title: mESC_DNA_cell1160


title: mESC_DNA_cell1158

status: Public on May 14 2021

type: SRA

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

country: China

institute: Peking University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.

molecule: genomic DNA

organism: Mus musculus

source_name: cell line

growth_protocol: mESCs were cultured at 37 °C with 5% CO2 and was maintained in high glucose DMEM

extract_protocol:
folloing CoTECH protocol
After PCR enrichment using Q5 polymerase, the 300-1,000 bp fragments were isolated using the 1.5% (w/v) agarose gel and purified once with 0.8 x AMpure XP beads

treatment_protocol: The mESCs were dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for CoTECH

tag: cell type

value: cultured mouse embryonic stem cells

tag: strain

tag: chip antibody


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title: mESC_DNA_cell530


title: mESC_DNA_cell554


title: mESC_DNA_cell528


title: mESC_DNA_cell527


title: mESC_DNA_cell526


title: mESC_DNA_cell543


title: mESC_DNA_cell522


title: mESC_DNA_cell525


title: mESC_DNA_cell523


title: mESC_DNA_cell551


title: mESC_DNA_cell529


title: mESC_DNA_cell534


title: mESC_DNA_cell519


title: mESC_DNA_cell521


title: mESC_DNA_cell520


title: mESC_DNA_cell531


title: mESC_DNA_cell518


title: mESC_DNA_cell532


title: mESC_DNA_cell517


title: mESC_DNA_cell514


title: mESC_DNA_cell511


title: mESC_DNA_cell515


title: mESC_DNA_cell516


title: mESC_DNA_cell508


title: mESC_DNA_cell512


title: mESC_DNA_cell524


title: mESC_DNA_cell504


title: mESC_DNA_cell513


title: mESC_DNA_cell505


title: mESC_DNA_cell506


title: mESC_DNA_cell510


title: mESC_DNA_cell503


title: mESC_DNA_cell499


title: mESC_DNA_cell507


title: mESC_DNA_cell500


title: mESC_DNA_cell501


title: mESC_DNA_cell502


title: mESC_DNA_cell498


title: mESC_DNA_cell497


title: mESC_DNA_cell494


title: mESC_DNA_cell496


title: mESC_DNA_cell495


title: mESC_DNA_cell491


title: mESC_DNA_cell492


title: mESC_DNA_cell490


title: mESC_DNA_cell493


title: mESC_DNA_cell487


title: mESC_DNA_cell509


title: mESC_DNA_cell489


title: mESC_DNA_cell481


title: mESC_DNA_cell486


title: mESC_DNA_cell484


title: mESC_DNA_cell478


title: mESC_DNA_cell479


title: mESC_DNA_cell537


title: mESC_DNA_cell485


title: mESC_DNA_cell482


title: mESC_DNA_cell477


title: mESC_DNA_cell473


title: mESC_DNA_cell476


title: mESC_DNA_cell469


title: mESC_DNA_cell470


title: mESC_DNA_cell474


title: mESC_DNA_cell472


title: mESC_DNA_cell471


title: mESC_DNA_cell465


title: mESC_DNA_cell467


title: mESC_DNA_cell468


title: mESC_DNA_cell488


title: mESC_DNA_cell466


title: mESC_DNA_cell464


title: mESC_DNA_cell480


title: mESC_DNA_cell483


title: mESC_DNA_cell462


title: mESC_DNA_cell475


title: mESC_DNA_cell463


title: mESC_DNA_cell459


title: mESC_DNA_cell460


title: mESC_DNA_cell456


title: mESC_DNA_cell461


title: mESC_DNA_cell455


title: mESC_DNA_cell457


title: mESC_DNA_cell450


title: mESC_DNA_cell453


title: mESC_DNA_cell454


title: mESC_DNA_cell447


title: mESC_DNA_cell446


title: mESC_DNA_cell445


title: mESC_DNA_cell443


title: mESC_DNA_cell444


title: mESC_DNA_cell442


title: mESC_DNA_cell451


title: mESC_DNA_cell440


title: mESC_DNA_cell439


title: mESC_DNA_cell438


title: mESC_DNA_cell436


title: mESC_DNA_cell437


title: mESC_DNA_cell441


title: mESC_DNA_cell435


title: mESC_DNA_cell458


title: mESC_DNA_cell452


title: mESC_DNA_cell432


title: mESC_DNA_cell433


title: mESC_DNA_cell431


title: mESC_DNA_cell430


title: mESC_DNA_cell449


title: mESC_DNA_cell428


title: mESC_DNA_cell427


title: mESC_DNA_cell429


title: mESC_DNA_cell426


title: mESC_DNA_cell434


title: mESC_DNA_cell424


title: mESC_DNA_cell422


title: mESC_DNA_cell448


title: mESC_DNA_cell423


title: mESC_DNA_cell425


title: mESC_DNA_cell421


title: mESC_DNA_cell420


title: mESC_DNA_cell419


title: mESC_DNA_cell418


title: mESC_DNA_cell417


title: mESC_DNA_cell413


title: mESC_DNA_cell414


title: mESC_DNA_cell416


title: mESC_DNA_cell411


title: mESC_DNA_cell415


title: mESC_DNA_cell410


title: mESC_DNA_cell408


title: mESC_DNA_cell412


title: mESC_DNA_cell409


title: mESC_DNA_cell405


title: mESC_DNA_cell403


title: mESC_DNA_cell402


title: mESC_DNA_cell407


title: mESC_DNA_cell406


title: mESC_DNA_cell400


title: mESC_DNA_cell399


title: mESC_DNA_cell404


title: mESC_DNA_cell397


title: mESC_DNA_cell392


title: mESC_DNA_cell398


title: mESC_DNA_cell396


title: mESC_DNA_cell395


title: mESC_DNA_cell391


title: mESC_DNA_cell389


title: mESC_DNA_cell394


title: mESC_DNA_cell388


title: mESC_DNA_cell393


title: mESC_DNA_cell390


title: mESC_DNA_cell386


title: mESC_DNA_cell385


title: mESC_DNA_cell384


title: mESC_DNA_cell382


title: stuA_Keratin_96h_III

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

library_source: transcriptomic

data_processing:
FastQC v0.11.7 was used to visualize the libraries quality before and after trimming.
Trimmomatic v0.36 was used to remove adapters and quality filtered setting the cutoff threshold for average base quality score at 15 over a window of 4 bases. Reads shorter than 36 bases post-trimming were excluded.
Filtered reads were mapped onto the T. rubrum genome using the STAR v2.5.2b.
Gene level read-counts were quantified using STAR’s –quantMode GeneCounts parameter.
The data were analyzed using the R package DESeq2. The samples were normalized, and the dispersions were estimated using the default settings. The package was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) >= 1.5 (upregulation) or <= -1.5 (downregulation) were called as differentially expressed.
Genome_build: Broad T. rubrum strain CBS118892 genome
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

molecule: total RNA

organism: Trichophyton rubrum

source_name: delta-stuA - Keratin - 96 hours, replicate III

growth_protocol: T. rubrum wild strain CBS 118892 and the null mutant strain ΔstuA were initially grown on malt extract agar solid medium (MEA: 2% glucose, 2% malt extract, 0.1% peptone, 2% agar, pH 5.7) at 28 °C for 20 days.

extract_protocol:
The obtained mycelium was harvested,  and stored at - 80 °C until RNA isolation. Total RNA was isolated using an Illustra RNAspin mini isolation kit (GE Healthcare, Chicago, IL, USA) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: About 1×10^6 conidia were inoculated into 100 mL of Sabouraud. Culture was held at 28 °C for 96 h under constant agitation (120 rpm). The resulting mycelia were washed with sterile water and transferred to 100 mL of minimal medium (Cove, 1966) containing 70 mM sodium nitrate  and either 50mM glucose, or 0.5% bovine keratin (m/v) as test condition. The cultures were incubated under agitation at 28 °C for 24 h, 48 h, or 96 h.

