title: Sample_463

value: Blood


title: ileum, DMSO, rep1

status: Public on Feb 21 2024

type: SRA

city: Lebanon

first: Mark

last: Sundrud

state: NH

address: Dartmouth Hitchcock Medical Center One Medical Center Drive

department: Microbiology and Immunology

country: USA

institute: Dartmouth Hitchcock Medical center

description: processed data in countsmatrix.csv column 2, named ‘170987_0001’, removed from analysis for having different DMSO concentration

library_source: transcriptomic

data_processing:
Quality control performed on reads using FastQC
Reads trimmed using cutadapt. max-n parameter set to 0.8
Aligned to genome using HISAT2 aligner
Sequence metrics and rRNA identified using Picard
Duplicate marking using Picard
Assembly: Gencode GRCm39
Supplementary files format and content: A counts matrix stored as a gz compressed csv. Each row represents a gene, and each column represents a sample. The first row and column contain the name of each of the genes and samples respectively.

molecule: total RNA

organism: Mus musculus

source_name: ileum

extract_protocol:
Total RNAs were harvested using TRIzol (Invitrogen) and Rneasy Mini Kit (Qiagen) with Dnase I treatment (Qiagen). 100 ng of total RNAs was used for the construction of sequencing libraries.
cDNA libraries were prepared using QuantSeq 3' mRNA-seq V2 Library Prep Kit with UDI (Lexogen)

treatment_protocol:
Ileal fragments were treated with DMSO, tauroCDCA, or bile acid extraction with or without bile acid depletion for 8 hours.
Medium is Advanced DMEM/F12 (Gibco) containing 100 U/ml penicilin, 100 ug/ml streptomycin, 10 mM HEPES, 2 mM GlutaMAX (Gibco)

tag: tissue

value: ileum

tag: strain

tag: genotype

value: wild-type

tag: Sex

value: male

tag: treatment

value: 0.5% DMSO

tag: time

value: 8 hours


title: GEX single cell RNA-seq on T cells from skin from Ramp1 KO and WT mice following 2 weeks of S. epi treatment

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

data_processing:
Data were filtered and mapped to mm10 reference genome using cellranger 7.0.0 (10X Genomics). Data were normalized in Seurat and were displayed as uniform manifold approximation and projection (UMAP). Three out of thirteen Seurat clusters were excluded from the analyses shown, as each of those outlier clusters only represented zero to ten cells (less than one percent) per cluster per animal. Differential gene expression for each cluster was performed using the Seurat FindAllMarkers function with a single cell-tailored test MAST and default parameters.
Assembly: mm10
Supplementary files format and content: Seurat object (rds)
Supplementary files format and content: 10X Genomics cellranger count output

source_name: skin

extract_protocol:
Skin CD8+ lymphocytes labeled with TotalSeqC hashtag antibodies (BioLegend) from S. epidermidis-associated mice (six Lck-Cre- Ramp1 fl/fl animals and six Lck Cre+ Ramp1 fl/fl animals) were sorted as DAPI- CD90.2+ TCRb+ CD4- CD8b+ TCRgd- CD49f- NK1.1- B220- CD11b- CD11c- MHCII-, using a Sony MA900 cell sorter.
Libraries were constructed with the 10X Genomics 5' kit.
All samples were pooled together, and approximately 15,000 sorted cells were loaded onto the Chromium Single Cell Controller (10X Genomics) to encapsulate cells into droplets. The library was prepared using a Chromium Single Cell 5’ Reagent Kits v2 (10X Genomics) following manufacturer's instructions, and then sequenced on an Illumina Nextseq500 (Next Seq 500/550 High Output Kit v2, Illumina).

value: skin

tag: cell type

value: CD8 T cells

value: Ramp1 KO and WT

value: Staphylococcus epidermidis


title: A699-32

type: RNA

city: Graz

first: Silvia

last: Groiss

address: Neue Stiftingtalstraße 6

department: Institute of Pathology

country: Austria

institute: Medical University of Graz

description:
Pat9 >20% other t3
cDNA, from amplified total RNA

hyb_protocol: Affymetrix GeneChip Human Genome U219 Array Plate (Cat No. ???); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0001 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000

data_processing: Affymetrix Geneexpression Console (Expression Console EC1.2.1.20) using Affymetrix default analysis settings for generation of CEL-files. Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); paired t-test

label: Biotin

organism: Homo sapiens

source_name: liver

label_protocol: Affymetrix GeneChip® 3’ IVT Express Kit (P/N 702646 Rev. ; Cat.No. 901228

extract_protocol: not provided

value: liver

tag: patient

value: pat 9

tag: disease

value: other

tag: steatosis

tag: time point


title: Adult mouse Striatum, replicate 2

city: Los Angeles

first: Kay

last: Linker

state: California

address: 10833 Le Conte Avenue, 53-263 CHS

department: Physiology

institute: UCLA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger 4.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
scRNA-seq was performed to profile the whole cortex, hippocampus, and striatum of C57BL/6NTac mice at 8-10 weeks of age. The brain was immediately dissected out and was sectioned into 400 mm slices in ice-cold artificial cerebrospinal fluid (ACSF) oxygenated with 95% O2 and 5% CO2 and immediately transferred to an oxygenated recovery solution. The cortical, hippocampal, or striatal tissue was dissected out in ice-cold ACSF and cut into small pieces. The tissue was digested in ACSF containing 1 mg/ml pronase at 34 °C for 30 min. The digested tissue was dissociated in ice-cold oxygenated ACSF containing 1% fetal bovine serum. The dissociated cells were filtered through a 20 mm filter and washed with ice-cold ACSF. To remove myelin, the cell pellet was resuspended in PBS and processed with debris removal kit (Miltenyi Biotec). Isolated cells were diluted to 1000 cells/ml in 0.04% BSA/PBS and processed with 10X Genomics platform.  The library preparation and sequencing were performed following 10X Genomics Chromium protocols.
Single cell suspension from mouse brain tissues were prepared using 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 and v3 (10X Genomics, Pleasanton, CA) according to manufacture’s protocol. Quantity and quality of cDNA were assessed by Agilent 2100 expert High Sensitivity DNA Assay. cDNA samples were sequenced on NovaSeq 6000 or NextSeq 500 platform at UCLA Technology Center for Genomics and Bioinformatics.

value: Brain

value: Glia enriched

tag: age

value: 8-10 weeks


title: Sample_455

city: Chicago

first: Gayatry

last: Mohapatra

state: IL

address: 840 S Wood Street

department: Pathology

institute: University of Illinois at Chicago

data_processing:
FASTQ files corresponding to the forward and reverse reads for 189 samples in total, 96 FM and 93 control were obtained from Basespace and used for analysis. The files were processed using the Trim Galore (Babraham Bioinformatics) and Cutadapt (DOI:10.14806/ej.17.1.200) tools to perform a quality trimming by removing short, low quality reads and the adapters. RNA-seq reads were mapped to the reference genome (Gencode.v38) and aligned using STAR aligner. Duplicate reads were removed and uniquely mapped transcripts were selected using Samtools. The TPMs (Transcripts per million) were computed using StringTie corrected by IsoformSwitchAnalyzeR and normalized using TMM (Trimmed Means of M value). Differential expression analysis was performed using DESeq2, using all annotated genes. Ontological analysis of gene expression was carried out using the Qiagen Ingenuity Pathway Analysis (IPA), and Gene Set Enrichment Analysis (GSEA). The Interactome analysis was carried out by Pearson Correlation clustering using the 914 most differentially expressed genes for FM1 and the 361 most differentially expressed genes for FM2 using Cytoscape,  the clusters were determined by AlegroMcode (AllegroViva Corporation, 2011) using default parameters.
Assembly: HG38
Supplementary files format and content: Log of normalized transcripts per million

molecule: polyA RNA

source_name: Blood

extract_protocol:
Total RNA was extracted using QIAamp RNA blood mini kit
RNA libraries were prepared using Agilent SureSelectXT RNA Direct workflow following manufacturer’s instructions.
Hybridization capture method, paired-end sequencing

value: Blood cells from Healthy patient (CONTROL)

value: Female

tag: disease state

value: Healthy patient (CONTROL)


title: Sample_457

value: Blood

value: Male


title: DRG_isletCre_Meis2KO_rep3

city: Lyon

first: Kiran

last: Padmanabhan

address: 32-34 avenue Tony Garnier

department: IGFL

country: France

institute: ENS-Lyon

data_processing:
UMI sequences were extracted with UMI tools (version 1.1.2)
Reads were mapped to GrCM38/mm10 by STAR (version 2.7.10), PCR duplicate were removed with UMI tools
HT-seq count (version 0.6) was used to aggregate read counts per gene followed by differential gene expression analysis with Limma voom on Galaxy (version 3.50.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts and differencial analysis

source_name: DRG

extract_protocol:
RNA was extracted with Rneasy Qiagen kits followed by mRNA purification using the NEBNext® Poly(A) mRNA Magnetic Isolation (NEB)
Libraries were prepared with the CORALL mRNA-Seq Library Prep Kits with UDIs (Lexogen) following manufacturer's recommendations

value: DRG

tag: developmental stage


title: A699-31

description:
Pat8 <5% CRC Met t2
cDNA, from amplified total RNA

value: pat 8

value: CRC Met


title: A699-28

description:
Pat8 <5% CRC Met t3
cDNA, from amplified total RNA


title: DRG_isletCre_Meis2KO_rep2


title: DRG_isletCre_Meis2KO_rep1


title: HTO single cell RNA-seq on T cells from skin from Ramp1 KO and WT mice following 2 weeks of S. epi treatment

value: skin

value: CD8 T cells


title: Sample_453


title: DRG_isletCre_rep2


title: DRG_isletCre_rep3


title: A699-29

description:
Pat8 <5% CRC Met t0
cDNA, from amplified total RNA


title: A699-27

description:
Pat7 <5% CRC Met t2
cDNA, from amplified total RNA

value: pat 7


title: A699-30

description:
Pat8 <5% CRC Met t1
cDNA, from amplified total RNA

value: liver


title: DRG_isletCre_rep1


title: Sample_447

value: Blood cells from Fibromylagia patient (FMA)

value: Fibromylagia patient (FMA)


title: Adult mouse Striatum, replicate 1

description: 10x Genomics

value: Brain


title: Sample_451


title: Sample_449


title: DRG_WT_rep2

value: WT


title: DRG_WT_rep1


title: RNAseq_neutrophils_9h_DR_rep3

data_processing:
RNA-seq reads were mapped with STAR (Dobin et al., 2013) to the mm10 reference genome with default parameters. Read counts were assessed with HOMER’s (Heinz et al., 2010) analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for three replicates per condition. Differential gene expression was assessed with DESeq2 (Love et al., 2014) using HOMER’s getDiffExpression.pl using a false discovery rate (FDR) of 5% and a fold change of 1.5. Metascape (Tripathi et al., 2015) was used for analyzing enriched GO terms, and GSEA was used for gene set enrichment analysis. PCA was performed in R with prcomp, center = TRUE, scale. = TRUE.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample, IDR peaks

source_name: neutrophils from spleen

extract_protocol:
Mice were euthanized with CO2, perfused via the left ventricle of the heart with 10 mL PBS before tissues were harvested and placed in cold PBS. Bone marrow was flushed using cold PBS and processed through a 70 mM filter. Spleens were processed through a 70 mM filter
Whole bone marrow from femur or tibia was flushed in Trizol (Thermofisher). Total RNA extraction was performed with RNeasy mini kit (QIAGEN). DNase-treated total RNA (100 ng) was reverse transcribed into cDNA with Omniscript RT kit (QIAGEN) following manufacturer’s instructions. qPCR was performed using the Taq PCR Master Mix (Life Technologies) on a Quantstudio 6 Flex Real-Time PCR (Life Technologies). CD8+ TCM were sorted from the bone marrow and spleen of mice fed ad libitum or on DR. RNA was extracted using an Arcturus PicoPure RNA Isolation Kit (Applied Biosystems), as per manufacturer’s instructions. cDNA was synthesized with the Ultralow V4 kit (Clonetech) and sequencing libraries were subsequently prepared with the Nextera XT DNA prep kit (Illumina) and sequenced on NextSeq500.

