title: 841CON_INPUT-1

value: colon

tag: cell line

tag: cell type

tag: genotype

value: WT


title: Sample61.Prairie vole.204529320081_R01C01

status: Public on Aug 07 2023

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Ear species=Prairie vole

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

molecule: genomic DNA

organism: Microtus ochrogaster

source_name: Ear

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: tissue

value: Ear

tag: age

tag: confidenceinageestimate

tag: Sex

value: Male

value: Sex naïve

tag: animalid


title: Sperm_untreated_NanoNOME_Whole_genome

type: SRA

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

library_source: genomic

data_processing:
Base calling was performed on the raw FAST5 files with Guppy (v.3.0.3 or v.5.0.11, ONT), using a configuration file for high-accuracy DNA base calling on an R10.4.1 pore at 450 bases s–1. The resulting reads were then mapped to the mm10 mouse reference genome without alternate contigs using minimap2 v.2.11 with default settings for alignment of nanopore reads (-x map-ont). Reads that mapped with a quality score <50 were then filtered out using samtools v.1.7. CpG and GpC methylation were simultaneously called on the remaining reads using nanopolish v.0.11.1. Average CpG methylation was calculated for each group of CpGs that did not contain any GCGs. To visualize the methylation patterns of the reads with IGV v.2.12.2, we modified the individual reads in the alignment (BAM) files. All cytosines called as unmethylated were converted to thymine to simulate bisulfite conversion. This was achieved using code adapted from the Timp Laboratory’s nanopore-methylation-utilities (https://github.com/ timplab/nanopore-methylation-utilities). Once these converted files were loaded in IGV, we were then able to visualize methylation using IGV’s bisulfite mode. Tiled data file tracks showing aggregated CpG methylation levels were generated with igvtools v.2.4.16.
Assembly: mm10
Supplementary files format and content: methylation calls(tsv)
Library strategy: nanopore-methylation

organism: Mus musculus

source_name: Sperm

extract_protocol:
About 2 million sperm were on-ice lysed with hypotonic lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin) for 10 min. Sperm were pelleted down and resuspended in 500 ul of 1x GpC buffer containing 150 μl of 1 M sucrose, 1.5 μl of 32 mM S-adenosylmethionine (SAM; NEB, B9003) and 50 μl of M.CviPI (NEB, no. M0227L). The suspension was carefully mixed and incubated for 7.5 min at 37 °C, followed by a boost with an additional 25 μl of M.CviPI and 1.5 μl of SAM for 7.5 min. The reaction was stopped by the addition of 25 μl of 10% SDS, 5 μl of 0.5 M EDTA, 6 μl of 20mg/mL proteinase K, and 28 μl of 1M DTT followed by overnight incubation at 55 °C. The total sperm DNA was recovered by PCI and ethanol precipitation.
For whole-genome nanopore sequencing, 1 ug of sperm DNA was used for library preparation using Oxford Nanopore Ligation-based library prep kit (ONT, SQK-LSK110). For target-enriched sequencing, single-stranded CRISPR–Cas9 DNA oligonucleotides (20 nt) were designed using the ChopChop v.3 designer tool (chopchop.rc.fas.har- vard.edu) and purchased from IDT. sgRNA were prepared using EnGen@sgRNA synthesis kit (NEB, no. E3322S). RNP complexes were assembled individually by combining 8 μl of nuclease-free water, 1.5 μl of NEBuffer r3.1 (NEB), 3 μl of 300 nM sgRNA, 1 μl of Cas9 Nuclease (NEB, no. M0386), followed by a 20-min incubation at 25 °C. The different RNP complexes were then pooled in a single tube. Per experiment, 3-4 μg of sperm gDNA was dephosphorylated with 10 μl of rSAP (NEB, no. M0371S) and 16 μl of 10× rCutSmart buffer (NEB, no. B6004S) for 30 min at 37 °C, then heat inactivated at 65 °C for 5 min. DNA was then purified through PCI and ethanol precipitation. The dephosphorylated DNA sample was then combined with the pool of RNP complexes in a 1:9 ratio. The reaction was incubated for 30 min at 37 °C to enable Cas9 cleavage. After digestion, Cas9 was inactivated by the addition of a 1/25 volume of 20 mg/mL proteinase K followed by a 15-min incubation at 55 °C. Cleaved and purified DNA was purified by PCI and ethanol precipitation and was subjected to dA-Tailing using Klenow Fragment (NEB, no. E6053). Reactions were incubated for 30 min at 37 °C and immediately subjected to adapter ligation as per the manual of Oxford Nanopore Ligation-based library prep kit (ONT, SQK-LSK110).

value: Sperm

tag: treatment

value: GpC methylase (NEB)


title: Sample57.Prairie vole.204529320068_R03C02

description: genomic DNA methylation from tissue=Liver species=Prairie vole

source_name: Liver

value: Liver


title: S22

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
FastQC (Version 0.72) was performed on the concatenated replicate raw sequencing paired-end reads from each library to ensure minimal PCR duplication and sequencing quality.
Reads were aligned to the mouse mm10 genome using HISAT2 (Version 2.1.0) and annotated against Ensembl v90.
After removal of multiple-aligned reads, remaining reads were counted using featurecounts (Version 2.0.1) with default parameters, and filtered to remove genes with low counts (<10 reads across samples).
For male 48-hr CSDS RNA-seq, RUVg was performed to normalize read counts based on empirically determined control genes that do not vary between control and susceptible groups (i.e. genes with p-val > 0.5 based on a first-pass differential expression analysis performed prior to RUVg normalization). For female RNA-seq experiments and the serotonylation manipulation experiments with the Q5A virus, RUVr was performed to normalized read counts based on the residuals from a first-pass GLM regression of the unnormalized counts on the covariates of interest.
DESEQ2 (Version 2.11.40.6) was used to perform pairwise differential expression analyses between indicated comparisons.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing raw counts

molecule: polyA RNA

source_name: adult (6-wk) dorsal raphe nucleus tissue

extract_protocol:
RNA-seq, RNA was harvested using Rneasy Micro kit (Qiagen). 300 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Truseq RNA Library Prep Kit V2 following manufacturer's protocols.

tag: group

value: SUS

tag: condition

tag: virus


title: S19

value: adult (6-wk) dorsal raphe nucleus tissue

value: CON


title: 39_TublularAdenoma_22

city: Seoul

first: Jaeseung

last: Song

department: Life Science

country: South Korea

institute: Dongguk University

data_processing:
Base-calling were performed using real time analysis.
Raw data were cleaned with BBduk (ver 38.8.1).
Cleaned FASTQ files were aligned to reference genome using STAR aligner (ver. 2.7.3a) with default setting.
Aligned files were then converted into BAM files using Samtools (ver 1.10).
HTSeq (ver. 0.11.4) were used for extracting read counts.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Table in txt file format having Ensemble gene identifiers as rownames and Samples in column. Each values were normalized and transformed into log2(cpm +1).

molecule: total RNA

organism: Homo sapiens

source_name: Tubular adenoma

extract_protocol:
Dissected samples were treated with Trizol and stored at -80℃ in a deep freezer.
Library was constructed using SureSelectXT RNA Direct Reagent Kit (Agilent, Santa Clara, CA, USA) following manufacturer's protocol.

tag: patient id no.

value: M

tag: date

tag: diagnosis

value: Tubular adenoma in the background of hyperplastic polyp with low grade dysplasia

tag: location

value: Sigmoid colon

tag: other diseases

value: Hypertension, diabetes mellitus, dyslipidemia, cerebral infarction


title: Sample64.Prairie vole.204529320081_R04C01

value: Pair bonded


title: CCB070022

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Hisat2 mapping to genome
FeatureCount summarization to gene read count
addition of 3 reads to all values
quantile normalization
Assembly: CanFam3.1
Supplementary files format and content: tab delimited txt file of normalized counts

organism: Canis lupus familiaris

source_name: osteosarcoma tumor tisue

growth_protocol: fresh frozen tumor tissue

extract_protocol:
Ambion miRvana kit.
Illumina paired end RNA-Seq standard

value: osteosarcoma tumor tisue

tag: breed

value: Irish Wolfhound

tag: tumor location

value: Radius


title: 841CON_INPUT-2

city: Harbin

first: Jing

last: Tang

state: Heilongjiang

address: No. 157 Baojian Road, Nangang District

country: China

institute: Harbin medical university

data_processing:
The generated reads were processed using Cutadapt (v3.5) to remove adaptors and perform quality-based trimming.
The ribosome-protected fraction (RPF) and input reads were mapped to the GRCh38 reference genome using STAR (v2.7.9).
Reads with lengths of 25-50 nts and 50-150 nts were used for RPF and input mapping, respectively. HTseq (v2.0.2) was employed to analyze the Ribo-seq and RNA-seq data.
The Xtail R package was applied to analyze changes in translation efficiency (TE) of genes across different cells
Assembly: GRCh38
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Library strategy: Ribo-seq

source_name: colon

growth_protocol: DMEM for 293TN and HCT15, L15 for SW620, RPMI-1640 for HCT116, and EMEM for 841-CON. The culture media were supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin. Cell cultures were maintained at 37°C in a 5% CO2 chamber, except for SW620, which was cultured in an air incubator.

extract_protocol:
The samples were then subjected to ultracentrifugation (38,000 rpm, 3 hours, 4℃), and the ribosome-protected RNA fragments were isolated using the RNA Clean and Concentrator-25 kit (Zymo Research, USA).
Subsequent steps involved rRNA removal and construction of cDNA libraries using the Next Multiple Small RNA library preparation Set for Illumina (New England Biolabs, USA) as described previously, The constructed cDNA libraries were sequenced using the Illumina HiSeqTM ×10 platform

treatment_protocol: The cells were treated with  Cycloheximide (CHX) (100μg/mL) at 37℃ for 10 minutes.  The collected cells were lysed using a lysis buffer (20mM Tris-HCl, pH 7.4, 5mM Mgcl2, 150mM NaCl, 1% Triton X-100, RNase inhibitor, 1× protein inhibitor, 100μg/mL CHX and 1mM DTT). A 10%-50% sucrose gradient was prepared, and the cell lysate was centrifuged at 15,000 rpm for 15 minutes. The supernatant was loaded onto the prepared sucrose gradient solution and centrifuged at 4℃, 38,000 rpm for 3 hours using a Beckman rotor SW41Ti.

value: colon

tag: cell line

tag: cell type

value: normal colon epithelium cell

tag: genotype

value: WT


title: 35_TubulovillousAdenoma_6

source_name: Tublovillous adenoma

tag: age

value: F

value: Tubulovillous adenoma with low grade dysplasia

value: Transverse colon

value: Dyslipidemia


title: S18

tag: tissue

value: adult (6-wk) dorsal raphe nucleus tissue


title: Sperm_untreated_NanoNOME_Cas9_targeted

value: Sperm

value: GpC methylase (NEB)


title: S21

value: RES


title: Sample58.Prairie vole.204529320068_R04C02

value: Ear

tag: confidenceinageestimate

tag: Sex

value: Male

value: Sex naïve

tag: animalid


title: Sample59.Prairie vole.204529320068_R05C02

value: Female


title: Sample56.Prairie vole.204529320068_R02C02


title: Sample55.Prairie vole.204529320068_R01C02

value: Liver

value: Pair bonded


title: 34_TubularAdenoma_19

value: M

value: Tubular adenoma with low grade dysplasia

value: Rectum


title: 37_TubularAdenoma_20

value: Descending colon

value: Hypertension, diabetes mellitus, dyslipidemia


title: S20

tag: group

tag: condition


title: Patient 1 Group: Exercise (Baseline) L001

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing:
FASTQC toolkit was performed for quality control of FASTQ files
The fastp tool was performed to trim adapters and low-quality reads
Cleaned reads of total RNA sequencing were aligned to the reference genome using the STAR RNA sequencing aligner.
Feature counts were calculated by subread v2.0.02 from the bam files generated from STAR
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: rectosigmoid colon

extract_protocol:
Total RNA was extracted using direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA, USA) ac-cording to manufacturer’s instructions
Sample preparation, library construction, and RNA sequencing were performed at MDACC Ad-vanced Technology Genomics Core Facility using the NovaSeq6000 S1-200 (100nt PE format).

