed
Supplementary files format and content: The differentially expressed gene sets were used as candidate genes, and transcription factors (TFs) were predicted with TFDB database by hmmsearch for animal and human.(Human and mouse species only
Supplementary files format and content: Fusion Genes were detected using the Fusionmap software.(Human and mouse species only)

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo- attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.

value: UBA52 knockdown


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS16835A


title: EoE_1D

value: eosinophilic esophagitis


title: Case9 TET-3

description: Case9 TET-3


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS16040A


title: mESC-Igf2_Igf2_miICR~dIgf2~Sox2-BS16840A


title: EE_HIV_2B


title: EE_HIV_1J


title: siUBA52-2


title: DM11


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS16034A


title: DM5


title: Chx

description: ribosomal profiling of input fraction of cytosol region in dep neuron, replicate 1

value: primary neuronal culture (cortical)

value: Cycloheximide


title: siNC-3

value: negative control


title: HD17


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS16033A


title: EE_HIV_1D


title: siUBA52-1


title: HD14


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS16026A


title: siNC-2


title: EE_8D


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS16042A


title: DM12


title: HD9


title: siNC-1


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS16024A


title: EE_8B


title: HD4


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS16023A


title: NPC268_cell_line_WGBS

city: Subang Jaya

first: Sok Ching

last: Cheong

state: Selangor

address: No. 1, Jalan SS12/1A,

department: Translational Cancer Biology

country: Malaysia

institute: Cancer Research Malaysia

description: bisulfite-converted DNA

data_processing:
Trimmomatic was used to discard the adapter sequences and poor quality bases/reads.
BSMAP was used for mapping the high-quality reads onto the human genome and EBV genome.
Methylation levels at base-pair resolution were quantified using BSMAP.
BSMAP output files were converted into bedgraph files,which were subsequently converted into bigwig files for visualization on genome browser.
Assembly: hg19, NC_007605
Supplementary files format and content: bigwig

extract_protocol:
EpiTect Bisulfite Kit (Qiagen Cat# 59104)  was used for bisulfite conversion. The 0.5% Unmethylated  Lambda DNA (Promega Cat# D1521) was spiked  in for assessing the bisulfite conversion efficiency. For  the cell lines, WGBS was performed by Novogene.
Accel-NGS Methyl-Seq DNA Library Kit

value: Human nasopharyngeal carcinoma


title: EE_7D

value: environmental enteropathy


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS16018A


title: EE_HIV_1B


title: HD3


title: EE_8J


title: HepG2, sericin 1, Rep1

city: Bangkok

first: Jiraporn

last: Jantaravnid

state: Prathunwan

address: 254 Phrayathai road, Wang-Mai

country: Thailand

institute: Chulalongkorn University

description:
Illumina HiSeq/ Illumina Novaseq/ MGI2000
Sericin-1-A

data_processing:
Quality control was proceessed by CutAdapt software V1.9.1 (phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
Sequence reads were mapped to reference genome using Hisat2 (v2.0.1)
Expression analysis was performed by using HTSeq (v0.6.1) generating counts files.
Supplementary files format and content: tab-delimited text files include FPKM values for all Samples

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 20 ug of total RNA was used for the construction of sequencing libraries.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: HepG2 cells were treated by sericin at 0.125 mg/ mL and 1 mg/ mL for 24 hrs.

value: Hepatocellular carcinoma cells

value: Sericin 1 mg/ mL


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS16017A

state: New York


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS16016A


title: EE_7B


title: KO19

value: Tyrobp-KO


title: HepG2, sericin 0.125, Rep2

description:
Illumina HiSeq/ Illumina Novaseq/ MGI2000
Sericin-0.125-C

value: WT

value: Sericin 0.125 mg/ mL


title: EE_6J


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS16009A

value: mESC


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS16008A

value: C57BL6/6J x CAST/EiJ F1 hybrid


title: HepG2, untreated cells, Rep2

description:
Illumina HiSeq/ Illumina Novaseq/ MGI2000
Control-B

value: Untreated


title: KO15

value: female


title: WT8

value: male


title: HepG2, untreated cells, Rep1

description:
Illumina HiSeq/ Illumina Novaseq/ MGI2000
Control-A


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS16007A

value: Capture-seq


title: HepG2, sericin 1, Rep2

description:
Illumina HiSeq/ Illumina Novaseq/ MGI2000
Sericin-1-C


title: EE_6B


title: EE_7J


title: Differentiating cells Day 30 PA-IVS-1v

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

data_processing:
Samples were preprocessed using 10X Genomics Chromium Single Cell RNA v3 chemistry. Libraries were sequenced on an Illumina Novaseq instrument and counted with CellRanger v6.0.2 using hg38 reference genome.
Assembly: hg38
Supplementary files format and content: csv for count matrix, and metadata

growth_protocol: Human induced pluripotent stem cells were cultured in Essential 8 medium (Thermo Fisher Scientific). Cardiac differentiation was performed by sequential modulation of WNT signaling by small molecules (CHIR99021 for 2 days and IWR-1 for 2 days) as we previously published (PMID: 33645570).

extract_protocol:
Single-cell suspension was processed and loaded into a Chromium Next GEM Chip G (10x Genomics) to generate single-cell gel bead in emulsions on a 10x Genomics Chromium Controller.
Single-cell RNA-seq libraries were constructed using a Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics).

treatment_protocol: Differentiating cells were collected on Day 5, Day 10, Day 14, and Day 30 during cardiac differentiation of healthy control and PA-IVS-1v iPSCs.

