title: C2C12_AmAc_24h3

data_processing:
Sequencing and analysis were performed at the University of Michigan according to their pipeline. In brief, Snakemake was used to manage the bioinformatics workflow. FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of each sample.
TrimGalore (https://github.com/FelixKrueger/TrimGalore) (v0.4.5) and Cutadapt(v1.15) were applied using the following parameters: --nextera -e 0.1 –stringency 6 –length 20 –nextseq 20.
Trimmed reads were aligned to mm10 with Bowtie2 (v2.3.4.1) with the following parameters: -X 2000 –no-mixed –no-discordant, and defaults multi-seed length of 20bp with 0 mismatches. Duplicate reads were marked with Picard (http://broadinstitute.github.io/picard/) (v2.20.2). Alignments to autosomes were retained (while sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard were removed, and alignments below a MAPQ threshold were removed. These filtering steps were performed with SAMtools(30) (v1.2) and the flags: -q 10 -F 1024. Reads completely overlapping blacklisted regions (ENCODE Blacklist Regions) were removed with bedtools(31) (v2.28.0).
Sample-wise peaks were called with macs2(32) (v2.1.2) with flags: -f BAM –nomodel –shift -100 –extsize 200 –gsize mm. Peaks over all samples are then merged with bedops(33) (v2.4.36). MultiQC(34) (v1.7) generated a report combining FastQC, trimming, alignment, and duplicate calling over all the samples. For ATAC-specific QC metrics, ataqv (Ataqv)(35) was used (v1.0.0).
For each model and contrast, edgeR Bioconductor package(36) (v3.26.8) was used to identify regions of DAC. For each sample, the number of reads in the merged peaks is counted for each sample, and a library size normalization factor is determined. The common, trended, and tagwise negative binomial dispersions of replicates are calculated. Each model is fit using the glmQLFit function, and each contrast tested with an empirical Bayes quasi-likelihood F-test. The DAC are then annotated to genic and CpG island annotations using the annotatr Bioconductor package(37) (v1.10.0).
Genome_build: mm10
Supplementary_files_format_and_content: Excel, differential expression comparisons with each treatment group including annotated and non-annotated chromatin regions

source_name: C2C12 myotubes

growth_protocol: 10% fetal bovine serum in Dulbecco’s modified Eagle’s medium [DMEM] with 10% fetal calf serum until 80% confluence, replaced by 2% horse serum DMEM for 48 hours of differentiation.

extract_protocol:
Cells were pelleted and frozen at -80 degrees C. The Omni-ATAC protocol for cells was used for extraction and library preparation as described in Corces et al., 2017 without modifications. PMID: 28846090
ATACseq libraries were prepared at the UM Epigenomics Core by using the Omni-ATAC protocol for cells as described in Corces at al., 2017 without modifications. PMID: 28846090

treatment_protocol: Myotubes were either untreated or treated with 10mM ammonium acetate for 3 or 24 hours (n=3 biological replicates)

value: Differentiated C2C12 myotube

value: 24h 10mM ammonium acetate


title: Sham_f_SC_2

status: Public on Jul 27 2021

type: SRA

city: Sydney

first: Gila

last: Moalem-Taylor

state: NSW

address: Wallace Wurth Building, Level 3, Room 355B

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

description: processed data file: Injury_SC_TPM counts.xlsx

library_source: transcriptomic

data_processing:
Illumina NextSeq500 using a High Output v2 kit to generate 2 x 38 bp reads
Transcripts were quantified using Salmon v1.4
Raw read counts were processed and normalized in R using DESeq2’s median of ratio method and low abundance genes were filtered below a mean count of 5 reads/sample
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft excel workbook of gene counts

molecule: total RNA

organism: Mus musculus

source_name: Ipsilateral lumbar spinal cord (L3-5)

extract_protocol:
Each block of tissue was homogenised using a dounce glass tissue homogeniser. Mononuclear cells were separated through Percoll (GE Healthcare Life Sciences) 37%/70% gradient centrifugation. Mononuclear cells were isolated from the interface and stained on ice for 30 min with combinations of BV650 rat anti-mouse CD11b (marking myeloid cells; 1:300), FITC rat anti-mouse Ly6C (marking monocytes/macrophages; 1:300) and APC rat anti-mouse 4D4 (marking resident microglia; 1:1000) in blocking buffer containing 0.2% bovine serum albumin (BSA, Sigma-Aldrich) in HBSS. Cell sorting was performed using FACSAriaIII cell sorter (Becton Dickson). Microglial cells were identified as CD11b+ Ly6C- 4D4+
cDNA libraries were generated from sorted cells using the Smart-seq2 protocol

tag: strain

tag: treatment

value: Sham

tag: tissue

value: Ipsilateral lumbar spinal cord (L3-5)

tag: cell type

value: Microglia


title: PBMCs, Mi-3

city: Harbin

first: Jinwen

last: Zhang

address: NanGang

country: China

institute: College of Bioinformatics

data_processing:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie2 v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with gene reads count for every gene and every sample

organism: Homo sapiens

source_name: symptomatic

extract_protocol:
Total RNA was isolated and purified using TRIzol(Life, cat.265709, CA, USA) following the manufacturer's procedure.
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer® (Implen, cat.N60, Munich, Germany), poly (A) RNA is purified from 1μg total RNA using VAHTS® mRNA Capture Beads with Oligo (dT) (Vazyme, cat.N401-01, Nanjing, China) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme, cat.NR604, Nanjing, China) under 94℃   8min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by reverse transcription reagent, which were next used to synthesise U-labeled second-stranded DNAs. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, size selection was performed with VAHTS® DNA Clean Beads (Vazyme, cat. N411, Nanjing, China). Then the ligated products are amplified with PCR. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (Guangzhou Huayin Health Technology Co., Ltd. Guangzhou, China) following the vendor's recommended protocol.

tag: disease state

value: COVID-19 patient

tag: Sex

value: male

tag: age

tag: immune response

value: symptomatic

value: PBMCs


title: C2C12_AmAc_24h1

city: Cleveland

first: Srinivasan

last: Dasarathy

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

country: USA

institute: Cleveland Clinic Lerner Research Institute

library_source: genomic

molecule: genomic DNA


title: PBMCs, Mi-1

value: female


title: C2C12_AmAc_3h3

value: 3h 10mM ammonium acetate


title: PBMCs, Mo_1


title: Sham_f_SC_1


title: PBMCs, Mi-2


title: PBMCs, Con_25

source_name: uninfected

value: uninfected


title: PBMCs, Con_24


title: PBMCs, Con_23


title: CCI_m_PAG_6

description: processed data file: Injury_PAG_TPM_counts.xlsx

source_name: Periaqueductal gray and rostroventral medulla

value: CCI


title: PBS4_WT

data_processing:
Downstream analysis of RNAseq datasets was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene’s wrapped scripts.
Alignments were parsed using TopHat and differential expressions were determined through DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with FPKM for each sample and differential expression of genes

extract_protocol:
Total RNA was extracted using the RNeasy Plus minikit (Qiagen, Germantown, MD)
RNAseq libraries were generated using the RNeasy Plus minikit (Qiagen, Germantown, MD) and sequenced on an Illumina HiSEQ400 instrument (using protocols provided by manufacturer) by Novogene (Sacramento, CA).

treatment_protocol: In vivo studies in ammonia-treated or vehicle-treated mice were performed in 8–10-week-old wild type animals bred on a C57BL/6J background (Jackson Laboratory, Bar Harbor, ME). In brief, an Alzet miniosmotic pump (Model 2004, Alzet, Cupertino, CA, USA) pre-filled either with ammonium acetate (Am) (released at a rate of 2.5 mmol/kg/day) or sterile phosphate buffered saline (PBS) was implanted in the mice as described previously. Mice were sacrificed 4 weeks after pump implantation and gastrocnemius muscle was rapidly collected and flash frozen.

value: Phosphate buffered saline

value: skeletal muscle


title: C2C12_AmAc_3h2


title: PBMCs, Con_20


title: PBMCs, Con_22


title: PBMCs, Con_21


title: CCI_m_PAG_5

value: Periaqueductal gray and rostroventral medulla


title: CCI_m_PAG_4


title: PBMCs, Con_19


title: CCI_m_PAG_3


title: C2C12_AmAc_3h1


title: PBMCs, Con_16


title: PBMCs, Con_14


title: CCI_m_PAG_2


title: C2C12_UnT_2

value: Untreated


title: PBMCs, Con_12


title: PBMCs, Con_26


title: C2C12_AmAc_24h2

value: Differentiated C2C12 myotube


title: PBMCs, Con_11


title: Sham_m_PAG_6


title: PBMCs, Con_9


title: C2C12_UnT_1


title: PBMCs, Con_8


title: CCI_m_PAG_1


title: C2C12_UnT_3


title: PBMCs, Con_10


title: PBMCs, Con_7


title: Endometrial cancer with non-recurrence status, S51

type: RNA

city: Barretos

first: Rui

last: Reis

state: SP

address: Antenor Duarte Viléla Street, 1331

department: Molecular Oncology Research Center

country: Brazil

institute: Barretos Cancer Hospital

hyb_protocol: Samples were hybridized with 100ns of total RNA  for 21 hours at 65°C, followed by purification and immobilization in nCounter® PrepStation

scan_protocol: Data collection and image processing were carried out in the nCounter® Digital Analyzer with 280 FOV

data_processing: The gene expression data were normalized by the quantile method implemented in the NanoStringNorm package and transformed into a log2 scale

label: Not applicable

label_protocol: NanoString capture and reporter probe mix of NanoString PanCancer Pathway Panel as manufacturer’s instructions

growth_protocol: Not applicable

extract_protocol: RNA from FFPE slides (minimum 60% tumor area) was isolated with RecoverAll Total Nucleic Acid Isolation kit (Ambion by Life Technologies, Austin, TX, USA)

treatment_protocol: Not applicable

value: endometrial cancer

tag: recurrence status

value: NonRecurrence

tag: matching samples

value: Case 8b

tag: figo staging

value: IA


title: Sham_m_PAG_4

value: Sham

value: Microglia


title: PBMCs, Con_3

value: COVID-19 patient

value: male


title: PBMCs, Con_5

value: PBMCs


title: PBMCs, Con_2


title: PBMCs, Con_1


title: Endometrial cancer with non-recurrence status, S50

value: Case 9b


title: Sham_m_PAG_2


title: Endometrial cancer with non-recurrence status, S49

value: Case 3b

value: IB


title: Sham_m_PAG_1


title: PBMCs, RP_10

source_name: re-detectable positive patients

value: female

value: re-detectable positive patients


title: Endometrial cancer with non-recurrence status, S48

value: Case 4b


title: Endometrial cancer with non-recurrence status, S46

value: Case 10b


title: PBMCs, RP_8


title: Endometrial cancer with non-recurrence status, S47

value: Case 11b


title: PBMCs, RP_7


title: PBMCs, RP_9


title: Sham_m_PAG_5

value: Periaqueductal gray and rostroventral medulla


title: PBMCs, Con_6

value: uninfected


title: PBMCs, RP_6


title: PBMCs, Con_4


title: PBMCs, RP_5


title: Endometrial cancer with recurrence status, S44

value: endometrial cancer

value: Recurrence

value: Case 16


title: CCI_m_S1_4

description: processed data file: Injury_S1_TPM counts.xlsx

source_name: Contralateral posterior thalamus and S1 (hindlimb)