value: colorectal mucosa

tag: patient id

tag: race

value: White or Caucasian

tag: ethinicity

value: Not Hispanic or Latino

tag: gene mutated

value: Exercise

tag: visit

value: Baseline


title: CCB080013

value: osteosarcoma tumor tisue

tag: breed

value: Mixed Breed

value: Tibia


title: CCB080001

value: Great Pyrenees

tag: tumor location


title: 36_SessileSerratedAdenoma/Polyp_4

source_name: SSA/P

tag: patient id no.

value: F

tag: date

tag: diagnosis

value: Sessile serrated adenoma/polyp

tag: location

value: Ascending colon

tag: other diseases

value: Primary biliary cirrhosis, nonalcoholic steatohepatitis, hypertension, diabetes mellitus


title: CCB070015

tag: tissue

value: Belgian Sheepdog

value: Radius


title: S17

value: adult (6-wk) dorsal raphe nucleus tissue

value: CON

tag: virus


title: S13

value: RES


title: CCB060038

value: Rhodesian Ridgeback

value: Other Site


title: S14


title: CCB050020

value: Doberman Pinscher

value: Humerus


title: S16

value: SUS


title: Sample53.Prairie vole.204529320068_R05C01

value: Ear

tag: age

tag: confidenceinageestimate

tag: Sex

value: Female

value: Sex naïve

tag: animalid


title: CCB060083

value: osteosarcoma tumor tisue

value: Mixed Breed

value: Femur


title: Sample54.Prairie vole.204529320068_R06C01

value: Liver

value: Male


title: Sample51.Prairie vole.204529320068_R03C01


title: S12

tag: group

tag: condition


title: 30_TraditionalSerratedAdenoma_1

source_name: Traditional serrated adenoma

value: M

value: Traditional serrated adenoma with low grade dysplasia

value: Transverse colon


title: 31_TubularAdenoma_16

value: Tubular adenoma with low grade dysplasia

value: Sigmoid colon

value: Dyslipidemia


title: 32_TubularAdenoma_17

value: Tubular adenoma with 1) focal high grade dysplasia 2) low grade dysplasia


title: CCB050015

value: Golden Retriever

value: Humerus


title: 29_TubularAdenoma_15

value: Descending colon

value: Hypertension, allergic rhinitis


title: S11

value: adult (6-wk) dorsal raphe nucleus tissue

value: CON


title: 33_TubularAdenoma_18

value: Ascending colon


title: 28_TubularAdenoma_14


title: S15

value: SUS


title: CCB050001

value: osteosarcoma tumor tisue

value: Mixed Breed

value: Femur


title: S10


title: CCB040155

value: Ulna


title: Sample52.Prairie vole.204529320068_R04C01

value: Ear

value: Female

value: Pair bonded


title: S9

value: RES


title: CCB030334

value: Labrador Retriever


title: 27_NeuroendocrineTumor_1

source_name: Neuroendocrine tumor

value: M

value: Neuroendocrine tumor

value: Rectum

value: Hypertension, diabetes mellitus, cerebral infarction


title: 26_TubularAdenoma_13

value: F

value: Tubular adenoma with low grade dysplasia

value: Sigmoid colon


title: Sample50.Prairie vole.204529320068_R02C01

value: Sex naïve


title: Sample47.Prairie vole.204529320082_R05C02

value: Liver


title: Sample48.Prairie vole.204529320082_R06C02


title: Sample49.Prairie vole.204529320068_R01C01


title: S8

value: adult (6-wk) dorsal raphe nucleus tissue


title: CCB030328

value: osteosarcoma tumor tisue

value: Greyhound

value: Femur


title: Sample46.Prairie vole.204529320082_R04C02

value: Ear

value: Male


title: 25_AtypicalGlands_1

source_name: Atypical glands and adjacent hyperplastic mucosa

value: A few atypical glands and adjacent hyperplastic mucosa (insufficient for diagnosis) * 내시경 소견은 colon cancer

value: Hypertension, dementia


title: Sample44.Prairie vole.204529320082_R02C02

value: Pair bonded


title: Sample45.Prairie vole.204529320082_R03C02


title: 38_TubularAdenoma_21

value: M

value: Descending colon


title: CCB030306

value: Mixed Breed

value: Ulna


title: CCB030221

value: Labrador Retriever

value: Radius


title: 23_HighGradeDysplasia_1

source_name: High grade dysplasia

value: High grade dysplasia VS. Well differentiated adenocarcinoma

value: Ascending colon

value: Hypertension, prostate cancer


title: S5

value: adult (6-wk) dorsal raphe nucleus tissue

value: SUS


title: S6


title: 22_IntramucosalAdenocarcinoma_1

source_name: Intramucosal adenocarcinoma

value: Intramucosal adenocarcinoma, well differentiated arising in tubulovillous adenoma

value: Rectum

value: Hypertension


title: CCB030198

value: osteosarcoma tumor tisue

value: Australian Cattle Dog

value: Femur


title: S4


title: CCB030175

value: Great Dane


title: 21_TubulovillousAdenoma_5

value: M

value: Tubulovillous adenoma low grade dysplasia

value: Sigmoid colon

value: Hypertension, liver abscess


title: Sample43.Prairie vole.204529320082_R01C02

value: Liver

value: Male

value: Sex naïve


title: S3

value: CON


title: CCB030153

value: Labrador Retriever

value: Humerus


title: S7

value: adult (6-wk) dorsal raphe nucleus tissue

value: RES


title: 20_TubularAdenoma_11

value: F

tag: allergy

value: Without drugs

value: Tubular adenoma with 1) focal high grade dysplasia 2) low grade dysplasia

value: Rectum

value: Cholangiocarcinoma, hypertension, diabetes mellitus


title: 24_TublarAdenoma_12

value: Cecum

value: Hypertension, dyslipidemia, chronic kidney disease


title: Sample42.Prairie vole.204529320082_R06C01

value: Female


title: 19_TubularAdenoma_10

value: M

value: Ascending colon

value: Liver cirrhosis, hypertension, gout


title: S2


title: Sample41.Prairie vole.204529320082_R05C01

value: Liver

value: Pair bonded


title: CCB030143

value: osteosarcoma tumor tisue

value: Labrador Retriever

value: Radius


title: Sample39.Prairie vole.204529320082_R03C01

value: Ear

value: Male

value: Sex naïve


title: Sample40.Prairie vole.204529320082_R04C01


title: S1

value: adult (6-wk) dorsal raphe nucleus tissue

value: CON


title: CCB030129

value: Mixed Breed

value: Humerus


title: KD3

city: Guangzhou

first: Tingting

last: zhang

address: zhongshan 2rd road,72

institute: Sun Yat-sen University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA-seq libraries were checked for quality using the Agilent Bioanalyzer High Sensitivity chip.
Sequencing results were converted to FASTQ files using Illumina bcl2fastq software (version 5.01).
Raw data were demultiplexed, barcode and mapped to the goat reference genome using the Cell Ranger package (version 3.1.0).
Feature-barcode raw digital gene expression matrix (UMI counts per gene per cell) was filtered and normalized by using the R package Seurat  (Version 3.1.1).
Genes detected in fewer than one cell were filtered out, and cells were removed if they expressed fewer than 500 detected genes, UMI counts less than Inf, and the percent of mitochondrial-DNA derived gene-expression < 25%. The Doublet Finder package (version 2.0.3) was also used to remove doublets.
Assembly: Mus_musculus.GRCm38.96
Supplementary files format and content: Tab-separated values files and matrix files

source_name: aortic tissue

extract_protocol:
The aortic tissue of the mice was washed with 4°C normal saline solution containing 3% FBS (Thermo Fisher Scientific, Inc.) to remove attached blood clots. The tissue was cut into pieces as small as possible and dissociated into individual cells according to the protocol of the 10 × Genomics platform
The double-ended sequencing mode of the Illumina sequencing platform was used to carry out high-throughput sequencing of the constructed libraries.

value: aortic tissue

tag: genotype


title: 18_TubularAdenoma_9

value: Without drugs

value: Tubular adenoma with low grade dysplasia

value: Descending colon

value: Dyslipidemia


title: 17_InflammatoryPolyp_1

source_name: Inflammatory polyp

value: M

value: Inflammatory polyp


title: CCB030122

value: osteosarcoma tumor tisue

tag: breed

value: Weimaraner

value: Femur


title: KD2

description: 10x Genomics


title: Sample38.Prairie vole.204529320082_R02C01

source_name: Ear

value: Ear

value: Female


title: 15_TublarAdenoma_8

value: Cecum


title: CON3

description: 10x Genomics


title: CCB030081

value: Great Pyrenees

tag: tumor location

value: Radius


title: CCB030104

value: Irish Wolfhound


title: 16_TubulovillousAdenoma_4

tag: patient id no.

value: F

value: Tubulovillous adenoma with high grade dysplasia

value: Rectum

value: Hypertension, cerebral atherosclerosis, cervial radiculopathy


title: CCB030096

value: Labrador Retriever


title: 14_TubulovillousAdenoma_3

tag: date

value: Tubulovillous adenoma with 1) high grade dysplasia 2) focal carcinomatous change

value: Ascending colon

value: Diabetes mellitus, dyslipidemia


title: CCB030080

value: osteosarcoma tumor tisue

value: Mixed Breed

value: Ulna


title: CON2

description: 10x Genomics

value: aortic tissue


title: 13_TublarAdenoma_7

value: M

tag: diagnosis

value: Tubular adenoma with 1) focal carcinomatous change 2) high grade dysplasia

value: Hypertension, aortic dissection


title: CON1

description: 10x Genomics


title: CCB020248

value: Greyhound

value: Humerus


title: 12_TublarAdenoma_6

value: Allergy (Band-aid, patch)

value: Tubular adenoma with low grade dysplasia

tag: location

value: Sigmoid colon

value: Hypertension, dyslipidemia, coronary artery disease, gastric cancer, cataract