tag: background strain

tag: genotype

value: delta stuA

tag: carbon source

value: keratin

tag: time


title: stuA_Keratin_96h_I

source_name: delta-stuA - Keratin - 96 hours, replicate I


title: mESC_DNA_cell377


title: mESC_DNA_cell379


title: stuA_Keratin_24h_III

source_name: delta-stuA - Keratin - 24 hours, replicate III


title: mESC_DNA_cell401


title: stuA_Keratin_48h_III

source_name: delta-stuA - Keratin - 48 hours, replicate III


title: mESC_DNA_cell375


title: stuA_Keratin_96h_II

source_name: delta-stuA - Keratin - 96 hours, replicate II


title: stuA_Glucose_96h_II

source_name: delta-stuA - Glucose - 96 hours, replicate II

value: glucose


title: mESC_DNA_cell380


title: mESC_DNA_cell383


title: stuA_Keratin_48h_II

source_name: delta-stuA - Keratin - 48 hours, replicate II


title: stuA_Glucose_96h_III

source_name: delta-stuA - Glucose - 96 hours, replicate III


title: mESC_DNA_cell381


title: mESC_DNA_cell371


title: stuA_Keratin_48h_I

source_name: delta-stuA - Keratin - 48 hours, replicate I


title: mESC_DNA_cell370


title: mESC_DNA_cell378


title: stuA_Keratin_24h_I

source_name: delta-stuA - Keratin - 24 hours, replicate I


title: mESC_DNA_cell387


title: mESC_DNA_cell374


title: stuA_Keratin_24h_II

source_name: delta-stuA - Keratin - 24 hours, replicate II


title: mESC_DNA_cell373


title: mESC_DNA_cell376


title: mESC_DNA_cell372


title: stuA_Glucose_48h_II

source_name: delta-stuA - Glucose - 48 hours, replicate II


title: stuA_Glucose_48h_III

source_name: delta-stuA - Glucose - 48 hours, replicate III


title: stuA_Glucose_48h_I

source_name: delta-stuA - Glucose - 48 hours, replicate I


title: mESC_DNA_cell369


title: stuA_Glucose_24h_I

source_name: delta-stuA - Glucose - 24 hours, replicate I


title: mESC_DNA_cell366


title: mESC_DNA_cell364


title: stuA_Glucose_24h_III

source_name: delta-stuA - Glucose - 24 hours, replicate III


title: mESC_DNA_cell363

source_name: cell line


title: mESC_DNA_cell360


title: mESC_DNA_cell368


title: stuA_Glucose_24h_II

source_name: delta-stuA - Glucose - 24 hours, replicate II


title: mESC_DNA_cell362


title: mESC_DNA_cell359


title: mESC_DNA_cell357


title: mESC_DNA_cell367


title: mESC_DNA_cell358


title: stuA_Glucose_96h_I

source_name: delta-stuA - Glucose - 96 hours, replicate I


title: mESC_DNA_cell365


title: mESC_DNA_cell353


title: mESC_DNA_cell356


title: mESC_DNA_cell350


title: mESC_DNA_cell349


title: mESC_DNA_cell355


title: mESC_DNA_cell348


title: mESC_DNA_cell345


title: mESC_DNA_cell347


title: mESC_DNA_cell352


title: mESC_DNA_cell351


title: mESC_DNA_cell343


title: mESC_DNA_cell354


title: mESC_DNA_cell344


title: KSL cells from STZ-DM

type: RNA

city: Otsu

first: Miwako

last: Katagi

address: seta tukinowa-cho

country: Japan

institute: Shiga university of medical science

hyb_protocol: 2.0 μg of Cy3-labelled cDNA was filled up to 50 μl containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: ckit(+), Sca1(+), Lineage(-) cells (KSL cells) from STZ-induced diabetic mice (n=3)

label_protocol: cDNA was amplified by OvationR Pico WTA System V2（NuGEN Technologies) from 8.3 ng total RNA according to the manufacturer's instructions. Amplified cDNA yield was checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared with Genomic DNA Enzymatic Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: total RNA were extracted by Rneasy Micro Plus kit (Qigen)

tag: tissue

value: bone marrow cells

tag: Sex

value: female

tag: disease state

value: STZ-DM mice


title: mESC_DNA_cell342


title: mESC_DNA_cell340


title: mESC_DNA_cell339


title: mESC_DNA_cell341


title: mESC_DNA_cell338


title: mESC_DNA_cell346


title: KSL cells from nonDM

source_name: ckit(+), Sca1(+), Lineage(-) cells (KSL cells) from nondiabetic mice (n=3)

value: nondiabetic mice


title: mESC_DNA_cell337


title: mESC_DNA_cell334


title: mESC_DNA_cell331


title: mESC_DNA_cell332


title: mESC_DNA_cell361


title: mESC_DNA_cell330


title: mESC_DNA_cell328


title: mESC_DNA_cell329


title: mESC_DNA_cell336


title: mESC_DNA_cell326


title: mESC_DNA_cell325


title: mESC_DNA_cell327


title: mESC_DNA_cell324


title: mESC_DNA_cell323


title: mESC_DNA_cell321


title: mESC_DNA_cell320


title: mESC_DNA_cell322


title: mESC_DNA_cell319


title: mESC_DNA_cell318


title: mESC_DNA_cell335


title: mESC_DNA_cell333


title: mESC_DNA_cell317


title: mESC_DNA_cell316


title: mESC_DNA_cell314


title: mESC_DNA_cell315


title: XL04 scRNA-seq

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

country: USA

institute: Moffitt Cancer Center

data_processing:
Sequence reads for each sample were aligned and processed using cellranger/3.1.0
Individual samples are aggregated to create a combined dataset using cellranger/3.10
Genome_build: GRCh38
Supplementary_files_format_and_content: h5. filtered gene expression counts for called cells.

organism: Homo sapiens

source_name: single cell suspension of tumor

extract_protocol:
Upon collection, samples were immediately placed on ice and transferred for processing. For CSF specimens, cells were quantified and directly loaded for library preparation. Samples from brain and skin metastases were digested using Miltenyi Tissue Dissociation Kit (Bergisch Gladbach, Germany) and enriched for live cells using FACS sorting prior to quantification and loading
Sample were quantified and viability was analyzed using the Nexcelom Cellometer K2. The samples were then loaded onto 10X Genomics Chromium Single Cell Controller (10X Genomics, CA) to prepare single-cell RNA-sequencing libraries. Around 50,000 to 1,000,000 mean sequencing reads per cell were generated on Illumina NextSeq 500 instrument using v2.5 flow cells

tag: site

value: Cutaneous


title: XL06 scRNA-seq


title: XL05 scRNA-seq


title: XL03 scRNA-seq


title: XL07 scRNA-seq


title: XL09 scRNA-seq


title: XL01 scRNA-seq


title: MB-19 scRNA-seq

value: Brain metastasis


title: mESC_DNA_cell311


title: XL02 scRNA-seq


title: mESC_DNA_cell313


title: mESC_DNA_cell308


title: mESC_DNA_cell310


title: mESC_DNA_cell309


title: mESC_DNA_cell312


title: MB-17 scRNA-seq


title: MB-16 scRNA-seq


title: MB-20 scRNA-seq


title: mESC_DNA_cell307


title: MB-15 scRNA-seq


title: MB-13 scRNA-seq


title: mESC_DNA_cell304


title: mESC_DNA_cell306


title: mESC_DNA_cell303


title: MB-10 scRNA-seq


title: mESC_DNA_cell302


title: mESC_DNA_cell305


title: MB-14 scRNA-seq


title: MB-12 scRNA-seq


title: MB-09 scRNA-seq


title: mESC_DNA_cell299


title: MB-05 scRNA-seq


title: mESC_DNA_cell301


title: MB-08 scRNA-seq


title: MB-18 scRNA-seq


title: mESC_DNA_cell296


title: MB-04 scRNA-seq


title: CSF-N scRNA-seq

value: Cerebrospinal fluid


title: CSF-30 scRNA-seq


title: mESC_DNA_cell294


title: CSF-K scRNA-seq


title: CSF-28 scRNA-seq


title: mESC_DNA_cell298


title: CSF-27 scRNA-seq


title: mESC_DNA_cell292


title: mESC_DNA_cell297


title: CSF-26 scRNA-seq


title: mESC_DNA_cell293


title: mESC_DNA_cell291


title: mESC_DNA_cell300


title: mESC_DNA_cell290


title: CSF-22 scRNA-seq


title: mESC_DNA_cell289


title: CSF-20 scRNA-seq


title: CSF-21 scRNA-seq


title: mESC_DNA_cell288


title: CSF-29 scRNA-seq


title: CSF-18 scRNA-seq


title: CSF-17 scRNA-seq


title: mESC_DNA_cell286


title: mESC_DNA_cell285


title: mESC_DNA_cell295


title: CSF-16 scRNA-seq


title: CSF-15 scRNA-seq


title: mESC_DNA_cell284


title: mESC_DNA_cell282


title: CSF-13 scRNA-seq


title: CSF-12 scRNA-seq


title: mESC_DNA_cell280


title: mESC_DNA_cell279


title: CSF-23 scRNA-seq


title: CSF-09 scRNA-seq


title: CSF-10 scRNA-seq


title: CSF-08 scRNA-seq


title: mESC_DNA_cell287


title: HASMC_mimCnt_hypoOxP_rep2

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

data_processing:
Reads were first trimmed for poly(A), Illumina adapter and low-quality bases using cutadapt [version 2.8].
nf-core RNA-Seq pipeline [version 1.4.2] was used to align the reads to the GRCh37/hg19 human genome with the STAR aligner and count the reads in transcripts according to Ensembl GRCh37 release 87 gene annotations.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs

source_name: human aortic smooth muscle cells

growth_protocol: HUVECs and HAECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich); HASMC were cultrured in Medium 231 (Cascade Biologics®) supplemented with Smooth Muscle Growth Supplement (SMGS). CD14+/Macrophages were cultured in Medium RPMI 1640, supplemented with 10 % FBS, 100μg/ml streptomycin,100 U/ml penicillin, and 2 mM glutamine, 1 % Na-pyruvate, 1 % NEAA and supplemented with rHu M-CSF (50ng/ml; ThermoFisher Scientific).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (QIAGEN).
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer´s instructions. For each sample, 250 ng of total RNA was used for library preparation, and the libraries were sequenced using a read length of 78 bases (single-end) on an Illumina NextSeq 500 sequencer.

treatment_protocol: Hypoxia was achieved in Ruskinn Invivo2 400 hypoxia workstation (1% O2 and 5% CO2). OxPAPC has been generated from 1-palmitoyl-2-archidonoyl-sn-glycero-3-phophocholine [PAPC, 10 mg/ml (Avanti Polar Lipids, Inc)]. PAPC was exposed to air for 40h, then dissolved in chloroform and stored at -70 °C. At the start of the oxPAPC stimulation, chloroform was evaporated with nitrogen gas and lipids were re-suspended in growth medium to achieve a concentration of 30 μg/ml.