value: dietary restriction 9 hours post secondary infection

tag: organ

value: spleen

value: neutrophils


title: RNAseq_neutrophils_9h_DR_rep2


title: Sample_445

value: Blood cells from Healthy patient (CONTROL)

value: Female

value: Healthy patient (CONTROL)


title: RNAseq_neutrophils_9h_DR_rep1


title: Sample_443

value: Blood

value: Male


title: DRG_WT_rep3

value: DRG


title: RNAseq_neutrophils_9h_AL_rep3

value: ad libitum 9 hours post secondary infection


title: RNAseq_neutrophils_9h_AL_rep2


title: A699-22

description:
Pat6 <5% CRC Met t1
cDNA, from amplified total RNA

value: pat 6

value: CRC Met


title: A699-24

description:
Pat7 <5% CRC Met t3
cDNA, from amplified total RNA

value: liver

value: pat 7


title: A699-26

description:
Pat7 <5% CRC Met t1
cDNA, from amplified total RNA


title: Sample_441


title: A699-25

description:
Pat7 <5% CRC Met t0
cDNA, from amplified total RNA


title: A699-23

description:
Pat6 <5% CRC Met t2
cDNA, from amplified total RNA


title: RNAseq_monocytes_9h_DR_rep3

source_name: monocytes from spleen

value: monoctyes


title: RNAseq_neutrophils_9h_AL_rep1


title: Sample_439


title: Sample_437


title: RNAseq_monocytes_9h_DR_rep1


title: RNAseq_monocytes_9h_AL_rep2


title: Sample_435


title: RNAseq_monocytes_9h_DR_rep2


title: RNAseq_monocytes_9h_AL_rep3


title: ATACseq_Tmem_spleen_AL_rep1

library_source: genomic

molecule: genomic DNA

source_name: Tmem from spleen

value: ad libitum

value: Tmem


title: Sample_433


title: ATACseq_Tmem_spleen_AL_rep2


title: Sample_431


title: A699-20

description:
Pat6 <5% CRC Met t3
cDNA, from amplified total RNA


title: ATACseq_neutrophils_DR_rep2

source_name: neutrophils from bone marrow

value: dietary restriction

value: bone marrow


title: RNAseq_monocytes_9h_AL_rep1

value: spleen


title: ATACseq_neutrophils_DR_rep1

value: neutrophils


title: A699-18

description:
Pat5 <5% other t1
cDNA, from amplified total RNA

value: pat 5

value: other


title: A699-21

description:
Pat6 <5% CRC Met t0
cDNA, from amplified total RNA


title: ATACseq_neutrophils_AL_rep2


title: Sample_429

value: Blood

value: Blood cells from Healthy patient (CONTROL)

value: Female

value: Healthy patient (CONTROL)


title: ATACseq_Tmem_spleen_DR_rep1


title: ATACseq_neutrophils_AL_rep1


title: A699-14

description:
Pat4 <5% HCC t1
cDNA, from amplified total RNA

value: pat 4

value: HCC


title: A699-19

description:
Pat5 <5% other t2
cDNA, from amplified total RNA

value: liver


title: Sample_427

value: Blood cells from Fibromylagia patient (FMA)

value: Fibromylagia patient (FMA)


title: A699-17

description:
Pat5 <5% other t0
cDNA, from amplified total RNA


title: A699-15

description:
Pat4 <5% HCC t2
cDNA, from amplified total RNA


title: ATACseq_monocytes_DR_rep4

source_name: monocytes from bone marrow

value: monoctyes


title: A699-16

description:
Pat5 <5% other t3
cDNA, from amplified total RNA


title: ATACseq_monocytes_DR_rep3


title: Sample_425


title: ATACseq_monocytes_DR_rep1


title: ATACseq_monocytes_DR_rep2


title: ATACseq_monocytes_AL_rep4

value: ad libitum


title: Sample_423

value: Male


title: ATACseq_monocytes_AL_rep3

value: bone marrow


title: Sample_421


title: ATACseq_monocytes_AL_rep1


title: ATACseq_monocytes_AL_rep2


title: A699-12

description:
Pat4 <5% HCC t3
cDNA, from amplified total RNA


title: Sample_419


title: RNA-seq bam,hs-bam 38hr AHS rep1

city: Cambridge

first: Tamsin

middle: Joy

last: Samuels

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description:
38h_rRNA
RNA_seq_fpkm.csv

data_processing:
Trimmed reads were aligned to non-coding RNA reference sequences (flybase, dmel_r6.39) using Bowtie2
non rRNA reads were mapped to the Drosophila melanogaster reference genome dm6 using STAR
Transcript abundance was quantified and differentially expressed genes were identified using Cuffdiff v2.2.1
Assembly: dm6
Supplementary files format and content: .bw and .bigWig files are bigWig files for each sample
Supplementary files format and content: RNA_Seq_fpkm.csv contains FPKM values for every gene at each time point in the RNA-seq
Supplementary files format and content: Ribo_Seq_fpkm.csv contains FPKM values for every gene at each time point in the Ribo-seq

organism: Drosophila melanogaster

source_name: whole adult ovary

growth_protocol: Adult females were heatshocked at 37C for 1 hour then 34C for 2 hours, then returned to 25C. Samples were collected with no heat shock, or at different times after heat shock (AHS)

extract_protocol:
Ovaries were dissected for each sample in cold Dissection buffer (PBS 1X, 0.01% Tween 20, 100 μg/ml cycloheximide) and immediately stored at -80°C after dissection. Frozen samples were homogenised in Polysome extraction buffer (50 mM Tris pH 7.5, 5 mM MgCl2, 150 mM NaCl, 0.5% Triton x-100, 1 mM DTT, 100 μg/ml cycloheximide, protease inhibitor, 25 u/ml Turbo DNAse) using an electrical pestle and then further disrupted by passing 20 times through a 26-gauge needle. The lysate was centrifuged at 20,000g for 10 min at 4°C to pellet tissue debris. Total RNA was isolated by hot phenol-chloroform extraction and quantified using Qubit RNA High Sensitivity Assay Kit (Invitrogen).
1.5 μg of total RNA was used for rRNA depletion by binding of complementary oligos and treatment with RNase H. Libraries were generated using NEBNext®UltraTM Directional RNA Library Prep Kit for Illumina® according to manufacturer9s instructions. Libraries were multiplexed using the NEBNext® Multiplex Oligos for Illumina® and sequenced in paired-end 150 nt-long reads on an Illumina NovaSeq 6000.

value: whole adult ovary

value: after heat shock 38hr


title: Sample_417


title: RNA-seq bam,hs-bam 38hr AHS rep2

description:
38h_rRNA
RNA_seq_fpkm.csv


title: RNA-seq bam,hs-bam 28hr AHS rep2

description:
28h_rRNA
RNA_seq_fpkm.csv

value: after heat shock 28hr


title: A699-10

description:
Pat3 <NA CRC Met t2
cDNA, from amplified total RNA

value: pat 3

value: CRC Met


title: Sample_413

value: Blood

value: Blood cells from Healthy patient (CONTROL)


title: Sample_415

value: Healthy patient (CONTROL)


title: RNA-seq bam,hs-bam 9hr AHS rep2

description:
9h_rRNA
RNA_seq_fpkm.csv

value: after heat shock 9hr


title: RNA-seq bam,hs-bam 18hr AHS rep1

description:
18h_rRNA
RNA_seq_fpkm.csv

value: after heat shock 18hr


title: RNA-seq bam,hs-bam 9hr AHS rep1

description:
9h_rRNA
RNA_seq_fpkm.csv


title: RNA-seq bam,hs-bam 18hr AHS rep2

description:
18h_rRNA
RNA_seq_fpkm.csv


title: RNA-seq bam,hs-bam 5hr AHS rep2

description:
5h_rRNA
RNA_seq_fpkm.csv

value: after heat shock 5hr


title: A699-09

description:
Pat3 <NA CRC Met t1
cDNA, from amplified total RNA

value: liver


title: Sample_411


title: Sample_409

value: Female


title: RNA-seq bam,hs-bam 5hr AHS rep1

description:
5h_rRNA
RNA_seq_fpkm.csv


title: RNA-seq bam,hs-bam 0.5hr AHS rep1

description:
0_5h_rRNA
RNA_seq_fpkm.csv

value: after heat shock 0.5hr


title: Sample_407

value: Blood cells from Fibromylagia patient (FMA)

value: Fibromylagia patient (FMA)


title: A699-11

description:
Pat3 <NA CRC Met t3
cDNA, from amplified total RNA


title: A699-08

description:
Pat2 <5% CCC t3
cDNA, from amplified total RNA

value: pat 2

value: CCC


title: A699-13

description:
Pat4 <5% HCC t0
cDNA, from amplified total RNA

value: pat 4

value: HCC


title: A699-07

description:
Pat2 <5% CCC t1
cDNA, from amplified total RNA


title: A699-05


title: RNA-seq bam,hs-bam no HS rep2

description:
0h_rRNA
RNA_seq_fpkm.csv

value: whole adult ovary

value: no heat shock


title: A699-04


title: RNA-seq bam,hs-bam 28hr AHS rep1

description:
28h_rRNA
RNA_seq_fpkm.csv

value: after heat shock 28hr


title: Sample_405

value: Blood


title: Ctrl 4 miRNA

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: miRNAs of liver tissue obtained from control subject

data_processing:
HISAT2 was used for mapping trimmed reads to HG19. StringTie was used for the assembly of transcripts.
Trimmed reads were mapped on miRNA precursors using SHiMPS aligner/miRbase and the reads associated with mature miRNAs were counted.
Data were log2-transformed and baselined to the median of all samples. All detected transcripts and miRNAs were tested for differential expression using a moderated t-test (significance cutoff false discovery rate <0.05). Hierarchical clustering and principal component analyses were performed for the identification of sample cluster patterns and transcript/miRNA clusters
Assembly: HG19
Supplementary files format and content: mRNA samples are in .txt format with transcript ID, gene symbol, and FPKM.
Supplementary files format and content: miRNAs are presented in .txt format with miRNA ID and RPM.

source_name: Liver

growth_protocol: Tumors from patients with HCC, corresponding nontumorous liver tissues, and livers from subjects without liver disease as diagnosed by the institutional pathologists were analyzed.

extract_protocol:
For gene expression profiling, total RNA extracted from frozen tissues was processed using Illumina TruSeq Stranded Total RNA. For miRNA sequencing, small RNAs purified from 2 μg of total RNA using a 15% denaturing polyacrylamide gel were barcoded using adapters, and ligated small RNAs were purified, reverse transcribed and amplified by polymerase chain reaction using the following primers: forward, AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA; reverse, CAAGCAGAAGACGGCATACGA.
Ribo-Zero Library Prep per manufacturer’s standard protocol and sequenced using Illumina NovaSeq6000 S (150bp paired-end).

