title: Skin, KO-1

city: Guangzhou

first: Huan

last: Yang

state: Guangdong

address: No. 2 Lujing Road

department: Dermatology Department

institute: Dermatology Hospital of Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using hisat2 (v2.0.1)
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using stringtie-2.0.6 following the protocol from Pertea et al., Nature Protocols, 2016.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all Sample.

source_name: Skin

extract_protocol:
Skin were removed, flash frozen in liquid nitrogen, and RNA was extracted using Trizol reagent. Total RNA was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent  Technologies, Palo Alto, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GSDMD-/- and WT female mice were subcutaneous injected with BLM every other day for a total 28 days.

value: skin

tag: age

value: post natal week 8

value: GSDMD-/-

value: subcutaneous BLM (bleomycin) injection

value: bleomycin-induced murine model of scleroderma


title: PitNET30-24h

status: Public on Feb 16 2022

type: SRA

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

library_source: transcriptomic

data_processing:
The FASTQ files from NGS were analysed using CLC Genomics Workbench (v20.0.4). During read trimming any reads with Q (Phred score) < 30 were discarded. Reads also underwent trimming by length and any reads that did not fall into 15 - 55 nt length category were discarded. Trimmed reads were aligned to miRBase (V22) with the following settings: additional upstream / downstream bases = 2, missing upstream / downstream bases = 2, maximum mismatches = 2, sequence length = 15 to 28, minimum supporting count = 1. The counts were compiled and exported into DESeq2 compatible counts matrix format.
miRNA differential expression analysis was done in DESeq2 (v1.30.1) in R (v 4.0.3).
Genome_build: miRBase V22 for miRNA annotation and counting
Supplementary_files_format_and_content: counts table

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Total RNA from plasma samples was extracted using exoRNeasy Midi kit (Qiagen, Germany) according to manufacturer's instructions. Total RNA from tumor tissue samples was extracted using AllPrep DNA/RNA/miRNA Universal kit (Qiagen Germany) according to manufacturer's instructions
miRNA-seq libraries were prepared using Lexogen Small RNA-seq Library prep Kit according to manufacturer's instructions

tag: pitnet type

value: NF PitNET

tag: sample/tissue

value: Plasma


title: Skin, WT-2

country: China

organism: Mus musculus

tag: strain

tag: tissue

tag: genotype

value: wild type

tag: treatment

tag: disease state


title: Sample57_KASUMI-9_BR2

city: Solna

first: Rozbeh

last: Jafari

address: Tomtebodavägen 23B

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description:
total RNA (ribosomal depleted)
SD-2137-KASUMI-9-R2_S11

data_processing:
The sequenced reads were preprocessed  for adapter and quality-based trimming using cutadapt  v2.4 and then mapped to the human reference genome GRCh38 (gencode.v31.p12 primary assembly) using STAR aligner v2.7.1a (DOI: 10.1093/bioinformatics/bts635) with enabled chimeric reads detection.
The mapped reads were quantified at the gene level using featureCount.
The raw counts were processed to remove any techinical variation due to different RNA-seq library prepartion times using ComBat-seq method in sva R package (DOI: 10.1093/nargab/lqaa078).
The batch-corrected raw counts are provided in the processed data files
Genome_build: gencode.v31.p12 primary assembly
Supplementary_files_format_and_content: raw counts at gene level

source_name: Blood

growth_protocol: RPMI 1640 Media with 10% or 20% FBS

extract_protocol:
QIAGEN RNeasy Mini Kit with DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina protocols using Ribo-Zero and/or Ribo-Zero Gold Kit

tag: disease

value: childhood acute lymohoblastic leukemia

tag: cell type

value: BCP-ALL

value: B-cells

value: untreated


title: Skin, KO-2


title: Skin, WT-1


title: OE ERRg-1 in hiPSC-CMs (RNA-seq)

city: Philadelphia

first: Tomoya

last: Sakamoto

state: PA

address: Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421

department: Cardiovascular Institute

country: USA

institute: University of Pennsylvania

description:
Gene Expression Data
ERR-G-1

data_processing:
Transcript-level gene expression was quantified using Salmon (Nat Methods. 2017 Apr;14(4):417-419. PMID: 28263959)
Transcript data was aggregated to produce gene-level quantifications, and tests for differential expression were performed using DESeq2 (Genome Biol. 2014;15(12):550. PMID: 25516281)
We considered genes with FDR < 0.05 and fold change at least 1.5 in any direction for further analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file contains significantly regulated gene name, log2 fold change (ERRg/GFP), and adjusted p-values.

source_name: hiPSC-CMs overexpressed with ERRg

growth_protocol: hiPSC were cultured in TeSR-E8 (StemCell Technologies) and differentiated toward cardiomyocytes with the method published by Dr. Joseph Wu (Nat Methods. 2014 Aug;11(8):855-60. PMID: 24930130).

extract_protocol:
RNA was harvested using Qiazol (QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The quality of Total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). 1ug of Total RNA was used as starting material to construct RNA Seq library using Illumina's Truseq Stranded Total RNA Library preparation kit as per the instructions. First the total RNA is Ribo depleted to remove rRNA from total RNA. The remaining non-rRNA is fragmented into small pieces using divalent cations under elevated temperature. Following fragmentation, the first strand cDNA were synthesized using random primers and followed by second strand synthesis using DNA Polymerase I. The cDNA is then ligated with index adapters for each sample followed by purification and then enriched with PCR to create the final library. The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR.
The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR. Multiplexed libraries are pooled and single-end 50-bp sequencing was performed on one flow-cell of an Illumina Hiseq 2500.

treatment_protocol: At D22, OE GFP or ERRg was performed using adenovirus expressing each gene. Two days after the infection, RNA samples were harvested.

value: hiPSC-derived cardioyocytes

tag: differentiation

value: overexpressed ERRg


title: Sample58_LC4-1_BR2

description:
total RNA (ribosomal depleted)
SD-2137-LC4-1-R2_S12


title: OE ERRg-2 in hiPSC-CMs (RNA-seq)

description:
Gene Expression Data
ERR-G-2


title: wild type-rep1

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

data_processing:
Illumina Casava2.19 software used for basecalling.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.8 with default parameter.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using cufflinks version 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel with raw FPKM for every gene and every sample

source_name: embryo

extract_protocol:
E12.5 embryos was used for RNA extraction using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: embryo


title: PitNET44-x


title: Pdzk1ip1-in vivo-wk3 tp wk5 HTO

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
For CITE-Seq additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software and matrices were made
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and read counting performed using HT-seq to make count tables
BAM to bedgraph performed using bedtools bedgraph to bigwig performed using bedGraphToBigWig v4
FlipJump-seq reads were trimmed using cutadapt and mapped using bowtie2, all the BAM files were merged to find all the peaks on all files and count tables were made for each BAM files using BEDTools
For FlipJump: bowtie2 -x ${Ref_DIR} -1 ${R1} -2 ${R2} --end-to-end -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 -X 1000 | samtools view -Sb - > BAMs/${File_Name}.bam
For FlipJump: bedtools coverage -counts -b BAMtoBED.bed -a Peaks.bed > CounTable.bed
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (.bw), count tables (.txt), barcode (.txt), gene (.txt), matrix (.mtx), metadata (.tsv)

extract_protocol:
Bulk RNA-Seq: RNA from sorted cells was extracted using TRIzol Plus purification kit (ThermoFisher) and cDNA libraries were prepared with the Low input Clontech SMART-seq HT with Nxt HT.  Flip-Jump-Seq (MiSeq): Genomic DNA was extracted by NucleoSpin Tissue XS (Takara) (< 15,000 cells) or QIAamp Mini  kit (> 15,000 cells). Extracted DNA was further amplified with REPLI-g Mini Kit (Qiagen) for whole genome amplification (WGA).Three-arm LM-PCR-based method was optimized and adapted to clone FlipJump transposon integration sites from both 3TR and 5TR ends. Amplified DNA was quantified using Qubit 2.0 fluorometer (Thermo Fisher), and 1 ug was digested separately with MspI, HindIII or HaeIII for 5TR cloning, and MspI, DpnII or HaeIII for 3TR cloning. The digested DNA was purified using QIAquick PCR Purification Kit. To prepare the individual LM-PCR linker mix, the equal volume of 50 uM linker common (long strand)(5’ GACCCGGGAGATCTGAATTCAGTGGCACAGCAGTTAGGGGGCTGGTCG 3’) and 50 uM restriction enzyme (RE)-digested end-specific linker (Blunt end linker /5Phos/CGACCAGCCC/3AmMO/ for HaeIII or CG end linker /5Phos/CGCGACCAGCCC/3AmMO/ for MspI or GATC end linker/5Phos/GATCCGACCAGCCC/3AmMO/ for DpnII or AGCT end linker/5Phos/AGCTCGACCAGCCC/3AmMO/ for HindIII were mixed in a PCR tube. The linker mix was then denatured and annealed by heating it to 95° C for 5 mins and cooling slowly to room temperature. One third of purified digested DNA was ligated with the individual LM-PCR linker mix using PfuTurbo Hotstart DNA Polymerase (Agilent Technologies). The ligation reaction was then digested with EcoRV (internal RE site of PB at 5TR direction) or MluI (internal RE site of PB at 3TR direction) to remove any linker that has ligated onto the 5TR or 3TR end of DNA, respectively. The remaining DNA containing MspI, HindIII and HaeIII linkers were pooled for 5TR sampling and the remaining DNA containing MspI, DpnII and HaeIII were pooled for 3TR processing. The pooled DNA was set up for PCR amplification using linker primer 1 (5’ GACCCGGGAGATCTGAATTC3’) and TR-specific biotinylated primers (LM_5TR_inver_A2: /5Biosg/AGATAATCATGCGTCATTTTGACTCAC or LM_3TR_inverA: /5Biosg/TCGATATACAGACCGATAAAACACATG). Biotinylated PCR products were pulled down using Dynabeads kilobaseBINDER kit at room temperature for 4 hours. Further nested PCR amplification was conducted using a primer that was specific for 5TR (LM_5TR_inver_B2: AGCGGCGACTGAGATGTCC) or 3TR (LM_3TR_inverB: ATGCGTCAATTTTACGCATGATTATC), and a Miseq sequencing index primer (Supplementary Table 5) containing individual sample barcode. The PCR products were tagged with modified P5 and P7 primers for sequencing.CITE-seq:after magnetic bead-based lineage depletion, prior to FACS sorting, each sample was stained with a pool of mouse CITE-Seq antibodies , and sample-specific hashing mixtures. Post staining and sorting, cells were run through the standard 10x Chromium (v3) protocol up until cDNA amplification, with the following modification: during cDNA PCR, 2 pmol of antibody-derived tag (ADT) additive primer (5’CCTTGGCACCCGAGAATTCC) and 1 pmol of hashtagging oligonucleotide (HTO) additive primer (5’GTGACTGGAGTTCAGACGTGTGCTC) were added to the cDNA amplification master mix. Post cDNA amplification, a 0.6X SPRI cleanup was performed to separate the cDNA fraction (on beads) from the smaller ADT and HTO fractions (in supernatant). The cDNA fraction was converted into a 3’ tag gene expression library according to the 10x Genomics Single Cell Genomics Protocol (v3). Supernatant from cleanup was kept for ADT and HTO preparation. To the supernatant, another 1.4X SPRI was added to bring the total SPRI concentration to 2X. After washing the beads in 80% ethanol and eluting in water, a second round of 2X SPRI cleanup was performed to remove any residual primer carryover from the cDNA PCR. Post cleanup, eluate was taken into ADT PCR amplification (using TruSeq Small RNA RPIx primer (5’CAAGCAGAAGACGGCATACGAGXXXXXXXXGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA) and SI PCR primer (5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC)), and into hashtag amplification (using TruSeq D7xx (5’CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGC) and SI PCR primers). ). Libraries were pooled and sequenced on a 100 cycle Novaseq S1 flowcell. Additional protocol details can be found for CITE-Seq and cell hashing at www.cite-seq.com.
RNA and DNA  libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq, Flip-Jump-Seq, CITE-Seq

tag: genotype/variation

value: Pdzk1ip1CreER R26tdTomato

value: Bone marrow

value: Lin-Tomato+Flt3+ progenitor


title: PitNET42-x


title: Sample60_MOLT-17

description:
total RNA (ribosomal depleted)
SD-2137-MOLT-17_S14

value: T-ALL

value: T-cells


title: OE GFP-1 in hiPSC-CMs (RNA-seq)

description:
Gene Expression Data
GFP-1

source_name: hiPSC-CMs overexpressed with GFP

value: overexpressed GFP


title: Sample56_KASUMI-2_BR2

description:
total RNA (ribosomal depleted)
SD-2137-KASUMI-2-R2_S10


title: Pdzk1ip1-in vivo-wk3 tp wk5 RNA


title: PitNET43-x


title: OE GFP-2 in hiPSC-CMs (RNA-seq)

description:
Gene Expression Data
GFP-2


title: Input in ERRg KO2 (ChIP-Seq)

description: H3K27ac occupancy

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie2
Peaks were called using findPeaks command in the Homer package
Genome_build: hg38
Supplementary_files_format_and_content: bw

molecule: genomic DNA

source_name: ERRgamma KO hiPSC-CMs

growth_protocol: hiPSC were cultured in TeSR-E8 (StemCell Technologies) and differentiated toward cardiomyocytes with the method published by Dr. Joseph Wu (Nat Methods. 2014 Aug;11(8):855-60. PMID: 24930130). ERRg KO iPSCs were generated by pSpCas9n(BB)-2A-Puro plasmids (PX462, Addgene plasmid # 48141) containing distinct sgRNAs against ERRg.