tag: treatment

value: mimic miRNA-control transfected cells

tag: stimulus

value: control

tag: timepoint

value: 7 hours


title: HASMC_mimCnt_hypoOxP_rep3


title: HASMC_mimCnt_hypoOxP_rep1


title: mESC_DNA_cell277


title: mESC_DNA_cell275


title: mESC_DNA_cell273


title: mESC_DNA_cell272


title: mESC_DNA_cell271


title: mESC_DNA_cell276


title: mESC_DNA_cell274


title: mESC_DNA_cell278


title: HASMC_mim100_hypoOxP_rep3

value: mimic miR-100-5p transfected cells

value: Hypoxia+OxPAPC


title: mESC_DNA_cell283


title: HASMC_mim100_hypoOxP_rep1


title: HASMC_mim100_hypoOxP_rep2


title: HUVEC_mimCnt_hypoOxP_rep3

source_name: human umbilical vein endothelial cells


title: mESC_DNA_cell281


title: HUVEC_mimCnt_hypoOxP_rep2


title: mESC_DNA_cell268


title: mESC_DNA_cell266


title: CSF-11 scRNA-seq


title: HUVEC_mim100_hypoOxP_rep1


title: HUVEC_mim100_hypoOxP_rep3


title: HUVEC_mim100_hypoOxP_rep2


title: HUVEC_mimCnt_hypoOxP_rep1


title: mESC_DNA_cell269


title: mESC_DNA_cell265


title: mESC_DNA_cell264


title: INPUT_DMTI_REP2

city: Los Angeles

first: Emad

last: Darvishi

state: CA

address: 4650 Sunset Blvd

department: Cancer and Blood Disease Institute

institute: Children’s Hospital Los Angeles

data_processing:
ChIP-seq data processing was performed using Partek Flow (Partek Inc.).
All reads were filtered to retain only those with mean base quality score >20 and duplicate reads were removed.
Filtered reads were mapped to reference genome (Hg38) using STAR, allowing uniquely-mapped alignments only.
Peaks were called using MACS2.
Genome_build: Hg38
Supplementary_files_format_and_content: bigwig files

source_name: RMS cell line

growth_protocol: RH30 Cell line was grown in RPMI-1640 supplemented with 10%FBS and Pen/Strep in the presence or absence of 500nM Guadecitabine for 5 days.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Libraries were prepared from ChIP and Input DNAs using Illumina TruSeq ChIP Library Prep Kit (cat # IP-202-1012) and size selected by following the manufacturer’s instructions to obtain a 250-300 bp size-range of DNA fragments.

treatment_protocol: ChIP samples harvested after 1% formaldehyde fixation for 8 minutes, sonicated (Diagenode, Denville, NJ, USA), processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.

tag: cell line

value: Rhabdomyosarcoma

tag: antibody

tag: enrichment target

tag: target function


title: mESC_DNA_cell270

tag: cell type

value: cultured mouse embryonic stem cells

tag: strain


title: mESC_DNA_cell262

tag: chip antibody


title: mESC_DNA_cell260


title: INPUT_DMSO_REP1


title: H3K4me3_DMSO_REP2

value: H3K4me3 (Active Motif, cat #39159)

value: Active promoter mark


title: mESC_DNA_cell261


title: INPUT_DMSO_REP2


title: H3K4me3_DMTI_REP1


title: INPUT_DMTI_REP1


title: mESC_DNA_cell267


title: H3K4me3_DMTI_REP2


title: H3K4me3_DMSO_REP1


title: mESC_DNA_cell258


title: mESC_DNA_cell256


title: H3K4me1_DMTI_REP2

value: H3K4me1 (Active Motif, cat #39297)

value: Active enhancer mark


title: mESC_DNA_cell255


title: mESC_DNA_cell254


title: H3K4me1_DMSO_REP2


title: H3K27me3_DMTI_REP2

value: H3K27me3 (Active Motif, cat #39155)

value: Repressive mark


title: H3K4me1_DMSO_REP1


title: mESC_DNA_cell253


title: mESC_DNA_cell263


title: mESC_DNA_cell252


title: H3K27me3_DMTI_REP1


title: H3K27me3_DMSO_REP2


title: mESC_DNA_cell251


title: mESC_DNA_cell259


title: mESC_DNA_cell250


title: mESC_DNA_cell257


title: mESC_DNA_cell249


title: Sample 23: wtBRAF - GFP+ rep3

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore (options: "--quality 20 --length 25")
Trimmed reads were mapped to GRCh38 whole genome using STAR  v2.7.0d  (options: "--outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10")
Gene counts of mapped reads were obtained with the Subread package ("featureCounts" function with options: "-g gene_name -s 0")
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include counts of mapped reads for each Sample

source_name: Myeloid cells from bone marrow of NSG mice

growth_protocol: Cord blood-derived CD34+ cells were injected intravenously in sublethally irradiated 8-week old female NSG mice and harvested from the bone marrow 15 days after transplant

extract_protocol:
RNeasy Plus Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transduced ex-vivo with lentiviral vectors expressing BRAF-V600E and GFP, wtBRAF and GFP, GFP alone and mock control

value: Myeloid cells from bone marrow

tag: lentiviral vector

value: wtBRAF

tag: transduction status

value: yes


title: H3K27me3_DMSO_REP1


title: H3K4me1_DMTI_REP1


title: mESC_DNA_cell247


title: Sample 22: wtBRAF - GFP- rep3

value: no


title: Sample 21: BRAF_V600E – GFP+ rep5


title: Sample 19: GFP+ rep3

value: GFP


title: mESC_DNA_cell245


title: mESC_DNA_cell246


title: mESC_DNA_cell242


title: mESC_DNA_cell243


title: Sample 17: BRAF_V600E – GFP+ rep4


title: Sample 18: GFP- rep3


title: Sample 14: wtBRAF - GFP- rep2


title: mESC_DNA_cell240


title: mESC_DNA_cell241


title: Sample 16: BRAF_V600E – GFP- rep4


title: Sample 13: GFP- rep2


title: Sample 12: UT rep2

value: UT


title: mESC_DNA_cell239


title: mESC_DNA_cell238


title: mESC_DNA_cell237


title: Sample 10: BRAF_V600E – GFP- rep3


title: Sample 20: BRAF_V600E – GFP- rep5


title: mESC_DNA_cell248


title: mESC_DNA_cell244


title: Sample 9: BRAF_V600E – GFP+ rep2


title: mESC_DNA_cell235


title: mESC_DNA_cell234


title: mESC_DNA_cell236


title: mESC_DNA_cell233


title: Sample 7: GFP+ rep1


title: Sample 6: GFP- rep1


title: Sample 5: wtBRAF - GFP+ rep1


title: Sample 3: UT rep1


title: mESC_DNA_cell230


title: mESC_DNA_cell229


title: mESC_DNA_cell231


title: Sample 2: BRAF_V600E – GFP+ rep1


title: Sample 4: wtBRAF - GFP- rep1


title: Sample 11: BRAF_V600E – GFP+ rep3


title: mESC_DNA_cell228


title: mESC_DNA_cell227


title: mESC_DNA_cell232


title: mESC_DNA_cell223


title: mESC_DNA_cell225


title: mESC_DNA_cell226


title: mESC_DNA_cell221


title: Sample 8: BRAF_V600E – GFP- rep2


title: mESC_DNA_cell222


title: mESC_DNA_cell220


title: mESC_DNA_cell219


title: Sample 2 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ ANG KD

city: Dallas

first: Sara

middle: K

last: Hildebrand

state: TX

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

description:
FS47
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

data_processing:
Adapters were trimmed from fastq.gz files using cutadapt v1.9.dev4.
Trimmed fastq files were mapped to the mm10 genome with STAR v 2.7.3.
Full length reads and read fragments mapping to tRNA loci were quantified using bedtools2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: 20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx: Excel file containing tRNA read counts per sample.

source_name: T-cells

growth_protocol: T cells were isolated from mouse spleens with the indicated genotypes by using mouse Pan T Cell Isolation Kit II. T cells were stimulated in vitro with plate-bound anti-CD3 antibody (BD Biosciences, 5 μg/ml) plus anti-CD28 antibody (BD Biosciences, 5 μg/ml) in the culture medium (Advanced RPMI Medium 1640 with 2 mM L-Glutamine, 10% FCS/FBS and 100 U/mL penicillin/streptomycin).

extract_protocol:
mirVana miRNA Isolation Kit (Life Technologies) was used for RNA extraction.
cDNA library was prepared by using TruSeq Small RNA Library Prep kit (Illumina).

treatment_protocol: Resting T cells were treated with 1 mM H2O2 for 2 hours; activated T cells were stimulated with anti-CD3/CD28 for 24 hours in the presence or absence of 10 mM NAC.

