title: R178* (2)

first: Marc

last: Ostermeier

address: 3400 N. Charles St.

department: Chemical & Department of Chemical & Biomolecular Engineering

institute: Johns Hopkins University

description: NEB 5-alpha F'Iq Competent E. coli

data_processing:
Reads were analyzed for per base sequence quality using FastQC v0.11.8.
We indexed the genome of NEB 5-alpha cells (NCBI Reference Sequence: NZ_CP017100.1), aligned paired end reads, and mapped the reads to the transcriptome using STAR version 2.7.0c
Mapped reads were quantified and tabulated using featureCounts from the Subread package v1.6.4.
Normalized counts per million for the two biological replicates of RNA-Seq were tabulated with edgeR version 3.8.
Calculations for the fold-difference in gene expression and statistical analysis were performed in Microsoft Excel 2016.
Genome_build: Escherichia coli strain K-12 NEB 5-alpha
Supplementary_files_format_and_content: The processed data file consists of tabs for raw counts of mapped reads, fold-difference in gene expression, variance in fold-difference, and p-values. Each tab is organized with the sample name listed in columns and genes listed in rows.

organism: Escherichia coli

source_name: pSkunk1-R178* nonsense mutation, 1 mM IPTG, biological replica 2

growth_protocol: Frozen stocks of NEB 5-alpha LacIq cells containing single-codon substitutions of TEM-1 beta-lactamase were diluted into 10 ml media containing 50 μg/ml spectinomycin and 2% w/v glucose and incubated overnight at 37 °C. The overnight cultures were diluted to an OD of 0.020 in 100 ml media containing 50 μg/ml spectinomycin and 2% w/v glucose, and incubated at 37 °C with shaking until the OD was about 0.5. The culture was diluted back to an OD of 0.020 in 100 ml of media in a shake flask. At time zero, IPTG was added to a concentration of 1 mM and the flasks were incubated at 37°C with shaking until the OD of the controls was approximately 0.640 (5 generations of growth). The culture was then diluted back to an OD of 0.020 in 100 ml of prewarmed media in a separate shake flask and incubated at 37°C with shaking until 330 minutes had passed since first inducing the cultures.

extract_protocol:
Microcentrifuge tubes that had been chilled on ice were filled with 1.5 ml of bacteria culture and centrifuged at 6000 x g and 4°C for 5 minutes. Supernatant was decanted and the cell pellet resuspended in 200 μl of Max Bacterial Enhancement Reagent (Invitrogen) that had been preheated to 95°C. The tubes were incubated at 95°C for 4 minutes before 1 ml of TRIzol Reagent (Invitrogen) was added. Sample lysis, separation of the RNA aqueous phase, and subsequent precipitation and wash steps were performed according to the TRIzol user manual. The resulting RNA pellet was resuspended in 50 μl of nuclease-free water. A second RNA precipitation was performed to remove residual salt as recommended by the MICROBExpress Bacterial mRNA Enrichment Kit (Invitrogen). RNA was resuspended in 0.1X TE buffer (NEB). Concentration of RNA was measured by NanoDrop spectrophotometer. RNA integrity was examined by native agarose gel electrophoresis with 300 ng of total RNA loaded in each lane of a 1.0% TAE gel containing ethidium bromide. mRNA enrichment was completed using the MICROBExpress Bacterial mRNA Enrichment Kit. The enriched mRNA was treated with DNase using the TURBO DNA-free Kit (Invitrogen).
Double-stranded cDNA was synthesized, purified, and end prepped with the NEBNext Ultra II Directional RNA Library Prep Kit with Sample Purification Beads (NEB). NEBNext Adaptor for Illumina (NEB) was ligated to the cDNA. The ligation reactions were purified using NEBNext Sample Purification Beads and PCR enriched using a unique index primer from the NEBNext Multiplex Oligos for Illumina Kit (NEB) for each sample. PCR products were cleaned with NEBNext Sample Purification Beads and pooled for Illumina Tru-Seq (2 x 75 bp reads) at the Transcriptomics and Deep Sequencing core at Johns Hopkins University.

treatment_protocol: Monoculture growth at 37°C for 330 minutes.