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K27a-DNA complexes were isolated with H3K27ac antibody.
Libraries were prepared according to NuGen The Ovation® Ultralow Library System V2 (Part# 0801-0303) with 2 mg DNA sample.

tag: day

value: ERRgamma

tag: chip antibody


title: Sample53_COG-LL-394h

description:
total RNA (ribosomal depleted)
SD-2137-COG-LL-394h_S7


title: PitNET39-x

value: NF PitNET


title: Pdzk1ip1-in vivo-wk3 tp wk5 ADT


title: Sample51_COG-LL-319h_BR2

description:
total RNA (ribosomal depleted)
SD-2137-COG-LL-319h-R2_S5


title: Cx3cr1-in vivo-day2 to day 5 ADT

value: Lin-GFP+ progenitor


title: Sample54_COG-LL-402h

description:
total RNA (ribosomal depleted)
SD-2137-COG-LL-402h_S8


title: PitNET40-x

value: Plasma


title: Sample55_KASUMI-10

description:
total RNA (ribosomal depleted)
SD-2137-KASUMI-10_S9

value: childhood acute lymohoblastic leukemia


title: Input in WT1 (ChIP-Seq)

description: H3K27ac occupancy

source_name: Wild type hiPSC-CMs

value: Wild type


title: Cx3cr1-in vivo-day2 to day 5 HTO


title: PitNET41-x

value: GH secreting


title: Input in WT2 (ChIP-Seq)

description: H3K27ac occupancy


title: Sample50_CCRF-HSB2

description:
total RNA (ribosomal depleted)
SD-2137-CCRF-HSB2_S4

value: untreated


title: Mfn1/2.KO-5

city: Ann Arbor

first: Scott

last: Soleimanpour

state: Michigan

address: 1000 Wall St,

department: Internal Medicine

institute: University Of Michigan

data_processing:
Base calling was performed by RTA3 software integrated in the NovaSeq 6000 Sequencing System.
Sequence reads were trimmed for adapters using Cutadapt (v2.3). FastQC (v0.11.8) was used to ensure the quality of data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1). Alignment options followed ENCODE standards for RNA-seq.
DESeq2 (v1.26.0) was used to generate count matrices.
Genome_build: GRCm38
Supplementary_files_format_and_content: deseq2_raw_counts.txt: Tab-delimited text file includes raw counts for every samples generated using DESeq.
Supplementary_files_format_and_content: deseq2_depth_normalized_counts.txt: Tab-delimited text file includes normalized raw counts for every sample.

source_name: Pancreatic islet

growth_protocol: Pancreatic islets were isolated by collagenase digestion, and were incubated in an atmospheric CO2 incubator at 37°C in mouse islet culture media for 24 hours.

extract_protocol:
Total RNA was collected from islets using E.N.Z.A. Total RNA MicroElute Total RNA kit from Omega Bio-tek.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Sequencing was performed by the UM Advanced Genomics Core using 151bp paired-end cycles on the NovaSeq-6000 platform (Illumina).

value: Pancreatic islets

tag: gender

value: Male


title: PitNET37-x


title: Sample49_BE-13

description:
total RNA (ribosomal depleted)
SD-2137-BE-13_S3


title: PitNET45-x

value: PRL secreting


title: Input in ERRg KO1 (ChIP-Seq)

description: H3K27ac occupancy

value: hiPSC-derived cardioyocytes


title: Mfn1/2.KO-4


title: Sample52_COG-LL-355h_BR2

description:
total RNA (ribosomal depleted)
SD-2137-COG-LL-355h-R2_S6

value: BCP-ALL

value: B-cells


title: OE GFP-3 in hiPSC-CMs (RNA-seq)

description:
Gene Expression Data
GFP-3


title: LC28_T

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

description: small RNA

data_processing:
Sequenced reads were trimmed by the sequencing quality and/or adopter contaminations using Cutadapt (Martin et al. EMBnet.Journal 2011) with the following parameters: --overlap=6 -f fastq -a TGGAATTCTCGGGTGCCAAGG -m 18 -M 26.
The sequencing quality of trimmed reads were checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Trimmed reads were aligned to the reference human genome using the mapper (mapper.pl; the following parameters were used: -e -h -j -m -s) function of miRDeep2 (Friedländer et al. Nucleic Acids Res. 2012) with Bowtie (Langmead et al. Genome Biol. 2009).
Expression levels of all known miRNAs were estimated using the quantifier (quantifier.pl; the following parameters were used: -t has -g 2 -e 2 -f 5) function of miRDeep2.
Differentially expressed miRNAs between lung adenocarcinoma and adjacent normal tissues were identified using DESeq2 (Love et al. Genome Biol. 2014).
Genome_build: hg38

source_name: fresh tissue

extract_protocol:
The patients with untreated, primary, non-metastatic lung tumors, who underwent lung lobe resection with curative intent and provided informed consent, were included in this study. Following surgical resection, paired tumor and normal tissues were isolated and immediately transported to the research facility. The tumor and normal tissues were macroscopically examined for tumor positioning. Ten paired normal and cancer samples from lung adenocarcinoma patients were placed in RNAlater solution (Thermo Scientific, Cat.#AM7020) at 4°C within a few minutes of collection and left overnight to ensure RNA sefety. For further analysis, samples were stored at −20 °C with the RNAlater removed.
The integrity and amount of RNA was measured using the Agilent Bioanalyzer 2100. Approximately 1 μg total RNA was used to prepare a small RNA library, according to the protocol of the TruSeq Small RNA RNA library prep kit (Illumina, San Diego, CA). The libraries were quantified using KAPA Library Quantification kits for Illumina sequencing platforms, according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854), and were sequenced (single-end; 51 bp) using the Illumina HiSeq 2500 system (LC Sciences, Houston, TX) by the Macrogen Inc (Seoul).

value: Lung adenocarcinoma cells

value: lung adenocarcinoma


title: PitNET32-x


title: Cx3cr1-in vivo-day2 to day 5 RNA

value: Bone marrow


title: PitNET38-x


title: H3K27ac ChIP-Seq in WT1

description: H3K27ac occupancy

value: H3K27ac (Abcam, ab4729)


title: H3K27ac ChIP-Seq in ERRg KO2

description: H3K27ac occupancy

value: ERRgamma


title: PitNET35-x

value: NF PitNET


title: Sample45_TANOUE

description:
total RNA (ribosomal depleted)
P10201_146_S83

value: B-ALL


title: Sample48_ALL-PO_BR2

description:
total RNA (ribosomal depleted)
SD-2137-ALL-PO-R2_S2

value: childhood acute lymohoblastic leukemia


title: Mfn2.KO-5


title: Mfn2.KO-4


title: H3K27ac ChIP-Seq in ERRg KO1

description: H3K27ac occupancy


title: BA.1-GFP

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: Viral genomic RNA sequencing of a recombinant virus that expresses GFP and encodes the S gene of BA.1

data_processing:
Library strategy: RNA virus sequencing
Sequencing reads were trimmed using fastp (ver. 0.21.0).
Sequencing reads were mapped to the viral genome sequence of SARS-CoV-2 WK-521 (GISAID ID: EPI_ISL_408667) harboring GFP using BWA-MEM (ver. 0.7.17).
Variant calling and filtering were performed using BCFtools (ver. 1.9).
Variant annotation was performed using snpEff (ver. 5.0e).
Genome_build: SARS-CoV-2 WK-521 (GISIAID ID: EPI_ISL_408667) encoding GFP
Supplementary_files_format_and_content: Variant information  (tsv)

organism: Severe acute respiratory syndrome coronavirus 2

extract_protocol:
QIAamp viral RNA mini kit (Qiagen)
NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs)


title: Sample47_697_BR2

description:
total RNA (ribosomal depleted)
SD-2137-697-R2_S1


title: Mfn1/2.KO-3


title: H3K27ac ChIP-Seq in WT2

description: H3K27ac occupancy

value: Wild type


title: Delta-GFP

description: Viral genomic RNA sequencing of a recombinant virus that expresses GFP and encodes the S gene of Delta


title: Mfn1/2.KO-2

value: Female


title: PitNET30-x

value: Plasma


title: Mfn2.KO-3

value: Pancreatic islets


title: RWPE1 6hr Hypoxia rep1

city: Tucson

first: Gregory

middle: C.

last: Rogers

state: Arizona

address: 1515 N. Campbell Ave.

department: Department Cellular & Molecular Medicine

institute: University of Arizona Cancer Center

description: RNA >200bp

data_processing:
RNA-seq reads were checked for quality using FastQC
Trimmed using Trimmomatic.
The quality trimmed reads were mapped against human reference genome (hg38) using STAR software.
Genes were quantified using FeatureCounts.
The differentially expressed genes were analyzed using DESeq2 R package.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts of reads for genes in matrix format

growth_protocol: RWPE1 cells were cultures in Keratinocyte Serum Free Media (KSFM) supplemented with 0.05 mg/ml BPE (provided with KSFM kit), 5 ng/ml EGF (provided with KSFM kit), 100 IU penicillin, 100 mcg/ml streptomycin, and 0.25 mcg/ml amphotericin. Cells were passaged every 7 days using 0.1% trypsin and soybean trypsin inhibitor.

extract_protocol:
RNA was isolated using the Qiagen RNeasy mini kit (catalog number 74104). Genomic DNA was removed from samples using Qaigen RNase-Free DNase Set (catalog number 79254) as instructed in the RNeasy protocol
RNASeq builds were performed on an Apollo 324 Automation Platform in conjunction with an illumina Truseq Stranded RNA build kit and combinatorial dual indexing. The 12 samples were built in a single batch. The 12 samples were pooled equally and run on our NextSeq 500 instrument using a High Output 75 cycle sequencing run with single-ended reads

treatment_protocol: Media of cells grown in hypoxia was supplemented with 10mM HEPES buffer.