value: T-cells

tag: group


title: Sample 1 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ control shRNA

description:
M7
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 3 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ ANG KD

description:
FS48
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 3 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ control shRNA

description:
M9
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 2 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ control shRNA

description:
M8
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell218


title: Sample 1 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ ANG KD

description:
FS46
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 3 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ RNH1

description:
FS45
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell216


title: Sample 2 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ RNH1

description:
FS44
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell217


title: mESC_DNA_cell215


title: mESC_DNA_cell214


title: mESC_DNA_cell213


title: Sample 1: BRAF_V600E – GFP- rep1

tag: tissue


title: mESC_DNA_cell224


title: Sample 1 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ RNH1

description:
FS43
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 2 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ T1

description:
FS41
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell212


title: Sample 3 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ T1

description:
FS42
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 1 Activated Slfn2f/f; CD4-Cre transfected with Slfn2+ T1

description:
FS40
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 3 Activated Slfn2f/f; CD4-Cre transfected with Slfn2

description:
FS39
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell211


title: Sample 1 Activated Slfn2f/f; CD4-Cre transfected with Slfn2

description:
FS37
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 2 Activated Slfn2f/f; CD4-Cre transfected with Slfn2

description:
FS38
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell208


title: mESC_DNA_cell210


title: mESC_DNA_cell209


title: Male RUNX1 fl/+ OCP treated with MCSF+RANKL for 3d [JL_M_WT_MCSF.RANKL_3d_rep3]

city: New York

first: Kyung-Hyun

last: Park-Min

email: ParkminK@HSS.EDU, parkmink@gmail.com

state: NY

address: 535 East 70th Street

institute: Hospital for Special Surgery

data_processing:
Basecalling was performed using Real Time Analysis (RTA) software version 2.11.3
Sequenced reads were preprocessed with fastq (with parameters fastp -q 15 -n 10 -l 20)
Adter preprocessing, sequenced reads were mapped to mm10 whole genome using STAR v2.7.3a (with parameters --outFilterMultimapNmax 1  --outSAMstrandField intronMotif --quantMode GeneCounts), using gencode mm10 annotation
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts, filtered gene counts (min expression cutoff of 5 CPM), log CPMs, and differential expression results from edgeR for every gene and every sample

source_name: Male RUNX1 fl/+ mouse OCP treated with MCSF+RANKL for 3 days

growth_protocol: OCPs were isolated by flow cytometry activated cell sorting (FACS). The osteoclast precursor population (CD45R− CD3− CD11b−/lo CD115+) was sorted from bone marrow cells as described (11). Sorted cells were cultured with M-CSF with or without RANKL (30ng/ml) for six days.

extract_protocol:
RNA from the cultures was extracted using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturers instructions.
Libraries were prepared following the manufacturer's procotols for the Illumina TruSeq Stranded mRNA library preparation kit (part # 20020595).  Purified mRNA was isolated from total RNA using oligo-dT beads then converted into double stranded cDNA.  Fragmented cDNA libraries were individually indexed and properly ligated molecules were PCR enriched to generate final library.

treatment_protocol: Cells were treated with MCSF and RANKL for 3 days

tag: Sex

value: Male

value: MCSF+RANKL

value: Osteoclast precursor (OCP) cells


title: Male RUNX1 fl/+ OCP treated with MCSF+RANKL for 3d [JL_M_WT_MCSF.RANKL_3d_rep2]


title: mESC_DNA_cell206

value: cultured mouse embryonic stem cells


title: mESC_DNA_cell205


title: Sample 3 Activated Slfn2f/f; CD4-Cre +NAC

description:
FS36
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

value: Activated Slfn2f/f; CD4-Cre+NAC


title: mESC_DNA_cell204


title: Sample 2 Activated Slfn2f/f; CD4-Cre +NAC

description:
FS35
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 1 Activated Slfn2f/f; CD4-Cre +NAC

description:
FS34
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Female RUNX1 fl/+ OCP treated with MCSF+RANKL for 3d [JL_F_WT_MCSF.RANKL_3d_rep3]

source_name: Female RUNX1 fl/+ mouse OCP treated with MCSF+RANKL for 3 days

value: Female


title: mESC_DNA_cell203


title: Sample 3 Activated Slfn2f/f +NAC

description:
FS33
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

value: Activated Slfn2f/f +NAC


title: mESC_DNA_cell200


title: Female RUNX1 fl/+ OCP treated with MCSF+RANKL for 3d [JL_F_WT_MCSF.RANKL_3d_rep2]


title: mESC_DNA_cell201


title: mESC_DNA_cell202


title: Female RUNX1 fl/+ OCP treated with MCSF+RANKL for 3d [JL_F_WT_MCSF.RANKL_3d_rep1]


title: mESC_DNA_cell198


title: Sample 1 Activated Slfn2f/f +NAC

description:
FS31
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell196


title: mESC_DNA_cell197


title: Male RUNX1 fl/+ OCP treated with MCSF for 3d [JL_M_WT_MCSF_3d_rep3]

source_name: Male RUNX1 fl/+ mouse OCP treated with MCSF for 3 days

value: MCSF


title: mESC_DNA_cell207


title: Sample 2 Activated Slfn2f/f +NAC

description:
FS32
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell194


title: mESC_DNA_cell199


title: Sample 3 Resting Slfn2f/f; CD4-Cre +H2O2

description:
FS30
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

value: Resting Slfn2f/f; CD4-Cre+H2O2


title: mESC_DNA_cell195


title: Male RUNX1 fl/+ OCP treated with MCSF+RANKL for 3d [JL_M_WT_MCSF.RANKL_3d_rep1]


title: mESC_DNA_cell193


title: mESC_DNA_cell192


title: Sample 2 Resting Slfn2f/f; CD4-Cre +H2O2

description:
FS29
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 1 Resting Slfn2f/f; CD4-Cre +H2O2

description:
FS28
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Male RUNX1 fl/+ OCP treated with MCSF for 3d [JL_M_WT_MCSF_3d_rep1]


title: mESC_DNA_cell190


title: Female RUNX1 fl/+ OCP treated with MCSF for 3d [JL_F_WT_MCSF_3d_rep3]

source_name: Female RUNX1 fl/+ mouse OCP treated with MCSF for 3 days


title: mESC_DNA_cell189


title: Sample 3 Resting Slfn2f/f +H2O2

description:
FS27
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

value: Resting Slfn2f/f +H2O2


title: mESC_DNA_cell188


title: Female RUNX1 fl/+ OCP treated with MCSF for 3d [JL_F_WT_MCSF_3d_rep2]


title: mESC_DNA_cell185


title: Sample 2 Resting Slfn2f/f +H2O2

description:
FS26
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 1 Resting Slfn2f/f +H2O2

description:
FS25
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell184


title: Female RUNX1 fl/+ OCP treated with MCSF for 3d [JL_F_WT_MCSF_3d_rep1]


title: mESC_DNA_cell181


title: mESC_DNA_cell180


title: mESC_DNA_cell191


title: Sample 1 Activated Slfn2f/f; CD4-Cre

description:
FS22
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

value: Activated Slfn2f/f; CD4-Cre


title: mESC_DNA_cell178


title: mESC_DNA_cell186


title: mESC_DNA_cell187


title: Male RUNX1 fl/+ OCP treated with MCSF for 3d [JL_M_WT_MCSF_3d_rep2]


title: mESC_DNA_cell183


title: FLAG-METTL5 IP 3

city: New Haven

first: Sigrid

last: Nachtergaele

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

data_processing:
Base calling was performed with Illumina bcl2fastq software.
Quality of sequenced reads was assessed with FastQC v0.11.5.
Adapter trimming and quality filtering was performed with Cutadapt.
Files were aligned to the human genome hg38 using hisat2 in splice-aware mode. Resulting bam files were ssorted with samtools version 1.7.
DESeq2 and R v4.0.3 were used to use bam files to analyze differential expression between input and CLIP samples.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file includes gene ID, baseMean, log2FoldChange, log2FoldChange standard error (SE), stat (Wald statistic), pvalue, and padj.

source_name: HeLa with overexpressed FLAG-METTL5_IP

growth_protocol: HeLa cells were transfected with pCS2-FLAG-METTL5 using Lipofectamine LTX.

extract_protocol:
Cell pellets were lysed, lysate was clarified, and then anti-FLAG immunoprecipitation was performed to isolate FLAG-METTL5. Samples were digested with Proteinase K and then RNA extracted using Trizol followed by choloroform extraction and isopropanol precipitation
Sequencing libraries were prepared using the TruSeq Stranded mRNA library preparation kit (Illumina), using 30-40 ng of RNA for each input and IP sample.

treatment_protocol: 24 hours after transfection, the cells were treated with 100μM 4-thiouridine overnight, and then crosslinked with 254nm light.

value: HeLa with overexpressed FLAG-METTL5

tag: condition

value: immunoprecipitate


title: Sample 3 Activated Slfn2f/f; CD4-Cre

description:
FS24
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 1 Activated Slfn2f/f

description:
FS19
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

value: Activated Slfn2f/f


title: mESC_DNA_cell182


title: FLAG-METTL5 IP 2


title: Sample 2 Activated Slfn2f/f; CD4-Cre

description:
FS23
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: FLAG-METTL5 IP 1


title: Input 3

source_name: HeLa with overexpressed FLAG-METTL5_input

value: input


title: mESC_DNA_cell177

source_name: cell line


title: mESC_DNA_cell179


title: mESC_DNA_cell176


title: Sample 3 Activated Slfn2f/f

description:
FS21
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 2 Activated Slfn2f/f

description:
FS20
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: mESC_DNA_cell174


title: mESC_DNA_cell170


title: mESC_DNA_cell175


title: Input 2


title: Sample 1 Resting Slfn2f/f; CD4-Cre

description:
FS16
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

value: Resting Slfn2f/f; CD4-Cre


title: shCtrl [s10]

city: Amsterdam

first: Cansu

last: Tekin

state: Noord-Holland

address: Meibergdreef 9, G2-132, P.O. Box 22660

country: Netherlands

institute: Amsterdam University Medical Center

data_processing:
Read quality was assessed with FastQC v0.11.5
Trimmomatic version 0.36 for Illumina adapter liagtion
The remaining high-quality reads were used to align against the Genome Reference Consortium human genome build 38 (GRCh38)
Mapping was performed by HISAT2 version 2.1.0
Count data were generated by means of the HTSeq method
Genome_build: analyzed using the DESeq2 method in R
Supplementary_files_format_and_content: normalized counts

source_name: pancreatic ductal adenocarcinoma

growth_protocol: PANC-1 cells were grown on adherent surface with 10%FCS supplemented DMEM. Passaged weekly.