title: KD1

description: 10x Genomics


title: CCB020239

value: Old English Sheepdog

value: Radius


title: Sample36.Prairie vole.204529320084_R06C02

value: Liver

value: Male

value: Sex naïve


title: Sample35.Prairie vole.204529320084_R05C02

value: Ear

value: Female

value: Pair bonded


title: CCB020156

value: osteosarcoma tumor tisue

value: Golden Retriever


title: Sample33.Prairie vole.204529320084_R03C02


title: 11_HyperplasticPolyp_1

source_name: Hyperplastic polyp

value: M

value: Hyperplastic polyp

tag: other diseases


title: Sample34.Prairie vole.204529320084_R04C02

source_name: Liver

tag: tissue


title: Sample30.Prairie vole.204529320084_R06C01


title: Sample31.Prairie vole.204529320084_R01C02


title: Sample32.Prairie vole.204529320084_R02C02


title: 9_SessileSerraedAdenoma/Polyp_2

value: F

value: Sessile serrated adenoma/polyp

value: Ascending colon


title: CCB020143

value: Greyhound

value: Tibia


title: 10_SessileSerraedAdenoma/Polyp_3

value: Sessile serrated adenoma/polyp with no cytologic dysplasia

value: Cecum


title: CCB020116

value: Mixed Breed


title: CCB020110

value: Ulna


title: CCB020108

value: Femur


title: 6_TublarAdenoma_4

value: Tubular adenoma with low grade dysplasia (mild to moderate dysplasia)

value: Sigmoid colon

value: Hypertension, diabetes mellitus, dyslipidemia, atrial fibrillation, cerebral infarction, chronic kidney disease, gout, benign prostatic hyperplasia


title: 8_SessileSerraedAdenoma/Polyp_1


title: 7_TublarAdenoma_5

value: Tubular adenoma with low grade dysplasia

value: Hypertension, neurogenic bladder


title: CCB020096

value: osteosarcoma tumor tisue


title: 5_TubulovillousAdenoma_2

value: M

value: Tubulovillous adenoma with 1) focal high grade dysplasia, 2) low grade dysplasia (low to moderate dysplasia)

value: Transverse colon

value: Spinal cord injury, dyslipidemia


title: CCB020094

value: Greyhound


title: Sample29.Prairie vole.204529320084_R05C01

value: Liver

value: Female

value: Pair bonded


title: 4_TubulovillousAdenoma_1

value: Tubulovillous adenoma with low grade dysplasia (mild to moderate dysplasia)

value: Hypertension


title: Sample28.Prairie vole.204529320084_R04C01


title: CCB020085

value: Humerus


title: CCB020083


title: 3_TublarAdenoma_3

value: Hypertension, dyslipidemia, cerebral infarction


title: 2_TublarAdenoma_2

value: Ascending colon


title: 1_TublarAdenoma_1

value: Hypertension, dementia, benign prostatic hyperplasia


title: CCB020082

value: Labrador Retriever


title: Sample26.Prairie vole.204529320084_R02C01

value: Ear

value: Male


title: Sample27.Prairie vole.204529320084_R03C01

value: Sex naïve


title: Sample23.Prairie vole.204529320083_R05C02


title: Sample24.Prairie vole.204529320083_R06C02


title: Sample25.Prairie vole.204529320084_R01C01


title: CCB020078

value: osteosarcoma tumor tisue

value: Mixed Breed

value: Radius


title: CCB020063

value: Greyhound


title: C76_ETO (S787Nr24)

city: Zaragoza

first: Patricia

last: Sancho

state: Aragón

address: P. Isabel la Católica 1-3

department: Traslational Research Unit

country: Spain

institute: Hospital Miguel Servet IIS Aragón

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq
Adapters were trimmed with Skewer (version 0.2.2, Jiang et al. 2014).
The quality of FASTQ files was analyzed with FastQC (version 0.11.5, Andrews 2010).
Reads were aligned using STAR (version 2.5.3a)
Reads count were performed by HT-seq using annotation from gencode.genome.v27
Genome_build: human genome build 38
Supplementary_files_format_and_content: tab-delimited text file for raw read counts for each Sample

source_name: primary  pancreatic tumor line

growth_protocol: Cells were maintained in RPMI with 10% FBS

extract_protocol:
Trizol extraction following manufacturer´s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA)

treatment_protocol: For experiments, cells were seeded in DMEM/F12 supplemented with 0.2% B27 anf FGFb in the presence or absence of macrophage-conditioned medium or 20 uM etomoxir

tag: cell line

value: primary  pancreatic tumor line, C76

tag: treatment

value: Etomoxir


title: C76_MCM (S787Nr23)

value: Macrophage conditioned media


title: CCB020056

value: Femur


title: Sample21.Prairie vole.204529320083_R03C02

tag: age

tag: confidenceinageestimate

value: Female

value: Pair bonded


title: C75_ETO (S787Nr21)

value: primary  pancreatic tumor line, C75


title: CCB010092

value: Staffordshire Bull Terrier


title: C75_MCM (S787Nr20)


title: CCB010057

value: Tibia


title: Sample20.Prairie vole.204529320083_R02C02

value: Liver

tag: Sex

tag: animalid


title: Sample19.Prairie vole.204529320083_R01C02


title: C75_CONT (S787Nr19)

value: Control


title: Sample18.Prairie vole.204529320083_R06C01

value: Ear


title: CCB020081

value: Golden Retriever

value: Humerus


title: Sample22.Prairie vole.204529320083_R04C02


title: Sample17.Prairie vole.204529320083_R05C01

value: Sex naïve


title: Sample16.Prairie vole.204529320083_R04C01


title: 2256_2021 [D7]

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

data_processing:
Reads were aligned to the musmusculus reference genome version mm10 using STAR (v2.5.2) with default parameters. SAM files were converted to BAM and sorted using Sambamba (v0.7.1)
Count matrices were generated using The Rsubread R package with the GENCODE Mus_musculus.GRCm38.97 custom annotation
Assembly: mm10
Supplementary files format and content: Raw count matrix in xls separated format

source_name: Mouse Embryo E13.5

growth_protocol: Cells were seeded in 6-well plates (300 000 cells per well) in DMEM (10% FBS, pen/strep). The following day, media was replaced with iPSC media and cells were treated as described. RNA was harvested 72h after transfer to iPSC media.

extract_protocol:
RNA was harvested using Qiagen RNeasy kit (Cat. 74106) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (Cat#E7760), following manufacturer´s instructions and 10 cycles of amplification.

treatment_protocol: MEFs were grow in iPSC media. Doxy-OSKM were grown in iPSC media treated continuously with 1μg/mL doxycycline. Samples treated with vitamin B12 had 2 µM supplemented continuously throughout the 72h of growth (starting at the time of transfer to iPSC media)

tag: clone

tag: strain

tag: condition

value: doxy-OSKM

value: Mouse Embryo E13.5


title: C76_CONT (S787Nr22)

value: primary  pancreatic tumor line, C76


title: 2255_2021 [C7]


title: 241_6

city: San Francisco

first: Charlotte

last: Eaton

institute: UCSF

description:
Merlin rescue in meningioma mouse xenografts
10X Genomics

data_processing:
Cell ranger v6.1.2
R studio, v4.2.1
Seurat v4.3.0
SCTransform, v0.3.5
Assembly: hg19 & mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: Human cells in mouse xenograft

extract_protocol:
cell dissociation using collagenase and Trypsin
10X genomics single cell 3' kit, v3.1

value: Meningies

tag: cell type

value: Human Meningioma

tag: genotype

value: Merlin rescue

value: 200ug/ml doxycycline


title: 241_5


title: C354_CONT (S787Nr16)

value: primary  pancreatic tumor line, C354


title: 2252_2021 [B7]


title: 287_6


title: C76_ETO (S787Nr12)

value: Etomoxir


title: Sample13.Prairie vole.204529320083_R01C01

value: Male


title: C354_ETO (S787Nr18)


title: 241_8


title: Sample14.Prairie vole.204529320083_R02C01

value: Female

value: Pair bonded


title: C76_MCM (S787Nr11)

value: Macrophage conditioned media


title: 287_5


title: C354_MCM (S787Nr17)


title: 0078_2022 [H6]


title: 0077_2022 [G6]


title: C76_CONT (S787Nr10)

value: Control


title: Sample11.Prairie vole.204529320015_R05C02

value: Ear


title: 287_4


title: Sample12.Prairie vole.204529320015_R06C02


title: 241_2


title: C75_ETO (S787Nr9)

value: primary  pancreatic tumor line, C75


title: Sample15.Prairie vole.204529320083_R03C01

value: Sex naïve


title: Sample9.Prairie vole.204529320015_R03C02

value: Liver


title: 2254_2021 [F6]

value: MEF

value: Mouse Embryo E13.5


title: Sample10.Prairie vole.204529320015_R04C02


title: 241_4

value: Meningies

value: Merlin-deficient

value: No doxycycline


title: 2253_2021 [E6]


title: C75_MCM (S787Nr8)


title: 241_10

value: Human Meningioma


title: Sample8.Prairie vole.204529320015_R02C02


title: 2251_2021 [A7]

value: doxy-OSKM


title: Sample7.Prairie vole.204529320015_R01C02


title: C75_CONT (S787Nr7)


title: 2250_2021 [D6]


title: Sample5.Prairie vole.204529320015_R05C01


title: C354_ETO (S787Nr6)

value: primary  pancreatic tumor line, C354

value: Etomoxir


title: Sample6.Prairie vole.204529320015_R06C01

value: Female


title: 241_3


title: 287_3


title: C354_MCM (S787Nr5)


title: Replicate6_DAPT

status: Public on Aug 06 2023

city: Stanford

first: Sofia

last: Essayan-Perez

address: 265 Campus Drive

department: Molecular and Cellular Physiology

institute: Stanford University

description:
Human induced neurons on mouse glia, day 40, DAPT-treated
40M total reads (20M paired)

data_processing:
Kallisto (V0.44.0) was used for pseudoalignment to human / mouse transcriptome
DESeq2 package in R Studio was used to analyze differential gene expression (FDR alpha < 0.1; p-value < 0.05; log2 fold change > 0.25 or < -0.25)
Batch effects were controlled for and log2 fold change shrinkage was applied
P-values were corrected for using the Benjamini-Hochberg correction
Assembly: hg38, mm10
Supplementary files format and content: Kallisto output files for human transcripts include raw counts (abundance)
Supplementary files format and content: Kallisto output files for mouse transcripts include raw counts (abundance)

source_name: Co-cultures of human induced neurons grown on mouse glia feeder layer

growth_protocol: Human induced neurons (trans-differentiated from human H1 ESC cell line using Ngn2 overexpression) were grown on mouse glia to day 40 in vitro in growth media (MEM, B27, Glutamax, transferrin, 5% FBS) at 37˚C and 5% CO2.

extract_protocol:
RNA from 6 biological replicates was harvested using TRIzol for lysis, choloroform extraction, and column purification with the Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared for stranded mRNA using Illumina TruSeq Library Prep Kit following manufacturer's protocols.
Bulk RNA-seq

treatment_protocol: Gamma-secretase inhibition was performed starting day 10 until day 40 in vitro (30 days total). Treatment groups were vehicle (0.5% DMSO), DAPT (40 µM) or LY411575 (2.5 µM).