tag: cell line

value: Immortalized prostate epithelial cell

value: 1% oxygen for 6hr


title: Sample46_TMD5

description:
total RNA (ribosomal depleted)
P10201_147_S84

value: untreated


title: RWPE1 24hr Hypoxia rep1

description: RNA >200bp

value: 1% oxygen for 24hr


title: RWPE1 6hr Hypoxia rep3

description: RNA >200bp


title: BA.2-GFP

description: Viral genomic RNA sequencing of a recombinant virus that expresses GFP and encodes the S gene of BA.2


title: Sample41_SEM

description:
total RNA (ribosomal depleted)
P10201_141_S78

value: BCP-ALL

value: B-cells


title: Sample44_TALL-104

description:
total RNA (ribosomal depleted)
P10201_145_S82

value: T-ALL

value: T-cells


title: RWPE1 6hr Hypoxia rep2

description: RNA >200bp


title: RWPE1 24hr Hypoxia rep2

description: RNA >200bp


title: Sample42_SEM_BR2

description:
total RNA (ribosomal depleted)
P10201_142_S79


title: Sample43_SUP-B15

description:
total RNA (ribosomal depleted)
P10201_144_S81


title: Mfn2.KO-2

tag: age


title: B.1.1-GFP

description: Viral genomic RNA sequencing of a recombinant virus that expresses GFP and encodes the S gene of B.1.1


title: Sample40_RPMI-8402

description:
total RNA (ribosomal depleted)
P10201_140_S77


title: Mfn1/2.KO-1


title: Mfn1.KO-3


title: Sample38_REH

description:
total RNA (ribosomal depleted)
P10201_138_S75


title: RWPE1 Normoxia rep3

description: RNA >200bp


title: Mfn2.KO-1


title: RWPE1 12hr Hypoxia rep3

description: RNA >200bp

value: 1% oxygen for 12hr


title: Sample37_RCH-ACV

description:
total RNA (ribosomal depleted)
P10201_137_S74


title: RWPE1 12hr Hypoxia rep2

description: RNA >200bp


title: Mfn1.KO-4

value: Male


title: RWPE1 12hr Hypoxia rep1

description: RNA >200bp


title: RWPE1 Normoxia rep1

description: RNA >200bp


title: Sample36_PF-382

description:
total RNA (ribosomal depleted)
P10201_136_S73


title: Sample39_REH_BR2

description:
total RNA (ribosomal depleted)
P10201_139_S76


title: Mfn1.KO-1


title: Mfn1.KO-2


title: naïve-2

type: RNA

first: Stephanie

last: Daws

address: 3500 N Broad St

institute: Temple University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 12 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

organism: Rattus norvegicus

source_name: orbitofrontal cortex tissue, naïve

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated using the miRvana PARIS kit (AM1556) from Invitrogen according to the manufacturer's protocol.

treatment_protocol: Adult male Sprague Dawley rats were aged 8 weeks on arrival. For saline and heroin exposure, animals were acclimited to the animal facility for 1 week then underwent jugular vein catheterization. Following 1 week of recovery, animals self-administered either saline or heroin for 6 hours per day in 10 daily sessions. For sucrose self-administration and naive animals, animals did not undergo any surgical procedure. Sucrose animals self-administered chocolate sucrose pellets for 2 hours per day in 10 daily sessions. Naive animals were briefly handled then placed in the self-administration chamber for 2 hours daily in 10 daily sessions with no self-administration protocol activated. Immediately following the last session, animals were euthanized and their brains were frozen in ice cold isopentane. Orbitofrontal cortex tissue was dissected from each animal on dry ice then RNA extraction proceeded.

value: Sprague Dawley

tag: Sex

value: male

value: adult

value: orbitofrontal cortex

value: naive


title: RWPE1 Normoxia rep2

description: RNA >200bp


title: Sample34_P30-OHKUBO

description:
total RNA (ribosomal depleted)
P10201_134_S71

value: childhood acute lymohoblastic leukemia


title: Ctrl-6

value: Pancreatic islets

value: wild type


title: sucrose-2

description: 10 days of sucrose self-administration (SA)

source_name: orbitofrontal cortex tissue, sucrose exposed

value: sucrose


title: Donor 4 TIGIT+ CD4 T cells O1

city: New York

first: Christian

last: Forst

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Donor 4 TIGIT+ CD4 T cells

data_processing:
Paired-end reads were aligned to the human genome built GRCh38.v27 using STARaligner v2.7.0f with outFilterScoreMinOverLread = 0.3, outFilterMatchNminOverLread = 0.3, alignSJoverhangMin = 8, alignSJDBoverhangMin = 1. Otherwise default parameters were used.
Following read alignment, featureCounts (v2.0.1) was used to quantify the mRNA expression levels based on the genome model.
mRNAs with at least 2 CPM in at least 1 sample were considered expressed and hence retained for further analysis, otherwise removed.
The mRNA read counts data was normalized using trimmed mean of M-values normalization (TMM) method of the edgeR package (edgeR v3.30.0/limma v3.44.1 pipeline with R v4.0.0; Robinson et al., 2010. PMCID: PMC2796818) to adjust for sequencing library size difference.
Genome_build: GRCh38.v27

source_name: Donor 29

extract_protocol:
Total RNA was extracted from sorted cells by Qiagen RNAeasy kit
Genewiz constructed the library

value: Tonsil

value: TIGIT+ CD45RAnegCXCR5low

value: No treatment


title: naïve-3

description: no self-administration protocol activated


title: Donor 4 TIGIT- CD4 T cells O2

description: Donor 4 TIGIT- CD4 T cells

value: TIGIT- CD45RAnegCXCR5low


title: sucrose-3


title: Sample35_PEER

description:
total RNA (ribosomal depleted)
P10201_135_S72

value: T-ALL

value: untreated


title: Ctrl-5


title: naïve-1


title: saline-2

description: 10 days of saline self-administration (SA)

source_name: orbitofrontal cortex tissue, saline exposed

value: saline


title: Sample31_NALM-16

description:
total RNA (ribosomal depleted)
P10201_131_S68

value: BCP-ALL

value: B-cells


title: Sample30_NALL-1

description:
total RNA (ribosomal depleted)
P10201_130_S67


title: saline-3

value: Sprague Dawley

value: male


title: sucrose-1

value: adult

value: orbitofrontal cortex


title: Ctrl-4

value: Male


title: pDC-GFP-negative-3

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and read counting performed using HT-seq to make count tables
BAM to bedgraph performed using bedtools bedgraph to bigwig performed using bedGraphToBigWig v4
FlipJump-seq reads were trimmed using cutadapt and mapped using bowtie2, all the BAM files were merged to find all the peaks on all files and count tables were made for each BAM files using BEDTools
For FlipJump: bowtie2 -x ${Ref_DIR} -1 ${R1} -2 ${R2} --end-to-end -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 -X 1000 | samtools view -Sb - > BAMs/${File_Name}.bam
For FlipJump: bedtools coverage -counts -b BAMtoBED.bed -a Peaks.bed > CounTable.bed
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (.bw), count tables (.txt)

extract_protocol:
Bulk RNA-Seq: RNA from sorted cells was extracted using TRIzol Plus purification kit (ThermoFisher) and cDNA libraries were prepared with the Low input Clontech SMART-seq HT with Nxt HT.  Flip-Jump-Seq (MiSeq): Genomic DNA was extracted by NucleoSpin Tissue XS (Takara) (< 15,000 cells) or QIAamp Mini  kit (> 15,000 cells). Extracted DNA was further amplified with REPLI-g Mini Kit (Qiagen) for whole genome amplification (WGA).Three-arm LM-PCR-based method was optimized and adapted to clone FlipJump transposon integration sites from both 3TR and 5TR ends. Amplified DNA was quantified using Qubit 2.0 fluorometer (Thermo Fisher), and 1 ug was digested separately with MspI, HindIII or HaeIII for 5TR cloning, and MspI, DpnII or HaeIII for 3TR cloning. The digested DNA was purified using QIAquick PCR Purification Kit. To prepare the individual LM-PCR linker mix, the equal volume of 50 uM linker common (long strand)(5’ GACCCGGGAGATCTGAATTCAGTGGCACAGCAGTTAGGGGGCTGGTCG 3’) and 50 uM restriction enzyme (RE)-digested end-specific linker (Blunt end linker /5Phos/CGACCAGCCC/3AmMO/ for HaeIII or CG end linker /5Phos/CGCGACCAGCCC/3AmMO/ for MspI or GATC end linker/5Phos/GATCCGACCAGCCC/3AmMO/ for DpnII or AGCT end linker/5Phos/AGCTCGACCAGCCC/3AmMO/ for HindIII were mixed in a PCR tube. The linker mix was then denatured and annealed by heating it to 95° C for 5 mins and cooling slowly to room temperature. One third of purified digested DNA was ligated with the individual LM-PCR linker mix using PfuTurbo Hotstart DNA Polymerase (Agilent Technologies). The ligation reaction was then digested with EcoRV (internal RE site of PB at 5TR direction) or MluI (internal RE site of PB at 3TR direction) to remove any linker that has ligated onto the 5TR or 3TR end of DNA, respectively. The remaining DNA containing MspI, HindIII and HaeIII linkers were pooled for 5TR sampling and the remaining DNA containing MspI, DpnII and HaeIII were pooled for 3TR processing. The pooled DNA was set up for PCR amplification using linker primer 1 (5’ GACCCGGGAGATCTGAATTC3’) and TR-specific biotinylated primers (LM_5TR_inver_A2: /5Biosg/AGATAATCATGCGTCATTTTGACTCAC or LM_3TR_inverA: /5Biosg/TCGATATACAGACCGATAAAACACATG). Biotinylated PCR products were pulled down using Dynabeads kilobaseBINDER kit at room temperature for 4 hours. Further nested PCR amplification was conducted using a primer that was specific for 5TR (LM_5TR_inver_B2: AGCGGCGACTGAGATGTCC) or 3TR (LM_3TR_inverB: ATGCGTCAATTTTACGCATGATTATC), and a Miseq sequencing index primer (Supplementary Table 5) containing individual sample barcode. The PCR products were tagged with modified P5 and P7 primers for sequencing.
RNA and DNA  libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: GFP- pDC


title: rns3-2_cP_sRNAseq_rep2

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

data_processing:
RtcB sRNAseq:Low-quality reads were removed and adapters and RNA-linker were trimmed using cutadapt2.7. Clean reads in sizes of 10–40 nt were mapped to the reference genome (TAIR10) by bowtie (Langmead et al., 2009), allowing no mismatches. Genome-matched reads were then mapped to 5’ region of Arabidopsis tRNA sequences downloaded from the PlantRNA database. The expression level of each 5’ tsRNA and miRNA was normalized by total genome-matched reads to RPM (Reads per Million). If 5’ tsRNAs on a tRNA gene have an RPM ≥ 50 in total in each biological replicate, the tRNA was considered to be able to produce 5’ tsRNAs. 5’ tsRNAs ligated with RNA-linkers and SR adapters were 3’-cP-terminated 5’ tsRNAs. 5’ tsRNAs only ligated with SR adapters were 3’-OH-terminated 5’ tsRNAs. For a 5’ tsRNA, if its 3’-cP-terminated species has an RPM ≥ 10 and is ≥ 5 fold abundant than its 3’-OH-terminated species, the 5’ tsRNA was considered to be predominantly terminated with 3’-cP. The same rule was applied to define 5’ tsRNAs that are predominantly terminated with 3’-OH. Other 5’ tsRNAs were considered to be bimorphic.
mRNA-seq:PCR duplicates were removed using FastUniq (Xu et al., 2012) and unique molecular indexes were removed using Trimmomatic (v0.36) (Bolger et al., 2014). Trimmed reads were mapped to the reference genome (TAIR10) in strand-specific mode with default parameters. The expression level of each gene was normalized to Fragments Per Kilobase of transcript per Million mapped reads  (FPKM). Differential gene expression analysis was performed using Cuffdiff (Trapnell et al., 2010). Differentially expressed genes were defined by an FDR ≤ 0.05 with 1.5 fold-change as cutoff. Gene ontology analysis of differentially expressed genes was performed using Metascape (Zhou et al., 2019)
Genome_build: TAIR10
Supplementary_files_format_and_content: For RNA-Seq processed datasets,provided files is the expression matrix of genes . The expression level of mRNA are estimated  as FPKM. For RtcB sRNA-seq processed datasets, our provided files contain genome match small RNA sequences and their counts.