value: Liver

tag: subjectid

tag: diagnosis

value: No liver disease control

tag: tumor type

value: not applicable

tag: tissue location

value: control liver

tag: patient age

value: pediatric


title: A699-03

description:
Pat2 <5% CCC t0
cDNA, from amplified total RNA

tag: tissue

value: liver


title: RNA-seq bam,hs-bam no HS rep1

description:
0h_rRNA
RNA_seq_fpkm.csv

tag: genotype

tag: treatment


title: RNA-seq bam,hs-bam 0.5hr AHS rep2

description:
0_5h_rRNA
RNA_seq_fpkm.csv

value: after heat shock 0.5hr


title: Ctrl 2 miRNA


title: Sample_403

tag: cell type

value: Blood cells from Healthy patient (CONTROL)

tag: Sex

value: Female

value: Healthy patient (CONTROL)


title: HCC Tumor C10 miRNA

description: miRNAs of non-fibrolamellar hepatocellular carcinoma tumor

value: Hepatocellular carcinoma

value: Non-fibrolamellar

value: tumor


title: Sample_401

value: Male


title: HCC Background C10 miRNA

description: miRNAs of non-fibrolamellar hepatocellular carcinoma background liver tissue

value: background liver


title: A699-06

tag: patient

value: pat 2

tag: disease

value: CCC


title: Sample_399

value: Blood


title: HCC Tumor C2 miRNA

value: Liver


title: A699-01

description:
Pat1 <5% CCC t0
cDNA, from amplified total RNA

value: pat 1

tag: steatosis

tag: time point


title: A699-02

description:
Pat1 <5% CCC t1
cDNA, from amplified total RNA


title: HCC Tumor C1 miRNA

description: miRNAs of fibrolamellar hepatocellular carcinoma tumor

value: Fibrolamellar


title: HCC Background C1 miRNA

description: miRNAs of fibrolamellar hepatocellular carcinoma background liver tissue

value: pediatric


title: A839-69

description:
Tube E966-20
cDNA, from amplified total RNA

value: liver

value: CRC Met


title: Sample_397

value: Blood cells from Healthy patient (CONTROL)

tag: disease state


title: DR_rep4

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description: transcriptional profiling (RNA sequencing)

data_processing:
Fastq files quality check was performed using FastQC v0.11.5.
The fastq files were mapped to the mm9 genome using TopHat v2.1.0 with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene is calculated by HTSeq-Count 0.11.2 with -s no -a 0 -t exon -m intersection-nonempty parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Htseq-count text file

source_name: Mouse CD34+alpha6+ hair follicle stems cells

growth_protocol: C57BL/6J mice were obtained from Janvier. Mice were obtained from Janvier and maintained in the animal facilities of the Leibniz Institute for Age Research or from Hunan SJA Laboratory Animal Co. Ltd. (Hunan, China) and maintained in the animal facilities of Nanchang Royo Biotech under pathogen-free conditions on a 12-hour light/12-hour dark cycle

extract_protocol:
CD34+alpha6+ hair follicle stems cells were FACS purified from a pool of 3 mice per group and total RNA was isolated using MagMAX-96 Total RNA Isolation kit (Ambion). A DNA digestion step was included during the RNA purification process.
Quality check and quantification of total RNA was done using the Agilent Bioanalyzer 2100 in combination with the RNA 6000 pico kit (Agilent Technologies). Library preparation was done using Illumina’s TruSeq RNA v2 library preparation kit following the manufacturer’s description. Quantification and quality check of libraries was done using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 kit. Libraries were sequenced on a HiSeq2500 running in 51cycle/single-end/high-output mode

treatment_protocol: Mice were housed individually and received either of the following regimen: ad libitum (AL), fed with unlimited amount of food; dietary restriction diet (DR), fed daily with an amount of food corresponding to 70% of the amount of food consumed by body weight and gender matched mice in the AL group.

tag: strain

value: CD34+alpha6+ hair follicle stems cells

tag: group

value: Dietary restriction


title: Sample_395

value: Blood cells from Fibromylagia patient (FMA)

value: Female

value: Fibromylagia patient (FMA)


title: A839-67

description:
Tube E966-18
cDNA, from amplified total RNA


title: A839-68

description:
Tube E966-19
cDNA, from amplified total RNA


title: DR_rep2


title: DR_rep1


title: Sample_393


title: HCC Tumor C5 miRNA

tag: subjectid

value: Hepatocellular carcinoma

value: tumor


title: Sample_391


title: HCC Background C2 miRNA

tag: diagnosis

value: Non-fibrolamellar

value: background liver


title: AL_rep5

value: Unlimited amount of food(ad libitum)


title: AL_rep3


title: Sample_389

value: Blood

value: Healthy patient (CONTROL)


title: AL_rep2


title: AL_rep4


title: A839-66

description:
Tube E966-17
cDNA, from amplified total RNA


title: A839-65

description:
Tube E966-16
cDNA, from amplified total RNA


title: AL_rep1


title: Sample_382


title: PCLS_aG1_6

city: Berlin

first: Paul

last: Horn

address: Augustenburger Platz 1

department: Department of Hepatology and Gastroenterology

institute: Charité - Universitätsmedizin Berlin

data_processing:
Adapter and quality trimming were performed using fastp using the adapter sequence GATCGGAAGAGCACACGTCTGAACTCCAGTCAC and settings --trim_poly_g --trim_poly_x --cut_tail --cut_window_size=4 --cut_mean_quality=20 --disable_quality_filtering --low_complexity_filter --complexity_threshold=30 --length_required 36
Gene abundance was quantified using a decoy-aware transcriptome index (transcriptome Gencode version 29, genome GRCh38) and Salmon 1.5.9 with default settings.
Assembly: GRCh38, Gencode version 29
Supplementary files format and content: Salmon quantification output files.

growth_protocol: Cylinders of liver tissue were prepared by taking biopsies from explant livers using an 8 mm skin biopsy blade. Next, we embedded these cylinders in 3% low-melt Agarose (A9414, Sigma) in phenol-free Hank’s Buffered Salt Solution (HBSS, 14175095, Gibco) and cut 250 µm thick sections using a vibratome (VT1200S, Leica biosystems). The slices were then equilibrated in pre-warmed full PCLS culture medium (Williams E medium + 2% FBS + 1% penicillin-streptomycin-L-glutamine + 1x insulin-transferrin-selenium + 100nM dexamethasone) at 37°C for one hour, and in the meanwhile, treatment conditions were prepared in PCLS culture medium. Treatment solutions were then added at 1.5mL per well into 3µm transwell inserts in a 12-well plate (GD665631, SLS). Finally, one piece of PCLS was transferred into each respective transwell and the plates were incubated for 24h on an orbital rocker at 20rpm, 37°C in a humidified 5% CO2 atmosphere. At the end of the incubation period, liver slices were collected, snap-frozen in liquid N2 and stored at -80°C until further processing.

extract_protocol:
RNA was isolated using Tri Reagent (T9424, Sigma) and 1-bromo-3-chloropropane (B9673, Sigma) according to manufacturer's instructions. Following Tri Reagent extraction, RNA clean-up was performed using the RNeasy Mini Kit according to the manufacturer's instructions, including on-column DNA digestion.
Single-end 75 base-pair libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (015.96, Lexogen) with an RNA input of 100ng. Quality of libraries was then checked using the Agilent TapeStation D1000 ScreenTape (5067-5582, Agilent) and Qubit dsDNA High Sensitivity kit (Q32851, Invitrogen).

treatment_protocol: PCLS were treated with 100nM anti-Gremlin-1 or Isotype control antibody for 24 hours.

value: Liver

value: anti-Gremlin-1 Ab


title: DR_rep3


title: A839-63

description:
Tube E966-14
cDNA, from amplified total RNA

value: liver


title: PCLS_IMC_6

value: Isotype control Ab


title: PCLS_aG1_5


title: PCLS_IMC_5


title: Sample_380

value: Blood cells from Healthy patient (CONTROL)


title: Sample_378


title: PCLS_aG1_4


title: PCLS_IMC_4


title: Sample_376

value: Male


title: PCLS_aG1_3


title: PCLS_IMC_3


title: A839-64

description:
Tube E966-15
cDNA, from amplified total RNA

value: CRC Met


title: A839-61

description:
Tube E966-12
cDNA, from amplified total RNA


title: Sample_374


title: A839-60

description:
Tube E966-11
cDNA, from amplified total RNA


title: PCLS_aG1_1


title: PCLS_aG1_2


title: Sample_372


title: PCLS_IMC_1


title: PCLS_IMC_2


title: H1 D0 Rep 2

city: Toronto

first: De Hua Andy

last: Yang

state: Ontario

address: 160 College St

department: CCBR

country: Canada

institute: University of Toronto

data_processing:
The transcript reads from FASTQ files were aligned to the Ensembl GRCh38v94 human transcriptome and quantified using Kallisto following default parameters.
Kallisto count data was prepared for DESeq2 using tximport function and differential expression analysis was performed using DESeq2
Assembly: Ensembl GRCh38v94 human transcriptome
Supplementary files format and content: tab-delimited text file include normalized abundance values for each Sample : NormalizedAbundance_allsamples.txt
Supplementary files format and content: tab-delimited text file include differential gene expression analysis comparing F5L6.13 vs CHIR : Deseq2_FZDvCHIR_D16.txt

source_name: H1 hESC

extract_protocol:
Cells were dissociated, pelleted, and resuspended in TRIzol Reagent. RNA was extracted according to manufacturer’s protocol
Sequencing libraries prepared by Network Biology Collaborative Centre at the Lunenfeld-Tanenbaum Research Institute

treatment_protocol: Differentiated ventral midbrain progenitors at day 16 patterned with CHIR or F5L6.13

tag: cell line

value: H1 hESC

value: Undifferentiated


title: Sample_370


title: F5L6.13 D16 Rep 3

value: Differentiated with F5L6.13 D16


title: A839-62

description:
Tube E966-13
cDNA, from amplified total RNA


title: A839-58

description:
Tube E966-09
cDNA, from amplified total RNA


title: A839-59

description:
Tube E966-10
cDNA, from amplified total RNA


title: Sample_368

value: Blood cells from Fibromylagia patient (FMA)

value: Female

value: Fibromylagia patient (FMA)


title: H1 D0 Rep 1


title: A839-56

description:
Tube E966-07
cDNA, from amplified total RNA


title: A839-57

description:
Tube E966-08
cDNA, from amplified total RNA


title: F5L6.13 D16 Rep 2


title: A839-55

description:
Tube E966-06
cDNA, from amplified total RNA


title: Sample_366


title: F5L6.13 D16 Rep 1


title: Sample_364


title: CHIR D16 Rep 3

value: Differentiated with CHIR D16


title: CHIR D16 Rep 2


title: CHIR D16 Rep 1


title: Sample_360


title: Sample_362


title: HEK293 BioRep2 input

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

data_processing: Fastq reads were trimmed from illumine adapters using cutadapt (-m 10 -q 20 -O 3 -a CTGTCTCTTATACACATCT). Next, reads have been aligned to the human genome hg38 with bwa mem and alignments were saved into bam files. Picard MarkDuplicates was used to identify and remove duplicated reads. Total number of unique reads was quantified for each library. Regions with local enrichments were obtained by calling peaks with macs2 for each individual pull-down library paired to the corresponding input control. Consensus regions of each biological replicate was defined as the regions observed in 2 out of the 3 technical replicates (bedtools, multiIntersectBed).

growth_protocol: HEK293 cells were maintained in high-glucose DMEM supplemented with 10% (v/v) heat-inactivated Fetal Bovine Serum at 37°C.

extract_protocol:
For each ChIP and input, 750 ng chromatin was incubated in 90.0 μL blocking buffer (25 mM HEPES pH 7.5, 10.5 mM NaCl, 110 m KCl, 1 mM MgCl2 and 1% (w/v) bovine serum albumin; cat. #A7030, Merck) supplemented with 1.0 μL 1 mg/ml RNaseA (cat. # AM2271, ThermoFisher) for 60 min at 1400 rpm on a thermoshaker (Eppendorf) at 37 °C in a 1.5 mL DNA LoBind tube. 65 μL anti-flag M2 magnetic beads (cat. # M8823, Merck) were washed 3 times with 650 μL blocking buffer and stored in 1.30 mL blocking buffer at 16 °C on the thermoshaker (1400 rpm) for at least 1 h until required. For each ChIP, 10 pmol BG4 stock was added and incubated for 1 h at 16 °C with mixing at 1400 rpm. Input samples were processed in parallel with omission of the BG4 antibody immunoprecipitation step. Next, 50 μL of prepared bead solution was added and incubated for 1 h at 16 °C with mixing at 1400 rpm. Beads were magnetically captured, supernatant discarded and washed eight times with 250 μL pre-chilled wash buffer (10 mM Tris pH 7.4, 100 mM KCl, 0.1% (v/v) Tween 20; cat. # 11332465001, Merck) in the cold room. Beads were then resuspended in 250 μL wash buffer and incubated at 37 °C in a thermoshaker at 1400 rpm for 10 min. After a second warm wash, beads were resuspended in 75 μL of elution buffer (1 x TE buffer, 1 μL 20 mg/mL proteinase K; cat. # AM2546, ThermoFisher) and incubated at 65 °C with 1400 rpm shaking for 16 h. DNA was purified using MinElute Reaction Cleanup Kit according to the manufacturer’s instructions (cat. # 28206, Qiagen) and eluted in 20 μL EB buffer.
For library preparation, samples were quantified by Qubit dsDNA HS assay and 10ng of purified ChIP or input DNA was tagmentated (2.5 µL Tn5 (Illumina) in tagmentation buffer (Illumina)) in total reaction volume of 40 µL at 800 rpm shaking for 20 min at 37 °C. After purification by MinElute Reaction Clean up Kit, libraries were generated by mixing 20 µL tagmentated DNA, 2.5 µL each of Nextera Index i7 and Nextera Index i5 (Nextera index primer kit, Illumina) with 25 µL NEB Next High Fidelity 2 x PCR master mix (NEB) in a PCR reaction using the following conditions: 72 °C for 5 min, 98 °C for 30 sec followed by six cycles of 98 °C for 10 sec, 63 °C for 30 sec and 72 °C for 1 min. Libraries were purified by MinElute reaction clean-up kit and library quality and quantity were assessed by Bioanalyser and Qubit, respectively. Samples were sequences on a NextSeq platform (single-end, 75 bp reads).