value: CCI

value: Microglia


title: Endometrial cancer with recurrence status, S45

value: Case 17

value: IA


title: PBMCs, RP_4

value: COVID-19 patient

value: male

value: PBMCs


title: PBMCs, RP_3

value: female


title: CCI_m_S1_3

value: Contralateral posterior thalamus and S1 (hindlimb)


title: Endometrial cancer with recurrence status, S43

value: Case 15

value: IB


title: PBMCs, RP_1

value: re-detectable positive patients


title: Sham_m_PAG_3

value: Sham

value: Periaqueductal gray and rostroventral medulla


title: PBMCs, RP_12


title: PBMCs, RP_11


title: PBMCs, RP_2


title: CCI_m_S1_6


title: CCI_m_S1_2


title: CCI_m_S1_5


title: PBMCs, Re_14

source_name: recovering

value: recovering


title: PBMCs, Re_15


title: PBMCs, Re_11


title: Endometrial cancer with non-recurrence status, S41

value: endometrial cancer

value: NonRecurrence

value: Case 16b


title: Endometrial cancer with non-recurrence status, S42

value: Case 6b


title: CCI_m_S1_1

value: CCI

value: Microglia


title: Sham_m_S1_5


title: Endometrial cancer with non-recurrence status, S40

value: Case 12b

value: IA


title: Endometrial cancer with non-recurrence status, S39

value: Case 6a


title: PBMCs, Re_12

value: COVID-19 patient

value: female

value: PBMCs


title: Sham_m_S1_4

value: Contralateral posterior thalamus and S1 (hindlimb)


title: PBMCs, Re_9

value: male


title: PBMCs, Re_6


title: Endometrial cancer with non-recurrence status, S38

value: Case 1b


title: Endometrial cancer with non-recurrence status, S37

value: Case 17b


title: PBMCs, Re_7

value: recovering


title: PBMCs, Re_10


title: PBMCs, Re_8


title: Sham_m_S1_3

value: Sham


title: PBMCs, Re_13


title: PBMCs, Re_4


title: Sham_m_S1_2


title: PBMCs, Re_1


title: PBMCs, As_12

source_name: asymptomatic

value: asymptomatic


title: Endometrial cancer with non-recurrence status, S35

value: endometrial cancer

value: NonRecurrence

value: Case 13b


title: Sham_m_S1_6

value: Microglia


title: Endometrial cancer with non-recurrence status, S36

value: Case 4a


title: CCI_m_PFC_5

description: processed data file: Injury_PFC_TPM counts.xlsx

source_name: Prefrontal cortex, amygdala, hippocampus

value: CCI


title: PBMCs, As_9


title: PBMCs, Re_2


title: PBMCs, As_8


title: Sham_m_S1_1


title: CCI_m_PFC_6

value: Prefrontal cortex, amygdala, hippocampus


title: Endometrial cancer with non-recurrence status, S31

value: Case 16a

value: IA


title: Endometrial cancer with recurrence status, S33

value: Recurrence

value: Case 13


title: Sublibrary_Screen_KPCcells_beforetransplantation_rep2

city: Zurich

first: Gerald

last: Schwank

address: Winterthurerstrasse 190

department: Institute of Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

description:
Sublibrary CRISPR Screen in vivo
allreps_OTvsPre.gene_summary.txt

data_processing:
Illumina RTA3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 with parameters hisat2 -x; for sgRNA cassettes, sequences were mapped to the Brie library using MAGeCK 0.5.9 with parameters mageck count -l reference_library.txt
RNA-Seq: raw count matrix was generated in R Studio using the Rsubread package with the featureCounts function
RNA-Seq: Differential Gene expression was assessed using the R package edgeR
CRISPR Screen: Enriched/Depleted sgRNAs were analysed with MAGeCK 0.5.9 with the parameter mageck test -k .count_normalized.txt -t OT-1 -c CTRL --norm-method control --control-sgrna sgRNActrl.txt
Genome_build: mm10
Supplementary_files_format_and_content: rawcounts of RNA molecules per gene, edgeR analysis of differential gene expression, MAGeCK analysis

source_name: Pancreatic cancer

growth_protocol: KPC were culture in IMDM or transplanted orthotopically into the pancreas of mice

extract_protocol: genomic DNA extraction using Qiagen Maxi Prep kits, NGS library prep using Illumina primers to PCR-amplifiy the sgRNA cassette

treatment_protocol: CD8 T cells were added to KPC cells in vitro or injected into tumor-bearing mice

value: Pancreas

tag: cell line

value: KPC

tag: genotype

value: WT

value: no


title: Sublibrary_Screen_KPCcells_beforetransplantation_rep1


title: PBMCs, Re_5

value: COVID-19 patient

value: male

value: recovering

value: PBMCs


title: PBMCs, As_4

value: female

value: asymptomatic


title: CCI_m_PFC_4

value: Microglia


title: Sublibrary_Screen_invivo_withTcells_mouse10

value: CD8 T cells_invivo


title: CCI_m_PFC_3

value: CCI

value: Prefrontal cortex, amygdala, hippocampus


title: PBMCs, As_3


title: CCI_m_PFC_2


title: Endometrial cancer with recurrence status, S30

value: endometrial cancer

value: Case 12

value: IA


title: Sublibrary_Screen_invivo_withTcells_mouse9

value: Pancreas


title: Endometrial cancer with recurrence status, S29

value: Recurrence

value: Case 11


title: Endometrial cancer with recurrence status, S28

value: Case 10


title: CCI_m_PFC_1


title: Sublibrary_Screen_invivo_withTcells_mouse8

value: KPC

value: WT


title: PBMCs, As_1

value: COVID-19 patient

value: male


title: Endometrial cancer with non-recurrence status, S27

value: NonRecurrence

value: Case 13a


title: Sham_m_PFC_5

value: Sham

value: Microglia


title: Sham_m_PFC_6


title: Endometrial cancer with recurrence status, S26

value: Case 9


title: SS22_24h_NT_WT

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description:
rRNA depleted
22

data_processing:
Raw fastq was aligned to human reference genome GRCh38 with hisat2 v2.1.0
Gene wise counts were generated with featureCounts from the subread package v1.5.1 for genes annotated by ensembl GRCh38.92
Counts from separate sequencing lanes for the same sample were summed.
Genes were filtered for at least 2 CPM in half the samples
Genome_build: GRCh38
Supplementary_files_format_and_content: All_logTPMs_exprTable.txt contains counts normalized as log2 TPM for genes with at least 2 counts per million reads

source_name: placenta

growth_protocol: Hofbauer cells were cultured with Dulbecco’s modified Eagle’s medium/nutrient mixture F-12 (1:1) (DMEM/F-12 GlutaMax; Gibco) containing 10% FBSH and 50 U/ml penicillin and 50 µg/ml streptomycin (Invitrogen) (complete DMEM/F-12). The cells were cultured for 48 h before stimulation and for an additional 24 h (total of 72 h) prior to infection.

extract_protocol:
Cells were lysed in TRIzol reagent (Invitrogen). PureLink RNA extraction kit with on-column DNase treatment (Invitrogen) was used to isolate high quality RNA from Hofbauer cells.
Total RNA-seq libraries were generated with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB #E7760L) and NEBNext® rRNA Depletion Kit with sample purification beads (NEB #E6350) with an input amount of 200 ng total RNA per sample. Libraries were pooled and sequenced on an Illumina NovaSeq SP flowcell in paired-end 150 bp format (Illumina, San Diego, CA) to a read yield between 70 – 80 million reads (equivalent to 35 – 40 million clusters).

treatment_protocol: Hofbauer cells (48 h after plating) were untreated or stimulated for 24 h with lipopolysaccharide (LPS from Escherichia coli O55:B5; Sigma-Aldrich) and IFNg (recombinant; R&D systems) at the final concentrations of 100 ng/ml and 100 U/ml (5 ng/ml), respectively. The cell culture medium of control untreated cells was replaced with fresh media at the same time. 24 h post stimulation, the untreated and stimulated cells were infected or not (control) for 5 h or 24 h with wild type L. monocytogenes 10403S.

tag: time point

value: non-treated (NT)

tag: infection

value: WT L. monocytogenes infected (WT)

value: Fetal placental macrophages (Hofbauercells)

tag: agent

value: Wild type L. monoctogenes 10403S


title: Endometrial cancer with non-recurrence status, S25

value: endometrial cancer

value: Case 14b

value: IB


title: Sublibrary_Screen_invivo_withTcells_mouse6

value: Pancreas

value: CD8 T cells_invivo


title: Sham_m_PFC_4

value: Prefrontal cortex, amygdala, hippocampus


title: Sublibrary_Screen_invivo_withTcells_mouse5

value: KPC

value: WT


title: Sublibrary_Screen_invivo_withTcells_mouse4


title: SS18_5h_NT_WT

description:
rRNA depleted
18

value: 5 h


title: SS19_5h_S_NI

description:
rRNA depleted
19

value: IFNg/LPS stimulated (S)

value: Non-infected (NI)

value: Non infected


title: SS17_5h_NT_NI

description:
rRNA depleted
17


title: Endometrial cancer with non-recurrence status, S24

value: NonRecurrence

value: Case 7b


title: Endometrial cancer with non-recurrence status, S23

value: Case 8a


title: Sham_m_PFC_2

value: Sham

value: Microglia


title: SS14_24h_NT_WT

description:
rRNA depleted
14

value: non-treated (NT)

value: WT L. monocytogenes infected (WT)

value: Fetal placental macrophages (Hofbauercells)

value: Wild type L. monoctogenes 10403S


title: Sublibrary_Screen_invivo_withTcells_mouse7

value: Pancreas

value: CD8 T cells_invivo


title: Sham_m_PFC_3

value: Prefrontal cortex, amygdala, hippocampus


title: PBMCs, As_2

value: COVID-19 patient

value: male

value: asymptomatic

value: PBMCs


title: Sublibrary_Screen_invivo_withTcells_mouse3

value: KPC

value: WT


title: CCI_m_SC_6

value: CCI

value: Ipsilateral lumbar spinal cord (L3-5)


title: Sublibrary_Screen_invivo_withTcells_mouse2


title: SS11_5h_S_NI

description:
rRNA depleted
11

value: 5 h

value: IFNg/LPS stimulated (S)

value: Non-infected (NI)

value: Non infected


title: Sublibrary_Screen_invivo_withTcells_mouse1


title: SS10_5h_NT_WT

description:
rRNA depleted
10

value: non-treated (NT)