value: NEB 5-alpha LacIq


title: L138F (2)

status: Public on Oct 28 2019

type: SRA

city: Baltimore

state: MD

country: USA

description: NEB 5-alpha F'Iq Competent E. coli

library_source: transcriptomic

molecule: total RNA

source_name: pSkunk1-L138F α-helix mutation, 1 mM IPTG, biological replica 2

tag: strain


title: Patient_08_normal

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

data_processing:
To control RNA-seq data quality, the RNA-seq reads with Phred base quality ≥ 20 were filtered using Sickle (version 1.33).
The remaining reads were mapped to human reference genome (CRCh37/hg19) using STAR (version 2.5.2b) with parameters "--alignIntronmin 61 --alignIntronMax 265006 --outFilterMultiMapNmax 20 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.90 --outFilterMatchNminOverLread 0.90".
Read counts were estimated with BAM files using featureCounts (version 1.5.1) with parameters "--minOverlap 60 -s 2 -p -B -C".
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each samples.

organism: Homo sapiens

source_name: ESCC adjacent normal tissue

extract_protocol:
Total RNA was extracted from ESCC tissues using TRIzol reagent (Invitrogen) for construction of RNA-seq libraries.
The sequencing library was prepared from 1 ug of total RNA using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (RS-122-2203).

value: ESCC

value: normal


title: OSCC-4-2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (TGGAATTCTCGGGTGCCAAGG) trimmed and three bases trimmed from the start of the read
mapped using bowtie -v 1
To investigate the expression profiles of miRNAs, the frequency of miRNA counts were normalized to TPM using the following formula: normalized expression = actual miR read count / total clean read count × 1000000.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include miRNA TPM values for each sample

source_name: adjacent normal epithelia specimens

extract_protocol:
Total RNA was extracted by using TRIzol® reagent (Ambion) according to the manufacturer’s instructions, and RQ1 DNase (Promega) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis, and assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
Three μg of total RNA was used for small RNA cDNA library preparation with Balancer NGS Library Preparation Kit for small/microRNA (Gnomegen, San Diego, CA, USA) following manufacture's instruction. Briefly, RNAs were ligated to 3' and 5' adaptor sequentially, and then reverse transcribed to cDNA and PCR amplified. Whole library was applied to 10% native PAGE gel electrophoresis and bands corresponding to microRNA insertion were cut and eluted. After ethanol precipitation and washing, the purified small RNA libraries were quantified with Qubit Fluorometer (Invitrogen, Carlsbad, USA) and applied to the Illumina GAIIx (Illumina, San Diego, CA, USA) 73 nt single-end sequencing according to the manufacturer's instructions.

tag: tissue

value: normal epithelium


title: L122S

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-L122S α-helix mutation, 1 mM IPTG, biological replica 1


title: mrna_30_WT_w/o_CHX_1

city: Bethesda

first: Shardul

last: Kulkarni

address: 49 Convent Drive, Rm 2C08

institute: NICHD, NIH

data_processing:
The ribosome profiling and mRNA sequencing data were processed as described in Ingolia, N.T. (2010). Genome-wide translational profiling by ribosome footprinting.  Methods Enzymol. 470, 119–142. Breifly, the sequnce linker and the first nucleotide of each read were removed using fastx_toolkit/0.0.13 (fastx_clipper and fastx_trimmer, respectively). Ribosome RNAs were removed using bowtie/2-2.2.5  alignment agains year ribosome RNA sequences.The non-rRNA reads were mapped to yeast geneome sacCer3 (http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/chromFa.tar.gz)using TopHat/2.0.13.
Wiggle files were produced from the alignment files using RiboSeq (https://github.com/ingolia-lab/RiboSeq). each for genes on the Watson or Crick strand. A combined alignment file (Bam file) was generated using two alignment files (one for each of the two biological replicates). The combined files were generated for both RPF samples (ribo-seq) and total RNA samples (mrna) for 20 °C, 30 °C and 37 °C. Wiggle files were generated from this combined alignment file. Files were generated for each gene on the Watson or Crick strand. The tracks were visualized using Integrative Genomics Viewer (IGV 2.4.14). The tracks were normalized according to total number of mapped reads in the combined file by adjusting the scale.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7  in synthetic complete medium at 30°C,without treatment with cycloheximide before harvesting.