organism: Arabidopsis thaliana

source_name: 14-day-old seedlings

growth_protocol: Arabidopsis seeds were germinated and grown in 1/2 MS medium under long-day conditions with daily cycles of 16 h of light at 22 °C and 8 h of dark at 22 °C in a growth chamber

extract_protocol:
Total RNAs were extracted from 14-d-old seedlings by TRIzol reagent (Takara, 9109), precipitated using isopropanol and then dissolved in DEPC-treated water. Total RNAs were incubated with 5% PEG8000 (Sigma, P5413) and 0.5 M NaCl (Sigma, S3014) on ice for 30 min to selectively precipitate large RNAs. Low molecular weight RNAs were subjected to ethanol precipitation and resolved on 15% urea PAGEs. 10–40-nt RNAs on the gel were purified and split in 4 aliquots;
cP-sRNA sequencing (cP-sRNA-seq) libraries were constructed essentially as described (Honda et al., 2016). Briefly, 10–40-nt sRNAs were gel-purified and incubated with CIP (NEB, M0290, final concentration: 0.2 U/μL) in CutSmart buffer at 37°C for 40 min in the presence of RNasin® Ribonuclease Inhibitor. RNAs were purified and then incubated with NaIO4 (freshly prepared, final concentration: 10 mM) on ice for 40 min in the dark. RNAs were purified and incubated with T4 PNK (NEB, M0201, final concentration: 0.33 U/μL) in T4 PNK reaction buffer at 37°C for 40 min in the presence of ATP and RNasin® Ribonuclease Inhibitor. The libraries were constructed using NEBNext Multiplex Small RNA Library Prep Kit for Illumina (NEB, E7560S). Briefly, purified sRNAs were first ligated with the 3′ SR adaptor. To prevent adaptor-dimer formation, SR RT primer was hybridized to the excess of 3′ SR Adaptor. The products were further ligated with the 5′ adaptor. sRNAs with adapters ligated at both ends were used as templates for reverse transcription and PCR amplification. The libraries were single-end sequenced on an Illumina HiSeqX-PE150 platform by Annoroad Gene Technology (Beijing).

tag: sample type

value: 14–40-nt sRNAs


title: Sample33_P12-ICHIKAWA

description:
total RNA (ribosomal depleted)
P10201_133_S70

value: childhood acute lymohoblastic leukemia

value: T-cells


title: saline-1

tag: strain


title: Donor 2 GC-Tfh CD155 stimulation + IgG M1

description: Donor 2 GC-Tfh CD155 stimulation + IgG

source_name: Donor 39

treatment_protocol: Control IgG (10 μg/ml) antibodies were added on day 0 and day 2.

tag: tissue

value: Tonsil

value: GC-Tfh (CXCR5hiICOShi)

value: Day 3 CD155 L cell stimulation and IgG control

tag: cell stimulation protocol

value: CD155 L cells (2.5e4/well) + anti-human CD3 (OKT3; 0.2-0.5 ug/ml) were mixed with indicated sorted CD4 T cell subset (5e4/well) for 3 days


title: Ctrl-3

value: Pancreatic islets

value: Female

tag: genotype

value: wild type


title: Donor 3 TIGIT- CD4 T cells N2

description: Donor 3 TIGIT- CD4 T cells

source_name: Donor 22

value: TIGIT- CD45RAnegCXCR5low

tag: treatment

value: No treatment


title: Sample32_NALM-6

description:
total RNA (ribosomal depleted)
P10201_132_S69

tag: disease

value: BCP-ALL

value: B-cells

value: untreated


title: Donor 2 Naive WT stimulation L3

description: Donor 2 Naive WT stimulation

treatment_protocol: No additional treatment

tag: cell type

value: Day 3 WT L cells stimulation

value: WT L cells (2.5e4/well) + anti-human CD3 (OKT3; 0.2-0.5 ug/ml) were mixed with indicated sorted CD4 T cell subset (5e4/well) for 3 days


title: PDC-GFP-negative-1

value: Bone marrow

value: GFP- pDC


title: Ctrl-2


title: Donor 3 TIGIT+ CD4 T cells N1

description: Donor 3 TIGIT+ CD4 T cells

value: TIGIT+ CD45RAnegCXCR5low


title: rns3-2_cP_sRNAseq_rep1

value: 14–40-nt sRNAs


title: heroin-2

description: 10 days of heroin self-administration (SA)

source_name: orbitofrontal cortex tissue, heroin exposed

value: Sprague Dawley

value: male

value: adult

value: orbitofrontal cortex

value: heroin


title: Ctrl-1

value: Pancreatic islets

value: Female

value: wild type


title: Donor 2 GC-Tfh CD155 stimulation + anti-CD226 M3

treatment_protocol: Blocking anti-CD226 (10 μg/ml; LeoA1; Millipore Sigma) antibodies were added on day 0 and day 2.

value: Tonsil

value: GC-Tfh (CXCR5hiICOShi)

value: Day 3 CD155 L cell stimulation and anti-CD226 blockade

value: CD155 L cells (2.5e4/well) + anti-human CD3 (OKT3; 0.2-0.5 ug/ml) were mixed with indicated sorted CD4 T cell subset (5e4/well) for 3 days


title: Donor 2 Pre-Tfh CD155 stimulation L2

description: Donor 2 Pre-Tfh CD155 stimulation

value: Pre-Tfh (CXCR5lowICOSlow)

value: Day 3 CD155 L cells stimulation


title: Sample29_MOLT-4

description:
total RNA (ribosomal depleted)
P10201_129_S66

value: childhood acute lymohoblastic leukemia

value: T-ALL

value: T-cells

value: untreated


title: rns1-3_cP_sRNAseq_rep1

value: 14–40-nt sRNAs


title: PDC-GFP-negative-2

value: Bone marrow

value: GFP- pDC


title: heroin-3

value: Sprague Dawley

value: male

value: adult

value: orbitofrontal cortex

value: heroin


title: Donor 2 Naive CD155 stimulation L4

description: Donor 2 Naive CD155 stimulation

value: Tonsil


title: Donor 2 Pre-Tfh WT stimulation L1

description: Donor 2 Pre-Tfh WT stimulation

value: Day 3 WT L cells stimulation

value: WT L cells (2.5e4/well) + anti-human CD3 (OKT3; 0.2-0.5 ug/ml) were mixed with indicated sorted CD4 T cell subset (5e4/well) for 3 days


title: Donor 1 GC-Tfh CD155 stimulation + IgG H1

description: Donor 1 GC-Tfh CD155 stimulation + IgG

source_name: Donor 44

value: GC-Tfh (CXCR5hiICOShi)

value: Day 3 CD155 L cell stimulation and IgG control

value: CD155 L cells (2.5e4/well) + anti-human CD3 (OKT3; 0.2-0.5 ug/ml) were mixed with indicated sorted CD4 T cell subset (5e4/well) for 3 days


title: Sample27_MOLT-16

description:
total RNA (ribosomal depleted)
P10201_127_S64

source_name: Blood

value: childhood acute lymohoblastic leukemia

value: T-ALL


title: rns1-3_cP_sRNAseq_rep2


title: Sample28_MOLT-3

description:
total RNA (ribosomal depleted)
P10201_128_S65

value: T-cells

value: untreated


title: prostate, etanercept50

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:
fastp was used to observe read quality
fastp was used to trim data
STAR  (v2.6.1d)  to align reads to the reference genome
FeatureCounts  (v1.5.0-p3) was used to count reads mapping to genes
DESeq2 Bioconductor package (v1.26.0) to identify differentially expressed genes
Genome_build: Ensembl reference genome for Mus musculus mm10
Supplementary_files_format_and_content: readcount.txt (raw abundance measurements)

source_name: NOD prostate tissue

growth_protocol: NOD mice tissues harvested at 30 weeks

extract_protocol:
Tissue homogenization, Trizol RNA extraction, Qiagen RNeasy Plus Mini kit for RNA cleanup
poly A enrichment
2x150 on a NovaSeq 6000 PE150

treatment_protocol: NOD mice treated with 4 mg/kg etanercept or PBS control twice weekly for five weeks

value: NOD

value: prostate

value: etanercept


title: pDC-GFP-positive-3

value: Bone marrow

value: GFP+ pDC


title: prostate, etanercept17


title: Sample26_MOLT-13

description:
total RNA (ribosomal depleted)
P10201_126_S63


title: Sample25_MN-60

description:
total RNA (ribosomal depleted)
P10201_125_S62

value: B-ALL

value: B-cells


title: pDC-GFP-positive-2


title: Col0_cP_sRNAseq_rep2

value: 14–40-nt sRNAs


title: heroin-1

value: Sprague Dawley

value: male

value: adult

value: orbitofrontal cortex

value: heroin


title: Sample20_KOPN-8

description:
total RNA (ribosomal depleted)
P10201_120_S57

value: childhood acute lymohoblastic leukemia

value: BCP-ALL


title: Sample24_MHH-CALL-4

description:
total RNA (ribosomal depleted)
P10201_124_S61


title: Donor 2 GC-Tfh CD155 stimulation + anti-CD226 H3

value: Tonsil

value: GC-Tfh (CXCR5hiICOShi)

value: Day 3 CD155 L cell stimulation and anti-CD226 blockade

value: CD155 L cells (2.5e4/well) + anti-human CD3 (OKT3; 0.2-0.5 ug/ml) were mixed with indicated sorted CD4 T cell subset (5e4/well) for 3 days


title: Donor 1 Pre-Tfh WT stimulation G1

description: Donor 1 Pre-Tfh WT stimulation

value: Pre-Tfh (CXCR5lowICOSlow)

value: Day 3 WT L cells stimulation

value: WT L cells (2.5e4/well) + anti-human CD3 (OKT3; 0.2-0.5 ug/ml) were mixed with indicated sorted CD4 T cell subset (5e4/well) for 3 days


title: Sample19_KASUMI-9

description:
total RNA (ribosomal depleted)
P10201_119_S56

value: untreated


title: Col0_cP_sRNAseq_rep1


title: prostate, etanercept52

value: NOD

value: prostate

value: etanercept


title: Sample23_MHH-CALL-3

description:
total RNA (ribosomal depleted)
P10201_123_S60

value: B-cells


title: Col0_cP_sRNA-seq

value: 14–40-nt sRNAs


title: prostate, etanercept19


title: Sample18_KASUMI-2

description:
total RNA (ribosomal depleted)
P10201_118_S55


title: Sample22_MHH-CALL-2

description:
total RNA (ribosomal depleted)
P10201_122_S59


title: Donor 1 Naive CD155 stimulation G4

description: Donor 1 Naive CD155 stimulation

value: Day 3 CD155 L cells stimulation


title: Donor 1 Naive WT stimulation G3

description: Donor 1 Naive WT stimulation


title: Bc_cP_sRNAseq_rep1

source_name: B.cinerea-inoculated seedlings


title: prostate, control3

value: control


title: AGO1IP_cP_sRNAseq_rep2

value: AGO1-associated 14–40-nt sRNAs


title: Donor 1 Pre-Tfh CD155 stimulation G2

description: Donor 1 Pre-Tfh CD155 stimulation


title: 35S:CYP71A13_rep2_RNAseq

molecule: polyA RNA

extract_protocol:
Total RNAs were purified from 14-d-old Arabidopsis seedlings using RNeasy Plant Mini Kit (QIAGEN, 74904). After DNA digestion, poly(A)+ RNAs were purified using Dynabeads mRNA Purification Kit (Invitrogen, 61006). Briefly, the sample was incubated at 65°C for 2 min and then immediately put on ice to disrupt RNA secondary structures. The denatured poly(A)+ RNAs were incubated with Dynabeads in the binding buffer at room temperature for 5 min  on a shaker to allow the annealing of poly(A)+ RNAs to oligo (dT)25 on the Dynabeads. The Dynabeads were washed twice with washing buffer and then incubated with 10 mM Tris-HCl (pH 7.5) to elute poly(A)+ RNAs.
Briefly, RNAs were fragmented and then the first strands and second strands of cDNAs were synthesized using First Strand Synthesis Mix and Second Strand Synthesis Mix, respectively. cDNA size selection and purification were performed using AMPure XP beads (Beckman, A63881). After the addition of a single nucleotide “A”, cDNAs were subjected to adapter ligation. The products were purified with AMPure XP beads and then used as templates for PCR amplification. The libraries were sequenced on a HiSeqX-PE150 sequencing platform by Annoroad Gene Technology (Beijing).