value: Human Induced Neurons from H1 ESC (WA01)

value: Human induced neurons, day 40 / mouse primary glia

value: Wild-type human induced neurons / CD1 mouse glia

value: DAPT (40 uM), day in vitro 10-40


title: 0076_2022 [B6]


title: 0075_2022 [A6]


title: Sample4.Prairie vole.204529320015_R04C01

value: Pair bonded


title: 287_2


title: Replicate5_DAPT

value: Co-cultures of human induced neurons grown on mouse glia feeder layer


title: Replicate4_LY411575

description:
Human induced neurons on mouse glia, day 40, LY411575-treated
40M total reads (20M paired)


title: Replicate5_CtrlV

description:
Human induced neurons on mouse glia, day 40, vehicle-treated control
40M total reads (20M paired)

value: Vehicle (0.5% DMSO), day in vitro 10-40


title: Replicate5_LY411575


title: Replicate6_LY411575


title: 2249_2021 [C6]

value: MEF


title: Replicate2_LY411575


title: Sample2.Prairie vole.204529320015_R02C01

value: Liver

value: Sex naïve


title: Replicate3_DAPT


title: Replicate4_CtrlV


title: Replicate1_LY411575


title: Replicate3_CtrlV


title: Replicate2_CtrlV


title: Replicate1_DAPT


title: C354_CONT (S787Nr4)

value: Control


title: Replicate2_DAPT


title: Replicate1_CtrlV


title: Replicate6_CtrlV


title: Gli1+ MuSCs-3

city: Shanghai

first: jiayin

last: Peng

address: Yueyang Road

institute: Center for Excellence in Molecular Cell Science

data_processing:
The image data measured by the high- throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. 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 N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non- splice mapping tools.
Supplementary files format and content: all_compare file includes raw counts for each sample
Supplementary files format and content: all_compare file includes FPKM values for each sample

source_name: Muscle stem cell

growth_protocol: Gli1+ MuSCs (tdT+) or Gli1- MuSCs (tdT-) were FACS isolated from Gli1-CreERT2; R26-tdT mice at 3 days after TAM injection. Gli1+ MuSCs (tdT+) or Gli1- MuSCs (tdT-) were enriched by FACS sorting into wash medium and centrifuged at 500 g at 4°C for 5 min.

extract_protocol:
Total RNA was extracted from Gli1+ or Gli1- MuSCs using Trizol reagent (Invitrogen)  according to the manufacturer’s instructions. The integrity of the isolated RNA was verified using a Bioanalyzer (Agilent 2100).
Library construction was performed with 1 ng of input total RNA using the VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s instructions and sequenced on an Illumina NextSeq sequencer.

value: Muscle stem cell

value: Gli1-CreERT2; R26-tdT

tag: cell population

value: Gli1+ MuSCs (tdT+)

tag: strain background


title: Gli1+ MuSCs-4


title: Gli1+ MuSCs-2


title: Gli1+ MuSCs-1


title: Gli1- MuSCs-2

value: Gli1- MuSCs (tdT-)


title: Replicate3_LY411575


title: Sample1.Prairie vole.204529320015_R01C01

value: Ear


title: Replicate4_DAPT


title: Gli1- MuSCs-1


title: Sample3.Prairie vole.204529320015_R03C01

value: Male


title: 999038_4

first: exRNA

last: BRL

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Homebrew Kit.
Library construction kit was Homebrew Kit. Samples were multiplexed. Type of Starting Material was total RNA.