treatment_protocol: 30 million HEK293 cells were fixed with 1% formadehyde for 10 min at room temperature. Chromatin was isolated using 250 μL of the Lysis and Hypotonic Buffer for Sonication kit (cat. # 500239, Chromatrap). Lysed nuclei suspensions were sonicated for 30 s on/60 s off (high setting) using a water-cooled bath sonicator (Bioruptor Plus, Diagenode) until genomic DNA was sheared to an average size of 100–500 bp.

value: human embryonic kidney

tag: chip antibody


title: Sample_358

value: Blood


title: HEK293 BioRep3 tech3

description: yuqi_HEK293_SLX-19000_biorep3.peaks.multi2.bed


title: A839-54

description:
Tube E966-05
cDNA, from amplified total RNA


title: A839-52

description:
Tube E966-03
cDNA, from amplified total RNA


title: A839-53

description:
Tube E966-04
cDNA, from amplified total RNA


title: Sample_356

value: Healthy patient (CONTROL)


title: HEK293 BioRep2 tech1

description: yuqi_HEK293_SLX-19000_biorep2.peaks.multi2.bed


title: Sample_354


title: HEK293 BioRep2 tech2


title: HEK293 BioRep2 tech3


title: WT Rep 2 Total RNA

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Department of Biochemistry and Biophysics

institute: UCSF

description:
Total RNA for WT Rep 2
RNAseq_TAF15_counts.tsv

data_processing:
To process the reads, the Ribo-seq reads were first trimmed using cutadapt (v2.3) to remove the linker sequence AGATCGGAAGAGCAC. The fastx_barcode_splitter script from the Fastx toolkit was then used to split the samples based on their barcodes. Since the reads contain unique molecular identifiers (UMIs), they were collapsed to retain only unique reads. The UMIs were then removed from the beginning and end of each read (2 and 5 Ns, respectively) and appended to the name of each read. Bowtie2 (v2.3.5) was then used to remove reads that map to ribosomal RNAs and tRNAs, and the retained reads were then aligned to mRNAs (we used the isoform with the longest coding sequence for each gene as the representative). Subsequent to alignment, umitools (v0.3.3) was used to deduplicate reads.
The quality check and downstream processing of the processed reads was performed using Ribolog v0.0.0.9 (Navickas et al. 2021). To distinguish stalling peaks from stochastic sequencing artifacts, we followed a multi-step procedure. We calculated P-site offsets and identified the codon at the ribosomal A-site for each RPF read using the riboWaltz package. A loess smoother was used to de-noise codon-wise RPF counts. The loess span parameter varied depending on the transcript length and allowed borrowing information from approximately 5 codons on either side of the A-site. We calculated an excess ratio at each codon position by dividing the loess-smoothed count by the transcript’s background translation level (median of no-zero loess-smoothed counts). After median normalization of the corrected counts and removal of transcripts with 0 counts, the ribosome occupancy testing was performed using logistic regression in Ribolog.
Library strategy: Ribo-Seq

growth_protocol: All cells were cultured in a 37°C 5% CO2 humidified incubator. The 293T cells (ATCC CRL-3216) were cultured in DMEM high-glucose medium supplemented with 10% FBS, glucose (4.5 g/L), L-glutamine (4 mM), sodium pyruvate (1 mM), penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco). The K562 cell line was cultured in RPMI-1640 medium supplemented with 10% FBS, glucose (2 g/L), L-glutamine (2 mM), 25 mM HEPES, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco). All cell lines were routinely screened for mycoplasma with a PCR-based assay.

extract_protocol:
Ribosome profiling was performed as previously described (McGlincy and Ingolia 2017). Briefly, approximately 10x106 cells were lysed in ice-cold polysome buffer (20 mM Tris pH 7.6, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide) supplemented with 1% v/v Triton X-100 and 25 U/mL Turbo DNase (Invitrogen). The lysates were triturated through a 27G needle and cleared for 10 min at 21,000 x g at 4°C. The RNA concentration in the lysates was determined with the Qubit RNA HS kit (Thermo). Lysate corresponding to 30 µg RNA was diluted to 200 µl in polysome buffer and digested with 1.5 µl RNaseI (Epicentre) for 45 min at room temperature. The RNaseI was then quenched by 10 µl SUPERaseIN (Thermo).  Monosomes were isolated using MicroSpin S-400 HR (Cytiva) columns, pre-equilibrated with 3 mL polysome buffer per column. 100 µl digested lysate was loaded per column (two columns were used per 200 µl sample) and centrifuged 2 min at 600 x g. The RNA from the flow-through was isolated using the Zymo RNA Clean and Concentrator-25 kit. In parallel, total RNA from undigested lysates was isolated using the same kit.  Ribosome-protected footprints (RPFs) were gel-purified from 15% TBE-Urea gels as 17-35 nt fragments. RPFs were then end-repaired using T4 PNK (NEB) and pre-adenylated barcoded linkers were ligated to the RPFs using T4 Rnl2(tr) K227Q (NEB). Unligated linkers were removed from the reaction by yeast 5’-deadenylase (NEB) and RecJ nuclease (NEB) treatment. RPFs ligated to barcoded linkers were pooled, and rRNA-depletion was performed using riboPOOLs (siTOOLs) as per the manufacturer’s recommendations. Linker-ligated RPFs were reverse transcribed with ProtoScript II RT (NEB) and gel-purified from 15% TBE-Urea gels. cDNA was then circularized with CircLigase II (Epicentre) and used for library PCR. First, a small-scale library PCR was run supplemented with 1X SYBR Green and 1X ROX (Thermo) in a qPCR instrument. Then, a larger scale library PCR was run in a conventional PCR instrument, performing a number of cycles that resulted in ½ maximum signal intensity during qPCR. Library PCR was gel-purified from 8% TBE gels and sequenced on a SE50 run on Illumina HiSeq4000 instrument at UCSF Center for Advanced Technologies.
RNA-seq libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara).

treatment_protocol: K562 cells expressing dCas9-KRAB fusion protein were constructed by lentiviral delivery of pMH0006 (Addgene #135448) and FACS isolation of BFP-positive cells.  The lentiviral constructs were co-transfected with pCMV-dR8.91 and pMD2.D plasmids using TransIT-Lenti (Mirus) into 293T cells, following the manufacturer’s protocol. The virus was harvested 48 hours post-transfection and passed through a 0.45 µm filter. Target cells were then transduced overnight with the filtered virus in the presence of 8 µg/mL polybrene (Millipore).  Guide RNA sequences for CRISPRi-mediated gene knockdown were cloned into pCRISPRia-v2 (Addgene #84832) via BstXI-BlpI sites. After transduction with sgRNA lentivirus, K562 cells were selected with 2 µg/mL puromycin (Gibco). Knockdown of target genes was assessed by RT-qPCR using PerfeCTa SYBR Green SuperMix (QuantaBio) per the manufacturer’s instructions. HPRT1 was used as endogenous control.

value: WT


title: A839-51

description:
Tube E966-02
cDNA, from amplified total RNA


title: A839-49

description:
Tube E856-49
cDNA, from amplified total RNA


title: Sample_334


title: HEK293 BioRep3 input


title: Sample_352


title: A839-50

description:
Tube E966-01
cDNA, from amplified total RNA


title: WT Rep 1 Total RNA

description:
Total RNA for WT Rep 1
RNAseq_TAF15_counts.tsv


title: HEK293 BioRep1 input


title: TAF15 KD Rep 2 Total RNA

description:
Total RNA for TAF15 KD Rep 2
RNAseq_TAF15_counts.tsv

value: TAF15 CRISPRi kD


title: HEK293 BioRep3 tech1


title: HEK293 BioRep3 tech2


title: HEK293 BioRep1 tech1

description: yuqi_HEK293_SLX-19000_biorep1.peaks.multi2.bed


title: Sample_332


title: A839-48

description:
Tube E856-48
cDNA, from amplified total RNA

value: liver


title: HEK293 BioRep1 tech3


title: TAF15 KD Rep 1 Total RNA

description:
Total RNA for TAF15 KD Rep 1
RNAseq_TAF15_counts.tsv


title: Sample_330


title: HEK293 BioRep1 tech2


title: A839-47

description:
Tube E856-47
cDNA, from amplified total RNA


title: A839-46

description:
Tube E856-46
cDNA, from amplified total RNA


title: TAF15 KD Ribo-seq

description: Multiplexed Ribosomal reads (barcode tags in barcodes.tsv)


title: Sample_328


title: Liver, Anesthetized with desflurane for 6 h

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

data_processing:
Terminal
Sequence reads were trimmed for adaptor sequence/low-quality sequence using sickle (parameter- -q 30 -l 20 )
Trimmed sequence reads were mapped to rn6 using hisat2 and samtools
Read count extraction and normalization were performed using Stringtie
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample

organism: Rattus norvegicus

source_name: Liver was recovered after maintaining the anesthetized state for 6h

extract_protocol:
Total RNAs were harvested using Rneasy Midi kit
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold Kit (illumina) according to manufacturer’s instruction.

treatment_protocol: Rats were subjected to inhalational anesthesia using either sevoflurane (4.5%) or desflurane (6%) and rats were sacrificed by decapitation immediately after their loss of consciousness or after subjection of inhalational anesthesia for 6 hours and then portions of their livers were recovered and immersed in RNAlater until RNA preparation.

value: wild type

value: Anesthetized with desflurane for 6 h


title: Control osteoblasts, confluent, control 3

city: Phoenix

first: Katherine

last: Wesseling-Perry

state: AZ

address: 1919 E. Thomas Rd

department: Nephrology

institute: Phoenix Children's Hospital

description:
24-C
1824 control confluent genes

data_processing:
The data was sequenced on Illumina NextSeq500 for a single-end 75bp run
Data quality check was done on Illumina SAV.
Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
Gene expression level was estimated using RSEM v1.2.15.
Assembly: The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
Supplementary files format and content: Combined data comparing expression in 9 end-stage kidney disease patients relative to 3 controls

source_name: trabecular bone

growth_protocol: Primary human osteoblasts from patients with end-stage kidney disease (CKD) and from healthy controls grown to confluence under standard culture conditions.