title: prostate, control69


title: AGO1IP_cP_sRNAseq_rep1


title: Bc_cP_sRNAseq_rep2


title: pDC-GFP-positive-1

value: Bone marrow

value: GFP+ pDC


title: prostate, control65


title: Sample15_HPB-ALL

description:
total RNA (ribosomal depleted)
P10201_115_S52

value: childhood acute lymohoblastic leukemia

value: T-ALL

value: T-cells


title: CFIm68_KD_rep3

city: Basel

first: Mihaela

last: Zavolan

state: BS

address: Klingelbergstrasse 50-70

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Remove read adapters: cutadapt (1.16), parameters: -b CCTTGGCACCCGAGAATTCCA -e 0.1 --times 1 --trim-n --cores=8 --minimum-length 10
Remove read tails: cutadapt (1.16), parameters: -b AAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTT -e 0.1 -O 1 --times 1 --trim-n --cores=8 --minimum-length 10
Align reads: STAR (2.7.1a), parameters: --runMode alignReads --twopassMode Basic --outSAMunmapped None --outSAMattributes All --outReadsUnmapped None --outFilterType BySJout --alignEndsType Local --outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 0 --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
Genome_build: hg38
Supplementary_files_format_and_content: Read counts for each gene excluding terminal exon in .txt format

source_name: HEK 293 cell line

growth_protocol: Cells were grown as described by ATCC

extract_protocol:
RNA was extracted with Accubiomed RNA extraction system. 1µg total RNA was used for library preparation with the TruSeq Stranded mRNA Library Prep Kit High Throughput
RNA libraries were prepared for sequencing using standard Illumina protocols with the TruSeq Stranded mRNA Library Prep Kit High Throughput

treatment_protocol: siRNA treatment was done using Lipofectamine RNAimax following manufacturers protocol

value: HEK 293

value: Kidney

value: CFIm68 knockdown


title: STTM-Ala-1_rep2_RNAseq


title: Sample21_LC4-1

description:
total RNA (ribosomal depleted)
P10201_121_S58

value: BCP-ALL

value: untreated


title: STTM-Ala-1_rep1_RNAseq


title: 35S:CYP71A13_rep3_RNAseq


title: Sample17_KARPAS-45

description:
total RNA (ribosomal depleted)
P10201_117_S54


title: CFIm25_OE_rep3

value: CFIm25 overexpression


title: CFIm68_OE_rep2

value: CFIm68 overexpression


title: prostate, control1

value: NOD

value: prostate


title: Sample13_DND-41

description:
total RNA (ribosomal depleted)
P10201_113_S50


title: CFIm68_KD_rep2


title: Sample16_JURKAT

description:
total RNA (ribosomal depleted)
P10201_116_S53


title: Sample12_COG-LL-356h

description:
total RNA (ribosomal depleted)
P10201_112_S49

value: Epstein-Barr virus transformed cells

value: B-cells


title: 35S:CYP71A13_rep1_RNAseq


title: Sample14_HAL-01

description:
total RNA (ribosomal depleted)
P10201_114_S51


title: Complemented strain 5' end mapping library replicate 1

city: Boston

first: Scarlet

middle: Sara

last: Shell

state: MA

address: 665 Huntington Ave, SPH 1 Room 802

department: Immunology and Infectious Diseases

institute: Harvard School of Public Health

data_processing:
Reads were aligned to the reference sequence using bwa mem.
Samtools was used to convert sam files to bam files
For expression libraries only, FeatureCount was used to assign mapped reads to genomic features (output included in processed file list)
For expression libraries only, DESeq2 was used to assess differential gene expression.
A custom perl script was used to place plus strand and minus strand reads in separate bam files for both library types.
For expression libraries, Bedtools Genomecov was used to make coverage files from strand-specific bam files, with the -pc option to fill in gaps between paired-end reads (output included in the processed file list).
For 5' end mapping libraries, a custom perl script was used to make bam files containing read 1 only.
For 5' end mapping libraries, Bedtools Genomecov with the -5 option was used to make coverage files for only for the first nt of read 1, which corresponds to the first nt of a transcript (output included in the processed file list).
Genome_build: NC_000962_3.gbk
Supplementary_files_format_and_content: .coverage files are output from Bedtools Genomecov. For expression libraries, they report read depth for each coordinate for the indicated strand. For 5' end mapping libraries, they report the depth for only the first nt of read 1, for the indicated strand.
Supplementary_files_format_and_content: The FeatureCounts excel file reports the output from FeatureCounts for the expression libraries (raw count assigned to each annotated gene).

organism: Mycobacterium tuberculosis H37Rv

source_name: Log phase growth

growth_protocol: Cultures were grown to OD approximately 0.4 in Middlebrook 7H9 supplemented with OADC, 0.2% glycerol, and 0.05% Tween 80.

extract_protocol:
Pellets were resuspended in Trizol and lysed by bead-beating. RNA was extracted with a Zymo Direct-zol kit, treated with DNase, and purified with a Zymo Clean and Concentrate kit.
rRNA was depleted by Ribo-Zero. Expression libraries were constructed with a KAPA stranded RNA-seq library preparation kit. 5' end mapping libaries were constructed as in https://doi.org/10.3389/fmicb.2019.00591, without RppH treatment.

value: H37Rv deletion of Rv2752c complemented with plasmid overexpressing Rv2752c


title: CFIm68_OE_rep1


title: Complemented strain 5' end mapping library replicate 3


title: Sample11_COG-LL-355h

description:
total RNA (ribosomal depleted)
P10201_111_S48

extract_protocol:
QIAGEN RNeasy Mini Kit with DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina protocols using Ribo-Zero and/or Ribo-Zero Gold Kit


title: CFIm25_OE_rep2


title: CFIm68_KD_rep1


title: Complemented strain expression library replicate 3

description:
FeatureCounts_table.xlsx
COMP_mtb_expr_rep3


title: rns3-2_rep3_RNAseq


title: Sample10_COG-LL-332h

description:
total RNA (ribosomal depleted)
P10201_110_S47


title: CFIm25_KD_rep2

value: CFIm25 knockdown


title: CFIm68_OE_rep3


title: Rv2752c deletion 5' end mapping library replicate 3

value: H37Rv deletion of Rv2752c transformed with empty vector


title: Sample8_COG-LL-317

description:
total RNA (ribosomal depleted)
P10201_108_S45

value: childhood acute lymohoblastic leukemia


title: Control_rep3

value: wild type


title: rns3-2_rep2_RNAseq


title: rns3-2_rep1_RNAseq


title: Rv2752c deletion 5' end mapping library replicate 2


title: rns1-3_rep1_RNAseq


title: Wildtype expression library replicate 2

description:
FeatureCounts_table.xlsx
WT_mtb_expr_rep2

value: H37Rv wildtype transformed with empty vector


title: cyp71A13-1_rep3_RNAseq


title: cyp71A13-1_rep1_RNAseq


title: MDA-MB-231 up3

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description:
VC3AI-ve/DAPI-ve/AnnexinV-ve
Replicate 3

data_processing:
Illumina basecalling.
Standard Illumina bioinformatics analysis were used to generate fastq files, followed by quality assessment [MultiQC v1.7 https://multiqc.info/], trimming and demultiplexing.
Rsubread v2.4.3 was used for mapping to the hg38 genome and creating a matrix of RNA-Seq counts. Rsamtools v2.6.0 was used to merge the two bam files for each sample (run in two different lanes).
Next, a DGElist object was created with the edgeR package v3.26.7.
After filtering (min.count = 10, min.total.count = 15) and normalization for composition bias, genewise exact tests were computed for differences in the means between groups.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file with normalized rpkm values for each sample

source_name: MDA-MB-231 cells

growth_protocol: Human breast cancer MDA-MB-231 cell line was obtained from American Type Culture Collection (ATCC). Cells were maintained in RPMI supplemented with 2 mM L-glutamine (ThermoFisher Scientific, 25030-24), non-essential amino acids (ThermoFisher Scientific, 11140-035), 1 mM sodium pyruvate (ThermoFisher Scientific, 11360-039), 10% FBS (Eurobio, CVFSVF00-01) and 5% penicillin/streptomycin (ThermoFisher Scientific, 15140-122).

extract_protocol:
Libraries were prepared from 600 ng total RNA using the TruSeq Stranded mRNA kit (Illumina) following the manufacturer’s instructions.
The different steps are the PolyA mRNA capture with oligo dT beads, cDNA double strand synthesis, adaptors ligation, library amplification and sequencing.
RNA sequencing was performed using the NextSeq500 Illumina sequencer in 75 bp paired-end.

treatment_protocol: Cells (3 x 10expexp6) were plated on a 75 mm transwell insert with a polycarbonate membrane pore size of 3 µm (Corning, 3420). Before seeding, the insert is coated with a layer of matrigel (300 µg/ml). A gradient of serum is then created between the two compartments of the transwell (0% FBS in the top compartment and 20% below) and is renewed 5 hours later. After 72 hours, the cells are recovered after washing the insert with PBS and incubation with trypsin. The cells that have migrated through the 3 µm pores are the “constricted cells” (refered to as “down” in the fastq files, or “bottom” throughout the text) while the ones that did not migrate are the “control cells” (refered to as “up” in the fastq files, or “Top” throughout the text).

value: control cells

value: caspase reporter + inducible tBID


title: rns1-3_rep3_RNAseq


title: Rv2752c deletion expression library replicate 3

description:
FeatureCounts_table.xlsx
JKO_mtb_expr_rep3


title: Complemented strain expression library replicate 1

description:
FeatureCounts_table.xlsx
COMP_mtb_expr_rep1


title: Sample9_COG-LL-319h

description:
total RNA (ribosomal depleted)
P10201_109_S46

data_processing:
The sequenced reads were preprocessed  for adapter and quality-based trimming using cutadapt  v2.4 and then mapped to the human reference genome GRCh38 (gencode.v31.p12 primary assembly) using STAR aligner v2.7.1a (DOI: 10.1093/bioinformatics/bts635) with enabled chimeric reads detection.
The mapped reads were quantified at the gene level using featureCount.
The raw counts were processed to remove any techinical variation due to different RNA-seq library prepartion times using ComBat-seq method in sva R package (DOI: 10.1093/nargab/lqaa078).
The batch-corrected raw counts are provided in the processed data files
Genome_build: gencode.v31.p12 primary assembly
Supplementary_files_format_and_content: raw counts at gene level


title: rns1-3_rep2_RNAseq


title: Sample3_A3

description:
total RNA (ribosomal depleted)
P10201_103_S40

value: T-ALL

value: T-cells


title: CFIm25_KD_rep1

value: HEK 293

value: Kidney


title: Sample5_ALL-SIL

description:
total RNA (ribosomal depleted)
P10201_105_S42

value: untreated


title: Rv2752c deletion expression library replicate 2

description:
FeatureCounts_table.xlsx
JKO_mtb_expr_rep2


title: Wildtype 5' end mapping library replicate 1


title: Sample7_CCRF-SB

description:
total RNA (ribosomal depleted)
P10201_107_S44


title: Sample6_CCRF-CEM

description:
total RNA (ribosomal depleted)
P10201_106_S43


title: Control_rep2


title: cyp71A13-1_rep2_RNAseq


title: MDA-MB-231 down3

description:
VC3AI+ve/DAPI-ve/AnnexinV-ve
Replicate 3

value: constricted cells


title: CFIm25_OE_rep1

value: CFIm25 overexpression


title: Control_rep1


title: Col0_rep5_RNAseq

source_name: 14-day-old seedlings,wild-type for 35S:CYP71A13 or cyp71A13-1


title: MDA-MB-231 down2

description:
VC3AI+ve/DAPI-ve/AnnexinV-ve
Replicate 2


title: Col0_rep8_RNAseq

source_name: 14-day-old seedlings,wild-type for STTM-Ala #1


title: ERR_KO_hiPSC-CMs_KO6_rep3 (RNA-seq)

description:
Gene Expression Data
KO6-3

data_processing:
Transcript-level gene expression was quantified using Salmon (Nat Methods. 2017 Apr;14(4):417-419. PMID: 28263959)
Transcript data was aggregated to produce gene-level quantifications, and tests for differential expression were performed using DESeq2 (Genome Biol. 2014;15(12):550. PMID: 25516281)
We considered genes with FDR < 0.05 and fold change at least 1.5 in any direction for further analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file contains significantly regulated gene name, log2 fold change (WT/KO), and adjusted p-values.