value: Human iPSC

tag: disease state

tag: time


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS16006A

tag: strain


title: WT6

state: NY

tag: genotype


title: EE_5B


title: WT2


title: mESC-LP300-BS15725A

tag: payload id


title: Differentiating cells Day 14 PA-IVS-1v


title: HepG2, sericin 0.125, Rep1

description:
Illumina HiSeq/ Illumina Novaseq/ MGI2000
Sericin-0.125-A


title: EE_4D


title: Differentiating cells Day 10 PA-IVS-1v


title: EE_4B


title: mESC-LP300-BS15526A

tag: clone id


title: Differentiating cells Day 5 PA-IVS-1v


title: WT1


title: EE_3D


title: WT7


title: EE_5D


title: mESC-Igf2_Igf2_inverted~dEnh~dCTCFinICR-BS15523A

tag: seq method


title: EE_6D


title: KO20


title: mESC-Igf2_Igf2_inverted~dEnh~dCTCFinICR-BS15294A


title: EE_2D


title: Differentiating cells Day 10 Control

value: Control


title: Differentiating cells Day 30 Control


title: mESC-Igf2_Igf2_inverted~dEnh~miICR-BS15288A


title: EE_2B


title: EE_3B


title: Differentiating cells Day 5 Control


title: EE_1D


title: mESC-Igf2_Igf2_inverted~dEnh~miICR-BS15290A


title: HCC827 cells, Osimertinib Resistance, 2

last: Zhang

data_processing:
Trimmed sequence reads were mapped to GRCh38/hg38 using bwa-mem
Mutations were identified following GATK best practice.
Duplicate reads were identified and removed by Picard, and Local Indel Realignment and Base Score Recalibration was applied to deduplicated reads using GATK
Somatic variants were called with Mutect2 and annotated by annovar.
Assembly: hg38
Supplementary files format and content: VCF file containing all mutations identified.
Library strategy: WES

extract_protocol:
We extract genomic DNA from the cultured cells following the manufacture's protocol (The QIAamp DNA Mini Kit (cat. nos. 51304 and 51306) ).
The exome sequences were efficiently enriched from 0.4 μg genomic DNA using Agilent liquidcapture system (Agilent SureSelect Human All Exon V6) according to the manufacturer’s protocol. Firstly, qualified genomic DNA was randomly fragmented to an average size of 180-280bp by Covaris S220 sonicator. Remaining overhangs were converted into blunt ends via exonuclease polymerase activities. Secondly, DNA fragments were end repaired and phosphorylated, followed by A-tailing and ligation at the 3’ends with paired-end adaptors. DNA fragments with ligated adapter molecules on both ends were selectively enriched in a PCR reaction. After PCR reaction, libraries hybridize with liquid phase with biotin labeled probe, then use magnetic beads with streptomycin to capture the exons of genes. Captured libraries were enriched in a PCR reaction to add index tags to prepare for sequencing. Products were purified using AMPure XP system (Beckman Coulter, Beverly, USA), DNA concentration was measured by Qubit®3.0 Flurometer (Invitrogen, USA), libraries were analyzed for size distribution by NGS3K/Caliper and quantified by real-time PCR (3 nM). At last, DNA library were sequenced on Illumina for pairedend 150bp reads.

treatment_protocol: Cells were treated with or without the osimertinib with gradually increased concentration, the primary osimertinib concentration is 100nM.

value: lung

tag: cell line

value: non-small cell lung cancer (NSCLC) cell line

value: Osimertinib Resistance


title: WTCW2

city: Qingdao 266237

first: Ma kexuan

last: Qin yuqi

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

institute: Shandong University

description: WTCW2 FPKM

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: All_samples.GeneExpression.FPKM.txt

organism: Penicillium oxalicum

source_name: fungal cell

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 1% bran + 1% microcrystalline cellulose as carbon resources for 18h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fungal cell

value: 114-2 (wild type)

tag: treatment

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: mESC-LP300-BS15724A


title: WTCW3

description: WTCW3 FPKM


title: WTCW1

description: WTCW1 FPKM


title: EE_1B

value: environmental enteropathy


title: mESC-Igf2_Igf2_inverted~dCTCFinICR-BS15286A


title: mESC-Igf2_Igf2_inverted~dCTCFinICR-BS15284A


title: HCC827 cells, Osimertinib Resistance, 1


title: DLD-1 cells, oeTNFRSF12A, rep3

first: Chuyue

address: Tianhe District, Guangzhou, Guangdong Province

institute: Sun Yat-Sen University

description: processed_counts.xlsx for all RNA-Seq samples

data_processing:
The sequencing data was filtered with SOAPnuke (v1.6.5) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
The clean data were mapped to the GRCh38/hg38 by HISAT (v2.2.1) , then were mapped to the assembled unique gene by Bowtie2 (v2.4.5)
The expression level of genes was calculated by RSEM (v1.3.1)
Assembly: GRCh38/hg38
Supplementary files format and content: xlsx format file includes raw counts for each sample

source_name: Large intestine; Colon

growth_protocol: DLD-1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) with 5% CO2 at 37℃

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen). A certain amount of RNA was used for library construction
(1) Sample QC (2) mRNA Isolation by oligo (dT) -attached magnetic beads (3) mRNA Fragmentation (4) cDNA Synthesis (5) End Repair, Add A and Adaptor Ligation (6) PCR (7) Library QC

treatment_protocol: TNFRSF12A overexpression was induced by treatment with 0.1 μg/mL Doxycycline for 48 h

value: Large intestine; Colon

value: epithelial cell

value: TNFRSF12A overexpression

value: Doxycycline treating 48 h