value: WT L. monocytogenes infected (WT)

value: Fetal placental macrophages (Hofbauercells)


title: Endometrial cancer with non-recurrence status, S20

value: endometrial cancer

value: NonRecurrence

value: Case 5a

value: IB


title: Endometrial cancer with non-recurrence status, S21

value: Case 5b


title: SS9_5h_NT_NI

description:
rRNA depleted
9


title: Endometrial cancer with non-recurrence status, S19

value: Case 11a

value: IA


title: BrieLibrary_Screen_withTcells_rep2

description:
Genome-wide CRISPR Screen
analysis_allreplicates.gene_summary.txt

value: Pancreas

value: KPC

value: WT

value: CD8 T cells


title: SS6_24h_NT_WT

description:
rRNA depleted
6

value: Wild type L. monoctogenes 10403S


title: CCI_m_SC_3

value: CCI

value: Ipsilateral lumbar spinal cord (L3-5)

value: Microglia


title: CCI_m_SC_5


title: Endometrial cancer with non-recurrence status, S18

value: Case 10a


title: Sham_m_PFC_1

value: Sham

value: Prefrontal cortex, amygdala, hippocampus


title: SS3_5h_S_NI

description:
rRNA depleted
3

value: 5 h

value: IFNg/LPS stimulated (S)

value: Non-infected (NI)

value: Fetal placental macrophages (Hofbauercells)

value: Non infected


title: BrieLibrary_Screen_withTcells_rep3


title: SS2_5h_NT_WT

description:
rRNA depleted
2

value: non-treated (NT)

value: WT L. monocytogenes infected (WT)


title: Sham_m_SC_6


title: BrieLibrary_Screen_Ctrl_rep3

value: Pancreas

value: KPC

value: no


title: BrieLibrary_Screen_Ctrl_rep2

value: WT


title: CCI_m_SC_4

value: CCI


title: Endometrial cancer with recurrence status, S14

value: endometrial cancer

value: Recurrence

value: Case 7

value: IB


title: Endometrial cancer with recurrence status, S22

value: Case 8


title: Endometrial cancer with non-recurrence status, S13

value: NonRecurrence

value: Case 1a

value: IA


title: KPC-Stat1KO_Tcells_rep3

description:
Gene expression
rawCounts.txt
Analysis_LFC1_Stat1-OToverCtrl-OT.txt

molecule: polyA RNA

extract_protocol: RNA was extracted using the Qiagen RNeasy Kit, DNA was extracted using the Qiagen Maxi Cell and Tissue Kit. RNA libraries were prepared for sequencing using standard Illumina protocols, for CRISPR screen standard PCR of the sgRNA cassette with Illumina adapters was done

value: CD8 T cells


title: BrieLibrary_Screen_withTcells_rep1


title: RRMS2_CD4

city: Tehran

first: zahra

last: salehi

state: Iran (the Islamic Republic of)

address: 16 Azar

department: Immunology

country: Iran

institute: Tehran University of Medical Sciences

description:
Raw_gene_counts_matrix.txt
abundance measurements.txt

data_processing:
Conversion of Illumina BCL (base calls) binary files into FASTQ format was carried out with the Illumina package bcl2fastq. Each sample had approximately 2×150-bp 30 million paired-end mappable sequencing reads.
After obtaining the raw reads, quality control of sequencing data was evaluated by FastQC software
According to the QC-results, trimming was conducted on low quality reads using Trimmomatic tool
The quality of the reads was re-assessed by FastQC to confirm quality improvements.
Qualified sequences were aligned to the human  genome reference (GRch38/hg38) using HiSat2 and Samtools.
Transcript assembly and abundance estimation were performed using StringTie
The DETs were determined with edgeR R packages.
The significant DETs were determined based on fold change (FC) and false discovery rate (FDR) obtained with Benjamini-Hochberg multiple testing corrections; |(〖log〗_2^|FC| )|>1 and FDR < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Normalized abundance measurements, output from edgeR.

source_name: CD4+ T cells

extract_protocol:
CD4+ T cells isolated from peripheral blood mononuclear cells (PBMCs) of RRMS patients and healthy controls. Total RNA was extracted using the Trizol isolation kit.
Library construction for RNA sequencing was performed with 1 ug of total RNA using Illumina’s TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Globin (Illumina, San Diego, CA, USA). Qualified samples were first proceeded to random fragmentation, with a median length of 150 bp, and converted to double-stranded cDNA. The adapter-ligated fragments were PCR amplified and gel purified. Then, the library was loaded into a flow cell, and cluster generation was executed. Sequencing was done by Illumina Novaseq6000 following the manufacturer’s protocol. Image analysis, per-cycle base calling, and quality score assignment was performed with Illumina primary analysis software, RTA (Real-Time Analysis).

value: Blood

value: RRMS patient at relapse phase


title: Endometrial cancer with non-recurrence status, S12

value: Case 3a


title: Sham_m_SC_3

value: Sham

value: Ipsilateral lumbar spinal cord (L3-5)

value: Microglia


title: CCI_m_SC_1


title: Endometrial cancer with non-recurrence status, S17

value: Case 12a


title: KPC-Vps4bKO_Tcells_rep3

description:
Gene expression
rawCounts.txt
Analysis_LFC1_Vps4b-OToverCtrl-OT.txt

value: Pancreas

value: KPC


title: Endometrial cancer with non-recurrence status, S16

value: endometrial cancer

value: Case 15b


title: Endometrial cancer with non-recurrence status, S10

value: Case 9a


title: SS1_5h_NT_NI

description:
rRNA depleted
1

value: 5 h

value: non-treated (NT)

value: Non-infected (NI)

value: Fetal placental macrophages (Hofbauercells)

value: Non infected


title: BrieLibrary_Screen_Ctrl_rep1

value: WT

value: no


title: Sham_m_SC_1


title: HC4_CD4

value: Blood

value: Healthy control


title: KPC-Rnf31KO_Tcells_rep3

description:
Gene expression
rawCounts.txt
Analysis_LFC1_Rnf31-OToverCtrl-OT.txt

value: CD8 T cells


title: RRMS4_CD4

value: RRMS patient at relapse phase


title: Endometrial cancer with non-recurrence status, S15

value: NonRecurrence

value: Case 15a

value: IB


title: CCI_m_SC_2

value: CCI

value: Ipsilateral lumbar spinal cord (L3-5)

value: Microglia


title: Sham_m_SC_5

value: Sham


title: KPC-Rnf31KO_rep3

value: Pancreas

value: KPC


title: HC2_CD4


title: RRMS3_CD4


title: Sham_m_SC_4


title: D30_IMQ_PolII_CNR_Rep2

city: New York

first: Samantha

middle: B

last: Larsen

state: NY

address: 435 East 30th Street

institute: NYU School of Medicine

description: PCR amplified library from genomic DNA

data_processing:
Library strategy: CUT&RUN-seq
Reads were aligned to reference genome (mm10) using Bowtie2 (version 2.2.9) and deduplicated with Picard tools (http://broadinstitute.github.io/picard, version 2.3.0). Reads were flittered to reads smaller or equal to 120bp using samtools (version 1.3.1). BAM files for each replicate were combined using samtools.  Bigwigs were generated using deeptools (version 3.1.2) with CPM (counts per million) normalization and presented by Integrative Genomics Viewer (IGV) software. Peaks were called using SEACR (Meers et al. 2019 ) using stringent setting and a numeric threshold of 0.01. Peaks were further filtered to have peaks scores greater than 0.5 for a set of high confident peaks per antibody and condition.
Genome_build: mm10

source_name: skin

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers. 400,000 cells were resuspended in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinked cells were quenched with glycine at a final concentration of 0.125M for 5 min at RT. Cells were washed with cold PBS and resuspended in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1 mM DTT, 0.1% triton X-100 supplemented with Roche complete protease inhibitor EDTA-free) and rotated for 10 min at 4’C. Nuclei were washed twice with CUT&RUN wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine supplemented with protease inhibitor) and incubated with concanavalin-A (ConA) beads washed with CUT&RUN binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2) for 10 min at 4’C. ConA-bead-bound nuclei were incubated overnight at 4’C in CUT&RUN antibody buffer (CUT&RUN wash buffer supplemented with 0.1% triton X-100 and 2mM EDTA) and antibody. After antibody incubation, ConA-bead-bound nuclei were washed once with CUT&RUN triton wash buffer (CUT&RUN wash buffer supplemented with 0.1% triton X-100) then resuspended and incubated at 4’C for 1hr in CUT&RUN antibody buffer and 2.5uL pAG-MNase (EpiCypher). ConA-bound-nuclei were then washed twice with CUT&RUN triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated on ice for 30 min. The reaction was stopped by addition of 100ul 2x stop buffer (30mM EGTA) and incubated at 37’C for 10 min. After incubation, ConA-boun-nuclei were captured using a magnet and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated at 70’C for 2hrs with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20’C. DNA was resuspended in 15uL of buffer EB. CUT&RUN sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primer Set 1 and 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer
NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: 2-3 postnatal day 60  murine backskin was treated with Imiquimod for 6 consecutive days

value: female

value: Epidermal Stem Cells

value: wildtype

tag: facs markers

value: ITGA6+, ITGB1+, Sca1+, CD34-

value: Imiquimod for 6 days


title: KPC-Stat1KO_rep3

value: no


title: RRMS1_CD4

value: Blood


title: RamDA-seq Neu_H12

city: Tsukuba

first: Hiroaki

last: Tateno

state: Ibaraki

address: Tsukuba Central 2, 1-1-1 Umezono

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

data_processing:
Library strategy: RamDA-seq
Quality check of reads in FASTQ files was performed using FastQC (version 0.11.5). The reads were trimmed by using fastq-mcf (version 1.0) with the parameters “-L 150 -l 50 -k 4.0 -q 30”. The trimmed reads were mapped to the human reference genome (GRCh38, primary assembly) using HISAT2 (version 2.1.0) with the parameters “--no-softclip”. The resulting SAM files were converted into BAM files using samtools (version 1.4). RSeQC (version 1.2) was used for quality check of read mapping. The featureCounts command in Subread (version 1.6.4) was used to quantify gene-level expression with the parameters “-M -O --fraction -p” and the reference gene model (GENCODE v32, primary assembly).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Neural progenitor cell

growth_protocol: 201B7 hiPSCs were cultured in 2 mL of mTeSR Plus (VERITAS ) on 6 well plate coated with Matrigel (Corning international ).

extract_protocol:
Single-cell cDNA library was prepared using GenNextⓇRamDA-seqTM Single Cell Kit (Toyobo Co., LTD. Tokyo, Japan) followed by manufacturer’s protocol.
cDNA library from each single cell was treated with NovaSeq 6000 S4 reagent Kit followed by manufacturer’s protocol.

treatment_protocol: 201B7 hiPSCs were cultured for 11 days using STEMdiff SMADi Neural Induction Kit (VERITAS) to differentiate into neural progenitor cells.