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill in cell lysis buffer containing 500 µg/ml cycloheximide. Total mRNA isolated from whole cell extract using miRNeasy minikt (Qiagen). Total RNA fragmentation, Size selection,  linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223. Ribo-Zero Gold rRNA Removal Kit (Illumina) was used to to remove ribosome contamination after linker ligation step.
RNA-Seq

tag: temperature


title: OSCC-4-1

source_name: Oral Squamous Cell Carcinoma

value: cancer


title: Patient_07_normal


title: H96C

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-H96C cysteine mutation, 1 mM IPTG, biological replica 1


title: Patient_07_cancer

source_name: ESCC tumor tissue


title: OSCC-3-2


title: Patient_06_cancer


title: OSCC-3-1


title: L148R (2)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-L148R α-helix mutation, 1 mM IPTG, biological replica 2


title: A18K

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-A18K signal sequence mutation, 1 mM IPTG, biological replica 1


title: A11D (2)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-A11D signal sequence mutation, 1 mM IPTG, biological replica 2


title: WT (2)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1, 1 mM IPTG, biological replica 2


title: Patient_05_normal


title: Patient_06_normal


title: OSCC-2-1


title: A25S (2)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-A25S signal sequence mutation, 1 mM IPTG, biological replica 2


title: ΔTEM-1 (2)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1 ΔTEM-1 gene deletion, 1 mM IPTG, biological replica 2


title: OSCC-2-2


title: Patient_05_cancer


title: R178* (1)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-R178* nonsense mutation, 1 mM IPTG, biological replica 1


title: Patient_02_cancer


title: OSCC-1-1


title: OSCC-1-2


title: Patient_04_cancer


title: C123S

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-C123S cysteine/α-helix mutation, 1 mM IPTG, biological replica 1


title: N52C

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-N52C cysteine mutation, 1 mM IPTG, biological replica 1


title: no IPTG (2)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1, no IPTG, biological replica 2


title: WT-NPA vs iaa13-NPA3

type: RNA

city: Bunkyo

first: Takaki

last: Yamauchi

country: Japan

institute: The University of Tokyo

description: Biological replicate 3 of 3. WT-NPA vs iaa13-NPA

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: The hybridized slides were scanned with a DNA microarray scanner G2505C (Agilent Technologies).

data_processing: Signal intensities were extracted using Feature Extraction software (version 10.5.1.1; Agilent Technologies).

organism: Oryza sativa

source_name: WT-NPA, adventitious roots, well-aerated hydroponic culture for 48 h

label_protocol: Total RNAs (400 ng) extracted from 10-mm-long root segments at 15-25 mm from the tips of adventitious roots were labelled with a Quick Amp Labeling Kit (Agilent Technologies) in accordance with the manufacturer’s instructions.

growth_protocol: Seeds of the rice iaa13 mutant and its background wild type (cv. Taichung 65) were germinated on petri dishes with deionized water in a growth chamber at 28oC under dark conditions. After 2 d, germinated seeds were placed on a meshfloat with an aerated quarter strength nutrient solution at 28oC under constant light conditions for 4 d. Six-day-old seedlings were transferred to aerated full-strength nutrient solution. After 7 d, 13-d-old rice plants were transferred newly prepared full-strength nutrient solution and further grown for 7 d.

extract_protocol: Total RNA extracted using RNeasy Plant Mini Kig following manufacturer's instructions.

treatment_protocol: Twenty-days-old rice seedlings were transferred to aerated nutrient solution with or without 0.5 µM N-1-naphthylphthalamic acid (NPA) and grown for 48 h.

tag: genotype/variation

value: wild type (cv. Taichung 65)

value: at 15 to 25 mm from the tips of adventitious roots

tag: treatment

value: Aerated -NPA for 48 h

source_name: iaa13-NPA, adventitious roots, well-aerated hydroponic culture for 48 h

value: iaa13 (background; Taichung 65)


title: Patient_03_cancer


title: Patient_04_normal

source_name: ESCC adjacent normal tissue


title: R43C

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-R43C cysteine mutation, 1 mM IPTG, biological replica 1


title: CD36KO-oxLDL_rep2

city: Milwaukee

first: Yiliang

state: WI

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

data_processing:
GSPMC NGS sequencer was used for base-calling
FastQC application provides quality control checks on raw sequence data. Then the software MAPRSeq3 was used to map the reads to reference genome and generate fetured counts
The software MAPRSeq3 also provide normalized values (RPKM)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include RPKM values for each sample

organism: Mus musculus

source_name: macrophage

growth_protocol: All cells were maintained in RPMI1640 plus 10% FBS until treatment

extract_protocol:
Total RNA were isolated using RNeasy Mini Kit (Qiagen) according to the user manual
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 20μg/ml oxLDL for 8h before cell lysis for RNA isolation

tag: cell type

value: peritoneal macrophage

tag: genotype

value: CD36 KO


title: Patient_01_cancer


title: A25S (1)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-A25S signal sequence mutation, 1 mM IPTG, biological replica 1