value: Plasma

value: Type 1 Diabetes Mellitus

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Homebrew Kit

tag: time frame sequentially collected every 1-3 months


title: 999226_12

tag: tissue


title: 999167_9


title: 999204_11


title: 999030_2


title: 999100_4


title: 999250_13


title: 999255_10


title: 999155_8


title: 999070_3


title: 999054_5


title: 999191_10


title: 998998_1


title: 999008_2


title: 999045_3


title: 999019_2


title: 999283_9


title: 999146_5


title: 961673_1


title: 999304_10


title: 999316_11


title: 999093_7


title: 999321_14


title: 999056_4


title: 999101_6


title: 999027_3


title: 999193_8


title: 999249_7


title: 999117_6


title: 999217_6


title: 999114_8


title: 956840_1


title: 999138_7


title: 999297_10


title: 999064_4


title: 999298_12


title: 999020_2


title: 999330_12


title: 999040_3


title: 999310_13


title: 999201_9


title: 999007_1


title: 999306_11


title: 999125_7


title: 999270_11


title: 999072_5


title: 999241_8


title: 999094_5


title: 999288_9


title: 269717_4


title: 999326_12


title: 236929_4


title: 236929_1


title: 269717_3


title: 999238_14


title: 999066_6


title: 999162_10


title: 980539_1


title: 999132_7


title: Sample37.Prairie vole.204529320082_R01C01

value: Female


title: 999225_11


title: 999248_12


title: 269717_8


title: 269717_2


title: 999088_6


title: 999044_4


title: 999065_5


title: 236929_5


title: 999036_3


title: 999128_8


title: 236929_9


title: 236929_7


title: 999182_11


title: 999203_10


title: 999221_13


title: 999079_5


title: 999200_12


title: 269717_7


title: 269717_1


title: 269717_9


title: 236929_8


title: 999024_3


title: 999106_7


title: 997202_1


title: 236929_6


title: 999259_15


title: 999179_9


title: 999147_9


title: 269717_6


title: 999000_2


title: 269717_5


title: 999160_8


title: 999014_2


title: 236929_2


title: 236929_10


title: 206598_5


title: 219012_6


title: 999104_6


title: 999268_13


title: 206598_3


title: 269757_7


title: 219012_9


title: 206598_7


title: 236929_3


title: 219012_7


title: 269757_6


title: 208376_6


title: 206598_10


title: 203678_1


title: 206598_12


title: 206598_2


title: 219012_13


title: 219012_4


title: 999061_4


title: 206598_4


title: 269757_4


title: 208376_3


title: 206598_1


title: 208376_7


title: 208376_5


title: 269757_3


title: 269757_1


title: 219012_10


title: 269757_5


title: 219012_12


title: 219012_5


title: 206598_9


title: 203678_5


title: 269757_12


title: 203678_2


title: 203678_4


title: 208376_2


title: 208376_4


title: 219012_3


title: 269757_2


title: 219012_2


title: 206598_6


title: 206598_8


title: 269757_11


title: 219012_8


title: 206598_11


title: 208376_1


title: 269757_13


title: 203678_3


title: 999089_8


title: 269757_9


title: 269757_10


title: 999184_13


title: 272825_5


title: 272825_7


title: 272825_6


title: 237280_2


title: Gli1- MuSCs-3


title: 272825_4


title: 219012_1


title: 237280_6


title: 999047_4


title: 272825_8


title: 954129_1


title: 237280_7


title: 999071_7


title: 999229_15


title: 999206_14


title: 999157_11


title: 272825_3


title: 219012_11


title: 999237_13


title: 269757_8


title: 999139_10


title: 237280_10


title: 237280_12


title: 999015_2


title: 999067_5


title: 272825_2


title: 999140_8


title: 999063_6


title: 999195_11


title: 237280_11


title: 999033_4


title: 999116_9


title: 999016_3


title: 237280_9


title: 999180_10


title: 237280_4


title: 237280_8


title: 999032_3


title: 999256_14


title: 999003_2


title: 999051_5


title: 272825_1


title: 999083_6


title: 999115_7


title: 999001_1


title: 237280_1


title: 999158_9


title: 237280_3


title: 999215_12


title: 999169_12


title: 237280_5


title: 213183_7


title: 213183_9


title: 242343_1


title: 201118_5


title: 270895_2


title: 217956_6


title: 217462_6


title: 270895_3


title: 213183_4


title: 270895_1


title: 213183_6


title: 213183_8


title: 201118_2


title: 201118_4


title: 213183_5


title: 242343_4


title: 242343_6


title: 242343_8


title: 217956_3


title: 217956_5


title: 201118_6


title: 217462_4


title: 270895_6


title: 217956_7


title: 217462_5


title: 201118_3


title: 217956_4


title: 242343_7


title: 270895_7


title: 217956_8


title: 213183_3


title: 201118_7


title: 242343_5


title: 242343_3


title: 213183_2


title: 217462_1


title: 270895_5


title: 201118_8


title: 242343_2


title: 217956_1


title: 213183_10


title: 270895_4


title: 211712_6


title: 211712_4


title: 999129_6


title: 999212_12


title: 271363_7


title: 271363_5


title: 999216_11


title: 999041_3


title: 211712_11


title: 999057_4


title: 999263_13


title: 999165_8


title: 217956_2


title: 211712_3


title: 217462_2


title: 201118_1


title: 271363_6


title: 217462_3


title: 999183_9


title: 211712_2


title: 999153_7


title: 271363_4


title: 211712_5


title: 213183_1


title: 999025_3


title: 999149_9


title: 271363_3


title: 999060_4


title: 999013_2


title: 211712_12


title: 211712_1


title: 999196_10


title: 999075_5


title: 999242_12


title: 999011_2


title: 211712_9


title: 999127_8


title: 999252_14


title: 999231_13


title: 999166_10


title: 999082_5


title: 271363_2


title: 985450_1


title: 999186_11


title: 271363_8


title: 211712_8


title: 211712_10


title: 900605_1


title: 999091_5


title: 999095_6


title: 999178_8


title: 999105_7


title: 999198_8


title: 999211_9


title: 999269_12


title: 271363_1


title: 999081_4


title: 999048_3


title: 211712_7


title: 999305_12


title: 999068_4


title: 999230_10


title: 999131_7


title: 999175_7


title: 999251_11


title: 999108_6


title: 999022_2


title: 998653_1


title: 999280_11


title: 999233_9


title: 999141_5


title: 999254_10


title: 998999_1


title: 999320_14


title: 999260_12


title: 999029_2


title: 999039_3


title: 999021_2


title: 999317_13


title: 999130_1


title: 924339_1


title: 999103_5


title: 999187_9


title: 999224_10


title: 999102_4


title: 999190_6


title: 999296_13


title: 999164_7


title: SMC1A ChIP#2

first: Yiwen

last: Chen

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

institute: UT MD Anderson Cancer Center

description: SMC1A1P1.SMC1A1P2.pooled_peaks.narrowPeak

data_processing:
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l hct116.sgrna.library --control-sgrna hct116.sgrna.library.negctrl --norm-method control -n hct116.sgrna.count --sample-label D0,D21 --fastq files.fq”. DESeq2 was used to identify the differentially expressed sgRNAs between D0 and D21. The read counts were normalized by the mapped negative control sgRNAs using ratio median normalization, and the normalization factors were applied to all sgRNAs. The cryptic ORFs with at least 2 significantly depleted sgRNAs (log2Fold-Change <= -log2(1.5) and p < 0.05),
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V22 transcriptome, using STAR v.2.6.1b with the parameters: “--outSAMunmapped Within --outFilterType BySJout --twopassMode Basic --outSAMtype BAM SortedByCoordinate”. The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2(1.22.2). The filters of basemean >= 1, |log2Fold-Change| >= log2(1.5) and FDR <= 0.05 were used to define differentially expressed genes for downstream analysis.
For the ChIP-seq data: The ChIP-seq reads were first trimmed by Trim Galore (v0.6.5), a wrapper around two tools: cutadapt v2.8 and FastQC v0.11.5, and were then mapped to the human genome (GRCh38), using Bowtie2 (v2.4.1). The resulting sorted BAM files were converted into bedGraph and bigWig formats using BEDTools (v2.24.0) and UCSC bedGraphToBigWig (v4). The ChIP-seq peaks were identified by MACS2 (v2.1.2) with the parameters “macs2 callpeak -t ChIP.bam -c INPUT.bam -g hs --outdir output -n NAME 2> NAME.callpeak.log”. BETA (v1.0.7) was used to annotate the peaks that are associated with genes of interest.
For the Ribo-seq data: The ribosome-protected RNA fragments (RPF) reads were trimmed and the low-quality reads were filtered by Sickle (http://github.com/ucdavis-bioinformatics/sickle). The RPF reads after filtering were mapped to human rRNA sequences using bowtie and allowing for two mismatches. The reads that were not mapped to human rRNA sequences were then mapped to the human genome (GRCh38) with transcriptome annotations GENECODE v22, NCBI refseq, MiTranscriptome and lincRNA transcript annotations generated by Dr. John Rinn’s group, using STAR with parameters “--outFilterMismatchNmax 2 –outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 20000 --outMultimapperOrder Random --outSAMmultNmax 1 --alignEndsType EndToEnd”. Quality control was performed using Ribo-TISH quality module with all the uniquely mapped RPF reads in the annotated ORFs. The RPFs were grouped by their lengths and each aligned RPF read was represented by its 5′ end before estimation of the P-site offset. The metagene RPF count profile near the start/stop codon was constructed by summing the RPF count between −40 and +20 bp of the first base of the start/stop codon across all annotated protein-coding genes. The P-site offset was estimated based on the distribution of the 5′ end of the metagene RPF counts near the annotated start codons. The RPF count between the 15 bp upstream of the first base of the start codon and the 12 bp upstream of the first base of the stop codon were used to calculate the RPF count distributions across three reading frames. The fraction of the RPF counts in the dominant frame (fd) was calculated as the ratio between the maximum RPF count among all three reading frames and the sum of the RPF counts from all reading frames. The cryptic ORFs were predicted with Ribo-TISH predict module with regular riboseq data longest mode.
Genome_build: human hg38 genome
Supplementary_files_format_and_content: RNASeq: read count and differential expression result in Excel file, ChIP-seq: narrowpeak file for peaks, CRISPR screen: read count in text files and MAGECK call result in Excel files.

source_name: Colon carcinoma

growth_protocol: HCT-116 cells were cultured in McCoy's 5a medium (Coring #10-050-CV). DLD-1 cells were cultured in RPMI- 1640 (Hyclone #SH30027.1). All culture medium were supplemented with 10% FBS (Gibco #10437-028) and 1% penicillin/streptomycin (Corning # 30-002-CI). All cell lines were cultured in an incubator (Thermo, HEARCELL VIOS 160i) with 5% CO2 at 37 °C. SMC1A (#32363)

extract_protocol:
Total RNA was isolated from cells using RNeasy Mini kit (QIAGEN, #74104) and was treated with DNase I(QIAGEN #79254). Immunoprecipitated DNA purified using QIAquik PCR purification kit (QIAGEN, #28106).
RNA-seq libraries were prepared from 2 μg of total RNA, using TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594), according to the manufacturer’s instructions. ChIP-seq libraries were prepared from 10 ng of ChIP DNA using the TruSeq ChIP Library Preparation Kit, according to the manufacturer’s instructions. Sample preparation for ribosome profiling was conducted according to the manufacturer’s specifications for the TruSeq Ribo Profile (Mammalian) Library Prep Kit (Illumina).

treatment_protocol: Cells(2×107) were first crosslinked with 1% formaldehyde (methanol-free, 16% Thermo Scientific, #28908) at room temperature for 10 minutes and then quenched with 0.125M Glycine (final concentration) for 5 minutes. After washing with cold PBS for three times, the cells were harvested using a silicon scraper. Cell pellets were resuspended in 5mL lysis buffer 1(50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and rocked at 4 degree for 5 minutes, followed by centrifugation at 2000 g for 4 minutes at 4°C. The cell pellets were then incubated with 5 mL LB2 buffer (10 mM Tris-HCl, pH=8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) at 4°C for 5 minutes with gently rocking. Nuclei were pelleted down by centrifugation of the cells at 2000 g for 5 min and were resuspended in 1 mL LB3 buffer (10 mM Tris-HCl, pH=8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine). All lysis buffer contained protease inhibitors (Roche #04693112001). Chromatin was sonicated to around 200 bp DNA fragments, using a Diagenode Bioruptor (three rounds of 5 cycles, 30” on 30” off). Lysates were cleared by addition of Triton X-100 to a final concentration of 1% and centrifugation at 2000 g for 10 minutes at 4°C. A total of 50 μl lysates were saved from each sample for input and stored at – 80°C until use. To prepare antibody-bound beads, 30 μl of magnetic beads (Invitrogen, Dynabeads) were washed three times with blocking buffer (1× PBS, 0.5% BSA) and incubated overnight with 5 μg of the anti-SMC1A antibodies at 4°C. For each ChIP, 900 uL sonicated lysate from 2×107 cells was incubated with the antibody-bound beads overnight at 4°C. Beads were washed 6 times with RIPA wash buffer (50 mM Hepes-KOH, pH= 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and 1 time with TBS (20 Mm Tris-HCL, PH 7.6, 150Mm NaCl) for 5 minutes each time at room temperature with gently rocking. All washing buffers contain the protease inhibitors. The beads were eluted twice with 50 ul elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) for 10 minutes at 65°C with rocking. Crosslinking was reversed by adding 6 uL 5M NaCl to the eluates and incubated at 65°C overnight. RNAs were degraded by incubation with 1μl of 10 mg/ml RNase at 37°C for 30 minutes and proteins were digested by incubation with 2 μl of 20 mg/ml of Proteinase K(Thermo Fisher) at 56°C for 2 hours. DNAs were then purified using QIAquik PCR purification kit (QIAGEN, #28106). For shRNA, sgRNA mediated knockdown and knokout experiments, lentiviruses were collected 48 hours after transfection and were then used to infect indicated cell lines. The infected cells were then treated with puromycin to select the ones with stable shRNA/sgRNA transduction.

tag: cell line

tag: chip antibody

value: Bethyl Laboratories (A300-055A)


title: 999223_10


title: SMC1A ChIP#1


title: 999049_3


title: 999154_7


title: Input#2


title: 999159_6


title: Input#1


title: 969811_1


title: 999058_3


title: 999042_3


title: CB-SKNAS-TR-MYCN-240h-Tet3_2

city: Berlin

first: Steffen

last: Fuchs

address: Augustenburger Platz 1

department: Pediatric Oncology

country: Germany

institute: Charité - Universitätsmedizin Berlin

description: Tet3 Technical Replicate 2

data_processing:
Reads were aligned to GRCh38 using the GENCODE (v30) annotation and the STAR aligner (v2.7.1a) with the following non-standard parameters --sjdbOverhang 300 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --outSAMattributes NH NM MD AS XS nM HI.
Feature counting  was done using featureCounts (v1.5.1) with the following non-standard parameters when counting at the gene level -t exon -g gene_id -C -M --fraction -p -O -Q 4 -J
Genome_build: GRCh38 using the GENCODE (v30)
Supplementary_files_format_and_content: Table reporting unique mapping read counts

source_name: Neuroblastoma cell line

growth_protocol: SK-N-AS neuroblastoma cells stably transfected with a tetracycline-inducible MYCN expression system were generated with the tetracycline repressor (TR) system (pcDNA™6TR, Invitrogen). Single clones were maintained by adding 500 µg/ml G418-BC (Merck) and 5µg/ml Blasticidin (ThermoFisher Scientific) as selection antibiotic to the culturing medium.

extract_protocol:
250.000 cells per condition were harvested and RNA was isolated with Trizol. ERCC spike-in (Invitrogen, #445670) was freshly diluted 1:40 and 1µl was added to the cells homogenized in Trizol according to Loven et al. 2012 (PMID 23101621). RNA was isolated then according to the manufacturer.
Depletion of ribosomal RNA was performed by enzymatic digestion. The ribodepletion was validated by qRT-PCR and a depletion of 95-99% was regularly reached. The ribodepleted RNA was used for generation of total RNA sequencing libraries with the TrueSeq Stranded mRNA kit (Illumina San Diego, USA) according to the manufacturer. The final libraries were stored at -20°C until sequencing. Libraries were sequenced on a HiSeq4000 (Illumina, San Diego, USA) with a paired-end read length of 2 × 150 nucleotides. On average 100 Mio read pairs were generated per sample.

treatment_protocol: Induction of MYCN expression by addition of tetracyclin to the growth medium for 10d. Induction of MYCN was confirmed by qRT-PCR and Western Blot.

tag: cancer type

value: Neuroblastoma

tag: knockdown

value: Induction

value: SK-N-AS


title: CB-SKNAS-TR-MYCN-240h-Tet2_2

description: Tet2 Technical Replicate 2


title: CB-SKNAS-TR-MYCN-240h-Tet2_1

description: Tet2 Technical Replicate 1


title: 999059_4


title: CB-SKNAS-TR-MYCN-240h-Tet3_1

description: Tet3 Technical Replicate 1


title: 999170_3


title: 999282_10


title: 999234_11


title: 999122_5


title: CB-SKNAS-TR-MYCN-240h-Tet1_2

description: Tet1 Technical Replicate 2


title: CB-SKNAS-TR-MYCN-240h-Tet1_1

description: Tet1 Technical Replicate 1


title: CB-SKNAS-TR-MYCN-240h-ETOH3_2

description: ETOH3 Technical Replicate 2

value: Control


title: CB-SKNAS-TR-MYCN-240h-ETOH2_2

description: ETOH2 Technical Replicate 2


title: 999205_7


title: CB-SKNAS-TR-MYCN-240h-ETOH3_1

description: ETOH3 Technical Replicate 1


title: 999144_6


title: 999228_8


title: CB-SKNAS-TR-MYCN-240h-ETOH2_1

description: ETOH2 Technical Replicate 1


title: 999173_8


title: CB-SKNAS-TR-MYCN-240h-ETOH1_2

description: ETOH1 Technical Replicate 2


title: 999312_15


title: 999303_9


title: CB-SKNAS-TR-MYCN-240h-ETOH1_1

description: ETOH1 Technical Replicate 1


title: 999338_11


title: AB9279

city: Rehovot

first: Gil

last: Levkowitz

state: Rehovot

address: Wolfson Building of Biological Sciences, Department of Molecular Cell Biology, Weizmann Institute of Science, 234 Herzl Street

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT. Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Single cell analysis was performed using the Seurat package v 3.1.5 (Butler et al., 2018). Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples.
Expression values were normalized and scaled using the functions NormalizeData (normalization.method="LogNormalize", scale.factor= 10000) and ScaleData (vars.to.regress = c("nCount_RNA", "percent.mito"). Clusters were determined using FindNeighbors (dims=1:6) and FindClusters (reduction.type = "pca", resolution = 0.6).
paired-end (read2 used to read cell and molecule barcodes only)
Assembly: DanRer10
Supplementary files format and content: Text file containing the gene average log normalized expression per cluster

organism: Danio rerio

source_name: Neurohypophysis enriched cells

growth_protocol: 37-day post fertilization, 5 & 7 months zebrafish were raised at the Weizmann Institute fish facility.

extract_protocol:
5 pituitaries from each age group were dissected and pooled in 1ml ice-cold HEPES buffered saline (HBS), which was later changed to 250μl ice-cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C, thereafter resuspended in 500μl ice-cold resuspension buffer (Leibovitz L-15 with 0.3mM Glutamine, penicillin 50 U/mL + streptomycin 0.05 mg/mL, FBS 1%, BSA 0.04%) and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384-well plates.
The Mars-Seq single-cell library was prepared according to (Jaitin et al., 2014). In short, mRNA from the single cell was barcoded and converted to cDNA in the 384-well plate, then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated, reverse transcribed, and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine (Illumina, USA) at a median sequencing depth around 40,000 reads per cell.