value: human iPS-derived neural progenitor cell

value: Day 11 of differentiation


title: D30_Ctrl_PolII_CNR_Rep2

description: PCR amplified library from genomic DNA

treatment_protocol: 2-3 postnatal day 60  murine backskin was treated with vanicream for 6 consecutive days

tag: strain

value: control vanicream for 6 days


title: Endometrial cancer with recurrence status, S11

value: endometrial cancer

value: Recurrence

value: Case 6

value: IA


title: KPC-Vps4bKO_rep3

tag: treatment


title: D30_Ctrl_PolII_CNR_Rep1

description: PCR amplified library from genomic DNA


title: Sham_m_SC_2

value: Sham

tag: tissue

value: Ipsilateral lumbar spinal cord (L3-5)

value: Microglia


title: RamDA-seq Neu_H11

tag: cell type


title: Endometrial cancer with recurrence status, S09

value: Case 5

value: IB


title: HC3_CD4

tag: disease state

value: Healthy control


title: Endometrial cancer with non-recurrence status, S08

value: NonRecurrence

value: Case 14a


title: D6_IMQ_PolII_CNR_Rep1

description: PCR amplified library from genomic DNA

tag: Sex

value: female

value: Epidermal Stem Cells

value: wildtype

value: ITGA6+, ITGB1+, Sca1+, CD34-

value: Imiquimod for 6 days


title: D30_IMQ_PolII_CNR_Rep1

description: PCR amplified library from genomic DNA


title: KPC-WT_Tcells_rep3

description:
Gene expression
rawCounts.txt

value: Pancreas

value: KPC

value: WT

value: CD8 T cells


title: Endometrial cancer with non-recurrence status, S07

value: endometrial cancer

value: Case 2b

tag: age


title: KPC-WT_rep3

description:
Gene expression
rawCounts.txt

value: no


title: Endometrial cancer with non-recurrence status, S06

value: Case 2a


title: RamDA-seq Neu_G12

value: human iPS-derived neural progenitor cell

value: Day 11 of differentiation


title: KPC-Stat1KO_Tcells_rep2


title: D30_PIMQ_FOS_4hr_TPA_CNR_Rep2

description: PCR amplified library from genomic DNA

treatment_protocol: 2 postnatal day 60  murine backskin was treated with Imiquimod for 6 consecutive days. At P90 backskin was treated with 0.125mg/mL 12-O-Tetradecanoylphorbol-13-acetate (TPA).


title: Endometrial cancer with recurrence status, S05

value: Recurrence

value: Case 4

value: IA


title: RamDA-seq Neu_H10


title: CHEQ-seq SOX10-KD MM087 plasmid rep 3

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

description:
processed data file:
CHEQ-seq_SOX10-KD_processed.tsv

data_processing:
Library strategy: CHEQ-seq
Enhancer - barcode assignment files are processed with a custom script. Enhancers and barcodes are separated with cutadapt. Enhancers are mapped to the human hg19 genome using minimap.
Raw cDNA and plasmid reads are first processed with a custom script to extract and count each barcode before associating them to the corresponding enhancer based on the enhancer - bc assignment list.
Enhancer activity from MPRA assay is estimated via a custom R script. Enhancers are first filtered based on the number of BCs identified in the sequencing reads. Thresholds of 5 (for the H3K37ac library and enhancer tiling library), 10 (for ATAC-seq library) or 20 (for the SOX-MITF combinations library) BCs per enhancer are selected based on the complexity of the library and the sequencing saturation of the enhancer - BC assignment samples. For the remaining enhancers, BC counts are aggregated per enhancer and then a count per million (CPM) normalisation is applied. Plasmid (input) and cDNA (output) samples are merged by keeping only enhancers remaining in both samples after filtering. Input normalisation is done by dividing CPM normalised cDNA counts by CPM normalised plasmid counts resulting in a FC value. For libraries with shuffled sequences, a basal expression normalisation is further applied by dividing the FC value of the enhancer by the median FC value of the shuffled sequences. For CHEQ-seq SOX10-KD library, enhancer activity from cDNA and plasmid barcode counts is performed with DEseq2.
Genome_build: hg19
Supplementary_files_format_and_content: Enhancer to barcode assignment lists are tables containing two columns: Enhancer name; barcode associated to that enhancer. Enhancer activity matrices are table containing: Enhancer name; Enhancer class; Enhancer activity Fold Change (one column per cell line). DEseq2 result table contains the following columns: Enhancer name; baseMean; log2FoldChange; lfcSE; stat; pvalue; padj; enhancer class.
CHEQ-seq_5p_H3K27ac_enh-BC_list.tsv: Enhancer to barcode assignment list
CHEQ-seq_Intron_H3K27ac_enh-BC_list.tsv: Enhancer to barcode assignment list
CHEQ-seq_ATAC_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_Enhancer-tiling-A_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_Enhancer-tiling-B_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_SOX10-KD_enh-BC_list.tsv: Enhancer to barcode assignment list
CHEQ-seq_SOX-MITF_combinations_enh-BC_list.tsv.gz: Enhancer to barcode assignment list
CHEQ-seq_5p_H3K27ac_processed.tsv: Enhancer activity matrix for CHEQ-seq 5' H3K27ac
CHEQ-seq_Intron_H3K27ac_processed.tsv: Enhancer activity matrix for CHEQ-seq Intron H3K27ac
CHEQ-seq_ATAC_processed.tsv: Enhancer activity matrix for CHEQ-seq ATAC
STARR-seq_ATAC_processed.tsv: Enhancer activity matrix for STARR-seq ATAC
CHEQ-seq_Enhancer_tiling_A_processed.tsv: Enhancer activity matrix for CHEQ-seq Enhancer tiling A
CHEQ-seq_Enhancer_tiling_B_processed.tsv: Enhancer activity matrix for CHEQ-seq Enhancer tiling B
CHEQ-seq_SOX10-KD_processed.tsv: DEseq2 result table for CHEQ-seq SOX10-KD
CHEQ-seq_SOX-MITF_combinations_processed.tsv: Enhancer activity matrix for CHEQ-seq SOX - MITF combinations

source_name: Melanoma cell line

growth_protocol: Melanoma cell lines were cultured with Ham's F-10 nutrient mix + 10% FBS + 0.5% penicillin/streptomycin in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the cell with the innuPREP RNA Mini Kit 2.0 (Analytik Jena) , followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion). cDNA synthesis was performed with the GoScript RT kit and oligo dT primer (Promega). DNA was extracted with a plasmid extraction protocol from Qiagen.
Plasmid libraries, extracted plasmids and cDNA were prepared for sequencing with two rounds of PCR. The first PCR targets the random barcode present within the transcript. The second PCR adds sequencing indexes to the PCR product.

tag: molecule subtype

value: Plasmid


title: KPC-Stat1KO_rep2


title: Endometrial cancer with recurrence status, S34

tag: recurrence status

value: Case 14


title: RamDA-seq Neu_G11


title: RamDA-seq Neu_G10


title: RamDA-seq Neu_H09


title: KPC-Vps4bKO_Tcells_rep2


title: KPC-Rnf31KO_rep2


title: D30_Ctrl_FOS_4hr_TPA_CNR_Rep2

description: PCR amplified library from genomic DNA

treatment_protocol: 2 postnatal day 60  murine backskin was treated with vanicream for 6 consecutive days. At P90 backskin was treated with 0.125mg/mL 12-O-Tetradecanoylphorbol-13-acetate (TPA).

value: female

value: Epidermal Stem Cells

value: wildtype

value: ITGA6+, ITGB1+, Sca1+, CD34-

value: control vanicream for 6 days


title: Endometrial cancer with non-recurrence status, S03

value: NonRecurrence

tag: matching samples

value: Case 7a

value: IB


title: PBMCs, Re_3

value: COVID-19 patient

value: male

tag: immune response

value: recovering

value: PBMCs


title: Endometrial cancer with recurrence status, S02

value: endometrial cancer

value: Recurrence

value: Case 2

tag: figo staging


title: D6_Ctrl_PolII_CNR_Rep1

description: PCR amplified library from genomic DNA

tag: genotype


title: D30_PIMQ_FOS_4hr_TPA_CNR_Rep1

description: PCR amplified library from genomic DNA

value: Imiquimod for 6 days


title: D30_Ctrl_FOS_4hr_TPA_CNR_Rep1

description: PCR amplified library from genomic DNA


title: KPC-WT_Tcells_rep2

description:
Gene expression
rawCounts.txt

value: Pancreas

tag: cell line

value: KPC

value: WT

value: CD8 T cells


title: KPC-Vps4bKO_rep2

value: no


title: Endometrial cancer with recurrence status, S04

value: Case 3


title: KPC-Rnf31KO_Tcells_rep2


title: CHEQ-seq SOX10-KD MM087 plasmid rep 2

value: Plasmid


title: KPC-WT_rep2

description:
Gene expression
rawCounts.txt


title: D30_IMQ_H3K27me3_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

data_processing:
MINT-ChIP reads were processed as shown in van Galen et al (doi::10.1016/j.molcel.2015.11.003) with appropriate modifications made for the T7 barcode adaptor in read2 instead read 1 (van Galen et al). Reads were first demultiplexed by Illumina’s bcl2fastq2 and further demultiplexed using the additional the T7 barcode in read2 (van Galen et al). These demultiplexed reads were aligned to the mm10 genome from the Bsgenome.Mmusculus.UCSC.mm10 Bioconductor package (version 1.4.0) using Rsubread's align method in paired-end mode with fragments between 1 to 5000 base-pairs considered properly paired (Liao Y et al).  Normalized, fragment signal bigWigs were created using the rtracklayer package. For Homer peak calling,  reads were filtered as shown in van Galen et al., with the appropriate modifications for the T7 barcode in read2.  First reads where both pairs are multi mapping and improperly paired are removed and following this fragment duplicates and read pairs with T7 (read 2) duplicates are filtered (van Galen et al). Homer tag directories were created from the filtered BAM files and peak calls made using the Homer’s findPeaks with parameters (-region , -size 1000, -minDist 2500).
Genome_build: mm10