source_name: ERRa/g KO hiPSC-CMs line 6

extract_protocol:
RNA was harvested using miRNeasy kit (QIAGEN) from hiPSC-CMs at day22.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: ERRg KO iPSCs were generated by pSpCas9n(BB)-2A-Puro plasmids (PX462, Addgene plasmid # 48141) containing distinct sgRNAs against ERRg. After generating ERRg KO hiPSCs, ERRa/g KO hiPSCs were generated by pCas9-EGFP and pGuide kindly provided by Dr. Kiran Musunuru (University of Pennsylvania, PA). Wild type control cells were processed with the same treatment using empty vectors without gRNA expression.

value: hiPSC-derived cardiomyocytes

tag: line

tag: differentiation

value: ERRa/g KO


title: Sample4_ALL-PO

description:
total RNA (ribosomal depleted)
P10201_104_S41

value: BCP-ALL

value: B-cells


title: Col0_rep7_RNAseq


title: MDA-MB-231 up2

description:
VC3AI-ve/DAPI-ve/AnnexinV-ve
Replicate 2

tag: genotype/variation


title: MDA-MB-231 up1

description:
VC3AI-ve/DAPI-ve/AnnexinV-ve
Replicate 1


title: Sample2_697

description:
total RNA (ribosomal depleted)
P10201_102_S39


title: Wildtype expression library replicate 1

description:
FeatureCounts_table.xlsx
WT_mtb_expr_rep1


title: Col0_rep6_RNAseq


title: Col0_rep3_RNAseq

source_name: 14-day-old seedlings,wild-type for rns1-3 and rns3-2


title: MDA-MB-231 down1

description:
VC3AI+ve/DAPI-ve/AnnexinV-ve
Replicate 1


title: KYSE-30_M1_KD2_ReD

first: Shuibin

last: Lin

state: China

address: Zhongshan 2nd road, Guangzhou

department: Clincial for Translational Medicine

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

description:
small RNA
esophageal epithelial
M1_KD2_ReD
cleavage_score_for_TRAC-seq.txt

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

source_name: esophagus

growth_protocol: KYSE-30 cells were cultured in DMEM (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) and 1% Penicillin (Gibco, USA). Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37 °C in an incubator (Thermo Scientific, USA).

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

treatment_protocol: KYSE-30 cells were transfected with shRNA for stable knockdown of METTL1. KYSE-30 cells with normal expression of METTL1 were used as control.

value: esophageal squamous cell carcinoma cell line

value: demethylated by ALKB; NaBH4/Aniline induced reduction and cleavage

value: TRAC-seq


title: Sample1_380

description:
total RNA (ribosomal depleted)
P10201_101_S38

value: childhood acute lymohoblastic leukemia


title: LN-Fibroblasts_1205Lu CM_rep3

city: Nice

first: Virginie

last: Prod'homme

address: 151, route de Ginestère

institute: Inserm

description: Gene expression in lymph node fibroblasts after 48hr culture with 1205Lu conditioned medium

hyb_protocol: Labeled cRNA probe were hybridized on SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (Agilent). Four biological replicates were performed for each comparison.

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent).

source_name: Lymp node fibroblasts, 1205Lu conditioned medium, 48hr, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One-Color low RNA input QuickAmp kit (Agilent) (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was extracted using NucleoSpin RNA Plus kit (Macherey-Nagel) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Lymph node fibroblasts from healthy donors were cultured in DMEM supplemented with 0.5% heat-inactivated fetal bovine serum, or in 1205Lu conditioned medium (in DMEM) supplemented with 0.5% heat-inactivated fetal bovine serum . The cultures were incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Lymph node

value: fibroblasts

value: 1205Lu conditioned medium


title: ERR_KO_hiPSC-CMs_KO6_rep1 (RNA-seq)

description:
Gene Expression Data
KO6-1


title: LN-Fibroblasts_1205Lu CM_rep4

source_name: Lymp node fibroblasts, 1205Lu conditioned medium, 48hr, replicate 4


title: LN-Fibroblasts_1205Lu CM_rep2

source_name: Lymp node fibroblasts, 1205Lu conditioned medium, 48hr, replicate 2


title: LN-Fibroblasts_1205Lu CM_rep1

source_name: Lymp node fibroblasts, 1205Lu conditioned medium, 48hr, replicate 1


title: Col0_rep4_RNAseq


title: ERR_KO_hiPSC-CMs_KO6_rep2 (RNA-seq)

description:
Gene Expression Data
KO6-2


title: KYSE-30_M1_KD1_ReD

city: Guangzhou

description:
small RNA
esophageal epithelial
M1_KD1_ReD
cleavage_score_for_TRAC-seq.txt


title: ERR_KO_hiPSC-CMs_KO1_rep1 (RNA-seq)

description:
Gene Expression Data
KO1-1

source_name: ERRa/g KO hiPSC-CMs line 1


title: Col0_rep2_RNAseq


title: KYSE-30_ctrl1_ReD

description:
small RNA
esophageal epithelial
ctrl1_ReD
cleavage_score_for_TRAC-seq.txt

value: normal


title: KYSE-30_M1_KD2_DeM

description:
small RNA
esophageal epithelial
M1_KD2_DeM
tRAN_counts_for_TRAC-seq.txt

value: demethylated by ALKB


title: ERR_KO_hiPSC-CMs_KO1_rep2 (RNA-seq)

description:
Gene Expression Data
KO1-2


title: WT_control_hiPSC-CMs_rep1 (RNA-seq)

description:
Gene Expression Data
WT1

source_name: Wild type control hiPSC-CMs

value: Wild type


title: Col0_rep1_RNAseq


title: LN-Fibroblasts_Ctrl_rep4

description: Gene expression in lymph node fibroblasts after 48hr culture in control conditions

source_name: Lymp node fibroblasts, control culture medium, 48hr, replicate 4

value: control culture medium


title: input_Ikzf3_mut_thy

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

institute: RIKEN Yokohama

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
RNA-seq sequences were aligned on mm10 and read counts were calculated using STAR (version 2.7.0) with default parameters.
ChIP-seq sequences were aligned on mm10 using Hisat2 (version 2.1.0) with default parameters.
Peaks were called using MACS2 (version 2.1.1) with the following settings in addition to the default setting: For Ikaros, broad peak calling. For Aiolos, broad peak calling and upper (50-fold) and lower (2-fold) limit for model building.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw read count for each RNA-seq sample. BED6+3 format file for each ChIP-seq sample.

source_name: thymocyte

extract_protocol:
Lysates were purified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs)

value: thymus

value: none (input)


title: KYSE-30_ctrl2_DeM

description:
small RNA
esophageal epithelial
ctrl2_DeM
tRAN_counts_for_TRAC-seq.txt


title: LN-Fibroblasts_Ctrl_rep1

source_name: Lymp node fibroblasts, control culture medium, 48hr, replicate 1


title: KYSE-30_ctrl2_ReD

description:
small RNA
esophageal epithelial
ctrl2_ReD
cleavage_score_for_TRAC-seq.txt


title: LN-Fibroblasts_Ctrl_rep3

source_name: Lymp node fibroblasts, control culture medium, 48hr, replicate 3


title: ERR_KO_hiPSC-CMs_KO6_rep1 (ATAC-seq)

first: Tomoya

last: Sakamoto

address: Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421

institute: University of Pennsylvania

description: ATAC-seq

data_processing:
ATAC-seq reads were aligned to GRCh38 with Bowtie2
Differential peaks were called using Homer/DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

extract_protocol:
100,000 hiPSC-CMs were lyzed to isolate nuclear and transposed with Nextera DNA Library Prep Kit.
The purified transposed DNA was amplified with NEBNext High-Fidelity 2 X PCR Master Mix (New England Biolabs) with Nextera Index Kit (Illumina). The amplified DNA samples were purified with AMPure XP (BECKMAN COULTER).

value: hiPSC-derived cardiomyocytes


title: Col0_rep2_RtcB_RNAseq

description: 15–40-nt sRNAs

source_name: 14-day-old seedlings

extract_protocol:
Total RNAs were extracted from 14-d-old seedlings by TRIzol reagent (Takara, 9109), precipitated using isopropanol and then dissolved in DEPC-treated water. Total RNAs were incubated with 5% PEG8000 (Sigma, P5413) and 0.5 M NaCl (Sigma, S3014) on ice for 30 min to selectively precipitate large RNAs. Low molecular weight RNAs were subjected to ethanol precipitation and resolved on 15% urea PAGEs. 10–40-nt RNAs on the gel were purified and split in 4 aliquots;
14–40-nt sRNAs in 14-d-old Arabidopsis seedlings were gel-purified. After treatment with 1U/µg of DNase (Promega, M6101) for 30 min, 14–40-nt sRNAs were ethanol precipitated with 20 μg of glycogen supplemented. 14–40-nt sRNAs were then ligated with RNA-linker in a 20 μL reaction that contains 5 μM RNA-linker (5’ rUrCrArCrCrGrUrGrGrU 3’), 1 × RtcB buffer (NEB, M0458), 15 pmol of RtcB ligase (NEB, M0458), 100 μM GTP, 1 mM MnCl2, 20 units of RNase inhibitor (Promega, N2518). The reaction took place at 37°C for 2 h. RNAs were ethanol precipitated with 20 μg of glycogen supplemented and resuspended in 10 μL of RNase-free water. The libraries were constructed using NEBNext Multiplex Small RNA Library Prep Kit for Illumina (NEB, E7560S). Briefly, purified sRNAs were first ligated with the 3’ SR adaptor. To prevent adaptor-dimer formation, SR RT primer was hybridized to the excess of 3’ SR adaptor. The products were further ligated with the 5’ adaptor. sRNAs with adapters ligated at both ends were used as templates for reverse transcription and PCR amplification. The libraries were single-end sequenced on an Illumina HiSeqX-PE150 platform by Annoroad Gene Technology (Beijing).


title: Col0_rep3_RtcB_RNAseq

description: 15–40-nt sRNAs


title: LN-Fibroblasts_Ctrl_rep2

source_name: Lymp node fibroblasts, control culture medium, 48hr, replicate 2


title: input_Ikzf3_WT_thy


title: WT_control_hiPSC-CMs_rep3 (RNA-seq)

description:
Gene Expression Data
WT3


title: ERR_KO_hiPSC-CMs_KO1_rep2 (ATAC-seq)

description: ATAC-seq

value: ERRa/g KO


title: Col0_rep1_RtcB_RNAseq

description: 15–40-nt sRNAs


title: WT_control_hiPSC-CMs_rep2 (RNA-seq)

description:
Gene Expression Data
WT2


title: ChIP-seq_Aiolos_Ikzf3_WT_thy

value: Anti-Aiolos/Ikzf3 antibody, Clone:9D10, EMD Millipore Corp, Catalog No:MABE911,Lot No:2728873


title: ERR_KO_hiPSC-CMs_KO6_rep2 (ATAC-seq)

description: ATAC-seq


title: KYSE-30_ctrl1_DeM

description:
small RNA
esophageal epithelial
ctrl1_DeM
tRAN_counts_for_TRAC-seq.txt


title: ChIP-seq_Ikaros_Ikzf3_mut_thy

value: Anti-Ikaros/Ikzf1 antibody, Clone:4E9, EMD Millipore Corp, Catalog number:MABE912, Lot No:2759640


title: ChIP-seq_Ikaros_Ikzf3_WT_thy


title: mimics 7704 KC 3

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

institute: Karolinska Institutet

hyb_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

data_processing:
Expression data were analyzed by using Transcriptome Analysis Console 4.0. The follwoing criteria were used for data analysis:  Array Type: Clariom_S_Human  Analysis Type: Expression (Gene)  Analysis Version: version 2  Summarization Method: Gene Level - SST-RMA  Pos vs Neg AUC Threshold: 0,7  Genome Version: hg38 (Homo sapiens)  Annotation: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv  Condition (Comparison): circRNA kd; ctr
Genes with FC > 1.2 and P-value < 0.05 between the miRNA mimics- and the control mimics-transfected cells were considered to be significantly changed.

label: biotin

source_name: Keratinocytes transfected with miRNA 7704 mimics

label_protocol: One hundred fifty nanograms of total RNA was used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol

growth_protocol: Adult Human Epidermal Keratinocytes (HEKa) were cultured in EpiLife medium (Gibco™) supplemented with 10% Human Keratinocyte Growth Supplement (HKGS, Gibco™) and 1% penicillin/streptomycin (Gibco™) at 37°C in 5% CO2. Adult human dermal fibroblasts (HDFa) were cultured in Medium 106 supplemented with Low Serum Growth Supplement (LSGS, Gibco™) and 100 units/mL Penicillin and 100 μg/mL Streptomycin.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (ThermoFisher Scientific).