title: Patient_03_normal


title: L148R (1)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-L148R α-helix mutation, 1 mM IPTG, biological replica 1


title: SNU-398_input

city: Singapore

first: Chan-Shuo

last: Wu

address: 14 Medical Drive, #12-01

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
The paired-end RNA-seq reads were mapped by TopHat2 pipeline against human reference genome GRCh38 with gene annotation GENCODE 24.
PCR duplicates were removed in the paired-end alignments by samtools rmdup.
Alignments with mapping quality < 20 were also removed.
Based on the reads mapped in the transcriptome, gene expression levels in FPKM were determined by cuffdiff in the Cufflinks package.
Genome_build: hg38
Supplementary_files_format_and_content: txt file recoding FPKM values

source_name: input (untreated cells)

growth_protocol: RPMI medium supplemented with 10% FBS, 37degC, 5% CO2

extract_protocol:
Qiagen RNeasy Mini kit
Illumina ScriptSeq Complete Gold (human/mouse/rat) kit

treatment_protocol: Lentivirus transduction and puromycin selection

tag: cell line

value: liver

tag: disease state

value: hepatocellular carcinoma


title: scrSAHA6h Replicate 2

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

hyb_protocol: Cyanine-3 (Cy3) labeling with miRNA Complete Labeling and Hyb Kit  according to the manufacturer's instructions

scan_protocol: Agilent Microarray Scanner

data_processing: The scanned images were analyzed with Feature Extraction Software

source_name: U937 stable clones transfected with scramble vector upon 6h SAHA treatment at 5uM concentration REPLICATE 2

growth_protocol: U937 leukemic cells were cultured in RPMI-1640 medium (Sigma Aldrich) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (HyClone Laboratories), 100 units/mL penicillin G (Euro Clone), 100 μg/mL streptomycin (Euro Clone), 2 mM L-glutamine (Euro Clone), 250 mg/mL amphotericin B (Euro Clone) and 50 mg/mL G-418 sulfate (Invitrogen). The cells were incubated at 37°C at a ﬁxed concentration of CO2 (5%).

extract_protocol: RNA extraction by protocol reported in PMID: 24349422

treatment_protocol: The inhibitor SAHA (Merck) was dissolved in dimethyl sulfoxide (Sigma) and used at the final concentration of 5 μM for 6 hours of treatment.

value: acute myeloid leukemia cell line

value: scramble upon SAHA 6h


title: WT-NPA vs WT+NPA3

description: Biological replicate 3 of 3. WT-NPA vs WT+NPA

source_name: WT+NPA, adventitious roots, well-aerated hydroponic culture for 48 h

value: Aerated +NPA for 48 h


title: L138F (1)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-L138F α-helix mutation, 1 mM IPTG, biological replica 1


title: Patient_02_normal


title: WT-NPA vs iaa13-NPA1

description: Biological replicate 1 of 3. WT-NPA vs iaa13-NPA


title: WT-NPA vs iaa13-NPA2

description: Biological replicate 2 of 3. WT-NPA vs iaa13-NPA


title: WT-NPA vs WT+NPA1

description: Biological replicate 1 of 3. WT-NPA vs WT+NPA


title: SNU-387_SALL4B

source_name: overexpression of isoform SALL4B


title: SNU-387_SALL4A

source_name: overexpression of isoform SALL4A


title: Patient_01_normal


title: SNU-387_EV

source_name: empty vector


title: ΔTEM-1 (3)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1 ΔTEM-1 gene deletion, 1 mM IPTG, biological replica 1


title: V23D

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-V23D signal sequence mutation, 1mM IPTG, biological replica 1


title: SNU-398_SALL4_KD

source_name: SALL4 Knockdown (targets both isoforms)


title: WT (1)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1, 1 mM IPTG, biological replica 1


title: A11D (1)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1-A11D signal sequence mutation, 1 mM IPTG, biological replica 1


title: WT-NPA vs WT+NPA2

description: Biological replicate 2 of 3. WT-NPA vs WT+NPA

source_name: WT-NPA, adventitious roots, well-aerated hydroponic culture for 48 h


title: scr Replicate 2

source_name: U937 stable clones transfected with scramble vector  REPLICATE 2

label_protocol: Cyanine-3 (Cy3) labeling with miRNA Complete Labeling and Hyb Kit  according to the manufacturer's instructions

value: scramble


title: S23-D0

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

description:
PolyA RNA
processed data file: WT_vs_SOX21-KO.gene_expression.TPM.csv

data_processing:
Basecalls performed using CASAVA version 1.7.
Sequences are aligned to transcriptome with Salmon (v0.8.2).
Transcripts Per Million were calculated by Salmon (v0.8.2) by default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: *.gene_expression.TPM.csv: Comma-separated text files include TPM values for all samples.