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.049
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: female

value: Epidermal Stem Cells

value: wildtype

value: ITGA6+, ITGB1+, Sca1+, CD34-

tag: chip antibody


title: CHEQ-seq SOX10-KD MM087 cDNA rep 3

value: mRNA


title: RamDA-seq Neu_F11

value: human iPS-derived neural progenitor cell

tag: time point

value: Day 11 of differentiation


title: D30_IMQ_H3K27me3_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.048
NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: facs markers


title: RamDA-seq Neu_G03


title: D30_Ctrl_H3K27me3_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.045
NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: strain

value: control vanicream for 6 days


title: PBMCs, As_7

value: COVID-19 patient

value: asymptomatic

value: PBMCs


title: CHEQ-seq SOX10-KD MM087 cDNA rep 2


title: KPC-Stat1KO_Tcells_rep1

value: Pancreas

value: KPC

tag: treatment


title: CHEQ-seq SOX10-KD MM087 plasmid rep 1


title: CHEQ-seq SOX10-KD MM087 cDNA rep 1


title: RamDA-seq Neu_F10


title: RamDA-seq Neu_F09


title: KPC-Vps4bKO_Tcells_rep1

tag: tissue

value: CD8 T cells


title: KPC-Stat1KO_rep1

value: no


title: RamDA-seq Neu_G09

tag: cell type


title: RamDA-seq Neu_F03


title: D30_Ctrl_H3K27me3_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.044
NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: 2-3 postnatal day 60 mice backskin were treated with vanicream for 6 consecutive days


title: CHEQ-seq Intron H3K27ac MM099 cDNA

description:
processed data file:
CHEQ-seq_Intron_H3K27ac_processed.tsv


title: D6_IMQ_H3K27me3_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.041
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Imiquimod for 6 days


title: KPC-Vps4bKO_rep1


title: D6_IMQ_H3K27me3_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.040
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D6_Ctrl_H3K27me3_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.037
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: CHEQ-seq Intron H3K27ac MM047 plasmid

value: Plasmid


title: RamDA-seq Neu_F02


title: RamDA-seq Neu_E12


title: CHEQ-seq Intron H3K27ac MM047 cDNA


title: RamDA-seq Neu_E11


title: KPC-Rnf31KO_Tcells_rep1


title: KPC-Rnf31KO_rep1


title: KPC-WT_Tcells_rep1

description:
Gene expression
rawCounts.txt

value: WT


title: D30_IMQ_H3K4me1_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.033
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: female

value: Epidermal Stem Cells


title: KPC-WT_rep1

description:
Gene expression
rawCounts.txt


title: CHEQ-seq Intron H3K27ac MM099 plasmid


title: RamDA-seq Neu_E10


title: CHEQ-seq Intron H3K27ac MM029 cDNA


title: D6_Ctrl_H3K27me3_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.036
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: wildtype

value: ITGA6+, ITGB1+, Sca1+, CD34-


title: CHEQ-seq Intron H3K27ac MM087 cDNA rep 1

value: mRNA


title: D30_IMQ_H3K4me1_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.032
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: CHEQ-seq Intron H3K27ac MM029 plasmid


title: D30_IMQ_6hr_TPA_RNA_Rep2

description: PCR amplified library from cDNA

data_processing:
RNA reads were aligned and analyzed with Salmon (v 1.4.0) using the Gencode Release M25 (GRCm38.p6) transcriptome (Patro et al., 2017).
Genome_build: mm10

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers. RNA was isolated from 250,000 cells using Direct-zol RNA Miniprep Kit (Zymo Research) as per manufacturer's instructions.
Illumina TruSeq standard mRNA Library Kit


title: RamDA-seq Neu_E03

value: human iPS-derived neural progenitor cell

value: Day 11 of differentiation


title: RamDA-seq Neu_E09


title: healthy mouse left ventricle1

city: Shanghai

first: Lan

last: Wu

address: No.279 Zhouzhu Road

institute: 1Shanghai University of Medicine & Health Sciences

description: one sample from left ventricle

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells. We processed the unique molecular identifier (UMI) count matrix using the R package Seurat (version 3.1.1). To remove low quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, we apply a criteria to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers. Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where >10% of the counts belonged to mitochondrial genes. After applying these QC criteria, heart single cells in total remained and were included in downstream analyses. Library size normalization was performed in Seurat on the filtered matrix to obtain the normalized count.
Top variable genes across single cells were identified using the method described previously. Briefly, the average expression and dispersion were calculated for each gene, genes were subsequently placed into bins based on expression. Principal component analysis (PCA) was performed to reduce the dimensionality on the log transformed gene-barcode matrices of top variable genes. The 8,527 Cells were clustered based on a graph-based clustering approach and were visualized in 2-dimension using tSNE. Likelihood ratio test that simultaneously test for changes in mean expression and in the percentage of expressed cells was used to identify significantly differentially expressed genes between clusters. Here, we use the R package SingleR, a novel computational method for unbiased cell type recognition of scRNA-seq, with the reference transcriptomic datasets ‘Mouse Cell Atlas’ to infer the cell of origin of each of the single cells independently and identify cell types.
DEGs were identified using the FindMarkers function of Seurat (1) package. The most variable genes were selected using FindVariableGenes function (mean.function = FastExpMean, dispersion.function = FastLogVMR, nfeature = 4000) in Seurat. P value < 0.05 and foldchange > 50% was set as the threshold for significantly differential expression. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution. The Go analysis and KEGG pathways were checked based on the standard of ListHits>2, p<0.05.
CellPhoneDB (v2.0) was used to identify biologically relevant ligand-receptor interactions from single-cell transcriptomics (scRNAseq) data. We defined a ligand or a receptor as “expressed” in a particular cell type if 10% of the cells of that type had non-zero read counts for the ligand/receptor encoding gene. Statistical significance was then assessed by randomly shuffling the cluster labels of all cells and repeating the above steps, which generated a null distribution for each LR pair in each pairwise comparison between two cell types. After running 1,000 permutations, P-values were calculated with the normal distribution curve generated from the permuted LR pair interaction scores. To define networks of cell-cell communication, we linked any two cell types where the ligand was expressed in the former cell type and the receptor in the latter. R packages Igraph and Circlize were used to display the cell-cell communication networks.
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

source_name: heart

extract_protocol:
After collecting left ventricular region of normal healthy hearts, the tissue was digested with enzymes (2 mg/mL Collagenase IV [Worthington Biochemical], 1.2 units/mL Dispase II [Sigma-Aldrich]) for 15 minutes and used for subsequent single-cell sequencing.
Then cDNA fragments were 10× labeled. Next, gel beads containing barcode information were first combined with a mixture of cells and enzymes, and then surrounded by oil surfactant droplets located in the microfluidic "double cross" connection. The droplet was very small and can only hold one gel bead. After the droplet flowed into the reservoir and collected, the gel bead dissolved and released the primer sequence, the cDNA fragment was reverse transcribed, and the cDNA was used as a template for PCR amplification. The products containing barcode information in each droplet were mixed to construct a sequencing library. Then, the Biorupter ultrasonic disrupter was used to break the cDNA into fragments of about 200-300bp, the sequencing adapter P5 was added and sequencing primer R1 and other traditional second-generation sequencing library construction process, and finally perform PCR amplification to obtain the DNA library.

value: left ventricle

value: 12 weeks old


title: CHEQ-seq Intron H3K27ac MM074 plasmid


title: D30_Ctrl_H3K4me1_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.029
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: control vanicream for 6 days


title: CHEQ-seq Intron H3K27ac MM074 cDNA


title: RamDA-seq Neu_D12


title: D30_Ctrl_H3K4me1_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.028
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_IMQ_6hr_TPA_RNA_Rep1

description: PCR amplified library from cDNA


title: CHEQ-seq Intron H3K27ac MM057 plasmid


title: D6_IMQ_H3K4me1_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.025
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: RamDA-seq Neu_D11

extract_protocol:
Single-cell cDNA library was prepared using GenNextⓇRamDA-seqTM Single Cell Kit (Toyobo Co., LTD. Tokyo, Japan) followed by manufacturer’s protocol.
cDNA library from each single cell was treated with NovaSeq 6000 S4 reagent Kit followed by manufacturer’s protocol.


title: D30_Ctrl_6hr_TPA_RNA_Rep2

description: PCR amplified library from cDNA


title: D6_Ctrl_H3K4me1_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.021
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: CHEQ-seq Intron H3K27ac MM057 cDNA

extract_protocol:
Total RNA was extracted from the cell with the innuPREP RNA Mini Kit 2.0 (Analytik Jena) , followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion). cDNA synthesis was performed with the GoScript RT kit and oligo dT primer (Promega). DNA was extracted with a plasmid extraction protocol from Qiagen.
Plasmid libraries, extracted plasmids and cDNA were prepared for sequencing with two rounds of PCR. The first PCR targets the random barcode present within the transcript. The second PCR adds sequencing indexes to the PCR product.


title: D6_IMQ_H3K4me1_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.024
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: RamDA-seq Neu_D03


title: RamDA-seq Neu_D10


title: D6_Ctrl_H3K4me1_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.020
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: RamDA-seq Neu_D09


title: CHEQ-seq Intron H3K27ac MM001 cDNA


title: CHEQ-seq Intron H3K27ac MM001 plasmid


title: CHEQ-seq 5' H3K27ac MM099 plasmid

description:
processed data file:
CHEQ-seq_5p_H3K27ac_processed.tsv


title: D30_Ctrl_6hr_TPA_RNA_Rep1

description: PCR amplified library from cDNA


title: CHEQ-seq 5' H3K27ac MM099 cDNA


title: D30_IMQ_H3K27ac_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.017
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_Ctrl_H3K27ac_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.013
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: CHEQ-seq 5' H3K27ac MM047 plasmid


title: CHEQ-seq 5' H3K27ac MM047 cDNA


title: D6_IMQ_H3K27ac_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.008
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D6_IMQ_H3K27ac_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.009
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: CHEQ-seq 5' H3K27ac MM029 plasmid


title: LCS8019_MF_s7_2

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
FastQC v.0.11.3 was used to observe read quality and HISAT2
Cuadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases
Then sequence quality was verified using FastQC and HISAT2 to map reads to the genome of mus_musculus ftp://ftp.ensembl.org/pub/release-96/fasta/mus_musculus/dna/
The mapped reads of each sample were assembled using StringTie.
Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
After the ﬁnal transcriptome was generated, StringTie was used to estimate the expression levels of all transcripts and edgeR to identify differentially expressed genes.