treatment_protocol: Third passage HEKa or HDFa cells were seeded in 24-well plates. At 60-70% confluence, cells were transfected with 20nM miRNA mimics using Lipofectamine 3000 (ThermoFisher Scientific). After 24 hours, cells were harvested for RNA extraction.

tag: developmental stage

value: adult

value: Skin

value: transfected with miR-7704 mimics

value: miR-7704 overexpression


title: ChIP-seq_Aiolos_Ikzf3_mut_preB

source_name: cultured pre-B cell

value: bone marrow

tag: chip antibody


title: input_Ikzf3_WT_preB


title: KYSE-30_M1_KD1_DeM

description:
small RNA
esophageal epithelial
M1_KD1_DeM
tRAN_counts_for_TRAC-seq.txt

value: esophageal squamous cell carcinoma cell line

value: TRAC-seq


title: ChIP-seq_Aiolos_Ikzf3_WT_preB


title: input_Ikzf3_mut_preB


title: 2737 (WT tam male)

city: Bronx

first: christopher

middle: p

last: cardozo

address: 130 West Kingsbridge Road

department: CMSCI

institute: Bronx VA Medical Center

description:
RNA-sequencing reads
raw_count_m.tsv

data_processing:
Sequences were aligned to GRCm38 (mm10) mouse genome using Spliced Transcripts Alignment to a Reference (STAR) software
gene-level read counts were generated by FeatureCounts
Genes with expression of 0 in more than 30% of all samples were removed; data were normalized using limma/voom
We performed differential expression analysis using the c package v3.44.3 from Bioconductor
Benjamini-Hochberg adjusted P values of less than or equal to 0.1 and fold change greater than or equal to 1.2 were used as the thresholds for detecting DEGs.
Genome_build: GRCm38 (mm10)

source_name: gastrocnemius

extract_protocol: Gastrocnemius muscles were removed from mice deeply anesthetized using isoflurane then flash frozen in liquid nitrogen. Samples of frozen tissue were disrupted using a bead tissue homogenizer in Tirzol. RNA was extracted then further enriched using RNA Easy kits (Qiagen).

value: gastrocnemius

value: Numb(f/f)/NumbL(f/f)

value: Tamoxifen

tag: gender

value: Male


title: 2704 (WT veh male)

description:
RNA-sequencing reads
raw_count_m.tsv

value: Vehicle


title: ChIP-seq_Aiolos_Ikzf3_mut_thy

value: thymus


title: WT_control_hiPSC-CMs_rep1 (ATAC-seq)

city: Philadelphia

description: ATAC-seq

value: hiPSC-derived cardiomyocytes

value: Wild type


title: 2751 (WT veh male)

description:
RNA-sequencing reads
raw_count_m.tsv


title: 2721 (WT tam male)

description:
RNA-sequencing reads
raw_count_m.tsv


title: WT_control_hiPSC-CMs_rep2 (ATAC-seq)

description: ATAC-seq


title: 2735 (WT tam male)

description:
RNA-sequencing reads
raw_count_m.tsv


title: ERR_KO_hiPSC-CMs_KO1_rep1 (ATAC-seq)

description: ATAC-seq

value: ERRa/g KO


title: 1085 (male cKO)

description:
RNA-sequencing reads
raw_count_m.tsv

value: HSA-MCM/Numb(f/f)/NumbL(f/f)


title: RNA-seq_Ikzf3 G158Rhomo pre-B rep3

source_name: Pre-B cell

extract_protocol:
Bone marrow B220+ cells were purified using anti-CD45R coated MACS beads (Miltenyi Biotec) following manufacturer’s instruction. Pre-pro B cell (B220+AA4.1+IgM-CD43+CD24-) and pre-B cell (B220+AA4.1+IgM-CD43-CD24+) were isolated by flow cytometry. Total RNA was extracted by TRIzol reagent (Thermo Fisher Scientific), followed by DNA digestion by RNA Clean & Concentrator-5 (ZYMO RESEARCH), and mRNA was obtained by poly (A) selection with mRNA DIRECT kit (Thermo Fisher Scientific). RNA-seq libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocol.
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)


title: 2702 (WT veh male)

description:
RNA-sequencing reads
raw_count_m.tsv


title: 1055 (male cKO)

description:
RNA-sequencing reads
raw_count_m.tsv


title: Wildtype 5' end mapping library replicate 2

source_name: Log phase growth

value: H37Rv wildtype transformed with empty vector


title: ChIP-seq_Ikaros_Ikzf3_mut_preB

value: Anti-Ikaros/Ikzf1 antibody, Clone:4E9, EMD Millipore Corp, Catalog number:MABE912, Lot No:2759640


title: ChIP-seq_Ikaros_Ikzf3_WT_preB

growth_protocol: Bone marrow B220+IgM- cells were isolated and cultured on Tst-4 stromal cells in Iscove's Modified Dulbecco's Medium (IMDM, Thermo Fisher Scientific) containing 10 to 20 ng/ml of IL-7, 10 ng/ml of SCF, and 10 ng/ml of Flt3L.


title: RNA-seq_Ikzf3 G158Rhet pre-B rep2


title: mimics 516b-5p KC 2

scan_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

source_name: Keratinocytes transfected with miRNA 516b-5p mimics

value: adult

value: Skin

value: Adult Human Epidermal Keratinocytes (HEKa)

value: transfected with 516b-5p mimics

value: miR-516b-5p overexpression


title: RNA-seq_Ikzf3 G158Rhet pre-B rep1

value: bone marrow


title: 1062 (male cKO)

description:
RNA-sequencing reads
raw_count_m.tsv

value: gastrocnemius


title: mimics 7704 KC 2

value: transfected with miR-7704 mimics

value: miR-7704 overexpression


title: 1080 (male vehicle control)

description:
RNA-sequencing reads
raw_count_m.tsv

value: Tamoxifen

value: Male


title: mimics 7704 KC 1


title: mimics 516b-5p KC 3


title: 1063 (male vehicle control)

description:
RNA-sequencing reads
raw_count_m.tsv


title: RNA-seq_Ikzf3 G158Rhomo pre-B rep2


title: mimics 450b-5p KC 1

source_name: Keratinocytes transfected with miRNA 450b-5p mimics

value: transfected with 450b-5p mimics

value: miR-450b-5p overexpression


title: RNA-seq_Ikzf3 G158Rhet pre-B rep3


title: mimics 450b-5p KC 3


title: mimics 424-5p KC 3

source_name: Keratinocytes transfected with miRNA 424-5p mimics

value: transfected with 424-5p mimics

value: miR-424-5p overexpression


title: mimics 450b-5p KC 2


title: tam-2 (female genotyp control)

description:
RNA-sequencing reads
raw_count_f_ctrl.tsv

value: Numb(f/f)/NumbL(f/f)

value: Female


title: RNA-seq_Ikzf3 G158Rhomo pre-B rep1


title: mimics 218-5p KC 2

source_name: Keratinocytes transfected with miRNA 218-5p mimics

value: adult

value: transfected with 218-5p mimics

value: miR-218-5p overexpression


title: mimics 218-5p KC 3

value: Skin

value: Adult Human Epidermal Keratinocytes (HEKa)


title: 1039 (male vehicle control)

description:
RNA-sequencing reads
raw_count_m.tsv

value: HSA-MCM/Numb(f/f)/NumbL(f/f)


title: mimics 516b-5p KC 1

value: transfected with 516b-5p mimics

value: miR-516b-5p overexpression


title: RNA-seq_WT pre-B rep2

value: bone marrow


title: mimics 424-5p KC 1


title: mimics 424-5p KC 2


title: mimics 218-5p KC 1


title: tam-3 (female genotyp control)

value: gastrocnemius

value: Tamoxifen


title: RNA-seq_WT pre-B rep3


title: veh-3 (female genotyp control)

value: Vehicle


title: tam-1 (female genotyp control)


title: mimics 96-5p KC 2

source_name: Keratinocytes transfected with miRNA 96-5p mimics

value: transfected with 96-5p mimics

value: miR-96-5p overexpression


title: veh-2 (female genotyp control)


title: RNA-seq_Ikzf3 G158Rhomo pre-pro B rep3

source_name: Pre-pro B cell


title: 919 (female cKO)

description:
RNA-sequencing reads
raw_count_f_cko.tsv


title: RNA-seq_Ikzf3 G158Rhomo pre-pro B rep2


title: RNA-seq_Ikzf3 G158Rhet pre-pro B rep1


title: mimics 96-5p KC 3


title: RNA-seq_Ikzf3 G158Rhomo pre-pro B rep1


title: 921 (female cKO)


title: mimics ctl KC 2

source_name: Keratinocytes transfected with miRNA mimics control

value: Adult human dermal fibroblasts (HDFa)

value: transfected with mimics control

value: Control


title: RNA-seq_WT pre-pro B rep3


title: RNA-seq_Ikzf3 G158Rhet pre-pro B rep3


title: RNA-seq_Ikzf3 G158Rhet pre-pro B rep2


title: mimics ctl KC 3

value: adult


title: RNA-seq_WT pre-pro B rep2


title: 871 (female cKO)

value: Female


title: 920 (female vehicle control)


title: 922 (female vehicle control)


title: RNA-seq_WT pre-pro B rep1


title: mimics 424-5p FB 2

source_name: Fibroblasts transfected with miRNA 424-5p mimics

value: transfected with 424-5p mimics

value: miR-424-5p overexpression


title: mimics ctl KC 1

value: Skin


title: RNA-seq_WT pre-B rep1


title: Pca_dRM_IV

status: Public on Feb 15 2022

city: Dunedin

first: Peter

middle: Charles

last: Fineran

state: Otago

address: 720 Cumberland Street

country: New Zealand

institute: University of Otago

data_processing:
Alignment of raw reads to the P. carotovorum RC5297 genome was performed using Bowtie2 with default parameters (Langmead & Salzberg 2012, Nature Methods)
Conversion of the alignment to BAM format was performed using SAMtools (Li et al. 2009, Bioinformatics)
Identification of up- and downregulated transcripts was performed in Rstudio using DESeq2 (Love et al. 2014, Genome Biology)
Genome_build: P. carotovorum RC5297 genome
Supplementary_files_format_and_content: countsWTvdRM

organism: Pectobacterium carotovorum

source_name: bacterial culture

growth_protocol: 250 µL of an overnight culture of the desired strain was used to inoculate 25 mL LB medium and incubated shaking at 25°C up to an OD of 0.65 to 0.75