extract_protocol:
RNA was extracted from cells using the Rneasy Micro Kit
Libraries were prepared with KAPA Stranded RNA-Seq Kit

value: trabecular bone

value: primary osteoblasts, healthy control

value: healthy control

value: unknown


title: A839-45

description:
Tube E856-45
cDNA, from amplified total RNA

value: CRC Met


title: Control osteoblasts, confluent, control 2

description:
23-C
1821 control confluent genes


title: Sample_326

value: Blood cells from Healthy patient (CONTROL)


title: Liver, Control for DesAnes

source_name: Liver was recovered immediately after the induction of anesthetized state

value: Control for DesAnes


title: Sample_324

value: Female


title: CKD osteoblasts, confluent, patient 8

description:
20-C
1756 confluent genes

source_name: iliac crest

value: iliac crest

value: primary osteoblasts, chronic kidney disease

value: chronic kidney disease (end-stage)


title: Liver, Anesthetized with sevoflurane for 6 h

value: Anesthetized with sevoflurane for 6 h


title: CKD osteoblasts, confluent, patient 9

description:
21-C
1762 confluent genes


title: A839-43

description:
Tube E856-43
cDNA, from amplified total RNA

source_name: liver


title: Sample_322

value: Blood

value: Male

value: Healthy patient (CONTROL)


title: Liver, Control for SevoAnes

value: liver

value: wild type

value: Control for SevoAnes


title: Control osteoblasts, confluent, control 1

description:
22-C
1810 control confluent genes

value: trabecular bone

value: primary osteoblasts, healthy control


title: RNA-seq from skin CD4+ CCR6+ Th17 cells following S.epi treatment (rep3)

data_processing:
For T cells, cells were processed and analyzed for RNA-seq as described in Linehan et al., 2018.
For keratinocytes: Sequencing reads were mapped to the mm10 (GRCm38) mouse genome using STAR with stringent mapping conditions, where reads aligned to multiple regions of the genome were eliminated (-outFilterMultimapNmax 2).  Differential gene expression was calculated using HOMER’s getDiffExpression (Heinz et al. 2010). Genes with FDR < 0.05 and foldchange > 2 were considered differentially expressed transcripts. Retroelement and noncoding transcript expression was determined using HOMER, defining these transcripts based on the annotations provided by the Genome-based Endogenous Viral Element Database (gEVE) for GRCm38. For the analysis of individual loci, reads were analyzed using HOMER’s analyzeRepeats function (Heinz et al. 2010), along with a custom GFT file with the gEVE annotations. For the analysis of retroelement and noncoding transcript family motifs, reads were analyzed using the analyzeRepeats function with parameters “repeats mm10”.
Assembly: mm10 (GRCm38)
Supplementary files format and content: file format: txt
Supplementary files format and content: content for T cells: mean, foldchange and p-values; content for keratinocytes: TPM per replicate

source_name: skin

extract_protocol:
Tissues were harvested and cells were extracted (see manuscript for details) and sorted. T cells were sorted as CD4+ CD25- CCR6- for Th1 cells and CD4+ CD25- CCR6+ for Th17. Keratinocytes were sorted as  LD-Cd45-Cd31-Cd34-Cd49f+Sca1+. For more details for the protocol used to sort T cells refer to Linehan et al, 2018; For more details for the protocol used to sort keratinicytes refer to Lima-Junior et al., 2021
For T cells, cells were processed and analyzed for RNA-seq as described in Linehan et al., 2018. For keratiocytes: Keratinocytes from Lck-Cre Ramp1 fl/fl and WT mice were sorted as described in Lima-Junior et al., 2021.
For T cells: mRNA libraries were constructed using SMARTer Ultra Low Input RNA kit (Clonetech) + Nextera XT DNA library prep kit (Illumina). For keratinocytes: RNA libraries were construted using the mouse Tecan SoLo library preparation kit.

treatment_protocol: Mice were treated with S. epidermidis every other day with 4 topical applications in total. Cells were harvsted 2 weeks after the first topical application

value: skin

value: CD4+ CCR6+ Tcells

value: WT

value: Staphylococcus epidermidis


title: A839-42

description:
Tube E856-42
cDNA, from amplified total RNA

value: CRC Met


title: Sample_318

source_name: Blood

value: Blood cells from Healthy patient (CONTROL)


title: A839-40

description:
Tube E856-40
cDNA, from amplified total RNA


title: RNA-seq from skin CD4+ CCR6+ Th17 cells following S.epi treatment (rep2)


title: Sample_316


title: RNA-seq from skin CD4+ CCR6+ Th17 cells following S.epi treatment (rep1)


title: A839-41

description:
Tube E856-41
cDNA, from amplified total RNA


title: CKD osteoblasts, confluent, patient 5

description:
17-C
1726 confluent genes

value: iliac crest

value: primary osteoblasts, chronic kidney disease

value: unknown


title: Sample_314

value: Blood

value: Female


title: RNA-seq from skin CD4+ CCR6- Th1 cells following S.epi treatment (rep3)

value: CD4+ CCR6- Tcells


title: A839-44

description:
Tube E856-44
cDNA, from amplified total RNA

value: liver


title: CKD osteoblasts, confluent, patient 4

description:
16-C
1717 confluent genes

value: chronic kidney disease (end-stage)


title: Sample_312

value: Male

value: Healthy patient (CONTROL)


title: Sample_320


title: A839-38

description:
Tube E856-38
cDNA, from amplified total RNA


title: A839-39

description:
Tube E856-39
cDNA, from amplified total RNA


title: A839-37

description:
Tube E856-37
cDNA, from amplified total RNA


title: CKD osteoblasts, confluent, patient 7

description:
19-C
1742 confluent genes


title: RNA-seq from skin CD4+ CCR6- Th1 cells following S.epi treatment (rep2)


title: Sample_310

value: Blood cells from Fibromylagia patient (FMA)

value: Fibromylagia patient (FMA)


title: CKD osteoblasts, confluent, patient 2

description:
14-C
1708 confluent genes


title: Sample_308


title: CKD osteoblasts, confluent, patient 3

description:
15-C
1712 confluent genes


title: CKD osteoblasts, confluent, patient 6

description:
18-C
1730 confluent genes


title: RNA-seq from skin CD4+ CCR6- Th1 cells following S.epi treatment (rep1)

value: skin


title: MEFs, CPN-/-CRY2, rep 2

city: Taichung

first: Yi-Ying

last: Chiou

address: No.145, Xingda Rd., South Dist.

department: Graduate Institute of Biochemistry

country: Taiwan

institute: National Chung Hsing University

data_processing:
Reads alignment using RNA STAR(Galaxy 2.6.0b-1)
Strands split by Filter SAM or BAM, output SAM or BAM (Galaxy 1.8)
BigWig conversion by Genome Coverage (Galaxy 2.27.0.0) and then Wig/BedGraph-to-bigWig(Galaxy 1.1.1)
Raw counts using FeatureCounts (Galaxy 1.6.0.6)
Assembly: mm10
Supplementary files format and content: bigwig files for genome browser, R and M are different strands
Supplementary files format and content: tabular files are raw counts for each sample after FeatureCount, first column is the Geneid, second column is the counts

source_name: MEF

growth_protocol: DMEM with 10%FBS, 37oC, 5% CO2

extract_protocol:
The water phase after phase separation of Trizol extraction was used for RNA purification by RNA mini kit (Zymo)
illumina stranded-RNA library kit

treatment_protocol: No

value: MEF

value: Cry1-/-, Cry2-/-, Per1-/-, Per2-/-, Nr1d1-/-, Nr1d2-/-, Exogenous CRY2 expression


title: CKD osteoblasts, confluent, patient 1

description:
13-C
1703 confluent genes


title: MEFs, CPN-/-CRY2, rep 1


title: A839-35

description:
Tube E856-35
cDNA, from amplified total RNA

value: CRC Met


title: ZNF800 KD ATAC-seq Rep 3

description: ATAC-Seq of CRISPRi mediated KD of ZNF800 Rep 3

data_processing: ENCODE ATAC-seq pipeline (Lee et al. 2016) with default parameters was used for sequencing data processing and analysis. The differentially accessible peaks were identified with the DESeq2 package (Love, Huber, and Anders 2014) and annotated with the ChIPseeker package (Yu, Wang, and He 2015). To perform a comparison against published ChIP-Seq data, the processed ChIP-exo results were downloaded from GEO (GSE151287) (Lai et al. 2021)The data consisted of bed files containing 33 and 181 QKI peaks (two replicates) and a bigWig file with ZNF800 ChIP-exo signal (no ChIP-exo peaks were reported for ZNF800). In total, 234564 and 222350 ATAC-seq peaks for QKI and ZNF800, respectively, had coverage of at least 10 reads in more than one replicate and were used in the following tests. For QKI, the bed files with ChIP-exo peaks were merged, transferred to the hg38 genome assembly with UCSC liftOver and the numbers of differentially accessible (or not differentially accessible) QKI-KD ATAC-seq peaks that intersect (or do not intersect) ChIP-exo peaks were calculated using bedtools intersect (v.2.26.0) (Hinrichs et al. 2006; Quinlan and Hall 2010) followed by a one-sided ('greater') Fisher’s exact test on 2x2 contingency table. For ZNF800, bigWig files were converted to bed using UCSC bigWigToWig (v.377) and wig2bed from BEDOPS (v.2.4.38) (Kent et al. 2010; Neph et al. 2012), followed by UCSC liftOver to the hg38 genome assembly. The resulting regions were intersected with differentially accessible and not differentially accessible ZNF800-KD ATAC-seq peaks using bedtools intersect followed by comparison of ChIP-exo signal distribution in these two sets using non-parametric Mann-Whitney U test.

growth_protocol: K562 cells expressing dCas9-KRAB fusion protein were constructed by lentiviral delivery of pMH0006 (Addgene #135448) and FACS isolation of BFP-positive cells.  The lentiviral constructs were co-transfected with pCMV-dR8.91 and pMD2.D plasmids using TransIT-Lenti (Mirus) into 293T cells, following the manufacturer’s protocol. The virus was harvested 48 hours post-transfection and passed through a 0.45 µm filter. Target cells were then transduced overnight with the filtered virus in the presence of 8 µg/mL polybrene (Millipore).  Guide RNA sequences for CRISPRi-mediated gene knockdown were cloned into pCRISPRia-v2 (Addgene #84832) via BstXI-BlpI sites. After transduction with sgRNA lentivirus, K562 cells were selected with 2 µg/mL puromycin (Gibco). Knockdown of target genes was assessed by RT-qPCR using PerfeCTa SYBR Green SuperMix (QuantaBio) per the manufacturer’s instructions. HPRT1 was used as endogenous control.

extract_protocol:
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed according to the optimized Omni-ATAC protocol (Corces et al. 2017; Grandi et al. 2022). Briefly, samples containing 50,000 cells as input were pelleted, lysed, washed, and re-pelleted using the lysis and wash buffers specified in the Omni-ATAC protocol. A transposition mix containing Tn5 was then added to the samples, and the transposition reaction was carried out for 30 minutes at 37 °C in a thermomixer with 1000 rpm mixing. After transposition, the transposed DNA was purified using the DNA Clean & Concentrator-5 Kit (Zymo Research, cat. no. D4014).
The samples underwent two PCR steps. First, a pre-amplification was performed for 3 cycles to attach unique barcoded adapters to the transposed DNA sample. The concentration of each pre-amplified sample was quantified via qPCR using the NEBNext Library Quant Kit (New England Biolabs, cat. no. E7630). Afterward, samples underwent a second PCR amplification step to obtain the desired DNA concentration of 8 nM in 20 ul. DNA cleanup and qPCR quantification were performed again, and final libraries were diluted down to exactly 8 nM using sterile water. Samples were sequenced using paired-end 75-bp sequencing on an Illumina NextSeq sequencer.

value: ZNF800 KD


title: Sample_304


title: Sample_306


title: ZNF800 KD ATAC-seq Rep 2

description: ATAC-Seq of CRISPRi mediated KD of ZNF800 Rep 2


title: A839-34

description:
Tube E856-34
cDNA, from amplified total RNA

data_processing: Affymetrix Geneexpression Console (Expression Console EC1.2.1.20) using Affymetrix default analysis settings for generation of CEL-files. Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); paired t-test

extract_protocol: not provided


title: A839-36

description:
Tube E856-36
cDNA, from amplified total RNA


title: A839-32

description:
Tube E856-32
cDNA, from amplified total RNA


title: Sample_292


title: ZNF800 KD ATAC-seq Rep 1

description: ATAC-Seq of CRISPRi mediated KD of ZNF800 Rep 1


title: MEFs, CPN-/-CRY1, rep 1

value: Cry1-/-, Cry2-/-, Per1-/-, Per2-/-, Nr1d1-/-, Nr1d2-/-, Exogenous CRY1 expression


title: MEFs, CPN-/-, rep 2


title: WT ATAC-seq Rep 2

description: ATAC-Seq of WT K562 cells

value: wildtype


title: Sample_288


title: WT ATAC-seq Rep 1

description: ATAC-Seq of WT K562 cells


title: MEFs, CPN-/-, rep 1


title: QKI KD ATAC-seq Rep 3

description: ATAC-Seq of CRISPRi mediated KD of QKI Rep 3

value: QKI KD


title: Control Vector -3

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the mm10 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads) with parameters -p -T 10
Assembly: GRCm38.88
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: OVARY

growth_protocol: cultured in RPMI-1640 ((ATCC® 30-2001ATCCTM) containingl-glutamine, 10% FBS, without Pen/Strep

extract_protocol:
Total RNA was isolated using Trizol/Chloroform extraction method and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library prep Kit following manufacturer's protocols.