treatment_protocol: 5ul of 4.6mM β-Ala-Lys-Nε-AMCA (Biotrend #BP0352) was injected into 37-day-old juvenile, or 10ul into 5 or 7 months-old male Tg(pomca:EGFP). After 3 hours, the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.

value: AB, Tg(pomca:EGFP)

value: Neurohypophysis

tag: age

value: 5 months


title: 999142_5


title: AB9278

value: 7 months


title: AB9277


title: 999080_4


title: AB7418

value: 37 days post fertilization


title: 999281_8


title: 999290_13


title: 999244_11


title: 999194_9


title: M145tna

city: Liege

first: Brett

middle: C

last: Mommer

state: Wallonia

address: Tour Pharmacie (Bat. B36) Quartier Hôpital, Avenue Hippocrate 15

department: GIGA-Neurosciences

country: Belgium

institute: University of Liege

data_processing:
To enable chromosome mapping of predicted transcripts on a reference sequence, scaffolds from the NODAII quail genome (Kawahara-Miki et al. 2013) were mapped to the chicken genome assembly Galgal5.0 using BWA.  Galgal5.0 FASTA sequence was combined with the resulting variant calls from the quail genome to create a chicken genome backbone with the allelic variation of the quail using FastaAlternateReferenceMaker (McKenna et al. 2010).  We will refer to this assembly as `qGG5` assembly.  Lastly, predicted transcripts were mapped to qGG5 using BLAST, top best hit was considered as the chromosomal location of the transcript.
A total of 36 RNA-seq libraries were sequenced on a NEXT-Seq 500 to produce 1.2 billion reads.  Reads from all libraries were concatenated into a single forward and reverse read file and analyzed with Trinity to generate a brain specific transcriptome of the Japanese quail (Haas et al. 2013).
All reads were screened with Trimmomatic ({Bolger:2014ek}), Our assembly yielded a total of <800K> predicted transcripts, of which <100K> yielded predicted ORF and <80K> were predicted as protein peptides using TransDecoder.
Following transcriptome assembly, predicted transcript isoforms were annotated using the Trinnotate suite, where each transcript is cross referenced to sequence similarity to various online databases (online at : trinotate.github.io).  All steps, both required and optional were carried out.  To start, coding genes were predicted using transdecoder using the chicken transcriptome Galgal5.0 Ensembl 69 assembly as the training set.  Translated transcripts were compared to SwissProt, UNIPROT, and TrEMBL using BLASTTX , the top hit was kept.  Ribosomal RNA species were predicted based using RNAmer v1.2 (Lagesen et al. 2007).  Predicted peptides from TransDecoder were additionally compared to SwissProt,  and TrEMBL using BLASTP, top hit was kept.  Protein domains were predicted by comparing peptide sequences to Pfam domains using HMMER.  Signaling peptides and trans-membrane domains were predicted using SignalP, and TmHMM, respectively.  Lastly, gene ontology categories were obtained from eggNOG, both through mapping and assessment of predicted protein.  Final annotation was summarized using a DNC cutoff of 0.05.
Differential expression of genes/transcripts was done for each of the three brain regions (POM, TnA, VMN) in a pairwise fashion for the comparisons M vs F, M vs TM, F vs TF, TM vs TF, and M vs TF. The analysis was carried out using four different publicly-available algorithms (DESeq2, EdgeR, ROTS, voom) and the genes/transcripts found to be differentially expressed by at least two algorithms at FDR<0.01 were combined into gene lists. We employed the 0.01 FDR threshold as opposed to 0.05 so as to control the experiment-wise error rate for the five selected pairwise comparisons. Additionally the top 10% of genes/transcripts remaining below FDR<0.01 by a single algorithm and all falling within the FDR<0.01 threshold for DESeq2 were added to the lists. Each algorithm produced a read count for each gene/transcript adjusted for library size, resulting in normalized read counts.
Genome_build: qGG5 reference sequence
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

organism: Coturnix japonica

source_name: adult brain

extract_protocol:
Brains were sliced in 200um-thick coronal sections in a 2800 Frigocut E cryostat (Reichert-Jung) and the sections kept on Superfrost Plus (Thermo Scientific,) microscope slides previously cooled to the temperature of the cryostat. Brain nuclei were punched using a specialized 1.25mm diameter brain punch apparatus (Leica Biosystems) using the previously observed neuroanatomical distribution of quail aromatase-positive cell populations as a guide. RNA was extracted using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands), DNA digested on-column using the RNase-free DNase Set (Qiagen), RNA quantity measured on a NanoDrop 2000 spectrophotometer (Thermo Scientific), concentrated by vacuum centrifuge, resuspended in 10ul RNase-free water (Ambion), and quantified again on Nanodrop.
RNA samples underwent ribosomal depletion using Ribozero (Illumina, San Diego, CA), cDNA synthesis, barcoding, pooling by brain region (3 pools, each with n=12 samples/pool), and each pool was divided and run across all 4 lanes of a NextSeq500 chip (Illumina) for a total of three chips at the GIGA-Genotranscriptomics platform (ULg, Liege Belgium). The cDNA were read in paired-end, 75nt read length format, and adapter and barcode sequences trimmed prior to assembly.

treatment_protocol: At 2.5 weeks of age birds were anesthetized with isoflurane, an incision was made in the abdomen, and gonads were either inspected (sham) or removed. Following gonadectomy or inspection the incision was closed and animals were left to recover at least two weeks before additional treatments.  Individuals were assigned into one of four treatment groups according to the type of gonads observed (testes vs. Ovary) and whether they underwent gonadectomy or inspection: sham males (M), sham females (F), castrated males chronically treated with testosterone (Cx + T) and ovariectomized females chronically treated with testosterone (Ovx + T).  At 6 weeks of age, gonadectomized quail received two 20mm silastic implants filled with crystalline testosterone to mimic the elevation of circulating testosterone concentration and subsequent activation of behavior and adult features such as the development of the cloacal gland occurring between 4 and 7 weeks of age in gonadally intact males. Sham quail received two empty silastic implants. One week after the final test of sexual behavior (12 weeks of age) all individuals were sacrificed by rapid decapitation and brains were quickly dissected from the head, flash frozen on dry ice and stored at -80C for later analysis.

value: wild type

value: nucleus taenia of the amygdala

tag: treatment

value: Cx+T male


title: 999172_8

value: Plasma

value: Type 1 Diabetes Mellitus

value: Entire cardiovascular system


title: 999265_12

value: total cell-free biofluid RNA

value: Homebrew Kit


title: R25tna


title: AB9280

tag: strain


title: 999010_2

tag: condition


title: M195tna

value: Ovx+T female


title: M167tna


title: 999031_2


title: M94tna


title: 961489_1


title: 999197_4


title: 999137_6


title: 999218_5


title: 999152_2


title: R18tna

value: intact male


title: M191tna


title: AB7417


title: R15tna


title: 999236_6


title: 999257_7


title: M157tna

value: intact female


title: Arabidopsis ChIP_E2FB-GFP Bioreplicate 2

city: Gif Sur Yvette

first: Xiaoning

last: HE

address: 630,Rue Noetzlin

country: France

institute: universite-paris-saclay

description: Bioreplicate 2

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of TAIR10.fasta
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak  -t sample.bam -c Input.bam -g 119481543 -q 0.05  -B -n --outdir "
Bigwig generation: takes an alignment of reads or fragments as input (BAM file) and generates a coverage track
Assembly: TAIR10.fasta
Supplementary files format and content: Bigwig file, containing Chr, start position, end position.
Supplementary files format and content: Broad Peak file from macs2

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Arabidopsis plantlets were grown on half-strength MS for 12 days under long day conditions at 20°C

extract_protocol:
See Gombos et al for details
NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

treatment_protocol: No treatment

tag: cultivar

tag: genotypes

value: abcam, ab290


title: M42tna

tag: genotype


title: Arabidopsis ChIP_E2FA-GFP Bioreplicate 2

description: Bioreplicate 2


title: Arabidopsis ChIP_RBR-GFP

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of TAIR10.fasta
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak --broad -t sample.bam -c Input.bam -g 119481543 -q 0.05  -B -n --outdir "
Bigwig generation: read density was scored with s3norm with the default paramaters
Assembly: TAIR10.fasta
Supplementary files format and content: Bigwig file, containing Chr, start position, end position.
Supplementary files format and content: Broad Peak file from macs2

value: pRBR-RBR-GFP


title: Arabidopsis ChIP_E2FC-GFP


title: R49tna


title: 999319_10


title: 999264_9


title: M145vmn

value: ventromedial nucleus


title: Arabidopsis ChIP_E2FA-GFP


title: Arabidopsis ChIP_E2FB-GFP


title: Arabidopsis ChIP_RBR-GFP Bioreplicate 2

description: Bioreplicate 2


title: Day21 R6

data_processing:
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l hct116.sgrna.library --control-sgrna hct116.sgrna.library.negctrl --norm-method control -n hct116.sgrna.count --sample-label D0,D21 --fastq files.fq”. DESeq2 was used to identify the differentially expressed sgRNAs between D0 and D21. The read counts were normalized by the mapped negative control sgRNAs using ratio median normalization, and the normalization factors were applied to all sgRNAs. The cryptic ORFs with at least 2 significantly depleted sgRNAs (log2Fold-Change <= -log2(1.5) and p < 0.05),
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V22 transcriptome, using STAR v.2.6.1b with the parameters: “--outSAMunmapped Within --outFilterType BySJout --twopassMode Basic --outSAMtype BAM SortedByCoordinate”. The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2(1.22.2). The filters of basemean >= 1, |log2Fold-Change| >= log2(1.5) and FDR <= 0.05 were used to define differentially expressed genes for downstream analysis.
For the ChIP-seq data: The ChIP-seq reads were first trimmed by Trim Galore (v0.6.5), a wrapper around two tools: cutadapt v2.8 and FastQC v0.11.5, and were then mapped to the human genome (GRCh38), using Bowtie2 (v2.4.1). The resulting sorted BAM files were converted into bedGraph and bigWig formats using BEDTools (v2.24.0) and UCSC bedGraphToBigWig (v4). The ChIP-seq peaks were identified by MACS2 (v2.1.2) with the parameters “macs2 callpeak -t ChIP.bam -c INPUT.bam -g hs --outdir output -n NAME 2> NAME.callpeak.log”. BETA (v1.0.7) was used to annotate the peaks that are associated with genes of interest.
For the Ribo-seq data: The ribosome-protected RNA fragments (RPF) reads were trimmed and the low-quality reads were filtered by Sickle (http://github.com/ucdavis-bioinformatics/sickle). The RPF reads after filtering were mapped to human rRNA sequences using bowtie and allowing for two mismatches. The reads that were not mapped to human rRNA sequences were then mapped to the human genome (GRCh38) with transcriptome annotations GENECODE v22, NCBI refseq, MiTranscriptome and lincRNA transcript annotations generated by Dr. John Rinn’s group, using STAR with parameters “--outFilterMismatchNmax 2 –outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 20000 --outMultimapperOrder Random --outSAMmultNmax 1 --alignEndsType EndToEnd”. Quality control was performed using Ribo-TISH quality module with all the uniquely mapped RPF reads in the annotated ORFs. The RPFs were grouped by their lengths and each aligned RPF read was represented by its 5′ end before estimation of the P-site offset. The metagene RPF count profile near the start/stop codon was constructed by summing the RPF count between −40 and +20 bp of the first base of the start/stop codon across all annotated protein-coding genes. The P-site offset was estimated based on the distribution of the 5′ end of the metagene RPF counts near the annotated start codons. The RPF count between the 15 bp upstream of the first base of the start codon and the 12 bp upstream of the first base of the stop codon were used to calculate the RPF count distributions across three reading frames. The fraction of the RPF counts in the dominant frame (fd) was calculated as the ratio between the maximum RPF count among all three reading frames and the sum of the RPF counts from all reading frames. The cryptic ORFs were predicted with Ribo-TISH predict module with regular riboseq data longest mode.
Assembly: human hg38 genome
Supplementary files format and content: RNASeq: read count and differential expression result in Excel file, ChIP-seq: narrowpeak file for peaks, CRISPR screen: read count in text files and MAGECK call result in Excel files.