source_name: Human embryonic stem cell

extract_protocol:
Total RNA was isolated from cells collected at different time points using TRIzol Reagent (Invitrogen). Isolated RNA was enriched by Poly(A) tails and fragmented.
RNA sequencing libraries were prepared according to Illumina manufacturer instruction. Paired-end RNA-seq of 2x100 base pair reads were sequenced on Illumina Hiseq2000 platform, or 2x150 base pair reads were sequenced on Hiseq X-ten, or 50 base pair reads were sequenced on Illumina MiSeq.

value: human embryonic stem cell

tag: time point

value: Day 0


title: scrSAHA6h Replicate 1

source_name: U937 stable clones transfected with scramble vector upon 6h SAHA treatment at 5uM concentration REPLICATE 1


title: shHDAC2 Replicate 1

source_name: U937 stable clones transfected with shHDAC2 vector  REPLICATE 1

value: HDAC2 Knockdown


title: S13-D0


title: WT1-D0

value: wild type


title: no IPTG (3)

description: NEB 5-alpha F'Iq Competent E. coli

source_name: pSkunk1, no IPTG, biological replica 1

value: NEB 5-alpha LacIq


title: Fructose TAP-

city: Tartu

first: Kaspar

last: Valgepea

state: Tartumaa

address: Nooruse 1

department: Institute of Technology

country: Estonia

institute: University of Tartu

description:
cDNA library not processed with Tobacco Acid Pyrophosphatase (TAP; TAP-)
Differential RNA-seq

data_processing:
Basecalling was performed online during sequencing with the Real-Time Analysis (RTA) software version 2.4.1.1 and System Suite Version 2.0.2.2. Conversion of basecall files to gzipped fastq files was performed using the bcl2fastq script provided by Illumina.
Sequencing reads were aligned and mapped to the genome of C. autoethanogenum DSM 10061 (NC_022592.1) using the software Tophat2 (Kim et al., 2013).
Sequencing reads were processed with the TSSAR (TSS Annotation Regime) software (35) for automated de novo determination of transcription start sites from dRNA-Seq data using the following parameters: p-Value 1e-3, Noise threshold 10, Merge range 5.
Genome_build: NC_022592.1
Supplementary_files_format_and_content: Tab-delimited text file "TSSAR output - TSS data.txt" includes the TSSAR output with the determined TSSs and their metrics

organism: Clostridium autoethanogenum

source_name: bacterial cell

growth_protocol: Clostridium autoethanogenum was grown on gas and fructose anaerobically at 37C.

extract_protocol:
RNA was extracted from the cells using TRIzol, glass beads, and 1-bromo-3-chloropropane. DNA was removed using DNase Turbo (Life Sciences) followed by column purification with RNAeasy (Qiagen) and evaluation of RNA quality using the BioAnalyzer instrument (Agilent). Total RNA pools were treated with the Ribo-Zero rRNA Removal Kit (Epicentre) to deplete ribosomal RNA, which was verified by capillary electrophoresis.
The cDNA libraries were prepared using the 5′tagRACE method (Fouquier et al. 2011). Firstly, the 5′ Illumina TruSeq sequencing adapter carrying sequence tag TCGACA was ligated to the 5′-monophosphate groups (5′P) of processed transcripts (TAP- on Fig. 1A). Samples were then treated with Tobacco Acid Pyrophosphatase (TAP) to convert 5′-triphosphate (5′PPP) structures of primary transcripts into 5′P ends to which the 5′ Illumina TruSeq sequencing adapter carrying sequence tag GATCGA was ligated (TAP+ on Fig. 1A). Next, first-strand cDNA was synthesised using an N6 randomised primer to which the 3′ Illumina TruSeq sequencing adapter was ligated after fragmentation. The 5′ cDNA fragments were subsequently amplified with PCR using a proof reading enzyme and primers designed for TruSeq sequencing according to manufacturer’s instructions. Finally, 5′ cDNAs were purified using the Agencourt AMPure XP Kit (Beckman Coulter Genomics) and analysed by capillary electrophoresis.