treatment_protocol: Resting State in RPMI-1640 with 10% FBS

value: OVARY

value: High Grade Serous Ovarian Cancer

value: Control

value: resting state


title: Control Vector -2


title: A839-29

description:
Tube E856-29
cDNA, from amplified total RNA

value: liver


title: QKI KD ATAC-seq Rep 2

description: ATAC-Seq of CRISPRi mediated KD of QKI Rep 2


title: Sample_284

data_processing:
FASTQ files corresponding to the forward and reverse reads for 189 samples in total, 96 FM and 93 control were obtained from Basespace and used for analysis. The files were processed using the Trim Galore (Babraham Bioinformatics) and Cutadapt (DOI:10.14806/ej.17.1.200) tools to perform a quality trimming by removing short, low quality reads and the adapters. RNA-seq reads were mapped to the reference genome (Gencode.v38) and aligned using STAR aligner. Duplicate reads were removed and uniquely mapped transcripts were selected using Samtools. The TPMs (Transcripts per million) were computed using StringTie corrected by IsoformSwitchAnalyzeR and normalized using TMM (Trimmed Means of M value). Differential expression analysis was performed using DESeq2, using all annotated genes. Ontological analysis of gene expression was carried out using the Qiagen Ingenuity Pathway Analysis (IPA), and Gene Set Enrichment Analysis (GSEA). The Interactome analysis was carried out by Pearson Correlation clustering using the 914 most differentially expressed genes for FM1 and the 361 most differentially expressed genes for FM2 using Cytoscape,  the clusters were determined by AlegroMcode (AllegroViva Corporation, 2011) using default parameters.
Assembly: HG38
Supplementary files format and content: Log of normalized transcripts per million

extract_protocol:
Total RNA was extracted using QIAamp RNA blood mini kit
RNA libraries were prepared using Agilent SureSelectXT RNA Direct workflow following manufacturer’s instructions.
Hybridization capture method, paired-end sequencing

value: Blood

value: Blood cells from Healthy patient (CONTROL)

value: Female


title: A839-30

description:
Tube E856-30
cDNA, from amplified total RNA


title: MEFs, CPN-/-CRY1, rep 2


title: A839-31

description:
Tube E856-31
cDNA, from amplified total RNA


title: A839-33

description:
Tube E856-33
cDNA, from amplified total RNA


title: A839-27

description:
Tube E856-27
cDNA, from amplified total RNA


title: A839-28

description:
Tube E856-28
cDNA, from amplified total RNA


title: Sample_282

value: Healthy patient (CONTROL)


title: A839-26

description:
Tube E856-26
cDNA, from amplified total RNA


title: Control Vector -1


title: QKI KD ATAC-seq Rep 1

description: ATAC-Seq of CRISPRi mediated KD of QKI Rep 1


title: Sample_290

value: Blood cells from Fibromylagia patient (FMA)

value: Fibromylagia patient (FMA)


title: Sample_274


title: Sample_278

value: Male


title: ∆GAG-3

value: deleted GAG


title: Sample_272


title: Vehicle_C

city: Belfast

first: Francesca

last: Amoroso

address: 97 Lisburn Road

institute: Queen's University Belfast

data_processing:
Sequencing was performed on Illumina Next Seq 500 (High out output (150)) at 75 P.E at 25M reads/ sample.
Fastq files were generated using bcl2fastq version 2.19 using the default thresholds.
Reads were aligned to version GRCh37/hg19 of the human reference genome using STAR (version 2.4.2a).
Raw counts of reads mapped to genes were calculated using HT‐Seq (http://www‐huber.embl.de/users/anders/HTSeq/doc/overview.html)
Raw counts were used as input for differential expression analysis using DESeq2.
Genome_build: mm8
Supplementary_files_format_and_content: Gene sets were filtered to contain genes upregulated after treatment (FC >1) and downregulated (FC <0.5).

source_name: Prostate Cancer cells

growth_protocol: Cells were injected subcute in nude-nude mice (2x106 in matrigel). When the tumours were visible, the mice were treated as described above. The tumours were harvasted at maximum size of 1000 mm3 or after 21 days of daily treatment.

extract_protocol:
The RNA was extracted from the cells and collected utilizing the column-based method through the RNeasy MinElute Clean-up Kit (QIAGEN, Hilden, Germany).
The RNA library preparations were performed with the KAPA RNA HyperPrep Kit (KAPA Biosystems, Roche Holding AG) according to the manufacturer’s instructions.

treatment_protocol: To obtain single cells, the tumours were dissociated  through mechanical and enzymatic digestion with Collagenase IV (1%) at 37˚C.

tag: treatments

value: 0.1 ml 5% benzyl alcohol and 95% safflower oil solution via IP every day

tag: experiment

value: in vivo (xenograft)

value: nude-nude

value: tumour explant


title: Vehicle_B

tag: tissue


title: Sample_286


title: ∆GAG-2

value: OVARY

tag: genotype

tag: treatment


title: A839-25

description:
Tube E856-25
cDNA, from amplified total RNA

value: CRC Met


title: Vehicle_A


title: A839-23

description:
Tube E856-23
cDNA, from amplified total RNA


title: A839-24

description:
Tube E856-24
cDNA, from amplified total RNA


title: Sample_268

tag: cell type

tag: Sex


title: S545S-3

value: High Grade Serous Ovarian Cancer


title: Sample_270


title: Untr_B

value: Untreated


title: S545A-2

value: resting state


title: S545A-1


title: Untr_A


title: A839-22

description:
Tube E856-22
cDNA, from amplified total RNA

value: liver

tag: patient

tag: disease


title: A839-21

description:
Tube E856-21
cDNA, from amplified total RNA

tag: steatosis

tag: time point


title: ARM5_D

value: Mycophenolate mofetil (100mg/kg), Abiraterone (0.5 mmol/kg/d in vehicle) and prednisolone phosphate (20mg/kg).

tag: strain


title: ∆GAG-1


title: ARM5_C


title: OE4_miRNA

city: Nanning

first: Wen

middle: Jing

last: Liu

state: Guangxi

address: No 6 Shuangyong Road

country: China

institute: The first affiliated hospital of Guangxi Medical University

description: Bronchopulmonary dysplasia (BPD),duplicate sample 4

data_processing:
From the Gene Expression Omnibus, this work gathered the GSE125873 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE125873) comprising RNA-seq profiling of peripheral blood specimens from 11 BPD individuals and 21 controls on the GPL16791 platform
mRNAs with aberrant expression were selected in BPD relative to controls both in our RNA-seq and the GSE125873 datasets. The screening threshold values were set as p<0.05 and |log2fold change (FC)|>0.585. This analysis was completed by use of edgeR package. The shared mRNAs were eventually obtained for further analysis. With the same threshold values, aberrantly expressed miRNAs in BPD versus controls were screened. Such findings were visualized into volcano and heatmap diagrams.
CircRNAs that targeted aberrantly expressed miRNAs were inferred through the circBank (www.circbank.cn) that is a comprehensive database for human circRNAs. In addition, interaction pairs between aberrantly expressed miRNAs and circRNAs were obtained from the starBase database (http://starbase.sysu.edu.cn/). The shared circRNA-miRNA pairs were acquired. After integrating circRNA-miRNA and miRNA-mRNA pairs, circRNA-miRNA-mRNA networks were generated and visualized by use of Cytoscape software
The enrichment analysis on Gene Ontology (GO) was achieved via clusterprofiler package. GO comprises biological process, molecular function, and cellular component. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was conducted. False discovery rate (FDR)<0.05 was indicative of the significant enrichment.
By adopting GSEA, the differences in GO and KEGG pathways between groups were estimate in accordance with the reference gene set from the Molecular Signature Database. FDR<0.05 was utilized as the enrichment cutoff value.
WGCNA was carried out based upon the top 5000 genes of standard deviation among samples. Sample dendrogram was drawn, and outlier samples were discarded. Through Pearson’s test, gene relationships were acquired. Next, a similarity matrix was built. The optimal soft thresholding value was selected through considering scale independence along with mean connectivity. The similarity matrix was converted into the adjacency matrix. The construction of a hierarchical clustering dendrogram was achieved for detecting modules. The modules were then merged by use of dynamic tree cutting method. Pearson’s test was employed for computing the connections of merged modules with BPD and EIF2AK2. Gene significance across modules was compared. The module presenting the strongest connection with EIF2AK2 was determined. Genes in this module with coefficient >0.6 were regarded as EIF2AK2-relevant genes.
EIF2AK2-relevant genes were uploaded the STRING online source (https://string-db.org/). Protein interactions were predicted, and a PPI network was downloaded.
Consensus clustering analysis was carried out for estimating the number of molecular subtypes across the merged mRNA dataset in accordance with the transcriptome profiling of EIF2AK2-relevant genes by use of ConsensuClusterPlus package. The consensus matrix was built for determining the optimal number of clusters.
Through Student’s t or Wilcoxon test, the difference between groups was estimated. Receiver operator characteristic curve (ROC) was plotted for appraising the diagnostic efficacy of EIF2AK2. Correlation analysis was achieved by use of Pearson’s test. P<0.05 indicated statistical significance.
Assembly: hg38

source_name: Peripheral blood

growth_protocol: Peripheral blood specimens were collected from 9 infants with BPD and 9 age-matched healthy controls in the Eighth Affliatied Hospital of Guangxi Medical University.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The blood specimens were placed in anticoagulant tubes composed of potassium and sodium EDTA. Then, 0.1 mL was separated into RNase-free microcentrifuge tubes, and mixed with 0.3 mL RNAlater (Sigma-Aldrich), followed by storage at −80°C before sequencing.

tag: disease state

value: Bronchopulmonary dysplasia (BPD)

value: Peripheral blood


title: S534A-3


title: S534A-2


title: OE3_miRNA

description: Bronchopulmonary dysplasia (BPD),duplicate sample 3


title: A839-19

city: Graz

first: Silvia

last: Groiss

institute: Medical University of Graz

description:
Tube E856-19
cDNA, from amplified total RNA


title: S534A-1


title: OE2_miRNA

description: Bronchopulmonary dysplasia (BPD),duplicate sample 2


title: ARM5_A


title: ARM5_B


title: OE1_miRNA

description: Bronchopulmonary dysplasia (BPD),duplicate sample 1


title: A839-18

description:
Tube E856-18
cDNA, from amplified total RNA


title: OE5_miRNA

description: Bronchopulmonary dysplasia (BPD),duplicate sample 5


title: A839-17

description:
Tube E856-17
cDNA, from amplified total RNA


title: RNA-seq from skin keratinocytes 14 days following S.epi treatment in Ramp1 WT mice (rep3)