treatment_protocol:
The HCT-116 cells transduced with lentiCas9-EGFP (addgene, #63592) were sorted on a FACSAria cell sorter (BD Biosciences) and the cells with high EGFP expression were collected. These HCT-116 cells with high expression of SpCas9 were plated into ten 10-cm dishes and infected with lentiviruses containing the sgRNA library at an MOI of 0.2~0.3. Following puromycin (2 μg/ml) selection for 4 days, 3.5 ×107 cells were split into three replicates. For each replicate, 8× 106 were harvested to extract genomic DNAs (Day 0, D0), using QIAamp DNA Mini Kit (QIAGEN), and 3.7×106 cells (~500×coverage for each sgRNA per replicate) were passed every 3 days and cultured for 21 days. At day 21 (D21), 8× 106 cells were harvested for each replicate to extract genomic DNA. The next-generation-sequencing (NGS)-ready sgRNA libraries were prepared by two rounds of PCR with the KAPA HiFi HotStart ReadyMix (Roche # KK2602).
Cells(2×107) were first crosslinked with 1% formaldehyde (methanol-free, 16% Thermo Scientific, #28908) at room temperature for 10 minutes and then quenched with 0.125M Glycine (final concentration) for 5 minutes. After washing with cold PBS for three times, the cells were harvested using a silicon scraper. Cell pellets were resuspended in 5mL lysis buffer 1(50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and rocked at 4 degree for 5 minutes, followed by centrifugation at 2000 g for 4 minutes at 4°C. The cell pellets were then incubated with 5 mL LB2 buffer (10 mM Tris-HCl, pH=8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) at 4°C for 5 minutes with gently rocking. Nuclei were pelleted down by centrifugation of the cells at 2000 g for 5 min and were resuspended in 1 mL LB3 buffer (10 mM Tris-HCl, pH=8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine). All lysis buffer contained protease inhibitors (Roche #04693112001). Chromatin was sonicated to around 200 bp DNA fragments, using a Diagenode Bioruptor (three rounds of 5 cycles, 30” on 30” off). Lysates were cleared by addition of Triton X-100 to a final concentration of 1% and centrifugation at 2000 g for 10 minutes at 4°C. A total of 50 μl lysates were saved from each sample for input and stored at – 80°C until use. To prepare antibody-bound beads, 30 μl of magnetic beads (Invitrogen, Dynabeads) were washed three times with blocking buffer (1× PBS, 0.5% BSA) and incubated overnight with 5 μg of the anti-SMC1A antibodies at 4°C. For each ChIP, 900 uL sonicated lysate from 2×107 cells was incubated with the antibody-bound beads overnight at 4°C. Beads were washed 6 times with RIPA wash buffer (50 mM Hepes-KOH, pH= 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and 1 time with TBS (20 Mm Tris-HCL, PH 7.6, 150Mm NaCl) for 5 minutes each time at room temperature with gently rocking. All washing buffers contain the protease inhibitors. The beads were eluted twice with 50 ul elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) for 10 minutes at 65°C with rocking. Crosslinking was reversed by adding 6 uL 5M NaCl to the eluates and incubated at 65°C overnight. RNAs were degraded by incubation with 1μl of 10 mg/ml RNase at 37°C for 30 minutes and proteins were digested by incubation with 2 μl of 20 mg/ml of Proteinase K(Thermo Fisher) at 56°C for 2 hours. DNAs were then purified using QIAquik PCR purification kit (QIAGEN, #28106). For shRNA, sgRNA mediated knockdown and knokout experiments, lentiviruses were collected 48 hours after transfection and were then used to infect indicated cell lines. The infected cells were then treated with puromycin to select the ones with stable shRNA/sgRNA transduction.


title: ATAC-seq SKOV3 shPLD2 hypoxia, replicate 2

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

institute: IBiS, Universidad de Sevilla-CSIC

description: ATAC-seq

data_processing:
Alignment: reads were aligned to the reference genome using Bowtie2 software
Filtering duplicates: duplicated pairs were removed using Samtools software
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions
Visualization: bigWig files were visualized using UCSC Browser
Assembly: GRCh38/hg38
Supplementary files format and content: narrowPeak files with peaks called using MACS2 with q<0.05

source_name: SKOV3 cells

growth_protocol: SKOV3 cells were grown in RPMI and incubated at 37ºC with the corresponding oxygen concentration

extract_protocol:
Cells were collected and lysed in fresh
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

treatment_protocol: SKOV3 cells were cultured under normoxic (20% O2) or hypoxic (3% O2) atmospheres with 5% CO2 at 37ºC, transfected with empty, PLD2 or shPLD2 vectors

tag: cell type

value: ovarian cancer

tag: vector

value: Hypoxia 3% oxygen


title: M94vmn


title: Day21 R5


title: ATAC-seq SKOV3 PLD2 normoxia, replicate 2

description: ATAC-seq

value: Normoxia 20% oxygen


title: ATAC-seq SKOV3 shPLD2 hypoxia, replicate 1

description: ATAC-seq


title: R25vmn

value: wild type


title: ATAC-seq SKOV3 empty vector normoxia, replicate 1

description: ATAC-seq

value: empty vector


title: ATAC-seq SKOV3 empty vector hypoxia, replicate 2

description: ATAC-seq


title: Day21 R4


title: M167vmn


title: ATAC-seq SKOV3 empty vector normoxia, replicate 2

description: ATAC-seq


title: HCT116 RPF R3

description: HCT116.RPF.readcount.tsv: E

data_processing:
Library strategy: Ribo-Seq
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l hct116.sgrna.library --control-sgrna hct116.sgrna.library.negctrl --norm-method control -n hct116.sgrna.count --sample-label D0,D21 --fastq files.fq”. DESeq2 was used to identify the differentially expressed sgRNAs between D0 and D21. The read counts were normalized by the mapped negative control sgRNAs using ratio median normalization, and the normalization factors were applied to all sgRNAs. The cryptic ORFs with at least 2 significantly depleted sgRNAs (log2Fold-Change <= -log2(1.5) and p < 0.05),
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V22 transcriptome, using STAR v.2.6.1b with the parameters: “--outSAMunmapped Within --outFilterType BySJout --twopassMode Basic --outSAMtype BAM SortedByCoordinate”. The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2(1.22.2). The filters of basemean >= 1, |log2Fold-Change| >= log2(1.5) and FDR <= 0.05 were used to define differentially expressed genes for downstream analysis.
For the ChIP-seq data: The ChIP-seq reads were first trimmed by Trim Galore (v0.6.5), a wrapper around two tools: cutadapt v2.8 and FastQC v0.11.5, and were then mapped to the human genome (GRCh38), using Bowtie2 (v2.4.1). The resulting sorted BAM files were converted into bedGraph and bigWig formats using BEDTools (v2.24.0) and UCSC bedGraphToBigWig (v4). The ChIP-seq peaks were identified by MACS2 (v2.1.2) with the parameters “macs2 callpeak -t ChIP.bam -c INPUT.bam -g hs --outdir output -n NAME 2> NAME.callpeak.log”. BETA (v1.0.7) was used to annotate the peaks that are associated with genes of interest.
For the Ribo-seq data: The ribosome-protected RNA fragments (RPF) reads were trimmed and the low-quality reads were filtered by Sickle (http://github.com/ucdavis-bioinformatics/sickle). The RPF reads after filtering were mapped to human rRNA sequences using bowtie and allowing for two mismatches. The reads that were not mapped to human rRNA sequences were then mapped to the human genome (GRCh38) with transcriptome annotations GENECODE v22, NCBI refseq, MiTranscriptome and lincRNA transcript annotations generated by Dr. John Rinn’s group, using STAR with parameters “--outFilterMismatchNmax 2 –outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 20000 --outMultimapperOrder Random --outSAMmultNmax 1 --alignEndsType EndToEnd”. Quality control was performed using Ribo-TISH quality module with all the uniquely mapped RPF reads in the annotated ORFs. The RPFs were grouped by their lengths and each aligned RPF read was represented by its 5′ end before estimation of the P-site offset. The metagene RPF count profile near the start/stop codon was constructed by summing the RPF count between −40 and +20 bp of the first base of the start/stop codon across all annotated protein-coding genes. The P-site offset was estimated based on the distribution of the 5′ end of the metagene RPF counts near the annotated start codons. The RPF count between the 15 bp upstream of the first base of the start codon and the 12 bp upstream of the first base of the stop codon were used to calculate the RPF count distributions across three reading frames. The fraction of the RPF counts in the dominant frame (fd) was calculated as the ratio between the maximum RPF count among all three reading frames and the sum of the RPF counts from all reading frames. The cryptic ORFs were predicted with Ribo-TISH predict module with regular riboseq data longest mode.
Genome_build: human hg38 genome
Supplementary_files_format_and_content: RNASeq: read count and differential expression result in Excel file, ChIP-seq: narrowpeak file for peaks, CRISPR screen: read count in text files and MAGECK call result in Excel files.