source_name: subcutaneous TRAMPC2-Ras prostate tumor

growth_protocol: Tumors (subcutaneous, TRAMPC2-Ras) isolated in RNALater at day 26

extract_protocol:
RNA isolated using Rnasy Qiagen kit
Tru-Seq stranded Illumina protocol, per manufacturer instructions

treatment_protocol: prostate adenocarcinoma, TRAMPC2-Ras, C57/BL6

value: prostate adenocarcinoma

tag: state

value: pooled from 4-6 tumors

value: treated with IL27pepL


title: CHEQ-seq 5' H3K27ac MM029 cDNA


title: LCS8019_MF_s718_1

value: treated with IL27pepL and IL18 sequentially


title: LCS8019_MF_s7_1


title: CHEQ-seq 5' H3K27ac MM087 plasmid


title: RamDA-seq Neu_C12


title: D6_Ctrl_H3K27ac_Mint-ChIPseq_Rep4

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.005
NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: Sex


title: RamDA-seq Neu_C03


title: RamDA-seq Neu_C10


title: RamDA-seq Neu_D02


title: RamDA-seq Neu_C11


title: RamDA-seq Neu_C09


title: RamDA-seq Neu_C02


title: LCS8019_MF_s718_2


title: LCS8019_MF_MCS_2

value: treated with empty vector control (MCS)


title: D30_Ctrl_H3K27ac_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.012
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D6_Ctrl_H3K27ac_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.004
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: CHEQ-seq 5' H3K27ac MM087 cDNA rep 1


title: RamDA-seq Neu_B12


title: ATF3__AFOS_Dox_CNR_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers. 400,000 cells were resuspended in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinked cells were quenched with glycine at a final concentration of 0.125M for 5 min at RT. Cells were washed with cold PBS and resuspended in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1 mM DTT, 0.1% triton X-100 supplemented with Roche complete protease inhibitor EDTA-free) and rotated for 10 min at 4’C. Nuclei were washed twice with CUT&RUN wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine supplemented with protease inhibitor) and incubated with concanavalin-A (ConA) beads washed with CUT&RUN binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2) for 10 min at 4’C. ConA-bead-bound nuclei were incubated overnight at 4’C in CUT&RUN antibody buffer (CUT&RUN wash buffer supplemented with 0.1% triton X-100 and 2mM EDTA) and antibody. After antibody incubation, ConA-bead-bound nuclei were washed once with CUT&RUN triton wash buffer (CUT&RUN wash buffer supplemented with 0.1% triton X-100) then resuspended and incubated at 4’C for 1hr in CUT&RUN antibody buffer and 2.5uL pAG-MNase (EpiCypher). ConA-bound-nuclei were then washed twice with CUT&RUN triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated on ice for 30 min. The reaction was stopped by addition of 100ul 2x stop buffer (30mM EGTA) and incubated at 37’C for 10 min. After incubation, ConA-boun-nuclei were captured using a magnet and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated at 70’C for 2hrs with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20’C. DNA was resuspended in 15uL of buffer EB. CUT&RUN sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primer Set 1 and 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer
NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: 2 Days 1ug/mL doxycycline

value: Cultured Keratinocytes

value: Pgk-H2B-RFP;TRE-AFOS K14rtTA

value: RFP+

value: Doxycycline


title: CHEQ-seq 5' H3K27ac MM074 plasmid

value: Plasmid


title: LCS8019_MF_MCS_1


title: LCS8019_MF_M2718_2

value: treated with IL27 and IL18 sequentially


title: you1

city: Nanjing

first: Dandan

last: Wang

state: Jiangsu

address: 305 East Zhongshan Road

department: Department of Reproductive Medicine

institute: Affiliated Jinling Hospital, Medicine School of Nanjing University

data_processing:
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq2 was used for differential gene expression analysis between two samples with non biological replicates.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome. GO terms with q<0.05 were considered to be significantly enriched.
The KEGG enrichment of DEGs was implemented by the hypergeometric test, in which p-value was adjusted by multiple comparisons as q-value. KEGG terms with q<0.05 were considered to be significantly enriched.

source_name: uterus

extract_protocol:
Uterus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: uterus

tag: age

value: 6-8 weeks after birth


title: old4


title: old1


title: you4


title: ATF3_AFOS_NoDox_CNR_Rep1

description: PCR amplified library from genomic DNA

treatment_protocol: Untreated

value: Untreated


title: LCS8019_MF_M2718_1


title: Jun_AFOS_Dox_CNR_Rep1

description: PCR amplified library from genomic DNA


title: RamDA-seq Neu_B11

value: human iPS-derived neural progenitor cell

value: Day 11 of differentiation


title: Jun_AFOS_NoDox_CNR_Rep1

description: PCR amplified library from genomic DNA


title: you2


title: CHEQ-seq 5' H3K27ac MM057 plasmid

tag: molecule subtype


title: RamDA-seq Neu_B03


title: LCS8019_MF_M27_2

value: prostate adenocarcinoma

value: treated with IL27


title: RamDA-seq Neu_B02


title: CHEQ-seq 5' H3K27ac MM074 cDNA

value: mRNA


title: RamDA-seq Neu_B09


title: CHEQ-seq 5' H3K27ac MM001 plasmid


title: LCS8019_MF_M27_1

value: pooled from 4-6 tumors


title: RamDA-seq Neu_A12


title: D30_IMQ_4hrWound_Fos_CNR_Rep2

description:
PCR amplified library from genomic DNA
D30_IMQ_4hrWound_Fos_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)

value: female

value: Epidermal Stem Cells

value: wildtype

value: ITGA6+, ITGB1+, Sca1+, CD34-

value: Imiquimod for 6 days


title: D30_IMQ_4hrWound_Fos_CNR_Rep1


title: CHEQ-seq 5' H3K27ac MM001 cDNA


title: RamDA-seq Neu_A11


title: RamDA-seq Neu_B10


title: CHEQ-seq 5' H3K27ac MM057 cDNA


title: RamDA-seq Neu_A10


title: FQMR12

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
We assessed fastq sequence data quality using FastQC v0.11.5 (Andrews, 2010) and trimmed the reads to remove adapter sequences and low quality bases using DimerRemover
Single end reads were aligned using STAR v2.5.3a  to the GRCh38 human genome release
BAMS index were generated using Sambamba v0.6.6
DEGs and abundance measurements were identified using StringTie v1.3.1c and R package DESeq2 v1.18.1 (median of ratio)
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: tab-delimited text files (.tsv) include RAW count for each Sample and DESeq2 output

source_name: neural crest stem cells derivated from hIPS

growth_protocol: The hIPSc were differentiated into functional neural crest stem cells according to the protocol described in Mica et al. (PMID: 23583175)

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen) following manufacturer’s instructions. Quality, quantitation and sizing of total RNA was evaluated using the RNA 6000 Pico assay.  (Agilent Technologies Ref. 5067-1513) on an Agilent 2100 Bioanalyzer system.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: disease

value: BAMS (bosma arhinia microphthalmia syndrome)


title: LCS8019_MF_M18_1

value: treated with IL18


title: RV-KO 3

first: Michael

last: Tranter

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

data_processing:
All read mapping and analysis was performed using the CLC Genomics Workbench v20.0.2 (CLC Bio-Qiagen).
Reads were mapped using the following parameters:  min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Expression value= Total counts.

source_name: Heart; Right Ventricle

extract_protocol:
Hearts were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 12-14 weeks

value: Heart; Right Ventricle


title: FQMR10


title: LV-KO 3

source_name: Heart; Left Ventricle

value: Heart; Left Ventricle


title: RamDA-seq Neu_A02

extract_protocol:
Single-cell cDNA library was prepared using GenNextⓇRamDA-seqTM Single Cell Kit (Toyobo Co., LTD. Tokyo, Japan) followed by manufacturer’s protocol.
cDNA library from each single cell was treated with NovaSeq 6000 S4 reagent Kit followed by manufacturer’s protocol.


title: RamDA-seq Neu_A09


title: RamDA-seq Neu_A03


title: FQMR8


title: FQMR9


title: LV-KO 2


title: D6_IMQ_Stat3KO_Jun_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_IMQ_Stat3KO_Jun_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)

value: YFP+, "ITGA6+, ITGB1+, Sca1+, CD34-


title: LCS8019_MF_M18_2


title: D30_Ctrl_4hrWound_Fos_CNR_Rep1

description:
PCR amplified library from genomic DNA
D30_Ctrl_4hrWound_Fos_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)

value: control vanicream for 6 days


title: D6_IMQ_Stat3KO_Jun_CNR_Rep1


title: RamDA-seq iPS_H10

source_name: iPS cell

value: iPS


title: D30_Ctrl_4hrWound_Fos_CNR_Rep2


title: FQMR7


title: D30_IMQ_H3K27ac_Mint-ChIPseq_Rep3

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.016
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: LV-KO 1


title: RamDA-seq iPS_H09


title: D6_IMQ_CreNeg_TamPos_Jun_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_IMQ_CreNeg_TamPos_Jun_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: D6_IMQ_Stat3KO_Fos_CNR_Rep3

description:
PCR amplified library from genomic DNA
D6_IMQ_Stat3KO_Fos_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: D6_IMQ_CreNeg_TamPos_Jun_CNR_Rep1


title: FQMR11


title: RV-KO 2


title: RV-KO 1


title: FQMR6

value: FSHD1 mosaic


title: RamDA-seq iPS_H08


title: CHEQ-seq Intron H3K27ac MM087 plasmid

extract_protocol:
Total RNA was extracted from the cell with the innuPREP RNA Mini Kit 2.0 (Analytik Jena) , followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion). cDNA synthesis was performed with the GoScript RT kit and oligo dT primer (Promega). DNA was extracted with a plasmid extraction protocol from Qiagen.
Plasmid libraries, extracted plasmids and cDNA were prepared for sequencing with two rounds of PCR. The first PCR targets the random barcode present within the transcript. The second PCR adds sequencing indexes to the PCR product.

value: Plasmid


title: RV-WT 3

value: wild-type


title: RamDA-seq iPS_H07


title: RV-WT 2


title: RamDA-seq iPS_H06


title: FQMR5


title: RV-WT 1


title: FQMR3

value: FSHD1 mosaic isogenic Control


title: D6_IMQ_CrePos_TamPos_YFPneg_Fos_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_IMQ_CrePos_TamPos_YFPneg_Fos_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)

value: female


title: LV-WT 3


title: FQMR2

value: Control


title: LV-WT 2


title: D30_IMQ_P63_CNR_Rep2

description:
PCR amplified library from genomic DNA
D30_IMQ_P63_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)

value: Epidermal Stem Cells

value: wildtype


title: RamDA-seq iPS_H04


title: HC1_CD4

extract_protocol:
CD4+ T cells isolated from peripheral blood mononuclear cells (PBMCs) of RRMS patients and healthy controls. Total RNA was extracted using the Trizol isolation kit.
Library construction for RNA sequencing was performed with 1 ug of total RNA using Illumina’s TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Globin (Illumina, San Diego, CA, USA). Qualified samples were first proceeded to random fragmentation, with a median length of 150 bp, and converted to double-stranded cDNA. The adapter-ligated fragments were PCR amplified and gel purified. Then, the library was loaded into a flow cell, and cluster generation was executed. Sequencing was done by Illumina Novaseq6000 following the manufacturer’s protocol. Image analysis, per-cycle base calling, and quality score assignment was performed with Illumina primary analysis software, RTA (Real-Time Analysis).

value: Blood

tag: disease state

value: Healthy control


title: RamDA-seq iPS_H05


title: RamDA-seq iPS_H03


title: D30_IMQ_P63_CNR_Rep1

value: ITGA6+, ITGB1+, Sca1+, CD34-

value: Imiquimod for 6 days


title: FQMR1


title: RamDA-seq iPS_G09


title: D30_Ctrl_P63_CNR_Rep1

description:
PCR amplified library from genomic DNA
D30_Ctrl_P63_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: D6_IMQ_Stat3KO_Fos_CNR_Rep1


title: D6_IMQ_P63_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_IMQ_P63_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: D30_Ctrl_ATACseq_WT_Rep2

description: PCR amplified library from genomic DNA

data_processing:
Reads were aligned to the reference genome (mm10) with Rsubread's align method in paired-end mode as descrived in doi::10.1093/nar/gkz114. Peaks were called with MACS2 software in BAMPE mode.
Genome_build: mm10