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

institute: NIH

value: skin

value: keratinocytes

value: Ramp1 WT

value: Staphylococcus epidermidis


title: RNA-seq from skin keratinocytes 14 days following S.epi treatment in Ramp1 WT mice (rep2)


title: ARM4_D

value: Mycophenolate mofetil (100mg/kg) and ARN-509 (30mg/kg)


title: ARM4_C

value: in vivo (xenograft)


title: A839-15

address: Neue Stiftingtalstraße 6

description:
Tube E856-15
cDNA, from amplified total RNA


title: Ctrl4_miRNA

description: normal population,duplicate sample 4

value: healthy


title: Ctrl5_miRNA

description: normal population,duplicate sample 5


title: A839-16

description:
Tube E856-16
cDNA, from amplified total RNA


title: Ctrl3_miRNA

description: normal population,duplicate sample 3


title: A839-20

description:
Tube E856-20
cDNA, from amplified total RNA


title: ARM4_A

value: nude-nude

value: tumour explant


title: RNA-seq from skin keratinocytes 14 days following S.epi treatment in Ramp1 WT mice (rep1)


title: RNA-seq from skin keratinocytes 14 days following S.epi treatment in Ramp1 KO mice (rep3)

value: Ramp1 KO


title: RNA-seq from skin keratinocytes 14 days following S.epi treatment in Ramp1 KO mice (rep2)


title: A839-14

description:
Tube E856-14
cDNA, from amplified total RNA

value: CRC Met


title: Ctrl2_miRNA

description: normal population,duplicate sample 2


title: ARM3_B

value: ARN-509 at 30mg/kg- delivered daily by OG in a formulation solution consisting of 15% Vitamin E-TPGS and 65% of a 0.5% w/v CMC solution in 20 mM citrate buffer (pH 4.0)


title: RNA-seq from skin keratinocytes 14 days following S.epi treatment in Ramp1 KO mice (rep1)


title: Ctrl1_miRNA

description: normal population,duplicate sample 1


title: ARM3_A


title: Homo_B4_mRNA


title: ARM2_D

value: Abiraterone at 0.5mmol/kg/d in vehicle - delivered by IP in 5% benzyl alcohol, 95% safflower oil together with


title: Homo_B3_mRNA


title: Homo_B2_mRNA


title: ARM2_C


title: A839-11

description:
Tube E856-11
cDNA, from amplified total RNA

value: liver


title: A839-13

description:
Tube E856-13
cDNA, from amplified total RNA


title: A839-12

description:
Tube E856-12
cDNA, from amplified total RNA


title: ARM3_C


title: A839-09

description:
Tube E856-09
cDNA, from amplified total RNA


title: A839-10

description:
Tube E856-10
cDNA, from amplified total RNA


title: HeLa, 4sU 30min chase, Oligo(dT) + MTS pulldown RNA-seq

city: New York

first: Yeon

last: Choi

state: NY

address: 1470 Madison Ave

institute: Iicahn school of medicine at mount sinai

data_processing:
The initial parts of sequence analysis were done by using Cutadapt version 3.0 {Martin, 2011 #125}. For 5′ and 3′ end of each read, the low-quality bases below Phred quality of 30 were trimmed. After trimming, 3′ adaptor sequences of both the first and second read of each pair were removed (Table S6). Read pairs with any read shorter than 70 bases were removed after trimming and adopter clipping. To get the readcount for each gene and spike-in, a transcript reference was build based on spike-in sequences (Table S6), UCSC Genome Browser hg38 RefGene annotation (downloaded on February 20, 2020), and hg 38 genome, by RSEM (v1.3.1) {Li, 2011 #126}. Pre-mRNA transcript models were also generated and added to the transcript reference by in-house software, since un-spliced mRNAs might be included in the early stage mRNPs. The read pairs were aligned to the above transcript reference by STAR version 2.7.6a {Dobin, 2013 #127}. The read count of each gene and spike-in was calculated by RSEM (v 1.3.1) {Li, 2011 #126}. Spike-in normalization was done by the ratio of geometric mean of spike-in TPMs.
Assembly: GRCh38
Supplementary files format and content: genes.results contains gene expression level estimated by RSEM

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM (Welgene) supplemented with 9% FBS (Welgene, cat#S001-01) and cultured at 37°C with 5% CO2.

extract_protocol:
Cells were harvested without UV crosslinking and then treated with DNaseI. For spike-in RNAs, in vitro transcribed non-human RNAs were prepared with or without 4-thiouridine and then polyadenylated with ePAP (NEB). After adding spike-in RNAs to the same amount of lysate, the RIC protocol described above was used to enrich poly(A) RNA in the lysate except elution buffer (20 mM Tris-HCl pH 7.5, 1 mM EDTA, and 1mM DTT). The eluted samples were precipitated with ethanol. Enrichment of 4-thiouridine labeled RNA was performed based on the previously described protocol {Duffy, 2016 #160} with the following alterations. 50ug of poly(A) enriched RNAs were used for MTS-pulldown. MTS-biotin was diluted in N,N-Dimethylformamide (Sigma, cat#227056). RNAs were incubated with diluted MTS-biotin at room temperature for 2 hrs and purified with RNAclean XP (Beckman, cat#A63987). Dynabeads MyOne Streptavidin C1 (Invitrogen, cat#65002) were washed with nuclease-free water and high salt buffer (10 mM Tris, 1 mM EDTA, 100 mM NaCl, 0.05 % Tween-20 wt/vol) and then blocked with blocking buffer (10 mM Tris, 1 mM EDTA, 100 mM NaCl, 0.05 % Tween-20 wt/vol, 5 ug/ul glycogen) for an hour at room temperature. Biotinylated RNAs were heated at 65°C for 10 min and placed on ice. 10X High salt buffer was added to RNA solution to make it 1X concentration, and pre-washed beads were added to RNAs. Biotinylated RNA and streptavidin beads were incubated in dark for 15 min. The first supernatants were kept as flow-through. After washing beads with high salt buffer three times, 4-thiouridine labeled RNAs were eluted from beads with elution buffer (100 mM DTT, 5% 2-Mercaptoethanol, 20 mM HEPES pH 7.6, 1 mM EDTA, 100 mM NaCl, 0.05% Tween-20 wt/vol).
RNA-seq libraries were constructed using MGIEasy RNA Directional Library Prep Kit V2.0 (MGI, cat#1000006385) and sequenced by paired-end run on MGI sequencer.

treatment_protocol: One 150 mm culture dish of HeLa cell for each time point was used for the experiment. Followed by 10 min of 4-thiouridine labeling, cells were harvested after incubation for 0 min, 30 min, and 5 hrs of uridine supplemented media. As a negative control, a no-4-thiouridine-labeled sample (“No-4sU”) was also prepared.

value: HeLa

value: 4sU 30min chase


title: A839-08

description:
Tube E856-08
cDNA, from amplified total RNA


title: Homo_B1_mRNA

value: Bronchopulmonary dysplasia (BPD)

value: Peripheral blood


title: A839-07

description:
Tube E856-07
cDNA, from amplified total RNA


title: ARM2_A


title: ARM1_D

value: Mycophenolate mofetil (100 mg/kg) – delivered daily by OG in a 0.9% saline solution


title: HeLa, No4sU, Oligo(dT) enriched RNA-seq


title: HeLa, No4sU, Oligo(dT) + MTS pulldown RNA-seq


title: HeLa, 4sU 0min chase, Oligo(dT) + MTS pulldown RNA-seq

value: 4sU 0min chase


title: HeLa, 4sU 5hr chase, Oligo(dT) enriched RNA-seq

value: 4sU 5hr chase


title: ARM1_C


title: Homo_A3_mRNA

description: normal population,duplicate sample 3


title: Homo_A4_mRNA

description: normal population,duplicate sample 4


title: HeLa, 4sU 5hr chase, Oligo(dT) + MTS pulldown RNA-seq


title: ARM2_B


title: HeLa, 4sU 30min chase, Oligo(dT) enriched RNA-seq


title: Homo_A2_mRNA

description: normal population,duplicate sample 2


title: ARM1_B


title: Homo_A1_mRNA

description: normal population,duplicate sample 1


title: HeLa, 4sU 0min chase, Oligo(dT) enriched RNA-seq


title: ARM1_A


title: A839-03

description:
Tube E856-03
cDNA, from amplified total RNA


title: A839-05

description:
Tube E856-05
cDNA, from amplified total RNA


title: A839-04

description:
Tube E856-04
cDNA, from amplified total RNA


title: A839-06

description:
Tube E856-06
cDNA, from amplified total RNA


title: ChIP_H3.1_DAL_4h_R1

status: Public on Feb 20 2024

city: Chicago

first: Matthew

middle: J.

last: Schipma

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Reads were trimmed using cutadapt version 3.7
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.4.1
Peaks were called using HOMER v4.11.1
bigWig files were created using HOMER v4.11.1
Differential binding analysis was performed using HOMER v4.11.1
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: Peak files (histone) except for input files

growth_protocol: Cells were maintained in DMEM/F12 (no phenol red) supplemented with 5% charcoal stripped FBS, 1% Pen/Strep, 20 ng/ml EGF, 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, and 0.1 µg/ml cholera toxin.

extract_protocol:
Material was prepared using  Magna ChIP A/G kit (Millipore) according to manufacturer's instructions.
The library was amplified to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Cells were treated with 10 nM D-Alanine and mRNA was collected 4h or 24h after tratment.

value: WT

value: ChIP H3.1 4h after 10nM D-Alanine


title: ChIP_H3.3_Ctrl_R1

value: ChIP H3.3 Control


title: ChIP_H3.1_DAL_24h_R1

value: ChIP H3.1 24h after 10nM D-Alanine


title: ChIP_H3.3_DAL_4h_R1

value: ChIP H3.3 4h after 10nM D-Alanine


title: ChIP_H3.3_DAL_24h_R1

value: ChIP H3.3 24h after 10nM D-Alanine


title: ChIP_H3.1_Ctrl_R1

value: ChIP H3.1 Control


title: A839-02

description:
Tube E856-02
cDNA, from amplified total RNA

value: CRC Met


title: Input_H3.3_DAL_24h_Rep1

value: Input H3.3 24h after 10nM D-Alanine


title: A839-01

description:
Tube E856-01
cDNA, from amplified total RNA

value: liver


title: Input_H3.3_DAL_4h_Rep1

value: Input H3.3 4h after 10nM D-Alanine


title: Input_H3.1_Ctrl_Rep1

value: Input H3.1 Control


title: Input_H3.1_DAL_24h_Rep1

value: Input H3.1 24h after 10nM D-Alanine


title: Input_H3.3_Ctrl_Rep1

value: Input H3.3 Control


title: Input_H3.1_DAL_4h_Rep1

value: Input H3.1 4h after 10nM D-Alanine


title: P5_RGC

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

data_processing:
Sequence reads were mapped to the mm10 genome and transcriptome by Hisat2 and transcripts quantified using the Cufflinks/cuffdiff pipeline
Reads mapping to the loci for Nfe2l1-3 were extracted in BAM file format using SamTool 1.9
Assembly: mm10
Supplementary files format and content: csv file includes FPKM values for Nfe2l1-3 tanscripts expressed in P5 RGCs based on Cufflinks/Cuffdiff analysis

source_name: RGCs

extract_protocol:
Postnatal day 5 RGCs were purified by immunopanning for Thy1 (after immunopanning depletion of macrophages and amacrine cells).
cDNA libraries were prepared using RiboZero and ScriptSeq v2 kit (Epicentre/Illumina) which depletes rRNAs. Paired reads were sequenced in a DNA-strand-specific manner, 100 bp from each end, on HiSeq 2000 Sequencer (Illumina).

tag: strains

tag: age

value: postnatal day 5

value: RGCs


title: KN473 Control

city: Bordeaux

first: Amandine

last: Crombe

address: 229 cours de l'Argonne

institute: Institut Bergonié

description: KN473 control PRE

data_processing:
data analysis was performed by three different methods: the MAGeCK tool
the CRISPRCloud2 pipeline (https://crispr.nrihub.org)
the RIGER (RNAi gene enrichment ranking) method launched through GENE-E from the Broad Institute (https://software.broadinstitute.org/GENE-E/extensions.html). RIGER settings were adjusted as described previously in Joung et al (DOI: 10.1038/nprot.2017.016)
Assembly: hg19
Supplementary files format and content: 3 Excel files: Mageck analysis, Crisprcloud2 analysis and  GENE-E (RIGER) analysis
Library strategy: CRISPR‒Cas9 knockout screen

growth_protocol: KN473 cells were maintained in RPMI medium 1640 GlutaMAX Supplement in the presence of 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol:
After the treatment, the cells were centrifuged and the pellet was frozen at -20°C. Frozen cell pellets (CONTROL and NEO group) were thawed and genomic DNA was extracted with a Quick-gDNA MidiPrep kit (Zymo Research) according to the manufacturer’s protocol.
PCR was performed to prepare sequencing library with the NEBNext HF 2X PCR master mix
The library was sequenced on a MiSeq using the 2x150 bp paired-end sequencing protocol (Illumina).