extract_protocol:
Total RNA was isolated from shCtrl PANC-1 and shPAR1 PANC-1 cells using the NucleoSpin RNA miniprep kit (Macherey Nagel, Düren, Germany). Yield and purity (260 nm:280 nm) were determined by a Nanodrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA). The integrity (RNA integrity number (RIN) >9.0) of the resuspended total RNA was determined by using the RNA Nano Chip Kit on the Bioanalyzer 2100 and the 2100 Expert software (Agilent, Amstelveen, the Netherlands).
RNA-sequencing libraries were prepared from 250 ng total RNA using KAPA RNA HyperPrep with RiboErase (HMR) kits (Roche, Basel, Switzerland).

treatment_protocol: 5 groups received shPAR1 hairpin and another 5 groups received ctrl hairpin. Selection for transfection efficiency was performed with 2µg/ml puromycinn treatment. Knockdown efficiency was later on tested with qPCR for PAR1(F2R) gene.

tag: plasmid

value: shCtrl


title: Input 1

tag: treatment


title: mESC_DNA_cell164


title: shCtrl [s6]


title: mESC_DNA_cell172


title: mESC_DNA_cell171


title: mESC_DNA_cell173


title: shCtrl [s9]


title: mESC_DNA_cell169


title: mESC_DNA_cell168


title: shCtrl [s8]


title: Sample 2 Resting Slfn2f/f; CD4-Cre

description:
FS17
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

value: T-cells


title: Sample 2 Resting Slfn2f/f

description:
FS14
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx

value: Resting Slfn2f/f


title: mESC_DNA_cell167


title: mESC_DNA_cell162


title: shPAR1 [s5]


title: mESC_DNA_cell161


title: shCtrl [s7]


title: mESC_DNA_cell166


title: mESC_DNA_cell158


title: mESC_DNA_cell165


title: mESC_DNA_cell159


title: Sample 3 Resting Slfn2f/f

description:
FS15
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: shPAR1 [s3]


title: mESC_DNA_cell163


title: Sample 1 Resting Slfn2f/f

description:
FS13
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: Sample 3 Resting Slfn2f/f; CD4-Cre

description:
FS18
smRNA
20210224_Data_S1_T-cell_RNA-seq_Tao.xlsx


title: CXCR5neg_2: CXCR5neg rep2 RNA-seq

city: Birmingham

first: Csilla

last: Varnai

address: Haworth Building

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Raw paired-end reads were processed prior to alignment with Trimmomatic (Galaxy v0.38)
The processed reads were aligned to the mouse genome using Hisat2 (Galaxy v2.1.0) with default parameters
Gene expression levels were calculated with htseq-count (Galaxy version 0.9.1) using RefSeq gene models as the reference transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: Counts were generated using htseq-count (Galaxy version 0.9.1) using RefSeq gene models as the reference transcriptome

source_name: CD4 T cells

extract_protocol:
Spleens from infected mice were recovered 7 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi CXCR5lo 2W1S-specific CD4 T cells
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Libraries were constructed using the Smart-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT library prep kit and the Nextera XT index kit (Illumina)

treatment_protocol: Mice were infected with 107 actA-deficient L. monocytogenes expressing OVA-2W1S through intravenous injection in the tail vein.

value: Spleen

value: CD4 T cells


title: CXCR5neg_1: CXCR5neg rep1 RNA-seq


title: mESC_DNA_cell154

value: cultured mouse embryonic stem cells


title: mESC_DNA_cell160


title: shPAR1 [s2]


title: mESC_DNA_cell157


title: CXCR5neg_3: CXCR5neg rep3 RNA-seq


title: shPAR1 [s1]


title: mESC_DNA_cell155


title: mESC_DNA_cell156


title: mESC_DNA_cell152


title: CXCR5pos_3: CXCR5pos rep3 RNA-seq

extract_protocol:
Spleens from infected mice were recovered 7 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi CXCR5hi 2W1S-specific CD4 T cells
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Libraries were constructed using the Smart-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT library prep kit and the Nextera XT index kit (Illumina)


title: mESC_DNA_cell151


title: mESC_DNA_cell150


title: mESC_DNA_cell149


title: CXCR5pos_1: CXCR5pos rep1 RNA-seq


title: siYTHDF1_IFN_rep3

city: Chicago

first: Hideki

last: Terajima

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

data_processing:
FASTQ files were generated by the Sequencing Facility in the University of Chicago
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2 with parameters  -p 64 --dta --score-min L,0,-0.6
Transcripts Per Kilobase Million (TPM) were calculated using StringTie
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values

molecule: polyA RNA

source_name: A172 glioblastoma cell

extract_protocol:
RNA was harvested using Trizol reagent. poly (A)+ RNA was purified from the total RNA by using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). Truseq stranded mRNA sample preparation kit (Illumina) was used with 100 ng of poly (A)+ RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: A172 glioblastoma cell

tag: sirna

tag: agent

value: interferon


title: siYTHDF1_IFN_rep1


title: shPAR1 [s4]

tag: cell line


title: M28Ag_3: Memory Day 28 + Ag rep3 RNA-seq

extract_protocol:
Spleens from infected mice were recovered 3 hours after the peptide was administered, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi 2W1S-specific CD4 T cells
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Libraries were constructed using the Smart-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT library prep kit and the Nextera XT index kit (Illumina)

treatment_protocol: Mice were infected with 107 actA-deficient L. monocytogenes expressing OVA-2W1S through intravenous injection in the tail vein. At 28 dpi mice were injected iv with 100 ug 2W1S peptide and 2.5 ug LPS


title: siYTHDF1_IFN_rep2


title: CXCR5pos_2: CXCR5pos rep2 RNA-seq


title: mESC_DNA_cell146


title: mESC_DNA_cell148


title: siYTHDF1_mock_rep3

value: mock


title: mESC_DNA_cell145


title: mESC_DNA_cell147


title: mESC_DNA_cell143


title: mESC_DNA_cell144


title: siYTHDF1_mock_rep2


title: M28Ag_2: Memory Day 28 + Ag rep2 RNA-seq


title: mESC_DNA_cell142


title: M28Ag_1: Memory Day 28 + Ag rep1 RNA-seq


title: siYTHDF1_mock_rep1


title: mESC_DNA_cell140


title: siControl_IFN_rep3

value: control


title: M56_2: Memory Day 56 rep2 RNA-seq

extract_protocol:
Spleens from infected mice were recovered 56 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi 2W1S-specific CD4 T cells
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Libraries were constructed using the Smart-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT library prep kit and the Nextera XT index kit (Illumina)

treatment_protocol: Mice were infected with 107 actA-deficient L. monocytogenes expressing OVA-2W1S through intravenous injection in the tail vein


title: M56_3: Memory Day 56 rep3 RNA-seq


title: mESC_DNA_cell138


title: mESC_DNA_cell137


title: siControl_IFN_rep2


title: mESC_DNA_cell136


title: M56_1: Memory Day 56 rep1 RNA-seq


title: M28_3: Memory Day 28 rep3 RNA-seq

extract_protocol:
Spleens from infected mice were recovered 28 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi 2W1S-specific CD4 T cells
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Libraries were constructed using the Smart-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT library prep kit and the Nextera XT index kit (Illumina)


title: siControl_IFN_rep1


title: mESC_DNA_cell135

extract_protocol:
folloing CoTECH protocol
After PCR enrichment using Q5 polymerase, the 300-1,000 bp fragments were isolated using the 1.5% (w/v) agarose gel and purified once with 0.8 x AMpure XP beads


title: siControl_mock_rep3


title: mESC_DNA_cell131


title: M28_2: Memory Day 28 rep2 RNA-seq


title: mESC_DNA_cell134


title: mESC_DNA_cell132


title: siControl_mock_rep2


title: mESC_DNA_cell133


title: mESC_DNA_cell129


title: mESC_DNA_cell130


title: siControl_mock_rep1


title: M28_1: Memory Day 28 rep1 RNA-seq


title: N_3: Naïve rep3 RNA-seq

extract_protocol:
Spleens were recovered, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The naïve CD4 T cells were purfied as CD44lo CD62Lhi
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Libraries were constructed using the Smart-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT library prep kit and the Nextera XT index kit (Illumina)


title: mESC_DNA_cell127


title: mESC_DNA_cell126


title: mESC_DNA_cell128


title: mESC_DNA_cell139


title: mESC_DNA_cell124


title: N_2: Naïve rep2 RNA-seq


title: N_1: Naïve rep1 RNA-seq


title: PomcDsRed_E135

city: Ann Arbor

first: Malcolm

last: Low

state: MI

address: 1000 wall street

department: Molecular & Integrative Physiology

institute: University of Michigan

data_processing:
Cell ranger (v.2.2.0) was used to QC and generate filtered gene matrices for samples PomcDsRed_E115, PomcDsRed_E135, PomcDsRed_E155, and PomcDsRed_E175.
Cell ranger (v.3.0.0) was used to QC and generate filtered gene matrices for samples PomcDsRed_P5, and PomcDsRed_P12.
Seurat (v3.0) was used for downstream analysis. Cells with high mitochondrial contents, high hemoglobin subunit genes expression and low quality were removed.  Cells with Pomc UMI > 0 were filtered for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: txt file with the UMI count matrices of cells that meet the criteria

source_name: brain-hypothalamus

growth_protocol: Mice were housed in ventilated cages under controlled temperature and photoperiod (12-h light/12-h dark cycle, lights on from 6:00 AM to 6:00 PM), with free access to tap water and laboratory chow (5L0D, LabDiet).