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions; residual genomic DNA was removed by treatment with TurboDNase (Thermo Fisher) as per the manufacturer's instructions
Libraries were prepared by the Microbial Genome Sequencing (MiGS) Center (Pittsburgh, USA) using the QIAseq Stranded RNA Library kit (Qiagen)

treatment_protocol: 1 mL of the culture was centrifuged for 1 min at 17,000 g, the supernatant was discarded, and the pellet was resuspended in 1 mL RNAlater (Invitrogen) and stored at -20 °C

value: PcaI RM KO

tag: replicate


title: Pca_dRM_I


title: Pca_dRM_II


title: NANOPOPRE-seq total polyA+

city: Singapore

first: Chan-Shuo

last: Wu

address: 14 Medical Drive, #12-01

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

description: NANOPORE-direct_RNA-seq total polyA+ fraction

data_processing:
For ChIP-seq analysis, reads were mapped by bowtie2 against human reference genome GRCh38 (Langmead and Salzberg 2012).
Only uniquely mapped reads were used and PCR duplicates were removed with samtools rmdup.
The resulting bam files are converted to bigWig format by bedGraphToBigWig from bedGraph generated by bedtools.
For 4C-seq analysis, the long-range genomic interaction regions generated by the 4C-Seq experiment were analyzed by using the R package r3CSeq v1.30.0 on hg19.
Bam files are converted to read coverage by bedGraphToBigWig. The read coverage was normalized according to sequencing depth.
The resulting bedGraph files are converted to bigWig format.
The genome version of bigWig files was converted to hg38 by CrossMap.
For total RNA-seq analysis, the paired-end RNA-seq reads were trimmed for adaptor sequence by TrimGalore and then mapped by STAR to the human reference genome GRCh38 with reference gene annotation GENCODE 26.
PCR duplicates were removed in the paired-end alignments by samtools rmdup.
Alignments with mapping quality < 20 were removed.
Gene expression levels in FPKM were determined by cuffdiff in the Cufflinks package.
For fraction RNA-seq analysis, the paired-end RNA-seq reads were trimmed for adaptor sequence by TrimGalore and then mapped by STAR to the human reference genome GRCh38 with reference gene annotation.
The read count on each EZH2 peak region was generated by featureCount. The read count was normalized according to the sequencing depth.
For RIP-seq analysis, reads from the RIP data set and its control data set were mapped respectively by STAR against human reference genome GRCh38 with gene annotation.
Only uniquely mapped reads were used and PCR duplicates were removed with samtools rmdup.
Bam files was converted to bedGraph to represent read coverage by bedtools. The read coverage was normalized according to the size of transcriptome mapping.
The resulting bedGraph files are converted to bigWig format.
For NANOPOPRE-seq total polyA+ RNA, the reads were mapped to hg38 by Minimap2 with -ax splice -uf -k14.
The bam files were converted to bed12 by bamToBed and were converted to bigBed file by bedToBigBed. Only uniquely mapped reads were retained.
For NANOPORE-seq nuclear cDNA sequencing, the reads were mapped to hg38 by LAST with lastal -d90 -m50 -D10 and last-split -d2
The maf files were converted to psl file with maf-convert -j1e6 psl. The psl files were subsequently converted to bam file with psl2sam.pl and cigar_tweaker scripts within the SAMtools package.
The read alignments were then converted into bedGraph by BEDTools and into bigWig format by bedGraphToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq.genes.fpkm.txt: Tab-delimited text file includes FPKM values.
Supplementary_files_format_and_content: *.ReadCount.txt: Tab-delimited text files include read counts.
Supplementary_files_format_and_content: *bw: bigWig format
Supplementary_files_format_and_content: *.bigBed: bigBed format

source_name: K562 leukemia cell line

growth_protocol: K562 cells and its derivatives were cultured with RPMI supplemented with 10% fetal bovine serum. The cells were passage every 3 to 4 days.

extract_protocol:
1) RIP-seq: Cells were fixed with 1% formaldehyde. RNA was sonicated to around 3000 and protein-RNA complexes were pulled down by antibodies. 2) RNA-seq: Fractionated RNA was harvested by Trizol followed by DNaseI treatment. 3) NANOPRE-seq: Fractionated RNA was harvested by Trizol followed by DNaseI treatment. Superscript IV was used for nuclear cDNA preparation. 4) ChIP-seq: Cells were fixed with 1% formaldehyde and insoluble chromatin fraction was isolated. Chromatin was sonicated to 100 to 500 base pair and protein-DNA complexes were pulled down by antibodies. 5) 4C-seq: Cells were fixed with 2% formaldehyde. gDNA was digested first with DpnII and ligated. The ligated chromatin was digested again with NlaIII, MseI or MluCI and ligated.
1) ChIP-seq: Libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. 2) RIP-seq and RNA-seq: Libraries were prepared using Scriptseq V2 RNA-seq Library preparation kit (SSV21124) according to manufacturer's instruction.  Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. 3) NANOPORE-seq:  Library for nuclear cDNA was constructed with 1D cDNA library kit (SQK-LSK108) according to manufacturer's instruction. RNA library for total polyA+ RNA was constructed with direct-RNA sequencing kit (SQK-RNA001) according to manufacturer's instruction. 4) 4C-seq: 4C library was constructed with customized primers with Illumina adaptor and barcodes and KAPA HiFi HotStart ReadyMix (KK2602).

treatment_protocol: LEVER knock out was achieved using CRISPR-Cas9 gene editing method. LEVER knock down was achieved using inducible CRISPR-dCas9 strategy.

tag: cell line

value: Leukemia cell line

value: Wild type

tag: passage


title: mimics 424-5p FB 3


title: mimics ctl FB 3

source_name: Fibroblasts transfected with miRNA mimics control


title: mimics ctl FB 2


title: 902 (female vehicle control)

value: HSA-MCM/Numb(f/f)/NumbL(f/f)


title: mimics ctl FB 1


title: veh-1 (female genotyp control)

value: gastrocnemius

value: Numb(f/f)/NumbL(f/f)


title: Pca_wt_I

value: wild type


title: Pca_wt_II


title: Pca_wt_III


title: mimics 424-5p FB 1


title: mimics 96-5p KC 1

value: Adult Human Epidermal Keratinocytes (HEKa)

value: transfected with 96-5p mimics


title: Pca_dRM_III


title: Pca_dRM_V


title: NANOPORE-seq Nuclear

description: NANOPORE-cDNA-seq nuclear fraction


title: G12-3D7_S87 SCC Bulk RNAseq SCC101

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

data_processing:
Bulk RNAseq samples were processed using Galaxy, alighed with STARaligner
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

source_name: SCC-derived Treg Cells

extract_protocol:
RNA was extracted using SMART-Seq v4 Ultra Low Input RNA kit protocols for bulk RNA-seq
RNA was constructed using NexteraXT DNA sample preperation protocol for bulk RNA-seq

treatment_protocol: Tregs were sorted and cultured with either no stimulation, stimulation with anti-CD3/CD28/CD2 beads,  or stimulation with anti-CD3/CD28/CD2 beads and IL-1b for 1, 2, or 3 days.

tag: phenotype

tag: donors

tag: stimulation

value: anti-CD3/CD28/CD2 beads

tag: timepoint

value: Day 3

value: Squamous Cell Carcinoma


title: Pca_wt_V

tag: strain

tag: genotype


title: Pca_wt_IV


title: H11-3C5_S80 SCC Bulk RNAseq SCC101

value: anti-CD3/CD28/CD2 beads and IL-1b

tag: tissue


title: A12-3C7_S81 SCC Bulk RNAseq SCC101


title: H12-3D8_S88 SCC Bulk RNAseq SCC101


title: F12-3D5_S86 SCC Bulk RNAseq SCC101


title: D12-3D2_S84 SCC Bulk RNAseq SCC101

source_name: Peripheral Blood Treg Cells (SCC)

value: Peripheral Blood


title: E12-3D4_S85 SCC Bulk RNAseq SCC101


title: B11-3A5_S74 SCC Bulk RNAseq SCC098


title: C12-3D1_S83 SCC Bulk RNAseq SCC101


title: C11-3A7_S75 SCC Bulk RNAseq SCC098


title: H10-3B2_S72 SCC Bulk RNAseq SCC099


title: G10-3B1_S71 SCC Bulk RNAseq SCC099


title: G11-3C4_S79 SCC Bulk RNAseq SCC101


title: B12-3C8_S82 SCC Bulk RNAseq SCC101


title: F10-2D8_S70 SCC Bulk RNAseq SCC101

value: Day 2


title: F11-3C2_S78 SCC Bulk RNAseq SCC101


title: A11-3A4_S73 SCC Bulk RNAseq SCC098


title: D11-3A8_S76 SCC Bulk RNAseq SCC098


title: E10-2D7_S69 SCC Bulk RNAseq SCC101


title: D10-2D5_S68 SCC Bulk RNAseq SCC101


title: G9-2C7_S63 SCC Bulk RNAseq SCC101


title: B10-2D2_S66 SCC Bulk RNAseq SCC101


title: A10-2D1_S65 SCC Bulk RNAseq SCC101


title: H9-2C8_S64 SCC Bulk RNAseq SCC101


title: E9-2C4_S61 SCC Bulk RNAseq SCC101


title: C10-2D4_S67 SCC Bulk RNAseq SCC101


title: F9-2C5_S62 SCC Bulk RNAseq SCC101


title: B9-2B2_S58 SCC Bulk RNAseq SCC099


title: A9-2B1_S57 SCC Bulk RNAseq SCC099


title: D9-2C2_S60 SCC Bulk RNAseq SCC101


title: H8-2F8_S56 SCC Bulk RNAseq SCC093


title: F8-2F5_S54 SCC Bulk RNAseq SCC093


title: G8-2F7_S55 SCC Bulk RNAseq SCC093


title: C9-2C1_S59 SCC Bulk RNAseq SCC101


title: E11-3C1_S77 SCC Bulk RNAseq SCC101


title: E8-2F4_S53 SCC Bulk RNAseq SCC093


title: D8-2A8_S52 SCC Bulk RNAseq SCC098


title: B8-2A5_S50 SCC Bulk RNAseq SCC098


title: A8-2A4_S49 SCC Bulk RNAseq SCC098


title: C8-2A7_S51 SCC Bulk RNAseq SCC098


title: G6-1F7_S47 SCC Bulk RNAseq SCC093

value: Day 1


title: F6-1F6_S46 SCC Bulk RNAseq SCC093


title: D6-1F4_S44 SCC Bulk RNAseq SCC093


title: C6-1F9_S43 SCC Bulk RNAseq SCC093


title: H5-1E8_S40 SCC Bulk RNAseq SCC103


title: A6-1D9_S41 SCC Bulk RNAseq SCC102


title: E6-1F5_S45 SCC Bulk RNAseq SCC093


title: B6-1E9_S42 SCC Bulk RNAseq SCC103


title: G5-1E7_S39 SCC Bulk RNAseq SCC103


title: F5-1E6_S38 SCC Bulk RNAseq SCC103


title: C5-1E3_S35 SCC Bulk RNAseq SCC103


title: D5-1E4_S36 SCC Bulk RNAseq SCC103


title: B5-1E2_S34 SCC Bulk RNAseq SCC103


title: H4-1D8_S32 SCC Bulk RNAseq SCC102


title: E5-1E5_S37 SCC Bulk RNAseq SCC103


title: G4-1D7_S31 SCC Bulk RNAseq SCC102


title: F4-1D6_S30 SCC Bulk RNAseq SCC102


title: E4-1D5_S29 SCC Bulk RNAseq SCC102


title: D4-1D4_S28 SCC Bulk RNAseq SCC102


title: H6-1F8_S48 SCC Bulk RNAseq SCC093


title: C4-1D3_S27 SCC Bulk RNAseq SCC102


title: H3-1C8_S24 SCC Bulk RNAseq SCC101


title: A4-1D1_S25 SCC Bulk RNAseq SCC102


title: B4-1D2_S26 SCC Bulk RNAseq SCC102


title: G3-1C7_S23 SCC Bulk RNAseq SCC101


title: F3-1C6_S22 SCC Bulk RNAseq SCC101


title: D3-1C4_S20 SCC Bulk RNAseq SCC101


title: E3-1C5_S21 SCC Bulk RNAseq SCC101


title: F2-1B6_S14 SCC Bulk RNAseq SCC099


title: A3-1C1_S17 SCC Bulk RNAseq SCC101


title: H2-1B8_S16 SCC Bulk RNAseq SCC099


title: B3-1C2_S18 SCC Bulk RNAseq SCC101


title: E2-1B5_S13 SCC Bulk RNAseq SCC099


title: C3-1C3_S19 SCC Bulk RNAseq SCC101


title: G2-1B7_S15 SCC Bulk RNAseq SCC099


title: D2-1B4_S12 SCC Bulk RNAseq SCC099


title: C2-1B3_S11 SCC Bulk RNAseq SCC099


title: A2-1B1_S9 SCC Bulk RNAseq SCC099


title: B2-1B2_S10 SCC Bulk RNAseq SCC099


title: G1-1A7_S7 SCC Bulk RNAseq SCC098


title: E1-1A5_S5 SCC Bulk RNAseq SCC098


title: D1-1A4_S4 SCC Bulk RNAseq SCC098


title: A5-1E1_S33 SCC Bulk RNAseq SCC103


title: H1-1A8_S8 SCC Bulk RNAseq SCC098


title: C1-1C9_S3 SCC Bulk RNAseq SCC101


title: B1-1B9_S2 SCC Bulk RNAseq SCC099


title: A1-1A9_S1 SCC Bulk RNAseq SCC098