treatment_protocol: KN473 cas9 cells infected with the GeCKO library were untreated or treated with NEO2734 at 1µM for 72h

tag: cell line

value: UPS (undifferentiated pleomorphic sarcoma)

value: WT

value: vehicle


title: KN473 NEO2734 1µM 72h

description: KN473 NEO POST


title: SAFA_PlusTag_CLIP_Rep2

city: Pasadena

first: Jimmy

middle: K

last: Guo

address: 1200 E California Blvd

institute: Caltech

data_processing:
Paired-end RNA sequencing reads were trimmed to remove adaptor sequences using Trim Galore! v0.6.2 and assessed with FastQC v0.11.8. Read pairs were then aligned to a combined genome reference containing the sequences of repetitive and structural RNAs (ribosomal RNAs, snRNAs, snoRNAs, 45S pre-rRNAs, tRNAs) using Bowtie2. The remaining reads were then aligned to a combined genome reference containing the mouse (mm10) and human (hg38) genomes using STAR aligner181. PCR duplicates were removed using the Picard MarkDuplicates function. For mixing experiments, only reads that mapped uniquely in the genome and unambiguously to the human or mouse genomes were kept for further analysis. For experiments done in a single species, the appropriate reference genome and alignments were used (mm10 for mouse and hg38 for human). These reads were then used for downstream analysis.  For computing enrichments, all human (hg38) and mouse (mm10) annotated genes (RefSeq, downloaded from UCSC GRCh38 and GRCm38, respectively) were used as a reference set except for the genes encoding the transfected proteins. We treated exonic regions and intronic regions of each annotated gene as separate reference genes for computing enrichment. For each reference gene, we enumerated 100 nucleotide windows that span across the gene; for each window, we calculated: (i) the number of reads overlapping the window in the protein elution sample (e.g., CLIP or CLAP) and (ii) the maximum of either the number of observed reads over the window or the median read count over all windows within the gene in the input sample. Because all windows overlapping a gene should have the same expression level in the input sample, this approach provides a conservative estimation of the input coverage because it prevents windows from being scored as enriched if the input values over a given window are artificially low due to stochastic fluctuation, while at the same time accounting for any non-random issues that lead to increases in read counts over a given window (i.e., alignment artifacts leading to non-random assignment or pileups).  To directly compare the number of reads within each window between sample and input, we normalized each window count by the total number of reads sequenced and the overall complexity within each sample. For example, if one sample was sequenced twice as deeply as another, then we would expect to observe – on average – twice as many reads over a given window for that sample. To account for the differences in the number of mapped (aligned) reads between samples, we scaled the total number of sequenced reads by the proportion of aligned reads within each sample.  For each window, we computed enrichment by dividing the normalized sample counts by the normalized input counts. Nominal p-values were calculated for each window using a binomial test where k (number of successes) is defined as the number of reads in the protein elution samples within the window, N (number of trials) is the sum of the number of reads in the protein elution and input samples, and p (probability of success) is the expected number of reads in the elution sample divided by the sum of the expected number of reads per window in elution and input samples. (The expected number of reads is defined as the total number of reads scaled by the proportion of aligned reads within each sample). For plotting and reporting purposes, we considered all regions with a nominal binomial p-value < 10-6 as significant. However, the overall results reported are robust to the precise p-value cutoff used.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes gene window enrichment calculations
Supplementary files format and content: bedgraph

organism:
Homo sapiens
Mus musculus

source_name: HEK239T, PSM33

extract_protocol:
Cells were washed once with PBS and then crosslinked on ice using 0.25 J cm-2 (UV 2.5k) of UV at 254 nm in a Spectrolinker UV Crosslinker. Cells were then scraped from culture dishes, washed once with PBS, pelleted by centrifugation at 1500g for 4 min, and flash-frozen in liquid nitrogen for storage at -80 °C.
Cells were lysed in 1 mL lysis buffer (50mM Tris pH 7.5, 100mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 1X Promega PIC). For CLIP samples, RNA was digested with Ambion RNase I (1:3,000 dilution) to achieve a size range of 100-500 nucleotides in length. We used a fixed RNase condition for all experiments to enable comparison between proteins. Lysates were precleared by mixing with Protein G beads (Dynabeads) for 30 minutes at 4°C. Target proteins were immunoprecipitated overnight at 4°C from 10 million cells with 5 μg of antibody coupled to 40 μL of Protein G beads in 100 μL lysis buffer. Antibodies were pre-coupled to beads for 1 hour at room temperature with mixing, followed by 3 washes with lysis buffer to remove unbound protein. After immunoprecipitation, beads were washed four times with high salt wash buffer (50 mM TrisHCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and four times with wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% Tween-20). RNA and protein were eluted by incubating in NLS elution buffer (20 mM Tris-HCl pH 7.5, 10 mM EDTA, 2% N-lauroylsacrosine, 2.5 mM TCEP) supplemented with 100 mM DTT at 50°C for 20 minutes. Samples were then run through an SDS-PAGE gel and transferred to a nitrocellulose membrane using the iBlot transfer system. The region 70 kDa above the molecular weight of the protein of interest was isolated and treated with Proteinase K (NEB), followed by purification with RNA Clean & Concentrate-5 (Zymo). Anti-V5 antibody (Bethyl, A190-120A) was used for all CLIP experiments.  For CLAP samples, cells were resuspended in 1 mL of cold lysis buffer (50 mM HEPES pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with 1X Protease Inhibitor Cocktail (Promega), 200 U of RiboLock (NEB), 20 U of TURBO DNase (Ambion), and 1X manganese/calcium mix (0.5mM CaCl2, 2.5 mM MnCl2). Samples were incubated on ice for 10 minutes and then at 37°C for 10 minutes at 1150 rpm shaking on a ThermoMixer (Eppendorf). Lysates were cleared by centrifugation at 15000g for 2 minutes and the supernatant was collected for capture to HaloLink Resin (Promega). For each CLAP capture, 200 μL of 25% HaloLink Resin (50 μL of HaloLink Resin total) was used per 10 million cells. Resin was washed three times with 2 mL of 1X TBS (50 mM Tris pH 7.5, 150 mM NaCl) and incubated in 1X Blocking Buffer (50 mM HEPES, pH 7.5, 10 μg/mL Random 9-mer, 100 μg/mL BSA) for 20 minutes at room temperature with continuous rotation. After the incubation, resin was washed three times with 1X TBS. Cleared lysate was mixed with 50 μL of HaloLink Resin and incubated at 4°C overnight with continuous rotation. The captured protein bound to resin was washed three times with lysis buffer at room temperature and then three times at 90°C for 3 minutes while shaking at 1200 rpm with each of the following buffers: 1X ProK/NLS buffer (50 mM HEPES, pH 7.5, 2% NLS, 10 mM EDTA, 0.1% NP-40, 10 mM DTT), high salt buffer (50 mM HEPES, pH 7.5, 10 mM EDTA, 0.1% NP-40, 1M NaCl), 8M urea buffer (50 mM HEPES, pH 7.5, 10 mM EDTA, 0.1% NP-40, 8 M Urea), and Tween buffer (50 mM HEPES, pH 7.5, 0.1% Tween 20, 10 mM EDTA). After the last wash, samples were centrifuged at 7500g for 30 seconds and supernatant was discarded. For elution, HaloLink Resin was resuspended in 100 μL of ProK/NLS buffer + 10 μL of Proteinase K (NEB) and incubated at 50°C for 20 minutes while shaking at 1200 rpm. Elutions were then transferred to microspin cups (Pierce, Thermo Fisher), centrifuged at 2000g for 30 seconds, and purified with RNA Clean and Concentrate-5 (Zymo).

value: HEK239T, PSM33

value: Human embryonic kidney cells, Mouse embryonic stem cells


title: SUZ12_MinusTag_Input_Rep1

data_processing:
Paired-end RNA sequencing reads were trimmed to remove adaptor sequences using Trim Galore! v0.6.2 and assessed with FastQC v0.11.8. Read pairs were then aligned to a combined genome reference containing the sequences of repetitive and structural RNAs (ribosomal RNAs, snRNAs, snoRNAs, 45S pre-rRNAs, tRNAs) using Bowtie2. The remaining reads were then aligned to a combined genome reference containing the mouse (mm10) and human (hg38) genomes using STAR aligner181. PCR duplicates were removed using the Picard MarkDuplicates function. For mixing experiments, only reads that mapped uniquely in the genome and unambiguously to the human or mouse genomes were kept for further analysis. For experiments done in a single species, the appropriate reference genome and alignments were used (mm10 for mouse and hg38 for human). These reads were then used for downstream analysis.  For computing enrichments, all human (hg38) and mouse (mm10) annotated genes (RefSeq, downloaded from UCSC GRCh38 and GRCm38, respectively) were used as a reference set except for the genes encoding the transfected proteins. We treated exonic regions and intronic regions of each annotated gene as separate reference genes for computing enrichment. For each reference gene, we enumerated 100 nucleotide windows that span across the gene; for each window, we calculated: (i) the number of reads overlapping the window in the protein elution sample (e.g., CLIP or CLAP) and (ii) the maximum of either the number of observed reads over the window or the median read count over all windows within the gene in the input sample. Because all windows overlapping a gene should have the same expression level in the input sample, this approach provides a conservative estimation of the input coverage because it prevents windows from being scored as enriched if the input values over a given window are artificially low due to stochastic fluctuation, while at the same time accounting for any non-random issues that lead to increases in read counts over a given window (i.e., alignment artifacts leading to non-random assignment or pileups).  To directly compare the number of reads within each window between sample and input, we normalized each window count by the total number of reads sequenced and the overall complexity within each sample. For example, if one sample was sequenced twice as deeply as another, then we would expect to observe – on average – twice as many reads over a given window for that sample. To account for the differences in the number of mapped (aligned) reads between samples, we scaled the total number of sequenced reads by the proportion of aligned reads within each sample.  For each window, we computed enrichment by dividing the normalized sample counts by the normalized input counts. Nominal p-values were calculated for each window using a binomial test where k (number of successes) is defined as the number of reads in the protein elution samples within the window, N (number of trials) is the sum of the number of reads in the protein elution and input samples, and p (probability of success) is the expected number of reads in the elution sample divided by the sum of the expected number of reads per window in elution and input samples. (The expected number of reads is defined as the total number of reads scaled by the proportion of aligned reads within each sample). For plotting and reporting purposes, we considered all regions with a nominal binomial p-value < 10-6 as significant. However, the overall results reported are robust to the precise p-value cutoff used.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes gene window enrichment calculations
Supplementary files format and content: bedgraph
Library strategy: CLAP-seq


title: SUZ12_MinusTag_CLIP_Rep1


title: SAFA_PlusTag_Input


title: SUZ12_MinusTag_CLAP_Rep2


title: SUZ12_PlusTag_Input


title: SUZ12_MinusTag_CLAP_Rep1


title: SUZ12_PlusTag_CLIP


title: SUZ12_MinusTag_Input_Rep2


title: PHx-Control (3998897014_A)

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and batch-corrected on array barcode and date of surgery in Partek Genomic Suite

label: biotin

source_name: murine liver

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

value: Control

tag: surgery date


title: PHx-Control (3998897004_F)


title: PHx-Enbrel (3998897014_D)

value: LTRβ-/-

value: Etanercept


title: PHx-Enbrel (3998897014_B)


title: PHx-Enbrel (3998897014_F)


title: SUZ12_PlusTag_CLAP


title: PHx-Enbrel (3998897004_D)


title: SUZ12_MinusTag_CLIP_Rep2


title: SAFA_PlusTag_CLAP_Rep1


title: SAFA_PlusTag_CLIP_Rep1


title: PHx-Control (3998897014_C)


title: PHx-Control (3998897004_B)


title: PHx-Enbrel (3998897004_C)


title: PHx-WT rep3

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite

tag: op

value: PHx


title: PHx-KO rep3

value: LTBR KO


title: PHx-WT rep2


title: PHx-KO rep1


title: PHx-WT rep1


title: PTBP1_MinusTag_Input


title: PTBP1_PlusTag_Input


title: PHx-KO rep4


title: SAFA_MinusTag_CLIP


title: PHx-KO rep2


title: PTBP1_MinusTag_CLIP


title: PTBP1_PlusTag_CLIP_Rep1


title: SAFA_MinusTag_Input


title: PTBP1_PlusTag_CLIP_Rep2


title: GFP_PlusTag_Input_Rep2


title: GFP_PlusTag_Input_Rep1


title: GFP_PlusTag_CLIP_Rep2


title: SAFA_PlusTag_CLAP_Rep2


title: EZH2_PlusTag_CLAP_Rep2


title: GFP_PlusTag_CLAP_Rep2


title: EZH2_PlusTag_Input


title: EZH2_PlusTag_CLIP_Rep1


title: GFP_PlusTag_CLIP_Rep1


title: GFP_PlusTag_CLAP_Rep1