extract_protocol:
Embryonic hypothalami were dissected at E11.5, E13.5, E15.5, and E17.5. Postnatal hypothalami were isolated from pups at postnatal day 6 (P6) and P12. In each dissection, hypothalami from at least 6 pups were pooled together to acquire enough cells for fluorescence-activated cell sorting (FACS). Pooled tissue samples were digested in papain solution supplemented with DNAse for 20 mins (E11.5 and E13.5), 30 mins (E15.5), 40 mins (E17.5) or 1hr (P6, and P12) with gentle agitation. After incubation, digested tissue were centrifuged at 300 x g for 5min at 4°C and resuspended with EBSS medium. Tissue were further triturated with series of fire-polished pasteur pipets, centrifuged at 300 x g for 5min, resuspended with PBS and filtered with 20μm strainer. The isolated cells were underwent FACS for red fluorescent protein.
The Chromium™ Single Cell 3’ v2 Protocol was applied to samples PomcDsRed_E115, PomcDsRed_E135, PomcDsRed_E155, and PomcDsRed_E175. The Chromium™ Single Cell 3’ v3 Protocol was applied to samples PomcDsRed_P5, and PomcDsRed_P12. Both are standard library construction protocols from 10x Genomics.

treatment_protocol: Adult male POMCDsRed/+ mice were bred with female POMCDsRed/+ mice and the day of copulation plug detection was counted as embryonic day 0.5 (E0.5).

value: brain-hypothalamus

value: FACS sorted Pomc-DsRed cells

tag: developmental stage


title: PomcDsRed_E155


title: mESC_DNA_cell122


title: PomcDsRed_E115


title: mESC_DNA_cell121


title: CXCR5neg_1: Memory Day 7 CXCR5neg rep1 ATAC-seq

data_processing:
Raw sequencing reads were aligned to the genome using Bowtie2 (Galaxy Version 2.3.2.2)
bedGraph files were generated using MACS2callpeak (Galaxy version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using MACS2callpeak (Galaxy version 2.1.1)

extract_protocol:
Spleens from infected mice were recovered 7 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi CXCR5lo 2W1S-specific CD4 T cells
Cells were resuspended in 50 ul ATAC transposition reaction mix containing 25 ul 2x Tagment DNA Buffer (Illumina), 2.5 ul Tn5 transposase (Illumina), 0.5 µl 1% Digitonin (Promega) and incubated for 20-30 minute at 37C with gentle agitation. DNA was purified using the MinElute Reaction Clean up kit (Qiagen). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.


title: Sca1MACS Roxa 21 Tage 4

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Basecalling and demultiplexing was done using bcl2fastq verion 2.17.1.14
STAR version 2.5.2a was used to align the reads to the mm10 genome
featureCounts version 1.5.0-p1 was used to quantify reads for genes in mm10 version 84
Genome_build: mm10 gene version 84
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: Primary Cell from Mouse Kidney

growth_protocol: tissue culture (msc medium, FCS, antibiotics, 5% CO2, 20% O2, 37°C)

extract_protocol:
Trizol
non stranded mRNA Seq TruSeq standard according to the illimina protocol

treatment_protocol: 7 days roxadustat injection (33mg/kg, i.p.), digestion of kidney tissue and magnetic sorting for Sca-1

value: mesenchymal stem cell-like

value: kidney

tag: cell marker

tag: time (day)

value: roxadustat


title: mESC_DNA_cell120

tag: cell type


title: CXCR5pos_2: Memory Day 7 CXCR5pos rep2 ATAC-seq

extract_protocol:
Spleens from infected mice were recovered 7 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi CXCR5hi 2W1S-specific CD4 T cells
Cells were resuspended in 50 ul ATAC transposition reaction mix containing 25 ul 2x Tagment DNA Buffer (Illumina), 2.5 ul Tn5 transposase (Illumina), 0.5 µl 1% Digitonin (Promega) and incubated for 20-30 minute at 37C with gentle agitation. DNA was purified using the MinElute Reaction Clean up kit (Qiagen). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.

tag: strain


title: Sca1MACS Roxa 21 Tage 3


title: PomcDsRed_E175


title: mESC_DNA_cell117

tag: chip antibody


title: mESC_DNA_cell116


title: mESC_DNA_cell115


title: mESC_DNA_cell125


title: Sca1MACS Roxa 21 Tage 2


title: M56Ag_2: Memory Day 56 + Antigen rep2 ATAC-seq

extract_protocol:
Spleens from infected mice were recovered 3 hours after the peptide was administered, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi 2W1S-specific CD4 T cells
Cells were resuspended in 50 ul ATAC transposition reaction mix containing 25 ul 2x Tagment DNA Buffer (Illumina), 2.5 ul Tn5 transposase (Illumina), 0.5 µl 1% Digitonin (Promega) and incubated for 20-30 minute at 37C with gentle agitation. DNA was purified using the MinElute Reaction Clean up kit (Qiagen). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.

treatment_protocol: Mice were infected with 107 actA-deficient L. monocytogenes expressing OVA-2W1S through intravenous injection in the tail vein. At 56 dpi mice were injected iv with 100 ug 2W1S peptide and 2.5 ug LPS


title: Sca1MACS Roxa 21 Tage 1


title: mESC_DNA_cell114


title: mESC_DNA_cell113


title: CXCR5neg_2: Memory Day 7 CXCR5neg rep2 ATAC-seq


title: mESC_DNA_cell123


title: mESC_DNA_cell112


title: mESC_DNA_cell153


title: Sca1MACS Roxa 7 Tage 4


title: Sca1MACS Roxa 7 Tage 3


title: mESC_DNA_cell118


title: M28Ag_2: Memory Day 28 + Antigen rep2 ATAC-seq


title: mESC_DNA_cell109


title: mESC_DNA_cell119


title: CXCR5pos_1: Memory Day 7 CXCR5pos rep1 ATAC-seq


title: mESC_DNA_cell107


title: mESC_DNA_cell111


title: M56_2: Memory Day 56 rep2 ATAC-seq

extract_protocol:
Spleens from infected mice were recovered 56 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi 2W1S-specific CD4 T cells
Cells were resuspended in 50 ul ATAC transposition reaction mix containing 25 ul 2x Tagment DNA Buffer (Illumina), 2.5 ul Tn5 transposase (Illumina), 0.5 µl 1% Digitonin (Promega) and incubated for 20-30 minute at 37C with gentle agitation. DNA was purified using the MinElute Reaction Clean up kit (Qiagen). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.


title: mESC_DNA_cell110


title: mESC_DNA_cell108


title: mESC_DNA_cell106


title: M56_1: Memory Day 56 rep1 ATAC-seq


title: M28Ag_1: Memory Day 28 + Antigen rep1 ATAC-seq


title: Sca1MACS Roxa 0 Tage 2


title: mESC_DNA_cell105


title: mESC_DNA_cell102


title: M56Ag_1: Memory Day 56 + Antigen rep1 ATAC-seq


title: mESC_DNA_cell103


title: mESC_DNA_cell104


title: M28_2: Memory Day 28 rep2 ATAC-seq

extract_protocol:
Spleens from infected mice were recovered 28 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi 2W1S-specific CD4 T cells
Cells were resuspended in 50 ul ATAC transposition reaction mix containing 25 ul 2x Tagment DNA Buffer (Illumina), 2.5 ul Tn5 transposase (Illumina), 0.5 µl 1% Digitonin (Promega) and incubated for 20-30 minute at 37C with gentle agitation. DNA was purified using the MinElute Reaction Clean up kit (Qiagen). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.


title: mESC_DNA_cell141


title: mESC_DNA_cell101


title: mESC_DNA_cell100


title: mESC_DNA_cell99


title: M28_1: Memory Day 28 rep1 ATAC-seq


title: Sca1MACS Control 21Tage 4


title: Sca1MACS Control 21Tage 3


title: mESC_DNA_cell98


title: Sca1MACS Roxa 0 Tage 1


title: Sca1MACS Roxa 7 Tage 2


title: Sca1MACS Roxa 7 Tage 1


title: M7_1: Memory Day 7 rep1 ATAC-seq

extract_protocol:
Spleens from infected mice were recovered 7 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi 2W1S-specific CD4 T cells
Cells were resuspended in 50 ul ATAC transposition reaction mix containing 25 ul 2x Tagment DNA Buffer (Illumina), 2.5 ul Tn5 transposase (Illumina), 0.5 µl 1% Digitonin (Promega) and incubated for 20-30 minute at 37C with gentle agitation. DNA was purified using the MinElute Reaction Clean up kit (Qiagen). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.


title: mESC_DNA_cell96


title: mESC_DNA_cell95


title: N_2: Naïve rep2 ATAC-seq

extract_protocol:
Spleens were recovered, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The naïve CD4 T cells were purfied as CD44lo CD62Lhi
Cells were resuspended in 50 ul ATAC transposition reaction mix containing 25 ul 2x Tagment DNA Buffer (Illumina), 2.5 ul Tn5 transposase (Illumina), 0.5 µl 1% Digitonin (Promega) and incubated for 20-30 minute at 37C with gentle agitation. DNA was purified using the MinElute Reaction Clean up kit (Qiagen). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.