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Nuclei were extracted and genomic DNA was transposed per protocol outlines in doi::10.1038/nmeth.2688
Nextera DNA Library Preparation Kit


title: LV-WT 1

value: 12-14 weeks


title: SD-6_S6_L008_R1_001_HumanCir_2

data_processing:
Downstream analysis of RNAseq datasets was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene’s wrapped scripts.
Alignments were parsed using TopHat and differential expressions were determined through DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with FPKM for each sample and differential expression of genes

source_name: Vastus lateralis_with cirrhosis

extract_protocol:
Total RNA was extracted using the RNeasy Plus minikit (Qiagen, Germantown, MD)
RNAseq libraries were generated using the RNeasy Plus minikit (Qiagen, Germantown, MD) and sequenced on an Illumina HiSEQ400 instrument (using protocols provided by manufacturer) by Novogene (Sacramento, CA).

value: Human with cirrhosis

value: skeletal muscle


title: SD-5_S5_L008_R1_001_HumanCir_1


title: RamDA-seq iPS_G10


title: D6_IMQ_Stat3KO_Fos_CNR_Rep2

value: YFP+, "ITGA6+, ITGB1+, Sca1+, CD34-


title: SD-8_S8_L008_R1_001_HumanCir_4


title: RamDA-seq iPS_G04

value: iPS


title: D30_PI_ATACseq_WT_Rep2

description: PCR amplified library from genomic DNA


title: FQMR4


title: RamDA-seq iPS_G07


title: SD-7_S7_L008_R1_001_HumanCir_3


title: D30_PI_ATACseq_WT_Rep1

description: PCR amplified library from genomic DNA


title: D6_IMQ_ATACseq_WT_Rep2

description: PCR amplified library from genomic DNA


title: D6_Ctrl_P63_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_Ctrl_P63_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)

value: control vanicream for 6 days


title: D6_IMQ_ATACseq_WT_Rep1

description: PCR amplified library from genomic DNA


title: D6_Ctrl_P63_CNR_Rep1


title: D30_Ctrl_ATACseq_WT_Rep1

description: PCR amplified library from genomic DNA


title: D6_IMQ_P63_CNR_Rep1


title: D6_Ctrl_ATACseq_WT_Rep2

description: PCR amplified library from genomic DNA


title: RamDA-seq iPS_G06


title: RamDA-seq iPS_F10


title: SD-2_S2_L008_R1_001_HumanCtl_2

source_name: Vastus lateralis_without cirrhosis

value: Human without cirrhosis


title: RamDA-seq iPS_G03


title: D6_Ctrl_ATACseq_WT_Rep1

description: PCR amplified library from genomic DNA


title: SD-4_S4_L008_R1_001_HumanCtl_4


title: D30_IMQ_Atf3_CNR_Rep2

description:
PCR amplified library from genomic DNA
D30_IMQ_Atf3_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: D30_Ctrl_Atf3_CNR_Rep2

description:
PCR amplified library from genomic DNA
D30_Ctrl_Atf3_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: SD-1_S1_L008_R1_001_HumanCtl_1


title: RamDA-seq iPS_F08


title: D30_IMQ_Atf3_CNR_Rep1


title: C5_2

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
CITE-Seq files:ADTs
Hashing files: HTOs

data_processing:
Data were analyzed using Cell Ranger™ v3.0.2 pipelines which is available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix

source_name: CITEseq/Multiplex ILC1 and NK cells from WT and KO

extract_protocol:
Livers were harvested, cut into small pieces and digested in DMEM with 10 mM Hepes, DNase I and Collagenase D at 37°C and 100 rpm for 40 min. Suspensions were passed through 100 mm filters and lymphocytes enriched by 40%/80% percoll gradient (860 x g, 20 min, RT, no breaks). The interphase was washed with PBS and used for sorting.
ILC1 and NKs from WT and KO mice were isolated for single cell RNA-sequencing. In order to pool the 4 populations into the same reaction, we labeled with oligo-tagged antibodies targeting ubiquitously expressed cell surface markers (Hashtag antibodies, Biolegend). WT and KO populations were labelled with Hashtags (TotalSeq™-A0301 anti-mouse Hashtag 1 for KO and TotalSeq™-A0302 anti-mouse Hashtag 2 for WT). Cells were furthermore labeled with oligo-tagged antibodies targeting selected surface markers (CD11b, CD127, CD200R, CD27, CD69, CD902, NKp46, TotalSeq™-A, Biolegend) for cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq). ILC1 and NKs from WT and KO mice were sorted separately using a FACS Aria III (BD Biosciences) and then pooled all together with the desired proportion. The 4 populations will be identified according to hashtags, antibody tags and gene expression sequences. Immediately after sorting, the cells were encapsulated into droplets using 10X Genomics GemCode Technology and processed following manufacturer’s specifications for single-cell RNA-sequencing library preparation. Every cell and every transcript (including oligo tags of Hashtag and CITE-Seq antibodies) were barcoded using a unique molecular identifier (UMI) and cDNA ready for sequencing on Illumina platforms was generated using the Single Cell 3’ Reagent Kit v3 (10X Genomics). 3 distinct libraries were generated: a CITE-Seq library, a Hashtag library, and the cDNA library fraction (corresponding to the cell transcriptome). Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher), quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent) and sequencing was performed across a NovaSeq 6000 platform (Illumina) in 50bp paired-end mode to reach approximately 150,000 reads per single cell. For adequate read coverage, we sequenced the CITE-Seq library at 10%, the Hashtag library at 5%, and the cDNA library fraction at 85% of a lane according to the manufacturer’s recommendations (Biolegend).
Chromium single cell 3´v3 (10XGenomics)

value: mixed sample Hobit tdTomato/WT and KO

value: liver leukocytes


title: SD-3_S3_L008_R1_001_HumanCtl_3


title: starved HUVEC knockdown Rab5C stimulated VEGF 4 hours_exp 2

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

country: Netherlands

institute: Amsterdam University Medical Centers

description: rawCounts.txt

data_processing:
Alignment of sequence reads was performed for the individual samples against the GRCh38/hg38 reference genome using the HISAT2 aligner (v2.1.0) applying the default parameters and --dta-cufflinks --rna-strandness R
Counts were obtained using the corresponding genome annotation (v94) using HTSEq (v0.11) using the following parameters: -m union -f bam -r name -s reverse -a 10 -t exon -i gene_id
The obtained counts were used as input for the consecutive analysis using the statistical computing environment R (version 3.5.2, Bioconductor v3.8). Only features with CPM (counts per million mapped reads) of more than 2 in 3 or more samples were retained in the analysis (21502 features).
Counts were normalized by applying the trimmed mean of M-values method.
The count data was transformed to log2-counts per million (logCPM) using voom, estimating the mean-variance relationship.  Differential expression was assessed using a moderated t-test using the linear model framework from the limma package (v3.38.3).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file contains raw count data as obtained using HTSeq; rownames contain featurenames (ENSEMBL id); one column per sample.

source_name: HUVEC

growth_protocol: HUVECs were grown in endothelial growth medium (Promocell)

extract_protocol:
Cells were lysed in Trizol and RNA was extracted with RLT buffer
RNA libraries were prepared for sequencing using standard Illumina protocols. Kapa total RNA HyperPrep kit was used.

treatment_protocol: HUVECs were lentivirally transduced with scrambled sequences or pools of short hairpins targeting Rab5A or Rab5C, cloned in PLKO.1 (MISSION library) and next selected with puromycin for three days. Then they were replated, deprived of growth factors overniht and then stimulated or not with VEGF for the indicated time-points

value: primary endothelial cells from umbilical vein

tag: knockdown

tag: timepoint

value: 4 hr

tag: stimulation

value: VEGF


title: RamDA-seq iPS_F06

tag: cell line


title: D30_Ctrl_Atf3_CNR_Rep1

value: female

value: Epidermal Stem Cells

tag: genotype

value: wildtype


title: RamDA-seq iPS_F05


title: RamDA-seq iPS_F09


title: D6_IMQ_Atf3_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_IMQ_Atf3_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)

value: ITGA6+, ITGB1+, Sca1+, CD34-


title: D30_Ctrl_P63_CNR_Rep2


title: RamDA-seq iPS_F04


title: D6_IMQ_Atf3_CNR_Rep1

value: Imiquimod for 6 days


title: starved HUVEC knockdown Rab5A stimulated VEGF 4 hours_exp 2

description: rawCounts.txt


title: RamDA-seq iPS_F03


title: starved HUVEC knockdown Rab5A stimulated VEGF 1 hour_exp 2

description: rawCounts.txt

value: 1 hr


title: D6_Ctrl_Atf3_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_Ctrl_Atf3_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: D6_Ctrl_Atf3_CNR_Rep1


title: RamDA-seq iPS_E10


title: starved HUVEC knockdown Rab5C stimulated VEGF 1 hour_exp 2

description: rawCounts.txt


title: Sth1-AID + Rap1-AID degron induction nascent RNA-Seq biological replicate 3

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters "--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC -A AGATCGGAAGAGC -u -50 -U -50".
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to all S. cerevisiae genes downloaded from the Ensembl genome browser (assembly R64-1-1, release 90; Kersey et al., 2016). The parameters used were "--star-output-genome-bam --forward-prob 0", and all other parameters were kept as default.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: Ensembl R64-1-1 release 90
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in yeast extract-peptone-dextrose (YPD) medium in conical flasks at 30 °C, shaking at 300 RPM in incubators.