treatment_protocol: Cultures were sampled from the exponential growth phase (OD600nm~0.5-0.6), pelleted by centrifugation (4,000 × g for 10 min at room temperature) followed by resuspension in 1 mL of TRIzol.

tag: growth condition

value: Fructose-grown cells

tag: enriched for

value: processed (TAP-) transcripts


title: Gas TAP-

value: Gas-grown cells


title: shHDAC2 Replicate 2

source_name: U937 stable clones transfected with shHDAC2 vector  REPLICATE 2


title: Gas TAP+

description:
cDNA library processed with Tobacco Acid Pyrophosphatase (TAP; TAP+)
Differential RNA-seq

value: primary (TAP+) transcripts


title: WT2-D0


title: PI01

city: La Jolla

first: Paul

middle: A

last: Insel

state: CA

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

description: untreated 'control' cells

data_processing:
FASTQC
Kallisto v0.43.1
tximport
Genome_build: hg38
Supplementary_files_format_and_content: excel files with gene expression in TPM

source_name: Cardiac Fibroblasts

extract_protocol:
Cells were lysed in RLT buffer and RNA was isolated via Qiagen Rneasy mini kit, with on-column Dnase-1 digestion
Illumina Truseq stranded mRNA protocol

value: Cardiac Fibroblasts

tag: development stage

value: fetal


title: CHLONZA

description: untreated 'control' cells

source_name: Pulmonary Arterial Smooth Muscle Cells

value: Pulmonary Arterial Smooth Muscle Cells

value: adult


title: BL41 NGFRLMP1 LMP1 Signaling 2

city: Colorado Springs

first: Olivia

last: Hatton

state: CO

address: 14 E Cache La Poudre St

department: Molecular Biology

institute: Colorado College

description:
test LMP1 activation
XLINK2

data_processing:
Ct values (Matrix non-normalized) were first normalized to the median Ct value of the individual array (DCt, Matrix normalized), The  DCt of the miRNA in the activated LMP1 samples (n=2) was then normalized to the DCt from the matched unactivated LMP1 samples (n=2, DDCt).  Fold change was calculated as 2-DDCt (Fold Change).
Fold change reports 2^-DDCt, where -ΔΔCt = -[ΔCtxlink -ΔCtnoxlink]

label: FAM

source_name: BL41 NGFRLMP1 cells, 12 hr LMP1 signal

growth_protocol: BL41 NGFRLMP1 cells were maintained in complete media consisting of RPMI 1640 (Fisher Scientific of Life Technologies, Foster City, CA) supplemented with 10% fetal calf serum, 1% penicillin/streptomycin, and 0.7 mg/mL G418 and incubated in a humidified 37C, 5% CO2 incubator.

extract_protocol: Total RNA was extracted using TRIzol reagent.

treatment_protocol: LMP1 signaling was activated as previously described (Lambert and Martinez, Journal of Immunology, 2007).

tag: Sex

value: male

value: EBV- Burkitt's Lymphoma Line BL41 stably transfected to express NGFRLMP1

tag: time

value: 12 hours LMP1 signaling


title: RNA-seq, Dicer1 knockout Ago2Halo/+ mESCs, biological rep 5

status: Public on Oct 27 2019

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description:
Dicer1 gene was disrupted using CRISPR-cas9 at the RNase III 1 domain
processed data file: mESCs_dicer_RNAseq_counts_DEseq.csv
KO5_IGO_07620_9_S9_L001

data_processing:
RNA-seq reads were aligned to the standard mouse genome (mm10) using Hisat2 v0.1.6-beta
Aligned reads were counted at each gene locus using the GENCODE annotation vM22
Differential gene expression analysis was performed using DESeq2 v1.20.0
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing differential gene expression analysis results and gene counts

source_name: Dicer1 knockout Ago2Halo/+ mESCs

growth_protocol: mESCs were cultivated on irradiated MEFs in KnockOut DMEM supplied with 15% FBS, leukemia inhibitory factor, penicillin/streptomycin , GlutaMax, non-essential amino acids, nucleosides (Millipore) and 2-Mercaptoethanol.

extract_protocol:
Total RNAs were extracted from cells using TRIzol Reagent following the manufacturer's instructions , treated with DNase and cleaned up using the Qiagen RNeasy kit.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a  HiSeq 2500 in High Output mode  in a 50bp/50bp paired end run, using the TruSeq SBS Kit v4 (Illumina).