title: Sca1MACS Control 21Tage 1


title: mESC_DNA_cell93


title: mESC_DNA_cell94


title: N_1: Naïve rep1 ATAC-seq


title: mESC_DNA_cell91


title: mESC_DNA_cell90


title: Sca1MACS Control 7 Tage 4


title: Sca1MACS Control 7 Tage 3


title: mESC_DNA_cell92


title: mESC_DNA_cell89


title: mESC_DNA_cell88


title: Sca1MACS Control 7 Tage 2


title: mESC_DNA_cell87


title: M7_2: Memory Day 7 rep2 ATAC-seq


title: mESC_DNA_cell86


title: Sca1MACS Control 7 Tage 1


title: mESC_DNA_cell97


title: pIC rep3

city: Taipei

first: Yi-Ping

last: Hsueh

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
PIC_vs_ctrl_7_sample_CLC.xlsx
PIC_vs_ctrl_7_sample_edgeR_qlf.xlsx
WT3-PIC_S9_R1_001.fastq.gz

data_processing:
Illumina bcl2fastq2.17 was used to generate fastqs from bcl files
Sequenced reads were trimmed for adaptor sequence,low quality sequences, then mapped to GRCm38.p6 whole genome using CLC Genomics Workbench with parameters: mismatches=2, minimum fraction length =0.9, minimum fraction similarity=0.9, and maximum hits per read = 5.
Generalized Linear Model (GLM) and Wald Test were then used to analyzed differential expression of genes and statistical significance.
Hisat2 for raw sequence trimming and mapping, FeatureCount for read counts,
classic EdgeR and Fisher’s exact test for differential expression and statistical analysis.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Excel files include Raw, TPM, RPKM , fold change and p values for each Sample .

source_name: Bone-marrow-derived macrophage culture

growth_protocol: bone marrow cells were collected from tibiasand femurs of adult WT mice. The cells were then cultured in DMEM containing 10% FBS, Penicillin and Streptomycin, and 50uM B-mercaptoethanol plus 20% conditioned medium of L929 cells for 6 days

extract_protocol:
Total RNA was  using Trizol reagent according to the manufacturer’s instructions (Invitrogen).
2 ug of total RNA was used for RNA-seq library preparation using the TruSeq Stranded mRNA LT set A/B Sample Prep Kit.

treatment_protocol: Poly(I:C) (10ug/ml,InvivoGen), CL075 (4uM,InvivoGen) treat for 6hr

value: poly IC


title: pIC rep5

description:
PIC_vs_ctrl_9_sample_CLC.xlsx
PIC_vs_ctrl_9_sample_edgeR_qlf.xlsx
WT5-PIC_S15_R1_001.fastq.gz


title: mESC_DNA_cell85

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.


title: Sca1MACS Control 21Tage 2


title: mESC_DNA_cell84


title: pIC rep2

description:
PIC_vs_ctrl_6_sample_CLC.xlsx
PIC_vs_ctrl_6_sample_edgeR_qlf.xlsx
WT2-PIC_S6_R1_001.fastq.gz


title: Sca1MACS Control 0 Tage 2


title: pIC rep1

description:
PIC_vs_ctrl_5_sample_CLC.xlsx
PIC_vs_ctrl_5_sample_edgeR_qlf.xlsx
WT1-PIC_S3_R1_001.fastq.gz


title: mESC_DNA_cell83


title: mESC_DNA_cell82


title: mESC_DNA_cell81


title: CL075 rep5

description:
CL075_vs_ctrl_9_sample_CLC.xlsx
CL075_vs_ctrl_9_sample_edgeR_qlf.xlsx
WT5-CL075_S14_R1_001.fastq.gz


title: mESC_DNA_cell80


title: pIC rep4

description:
PIC_vs_ctrl_8_sample_CLC.xlsx
PIC_vs_ctrl_8_sample_edgeR_qlf.xlsx
WT4-PIC_S12_R1_001.fastq.gz


title: pir1_tm3198_10day

city: Riverside

first: Weifeng

last: Gu

state: California

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

data_processing:
The samples are debarcoded using the 8 nt barcodes
The 3' AGATCGGAA and beyond are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 2 mismatches are considered
Genome_build: C. elegans WS215
Supplementary_files_format_and_content: tabbed txt file containing sequence and read number for the analysis

organism: Caenorhabditis elegans

source_name: small RNA in 10-day pir-1 mutant

growth_protocol: Worms were grown on NGM or Ivermectin-containing NGM plates with OP50 at 20 °C.

extract_protocol:
RNAs were extracted with TRIzol
RNAs were linked with Truseq LT/V1/V2 linkers using the standard 5' and 3' ligation methods. Amplicons with ~20 nt inserts were selected for sequencing. The samples were multiplexed with 8 nt indexes in the 3' linker. Please refer to Li L et al. RNA. 2020 Feb;26(2):218-227.

treatment_protocol: For cloning ppp-RNAs, the sample is treated with 0.5 μM PIR-1 at 20 °C for 2 hours and for cloning only p-RNAs, no PIR-1 is required.

tag: genotype

value: whole worm

tag: rna fraction

value: All RNA


title: CL075 rep4

description:
CL075_vs_ctrl_8_sample_CLC.xlsx
CL075_vs_ctrl_8_sample_edgeR_qlf.xlsx
WT4-CL075_S11_R1_001.fastq.gz


title: mESC_DNA_cell78

city: Beijing

first: Haiqing

last: Xiong

institute: Peking University

treatment_protocol: The mESCs were dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for CoTECH


title: mESC_DNA_cell76


title: mESC_DNA_cell77


title: CL075 rep3

description:
CL075_vs_ctrl_7_sample_CLC.xlsx
CL075_vs_ctrl_7_sample_edgeR_qlf.xlsx
WT3-CL075_S8_R1_001.fastq.gz


title: CL075 rep2

description:
CL075_vs_ctrl_6_sample_CLC.xlsx
CL075_vs_ctrl_6_sample_edgeR_qlf.xlsx
WT2-CL075_S5_R1_001.fastq.gz


title: pir1_tm3198_7day_rep2

source_name: small RNA in 7-day pir-1 mutant


title: pir1_tm3198_7day_rep3


title: mESC_DNA_cell75


title: pir1_tm3198_7day_rep1


title: mESC_DNA_cell74


title: mESC_DNA_cell73


title: CL075 rep1

description:
CL075_vs_ctrl_5_sample_CLC.xlsx
CL075_vs_ctrl_5_sample_edgeR_qlf.xlsx
WT1-CL075_S2_R1_001.fastq.gz


title: mESC_DNA_cell72


title: mESC_DNA_cell71


title: mESC_DNA_cell70


title: mESC_DNA_cell69


title: Ctrl rep5

value: ctrl


title: Sca1MACS Control 0 Tage 1


title: mESC_DNA_cell68


title: mESC_DNA_cell67


title: Ctrl rep4


title: N2_nuclear_extract

source_name: nuclear RNA

value: Nuclear RNA


title: N2_input

source_name: total RNA used for isolating nuclear RNA


title: Ctrl rep3


title: Ctrl rep2


title: mESC_DNA_cell79


title: mESC_DNA_cell66


title: mESC_DNA_cell65


title: The_avr3x_L4-YA_rep2

source_name: small RNA in avr3x


title: mESC_DNA_cell64


title: The_avr3x_L4-YA_rep1


title: pir1_tm3198_3day

source_name: small RNA in 3-day pir-1 mutant


title: mESC_DNA_cell60


title: WT3

city: BOSTON

first: Rajat

middle: M

last: Gupta

state: MA

address: 77 Avenue Louis Pasteur

institute: THE BROAD INSTITUTE INC

description: 10X Genomics v2

data_processing:
Cellranger 2.1
Supplementary_files_format_and_content: counts

source_name: Aorta

growth_protocol: Whole mouse aortas were harvested from 12-week old female C57/BL6 mice on either chow diet or 8 weeks of Western Diet (Research Diets). Four mice were included in each group, with 2 dissociated aortas from each condition sequenced at low-depth (17,000 reads/cell) and 2 samples sequenced at high-depth (145,000 reads/cell). The high-depth samples from the chow diet (n=2) and Western diet (n=2) were used for subsequent analyses. All mouse protocols were approved by the Broad Institute IACUC and all protocols were in accordance with institutional guidelines. The aorta was dissected from the root (distal to the aortic valve) to the femoral artery bifurcation. The isolated aorta included aortic arch, ascending, descending, thoracic, and abdominal portions. Perivascular fat was dissected from the vascular tissue prior to dissociation.

extract_protocol:
Preparation of a single cell suspension of aortic cells was performed using a previously described enzymatic digestion protocol9. Briefly, the isolated whole aorta was finely cut and incubated in 1X Aortic Dissociation Enzyme Solution (125 U/mL collagenase type XI, 60 U/mL hyaluronidase type 1-s, 60 U/mL DNase I, and 450 U/mL collagenase type I) for 1 hour at 37°C. The cell suspension was strained through a 30 μm filter, treated with ACK lysis buffer for 5 minutes at room temperature, and washed twice with PBS. The cells were resuspended in 0.4% BSA-PBS at a final concentration of 8×105 cells/mL.
Single cells were processed through the GemCode Single Cell Platform using GemCode Gel Bead, Chip and Library Kits (10X Genomics) as per the manufacturer’s protocol. In brief, single cells were sorted into 0.4% BSA–PBS solution. 9,000 cells were added to each channel. The cells were then partitioned into Gel Beads in emulsion in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing and 5′ adaptor and sample index attachment. Libraries were sequenced on an Illumina Hiseq 2500.
10x genomics single cell v2

tag: age

value: 12-week old

tag: gender

value: female


title: Ctrl rep1


title: mESC_DNA_cell62

address: 5 Yiheyuan Road,  Haidian District

value: cultured mouse embryonic stem cells


title: mESC_DNA_cell58


title: GM12878_input

city: Tel Aviv

first: Gil

last: Ast

state: Israel

address: Haim Levanon 55

country: Israel

institute: Tel Aviv University

data_processing:
Illumina HiSeq 2500 System was used for base-calling. The sequenced reads are separated into consecutively numbered files that together can be treated as one continuous file. The names of the raw data files are in the following format:  <sample name>_<index>_<lane>_<R1 >_<number of file>. Index – The index that was used for multiplexing. Lane – The lane on which the read was sequenced. R1 / R2-  All files are marked with R1 or R2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 v2.1.0 with default parameters
Duplicate alignments were removed using samtools-1.10 markdup with defult parameters.
Lamin A/C broad enrichment domain peaks were identified using EDD (version 1.1.19). For GM12878 we specified 8-kb bin size and a gap penalty of 3 and for K562 we used 7-kb bin size and a gap penalty of 4.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: peak text files