extract_protocol:
For nascent RNA sequencing (nascent RNA-seq), RNA fragments associated with RNA polymerase II subunit Rpb3 endogenously tagged with 3xFLAG epitope at the C-terminus were isolated by affinity purification. Small batch cultures of yeast cells grown in YPD media were collected by centrifugation, the supernatant was aspirated, and cell pellets were immediately snap-frozen by submerging in liquid nitrogen to minimise changes in nascent transcription activity (e.g. in response to cell resuspension in cold lysis buffer with high concentrations of salts and detergents). Frozen cell pellets were dislodged from centrifuge tubes and stored at -80 °C. Cells were subjected to cryogenic lysis by freezer mill grinding under liquid nitrogen (SPEX 6875D Freezer/Mill, standard program: 15 cps for 6 cycles of 2 minutes grinding and 2 minutes cooling each). Yeast “grindate” powder was stored at -80 °C. 2 g of yeast grindate was resuspended in 10 mL of 1X cold lysis buffer (20 mM HEPES pH 7.4, 110 mM potassium acetate, 0.5% v/v Triton-X-100, 1% v/v Tween-20) supplemented with 10 mM MnCl2, 1X Roche cOmplete EDTA-free protease inhibitor, and 50 U/mL SUPERase.In RNase Inhibitor. Chromatin-bound proteins were solubilised by incubation with 1320 U of DNase I (RQ1 RNase-free DNase I, Promega) on ice for 20 minutes. Lysates containing solubilised chromatin proteins were clarified by centrifugation at 20,000 x g for 10 minutes (at 4 °C), and the supernatant was taken as input for immunoprecipitation using 500 μL of anti-FLAG M2 affinity gel suspension (A2220, Sigma-Aldrich) per sample (2.5 hours at 4 °C). After immunoprecipitation, the supernatant was removed and beads were washed 4 times with 10 mL of cold wash buffer each time (1X lysis buffer with 50 U/mL Superase.In RNase inhibitor and 1 mM EDTA). After the last wash, agarose beads were transferred to small chromatography spin columns (Pierce Spin Columns, Thermo Fisher), and competitive elution of protein complexes containing Rpb3-3xFLAG protein from the resin was performed by incubating beads with 300 μL of elution buffer (1X cold lysis buffer with 2 mg/mL 3xFLAG peptide) for 30 minutes at 4 °C (3xFLAG peptide provided by the Peptide Chemistry Science Technology Platform, The Francis Crick Institute). Elution was performed twice and 600 μL of eluate was subjected to acid phenol:chloform RNA extraction and ethanol precipitation. A significant amount of 3xFLAG peptide co-precipitates with the RNA as a contaminant, and is later removed by spin column purification.
Purified RNA was fragmented to a mode length of ~200 nucleotides using zinc ion-mediated fragmentation (Ambion AM870, 70 °C for 4 minutes). Fragmented RNA was purified using miRNeasy spin columns (miRNeasy mini kit, QIAGEN), which retain RNAs approximately 18 nucleotides or more in length. Purified RNA was quantified by Qubit (Thermo Fisher) and approximately 150 ng of RNA was subjected to rRNA depletion using the Ribo-Zero Gold rRNA Removal Kit (Yeast) (Illumina MRZY1324, now discontinued). Libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s instructions (14 PCR cycles). The libraries were multiplexed and sequenced on the HiSeq 4000 platform (Illumina), and generated ~28 million 101 bp strand-specific paired-end reads per sample on average.

treatment_protocol: Cells were either left untreated (wild-type samples), or treated during exponential growth (OD600 ~0.8) by adding 3-indole-acetic acid (3-IAA, Sigma-Aldrich I3750) to a final concentration of 500 μM from a 1 M stock dissolved in DMSO, or an equivalent volume of DMSO (vehicle).

tag: strain/background

value: FW7232 (MATa, his3D1, leu2D0, met15D0, ura3D0 LEU2::pGPD1-osTIR::LEU sth1::STH1-3V5-IAA7::KanMX6 rap1::RAP1-3V5-IAA7::KANMX6 rpb3::RPB3-3xFLAG::NATMX6) BY4741 derivative


title: Sth1-AID + Rap1-AID degron no induction nascent RNA-Seq biological replicate 2

value: DMSO


title: Sth1-AID + Rap1-AID degron induction nascent RNA-Seq biological replicate 1


title: Sth1-AID + Rap1-AID degron no induction nascent RNA-Seq biological replicate 3


title: starved HUVEC knockdown Rab5A_exp 2

description: rawCounts.txt

value: 0 hr


title: Sth1-AID + Rap1-AID degron induction nascent RNA-Seq biological replicate 2


title: D6_IMQ_Stat3_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_IMQ_Stat3_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)

tag: facs markers


title: RamDA-seq iPS_E09

value: iPS


title: Sth1-AID + Rap1-AID degron no induction nascent RNA-Seq biological replicate 1


title: starved HUVEC knockdown Rab5C_exp 2

description: rawCounts.txt


title: RamDA-seq iPS_E08


title: D6_IMQ_Stat3_CNR_Rep1

tag: strain


title: starved HUVEC stimulated with VEGF 1 hour_exp 2

description: rawCounts.txt


title: Rap1-AID degron induction  nascent RNA-Seq biological replicate 3

value: FW7238 (MATa, his3D1, leu2D0, met15D0, ura3D0 LEU2::pGPD1-osTIR::LEU rap1::RAP1-3V5-IAA7::KANMX6 rpb3::RPB3-3xFLAG::NATMX6) BY4741 derivative

tag: treatment


title: D6_Ctrl_Stat3_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_Ctrl_Stat3_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)

value: control vanicream for 6 days


title: starved HUVEC_exp 2

description: rawCounts.txt


title: starved HUVEC knockdown Rab5C stimulated VEGF 4 hours_exp 1

description: rawCounts.txt


title: RamDA-seq iPS_E05


title: RamDA-seq iPS_E04


title: Rap1-AID degron induction nascent RNA-Seq biological replicate 2


title: RamDA-seq iPS_E07


title: Rap1-AID degron induction nascent RNA-Seq biological replicate 1


title: D6_Ctrl_Stat3_CNR_Rep1


title: D30_IMQ_Jun_CNR_Rep2

description:
PCR amplified library from genomic DNA
D30_IMQ_Jun_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: starved HUVEC knockdown Rab5C stimulated VEGF 1 hour_exp 1

description: rawCounts.txt


title: RamDA-seq iPS_E03


title: starved HUVEC stimulated with VEGF 4 hours_exp 2

description: rawCounts.txt


title: starved HUVEC knockdown Rab5C_exp 1

description: rawCounts.txt


title: D30_IMQ_Jun_CNR_Rep1


title: D30_Ctrl_Jun_CNR_Rep1

description:
PCR amplified library from genomic DNA
D30_Ctrl_Jun_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: Rap1-AID degron no induction nascent RNA-Seq biological replicate 2


title: D30_Ctrl_Jun_CNR_Rep2


title: Sth1-AID degron induction nascent RNA-Seq biological replicate 3

value: FW7220 (MATa, his3D1, leu2D0, met15D0, ura3D0 LEU2::pGPD1-osTIR::LEU sth1::STH1-3V5-IAA7::KanMX6 rpb3::RPB3-3xFLAG::NATMX6) BY4741 derivative


title: starved HUVEC knockdown Rab5A stimulated VEGF 4 hours_exp 1

description: rawCounts.txt


title: Rap1-AID degron no induction nascent RNA-Seq biological replicate 1


title: starved HUVEC knockdown Rab5A stimulated VEGF 1 hour_exp 1

description: rawCounts.txt


title: D6_IMQ_Jun_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_IMQ_Jun_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: RamDA-seq iPS_D07


title: Sth1-AID degron induction nascent RNA-Seq biological replicate 2


title: RamDA-seq iPS_D10


title: starved HUVEC knockdown Rab5A_exp 1

description: rawCounts.txt


title: Rap1-AID degron no induction nascent RNA-Seq biological replicate 3


title: RamDA-seq iPS_D08


title: D6_IMQ_Jun_CNR_Rep1


title: starved HUVEC stimulated with VEGF 1 hour_exp 1

description: rawCounts.txt


title: Sth1-AID degron induction nascent RNA-Seq biological replicate 1


title: RamDA-seq iPS_D05


title: starved HUVEC stimulated with VEGF 4 hours_exp 1

description: rawCounts.txt


title: D6_Ctrl_Jun_CNR_Rep2

description:
PCR amplified library from genomic DNA
D6_Ctrl_Jun_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: RamDA-seq iPS_D09


title: D6_Ctrl_Jun_CNR_Rep1


title: Sth1-AID degron no induction nascent RNA-Seq biological replicate 3


title: Sth1-AID degron no induction nascent RNA-Seq biological replicate 2


title: RamDA-seq iPS_D04


title: D30_IMQ_Fos_CNR_Rep1

description:
PCR amplified library from genomic DNA
D30_IMQ_Fos_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: RamDA-seq iPS_D03


title: D30_Ctrl_Fos_CNR_Rep2

description:
PCR amplified library from genomic DNA
D30_Ctrl_Fos_CNR.peaks.bed (in CUTandRUN_bedfiles.tar.gz)


title: Sth1-AID degron no induction nascent RNA-Seq biological replicate 1


title: Wild-type nascent RNA-Seq biological replicate 3

value: FVW7228 (MATa, his3D1, leu2D0, met15D0, ura3D0 rpb3::RPB3-3xFLAG::NATMX) BY4741 derivative

value: no treatment


title: RamDA-seq iPS_C10


title: RamDA-seq iPS_D06


title: Wild-type nascent RNA-Seq biological replicate 2


title: Wild-type nascent RNA-Seq biological replicate 1


title: D30_Ctrl_Fos_CNR_Rep1


title: KD_1

city: 南京

last: Zheng

state: 江苏

address: 南京医科大学江宁校区

institute: 南京医科大学

data_processing:
Using the Illumina MicroRNA sequencing
Raw reads were processed with ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, and snoRNA) and repeats. Subsequently, unique sequences containing 18–26 bases were mapped to specific species precursors in miRBase 22.0 using a BLAST search to identify known miRNAs and novel miRNA-3p- and miRNA-5p-derived miRNAs. The mapped sequences were identified as known miRNAs. The remaining sequences were mapped to other selected species precursors in miRBase 22.0 by BLAST search. Differential expression of miRNAs as a function of normalized deep sequence counting was analyzed through the selective use of Student’s t-test. The significance threshold was set at <0.05.
The differentially expressed microRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: abundance measurements

growth_protocol: The human CRC cell lines HCT116 was purchased from the Shanghai Institute of Cell Biology, Chinese Academy of Sciences. HCT116 cells were cultured in RPMI 1640 medium (HyClone, South Logan, UT, USA), supplemented with 10% FBS (Gibco, Grand Island, NY, USA), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (Gibco). HCT116 cells were cultured at 37°C in a humidified incubator of 5% CO2.

extract_protocol:
Total RNA, including small RNAs from two groups of control and RANBP1-knockdown HCT116 cells, were extracted using the Total RNA Purification Kit from Norgen Biotek Corp (Thorold, Canada). Approximately 1 μg total RNA was used to prepare a small RNA library according to the protocol of the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA). Then, single-end sequencing (36 bp or 50 bp) was performed on the Illumina HiSeq 2500 System (LC Sciences, Houston, TX) according to the manufacturer’s recommended protocol.
MicroRNA sequencing Total RNA, including small RNAs, was extracted using a commercial extraction kit from Total RNA Purification Kit from Norgen Biotek Corp (Thorold, ON, Canada) in cultured mCECs in the SCIP assay. RNA quality and quantity were analyzed using a Bioanalyzer 2100 (Agilent, CA, USA) to ensure a RIN number > 7.0.

treatment_protocol: Human colon cancer cell line HCT116 was transfected with a control non-targeting shRNA to cells or transfected with shRNA targeting RANBP1 for 48 hours in RPMI medium.

tag: cell ine

tag: genotype/variation


title: RamDA-seq iPS_C09

tag: cell type


title: KD_2