tag: strain background

value: Ago2Halo/+; Dicer1 knockout

value: mouse embryonic stem cells (mESCs)


title: RNA-seq, Dicer1 knockout Ago2Halo/+ mESCs, biological rep 3

description:
Dicer1 gene was disrupted using CRISPR-cas9 at the RNase III 1 domain
processed data file: mESCs_dicer_RNAseq_counts_DEseq.csv
KO3_IGO_07620_7_S7_L001


title: RNA-seq, Dicer1 knockout Ago2Halo/+ mESCs, biological rep 1

description:
Dicer1 gene was disrupted using CRISPR-cas9 at the RNase III 1 domain
processed data file: mESCs_dicer_RNAseq_counts_DEseq.csv
KO1_IGO_07620_5_S5_L001


title: RNA-seq, Dicer1 knockout Ago2Halo/+ mESCs, biological rep 2

description:
Dicer1 gene was disrupted using CRISPR-cas9 at the RNase III 1 domain
processed data file: mESCs_dicer_RNAseq_counts_DEseq.csv
KO2_IGO_07620_6_S6_L001


title: Patient_13_normal

source_name: ESCC adjacent normal tissue

value: ESCC

value: normal


title: BL41 NGFRLMP1 LMP1 Signaling 1

description:
test LMP1 activation
XLINK1


title: BL41 NGFRLMP1 No LMP1 Signaling 1

description:
control
NOXLINK1

source_name: BL41 NGFRLMP1 cells, 0 hr LMP1 signal

value: 0 hours LMP1 signaling


title: Fructose TAP+


title: RNA-seq, Dicer1 knockout Ago2Halo/+ mESCs, biological rep 4

description:
Dicer1 gene was disrupted using CRISPR-cas9 at the RNase III 1 domain
processed data file: mESCs_dicer_RNAseq_counts_DEseq.csv
KO4_IGO_07620_8_S8_L001


title: RNA-seq, wild-type Ago2Halo/+ mESCs, biological rep 1

description:
processed data file: mESCs_dicer_RNAseq_counts_DEseq.csv
WT1_IGO_07620_1_S1_L001

source_name: wild-type Ago2Halo/+ mESCs

value: Ago2Halo/+; Dicer1 wild-type


title: RNA-seq, wild-type Ago2Halo/+ mESCs, biological rep 4

description:
processed data file: mESCs_dicer_RNAseq_counts_DEseq.csv
WT4_IGO_07620_4_S4_L001


title: RNA-seq, wild-type Ago2Halo/+ mESCs, biological rep 3

description:
processed data file: mESCs_dicer_RNAseq_counts_DEseq.csv
WT3_IGO_07620_3_S3_L001


title: scr Replicate 1

source_name: U937 stable clones transfected with scramble vector  REPLICATE 1

value: acute myeloid leukemia cell line

value: scramble


title: RNA-seq, wild-type Ago2Halo/+ mESCs, biological rep 2

description:
processed data file: mESCs_dicer_RNAseq_counts_DEseq.csv
WT2_IGO_07620_2_S2_L001


title: Input control library, Ago2Halo/+ mESCs, biological rep 2, technical rep 2

description:
LIZ_IC-WT2_IGO_07657_D_4_S11
processed data file: mESC_peaks.csv

data_processing:
The first 7 bases were removed from the beginning of reads and appended to the original read names
The 3’ adaptor (5’-GTGTCAGTCACTTCCAGCGGGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’) and bases with Phred quality score lower than 20 were trimmed from reads using cutadapt v1.15 or v1.17. After trimming, reads shorter than 18 nt were discarded.
For HEAP mRNA and input control libraries, processed reads were aligned to the UCSC mm10 mouse genome using STAR (version 2.5.3a). For HEAP miRNA libraries, processed small RNA reads were aligned to a miRNA genome index built from 1,915 murine pre-miRNA sequences from miRbase version 21 (ftp://mirbase.org/pub/mirbase/21/) using Bowtie (version 2.3.4), and these reads were considered true miRNA counts if they fell within plus or minus 4 bps at each of the 5’ and 3’ end of the annotated mature miRNAs.
Reads mapped to the same locus with identical barcodes were considered PCR duplicates and therefore collapsed. This was achieved by storing aligned reads using chromosome names, strand information, positions of the first bases and the 7 nt barcodes as keywords. Representative reads of these unique events were written into a BAM file.
Peaks were called using CLIPanalyze (https://bitbucket.org/leslielab/clipanalyze) from HEAP mRNA libraries using input control libraries as background signals.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing peaks identified in each context and (for miRNA libraries) miRNA counts

source_name: Input control library, Ago2Halo/+ mESCs

growth_protocol: Ago2Halo/+ mESCs were cultivated on irradiated MEFs in KnockOut DMEM supplied with 15% FBS, leukemia inhibitory factor, penicillin/streptomycin , GlutaMax, non-essential amino acids, nucleosides (Millipore) and 2-Mercaptoethanol.