extract_protocol:
Approximately 1×107 GM12878 or K562 cells per sample were harvested, resuspended at a concentration of 1×106 per ml medium and crosslinked in 1% formaldehyde for 10 minutes at 37 ºC with mixing. The crosslinking reaction was quenched by the addition glycine at a final concentration of 125 mM and incubation for 5 minutes at room temperature. Cells were washed twice with PBS, centrifuged, and pellets were frozen at -80 ºC. Pellets were thawed on ice for at least 15 minutes, resuspended in ice-cold Hi-C Lysis Buffer (0.2% NP-40, 10 mM NaCl, 10 mM Tris-HCl, pH 8, complete protease inhibitor cocktail (Roche)), and incubated on ice for at least 15 minutes. Nuclei were centrifuged, the supernatant was discarded, and nuclei were washed with ice-cold Hi-C Lysis Buffer and centrifuged. Nuclei pellets were re-suspended in RIPA FA buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, complete protease inhibitor cocktail (Roche)) and incubated for 10 minutes. Samples were sonicated with a Vibra-Cell VCX600 (Sonics & Materials) for 75 minutes total (2.2 seconds ON, 9.9 seconds OFF, 40% amplitude) to obtain DNA fragments with lengths averaging 150-350 nt (maximum 500 nt). After centrifugation at 20,000 g for 8 minutes, the supernatant was diluted 1:10 with Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, complete protease inhibitor cocktail (Roche)) and aliquoted. Chromatin from an equivalent of 10×106 cells was used per immunoprecipitation reaction. For Lamin A/C immunoprecipitation, 104 µl of protein-A and 104 µl of protein-G Dynabeads (Invitrogen) were washed twice with RIPA buffer (0.1% deoxycholate, 0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, pH 8.1, 1 mM EDTA, 140 mM NaCl), resuspended in ChIP Blocking Buffer (PBS, 0.5% TWEEN, 0.5% BSA), and incubated with 50 µg of anti-Lamin A/C antibody (Santa-Cruz Biotechnology, sc-7292x) for at least 2 hours at 4 ºC with rotation. Sonicated chromatin was added to the conjugated beads, and samples were incubated for 16 hours at 4 ºC. The beads were washed six times with RIPA buffer, twice with RIPA-high salt buffer (0.1% deoxycholate, 0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, pH 8.1, 1 mM EDTA, 360 mM NaCl), twice with LiCl wash buffer (250 mM LiCl, 0.5% NP-40 (Sigma IGEPAL), 0.5% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1) and twice with TE buffer (10 mM Tris-HCl, pH 8.1, 1 mM EDTA). DNA was eluted from the beads with Elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris-HCl, pH 8.1) in a 30-minute incubation in a thermo-shaker at 65 ºC. From this stage on, input tubes were processed similarly to elution tubes. To the input and elution samples was added 1 µl of 10 mg/ml RNase A (Sigma), and samples were incubated for 30 minutes at 37 ºC. Next, 1.5 µl Proteinase K (NEB) was added, and samples were incubated for 16 h at 65 ºC. DNA was purified using phenol:chloroform:isoamyl extraction. DNA was eluted in 30 µl Elution buffer (10mM Tris-HCl pH 8.5). Concentrations were measured using a Qubit assay (ThermoFisher).
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: B-Lymphocyte


title: GM12878_Lamin2

value: Anti-Lamin A/C antibody (Santa-Cruz Biotechnology, sc-7292x)


title: WT1

description: 10X Genomics v2


title: mESC_DNA_cell57


title: K562_input

value: human blood (chronic myelogenous leukemia)


title: mESC_DNA_cell56


title: mESC_DNA_cell55


title: GM12878_Lamin1


title: mESC_DNA_cell59


title: mESC_DNA_cell54


title: mESC_DNA_cell63


title: mESC_DNA_cell61


title: mESC_DNA_cell51


title: mESC_DNA_cell53


title: K562_Lamin2


title: K562_Lamin1


title: mESC_DNA_cell52


title: mESC_DNA_cell49


title: MX1357-C6RGTANXX-4-TATCGT

city: Vancouver

first: Wan

middle: L

last: Lam

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

data_processing:
Raw fastq files were processed by the miRMaster platform (March 2018, miRBase v21), using its default settings.
Predicted novel miRNA precursor sequences were excluded if not classified by miRMaster as ‘novel’. Predicted mature novel miRNA sequences were also excluded if they were present in miRBase v22.
For kno-sncRNA files: for mature sncRNAs derived from multiple precursor sequences, only the most highly-expressed precursor-mature pair is reported
For nov-miRNA files: for putative mature miRNA sequences that could be derived from multiple putative miRNA precursor sequences, only the precursor-mature pair with the highest probability (as assigned by miRMaster) is reported.
Genome_build: hg38
Supplementary_files_format_and_content: isomiR files: precursor (name of miRNA precursor), miRNA (name of mature miRNA from which isomiR is derived), iso_type (description of modifications to mature miRNA sequence [Fehlmann et al., 2017, PMID: 28911107]), RPM (expression of isomiR, normalized to reads-per-million); nov-miR files: chromosome, start (nucleotide position of the start of the putative miRNA precursor), stop (nucleotide position of the end of the putative miRNA precursor), probability (probability of the precursor being a true miRNA precursor), novomirank_score (novoMiRank score for the precursor [Backes et al., 2016, PMID: 26635395]), sequence (sequence of the putative mature miRNA), RPM (expression of the putative mature miRNA, normalized to reads-per-million); kno-sncRNA files: Reference (for miRNAs, piRNAs, and tRNAs: the name of the sncRNA sequence. For snRNAs and snoRNAs: Ensembl transcript ID of the sncRNA sequence), Subtype (type of sncRNA; one of miRNA, piRNA, snRNA, snoRNA, or tRNA), RPM (expression of sncRNA, normalized to reads-per-million); supplementary file: Reference (for known sncRNAs, identical to the sncRNA processed data files; for novel miRNAs, has the format chromosome|start|stop|sequence; for isomiRs, has the format precursor|miRNA|iso_type), Subtype (one of miRNA, piRNA, snRNA, snoRNA, tRNA, isomiR, nov-miR), subsequent columns denote reads-per-million expression in different samples.

source_name: Chorionic villi

extract_protocol:
Thirty milligram samples were taken from the chorionic villi on the fetal-facing side of the placenta. TRIzol was used to extract total RNA.
Sequencing was performed using the standard ribodepleted strand-specific RNA sequencing protocol of Canada’s Michael Smith Genome Sciences Centre in Vancouver, in line with The Cancer Genome Atlas miRNA sequencing protocol (Chu et al., 2015, PMID: 26271990). Briefly, after adaptor ligation, amplification was achieved through 15 cycles of PCR (98˚C for 15s, 62˚C for 30s, 72˚C for 15s), concluded by 5 minutes at 72˚C. Gel extraction from a 3% MetaPhor Agarose gel was used to select for RNAs shorter than 200 nucleotides, and hybridization was used to deplete the rRNA fraction. RNA quality was confirmed on an Agilent Bioanalyzer 2100 (Agilent, USA). Sequencing was performed on an Illumina HiSeq 2500.

value: Term

tag: neural tube defect

tag: tissue

value: placenta (chorionic villi)


title: MX1357-C6RGTANXX-4-GTAGCC


title: mESC_DNA_cell50


title: mESC_DNA_cell47


title: mESC_DNA_cell48


title: mESC_DNA_cell46


title: mESC_DNA_cell45


title: MX1357-C6RGTANXX-4-GCCTAA


title: Kidney, control-miRNA 1

city: Saitama

first: Akinori

last: Aomatsu

address: 1-847 Amanuma-cho, Omiya-ku

department: Nephrology

institute: Saitama Medical Center, Jichi Medical University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Ver.2.0 Microarray (Agilent, G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 074809_D_F_20171030). Quantile normalization was performed by the GeneSpring GX software using Agilent.SingleColor.74809 technology. Data were baseline shifted to the median of all samples.

source_name: IRI-AKI+control-miRNA-PEI-NPs model

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The kidney samples weighing 30 mg were homogenized using a glass homogenizer. Total RNA, including messenger RNA (mRNA), was purified from the kidney samples using an RNeasy Mini Kit (Qiagen).

tag: disease state

value: IRI-AKI+control-miRNA-PEI-NPs model


title: mESC_DNA_cell44

extract_protocol:
folloing CoTECH protocol
After PCR enrichment using Q5 polymerase, the 300-1,000 bp fragments were isolated using the 1.5% (w/v) agarose gel and purified once with 0.8 x AMpure XP beads


title: mESC_DNA_cell42


title: Kidney, IRI 34

source_name: IRI-AKI model

value: IRI-AKI model


title: mESC_DNA_cell40

source_name: cell line


title: Kidney, 5100 mimic 7

source_name: IRI-AKI+miRNA-5100-mimic-PEI-NPs model

value: kidney

value: IRI-AKI+miRNA-5100-mimic-PEI-NPs model


title: Kidney, 5100 mimic 6


title: mESC_DNA_cell39


title: mESC_DNA_cell37


title: mESC_DNA_cell41


title: Kidney, IRI 30


title: mESC_DNA_cell38


title: MX1357-C6RGTANXX-4-CATGGG