treatment_protocol:
HCT116 cells were treated with CHX (Sigma-Aldrich, final concentration 0.1mg/ml) for 1 minutes and the cells were lyszed by using Mammalian Lysis Buffer (including CHX at a concentration of 0.1mg/ml). Then 600 μl of lysate were taken and 15 ul of RNase I (100 U/μl, Thermo Fisher Scientific) were added and the mixtures were incubated for 45min at room temperature followed by adding 15 μl SUPERaseIn RNase inhibitor (Thermo Fisher Scientific) to stop the reaction. Ribosome recovery were done by illustra MicroSpin S-400 HR Columns (GE Healthcare) and the Ribosomal Protected Fragments (PFFs) were purified by RNA Clean & Concentrator (Zymo Research). Ribosomal RNA was subtracted using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat, Illumina). RPFs without ribosomal RNA were ran on a 15% Urea denaturing-PAGE gel, and the gel slides from 28nt~30nt were excised.
Cells(2×107) were first crosslinked with 1% formaldehyde (methanol-free, 16% Thermo Scientific, #28908) at room temperature for 10 minutes and then quenched with 0.125M Glycine (final concentration) for 5 minutes. After washing with cold PBS for three times, the cells were harvested using a silicon scraper. Cell pellets were resuspended in 5mL lysis buffer 1(50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and rocked at 4 degree for 5 minutes, followed by centrifugation at 2000 g for 4 minutes at 4°C. The cell pellets were then incubated with 5 mL LB2 buffer (10 mM Tris-HCl, pH=8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) at 4°C for 5 minutes with gently rocking. Nuclei were pelleted down by centrifugation of the cells at 2000 g for 5 min and were resuspended in 1 mL LB3 buffer (10 mM Tris-HCl, pH=8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine). All lysis buffer contained protease inhibitors (Roche #04693112001). Chromatin was sonicated to around 200 bp DNA fragments, using a Diagenode Bioruptor (three rounds of 5 cycles, 30” on 30” off). Lysates were cleared by addition of Triton X-100 to a final concentration of 1% and centrifugation at 2000 g for 10 minutes at 4°C. A total of 50 μl lysates were saved from each sample for input and stored at – 80°C until use. To prepare antibody-bound beads, 30 μl of magnetic beads (Invitrogen, Dynabeads) were washed three times with blocking buffer (1× PBS, 0.5% BSA) and incubated overnight with 5 μg of the anti-SMC1A antibodies at 4°C. For each ChIP, 900 uL sonicated lysate from 2×107 cells was incubated with the antibody-bound beads overnight at 4°C. Beads were washed 6 times with RIPA wash buffer (50 mM Hepes-KOH, pH= 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and 1 time with TBS (20 Mm Tris-HCL, PH 7.6, 150Mm NaCl) for 5 minutes each time at room temperature with gently rocking. All washing buffers contain the protease inhibitors. The beads were eluted twice with 50 ul elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) for 10 minutes at 65°C with rocking. Crosslinking was reversed by adding 6 uL 5M NaCl to the eluates and incubated at 65°C overnight. RNAs were degraded by incubation with 1μl of 10 mg/ml RNase at 37°C for 30 minutes and proteins were digested by incubation with 2 μl of 20 mg/ml of Proteinase K(Thermo Fisher) at 56°C for 2 hours. DNAs were then purified using QIAquik PCR purification kit (QIAGEN, #28106). For shRNA, sgRNA mediated knockdown and knokout experiments, lentiviruses were collected 48 hours after transfection and were then used to infect indicated cell lines. The infected cells were then treated with puromycin to select the ones with stable shRNA/sgRNA transduction.


title: ATAC-seq SKOV3 PLD2 normoxia, replicate 1

description: ATAC-seq


title: HCT116 RPF R2

description: HCT116.RPF.readcount.tsv: D


title: M195vmn


title: R49vmn


title: HCT116 RPF R1

description: HCT116.RPF.readcount.tsv: A


title: M172tna

value: nucleus taenia of the amygdala


title: R18vmn


title: R15vmn


title: Day21 R3


title: Day0 R3


title: Day21 R2


title: ATAC-seq SKOV3 empty vector hypoxia, replicate 1

description: ATAC-seq


title: Day0 R2


title: Day21 R1


title: bone marrow-derived macrophages cultured in 50% LL-2 conditional medium 24h 2

city: Chengdu

first: Ziqi

last: Zhang

state: Sichuan

address: No. 17, Block 3, Southern Renmin Road

department: National Clinical Research Center for Geriatrics,

institute: West China Hospital, Sichuan University

description: WT CM 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using IlluQC_PRLL.pl of NGSQCToolkit (parameter-  2 A -z g )
Trimmed sequence reads were mapped to Mus_musculus.GRCm38 using hisat2 (parameters- -p 20 -t )
Read count extraction and normalization were performed using featureCounts
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: primary bone marrow-derived macrophages

growth_protocol: Bone marrow was flushed out by RPMI-1640 medium. The bone marrow was centrifuged and resuspended by red blood cell lysis buffer. Then the cell pallets were centrifuged and resuspended by RPMI-1640 medium to remove red blood cell lysis buffer. Next, the cells were filtrated by 70 μm cell strainers and counted. Finally, the bone marrow cells were centrifuged and resuspended by RPMI-1640 medium supplied with 10% FBS, 1% penicillin/streptomycin, and 20 ng/mL M-CSF.

extract_protocol:
BMDMs were harvested and lysed in TRIzol (Invitrogen). The extraction and sequencing of RNA was performed by Novogene Bioinformatics Institute, Beijing, China.
After the RNA samples passed the test, eukaryotic mRNA was enriched with magnetic beads with Oligo(dT) (in case of prokaryotes, mRNA was enriched by removing rRNA with the kit) . The mRNA was then broken into short fragments by adding fragmentation buffer, and one-stranded cDNA was synthesized using six-base random primers (random hexamers) with mRNA as the template, followed by the addition of buffer, dNTPs and DNA polymerase I and RNase H to synthesize two-stranded cDNA, followed by the use of The purified double-stranded cDNA was firstly end-repaired, A-tailed and sequenced with AMPure XP beads, and then fragment size selection was performed with AMPure XP beads. Finally, PCR amplification was performed, and the PCR products were purified with AMPure XP beads to obtain the final library. After library construction, initial quantification was performed using Qubit 2.0 to dilute the library, followed by detection of the insert size of the library using Agilent 2100, and after the insert fragment met the expectation, the effective concentration of the library was accurately quantified using Q-PCR method to ensure the quality of the library.

treatment_protocol: For WT 1, WT 2, and WT 3, bone marrow-derived macrophages were cultured in RPMI-1640 medium supplied with 10% FBS, 1% penicillin/streptomycin, and 20 ng/mL M-CSF. For WT CM 1, WT CM 2, and WT CM 3, bone marrow-derived macrophages were cultured in equal volum of LL-2 conditional medium and RPMI-1640 medium supplied with 10% FBS, 1% penicillin/streptomycin, and 20 ng/mL M-CSF. Twenty four hours later, cells were lysed for RNA-seq.

value: primary bone marrow-derived macrophages

value: macrophages

value: WT

value: 50% LL-2 conditional medium

tag: time

value: Day 1


title: Day0 R1


title: bone marrow-derived macrophages cultured in 50% LL-2 conditional medium 24h 1

description: WT CM 1


title: bone marrow-derived macrophages cultured in 50% LL-2 conditional medium 24h 3

description: WT CM 3


title: M42vmn


title: M157vmn


title: M172vmn


title: untreated bone marrow-derived macrophages 3

description: WT 3

value: untreated


title: M145pom

value: pre-optic medial nucleus

value: Cx+T male


title: painless abortion sample rep3 by RNA-seq

city: Shenzhen

first: Jiajie

last: She

address: huafu street

institute: Shenzhen Second people's hospital

data_processing:
Trimmomatic (v.0.27) was used for quality control of paired-end sequencing data.
Reads obtained by sequencing that mapped to rRNA and tRNA sequences from the UCSC gene annotation (hg38) using bowtie2 (v.2.3.4) were discarded, and the remaining reads were aligned to the GRCh38 using hisat2-align (v.2.1.0).
MACS2 (v.2.1.1) was used to identify m6A peaks with the parameter ‘--nomodel’ and ‘-q 0.05’. ExomePeak2 package (v.1.2.0) was used for the identification of differentially methylated peaks.
The findMotifsGenome.pl Perl script from the Homer software suite was used for motif search with the ‘-mask -rna -len 6’ parameters.
Differentially expressed genes were identified using the RNA-seq data (the corresponding MeRIP-seq input library data) by the R package DEseq2 (v.1.32.0).
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using macs2
Supplementary_files_format_and_content: peak text files

source_name: villous tissues

growth_protocol: Villous tissue was at 7 to 8 weeks in the first trimester of pregnancy

extract_protocol:
Total RNA from each sample was isolated using TRIzol reagent (Invitrogen) and fragmented into ~100-nucleotide-long fragments by zinc acetate.
bound RNA was eluted by competition with 1 mg ml−1 N6-methyladenosine (Selleckchem) and used for library construction using the NEBNext Ultra RNA Library Prep Kit v2 for Illumina. After removal of ribosomal RNA using the Epicentre Ribo-zero rRNA Removal Kit (Epicentre), total RNA from each tissue was fragmented and a library was constructed using the NEBNext Ultra RNA Library Prep Kit v2 for Illumina (New England Biolabs) as input RNA.

tag: sample

value: painless abortion


title: M191vmn

value: intact male


title: shSMC1A#3

description:
DLD1_shNC_shSMC1A_diffexpr-results.csv
shSMC3


title: M94pom


title: untreated bone marrow-derived macrophages 2

description: WT 2


title: shSMC1A#2

description:
DLD1_shNC_shSMC1A_diffexpr-results.csv
shSMC2


title: untreated bone marrow-derived macrophages 1

description: WT 1


title: R25pom


title: TS1-iPSC

type: RNA

first: Detu

last: Zhu

state: Guangdong

institute: The Third Affiliated Hospital of Guangzhou Medical University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: TS patient-derived iPSC

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Both the WT and TS-iPSC lines were maintained in mTeSR medium (StemCell Technologies), and the CM lines were maintained in the PSC Cardiomyocyte Maintenance Medium (Gibco) following the manufacturer’s instructions.

extract_protocol: Total RNA was extracted and purified using miRNA Extraction Kit #TR205-200 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: disease

value: Turner syndrome (TS)

value: iPSC


title: shSMC1A#1

description:
DLD1_shNC_shSMC1A_diffexpr-results.csv
shSMC1


title: painless abortion sample rep1 by RNA-seq


title: WT3-iPSC

source_name: Healthy donor-derived iPSC


title: TS2-iPSC


title: bone-marrow-derived macrophage siCXCR4 rep3

city: Hangzhou

first: Ning

state: Zhejiang

address: 88 Jiefang Rd, Hangzhou, Zhejiang Province

institute: Second Affiliated Hospital, Zhejiang University College of Medicine

data_processing:
Basecalling was performed by Illumina NovaSeq 6000.
Sequenced reads were trimmed to remove adaptor sequences and masked to remove low-complexity or low-quality sequences.
Transcription levels are log2 read counts per kilobase of exon per million library reads (RPKM). All overlapping exons of a gene were merged to create one meta-transcript. Gene expression was quantified by the number of reads falling into annotated exons.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: bone-marrow-derived macrophages

extract_protocol:
Total RNA from MΦsiCXCR4 or MΦsiNC was extracted from cells with Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bone-marrow-derived macrophages

tag: sirna

value: LPS for 12 hours


title: bone-marrow-derived macrophage siCXCR4 rep2


title: shNC#3

description:
DLD1_shNC_shSMC1A_diffexpr-results.csv
shNC3

tag: cell line


title: painless abortion sample rep3 by meRIP-seq

tag: chip antibody

value: abcam ab151230


title: WT1-CM

source_name: WT iPSC-derived CMs

value: cardiomyocytes (CMs)


title: TS2-CM

source_name: TS iPSC-derived CMs


title: painless abortion sample rep2 by meRIP-seq


title: painless abortion sample rep2 by RNA-seq


title: TS3-CM


title: shNC#2

description:
DLD1_shNC_shSMC1A_diffexpr-results.csv
shNC2


title: M195pom

value: wild type

tag: tissue

value: Ovx+T female


title: TS1-CM


title: painless abortion sample rep1 by meRIP-seq


title: M167pom


title: WT2-CM


title: bone-marrow-derived macrophage siNC rep3

value: siNC


title: WT2-iPSC

value: WT


title: shNC#1

description:
DLD1_shNC_shSMC1A_diffexpr-results.csv
shNC1


title: WT3-CM