extract_protocol:
For HEAP mRNA and miRNA libraries, RNAs were isolated along with the HaloTag-Ago2 fusion protein using HaloTag ligands conjugated to sepharose beads. RNAs were extracted from sepharose beads using phenol/chloroform. For input control libraries, RNAs were extracted from whole-cell lysates after RNAse A treatment using DynaBeads MyOne Silane.
RNAs were ligated to RNA adaptors on both ends (3' RNA adaptor RL3: GUGUCAGUCACUUCCAGCGG; 5' RNA adaptor RL5D-6N: AGGGAGGACGAUGCGGNNNNNNG). After reverse transcription with a DNA primer DP3 (CCGCTGGAAGTGACTGACAC), the library was amplified with DNA primers DP3 and DP5 (AGGGAGGACGATGCGG). Illumina sequencing adaptors, sequencing primer binding sites and Illumina Truseq indexes for library multiplexing were introduced to the amplified libraries by PCR using primers DP3-barcode (CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCCCGCTGGAAGTGACTGACAC) and DSFP5 (AATGATACGGCGACCACCGACTATGGATACTTAGTCAGGGAGGACGATGCGG). After PicoGreen quantification and quality control by Agilent BioAnalyzer, libraries were run on a HiSeq 2500 in Rapid Mode in a 125/100bp single end run, using the HiSeq Rapid SBS Kit v2 (Illumina). Sequencing primers used were custom SSP1 primer (CTATGGATACTTAGTCAGGGAGGACGATGCGG) and the Illumina index read SP2 primer.

tag: molecule/library type

value: Input control control


title: HEAP mRNA library, Ago2Halo/+ mESCs, lefty2 wild-type

description:
5-ES-WT-mRNA_IGO_08827_B_5_S3
processed data file: mESC_lefty2mut_peaks.csv

value: Ago2Halo/+; Lefty2 wild-type

value: HEAP mRNA


title: Input control library, Ago2Halo/+ mESCs, biological rep 1, technical rep 1

description:
KIM_IC-WT1_IGO_07657_D_3_S12
processed data file: mESC_peaks.csv


title: HEAP miRNA library, Ago2Halo/+ mESCs, biological rep 3, technical rep 1

description:
KIM_6-WT3-miRNA-5_IGO_07657_D_13_S3
mESCs_mirna_counts.csv

source_name: HEAP miRNA library, Ago2Halo/+ mESCs

value: HEAP miRNA


title: HEAP miRNA library, Ago2Halo/+ mESCs, biological rep 3, technical rep 2

description:
LIZ_6-WT3-miRNA-5_IGO_07657_D_13_S3
mESCs_mirna_counts.csv


title: Input control library, Ago2Halo/+ mESCs, biological rep 1, technical rep 2

description:
LIZ_IC-WT1_IGO_07657_D_3_S12
processed data file: mESC_peaks.csv


title: Input control library, Ago2Halo/+ mESCs, lefty2 wild-type

description:
5-ES-WT-IC_IGO_08827_B_21_S21
processed data file: mESC_lefty2mut_peaks.csv


title: Input control library, Ago2Halo/+ mESCs, biological rep 2, technical rep 1

description:
KIM_IC-WT2_IGO_07657_D_4_S11
processed data file: mESC_peaks.csv


title: HEAP miRNA library, Ago2Halo/+ mESCs, biological rep 1, technical rep 2

description:
LIZ_4-WT1-miRNA-5_IGO_07657_D_11_S1
mESCs_mirna_counts.csv


title: HEAP miRNA library, Ago2Halo/+ mESCs, biological rep 2, technical rep 1

description:
KIM_5-WT2-miRNA-5_IGO_07657_D_12_S2
mESCs_mirna_counts.csv


title: BL41 NGFRLMP1 No LMP1 Signaling 2

description:
control
NOXLINK2


title: HEAP mRNA library, Ago2Halo/+ mESCs, biological rep 3, technical rep 2

description:
LIZ_6-WT3-mRNA-6_IGO_07657_D_16_S16
processed data file: mESC_peaks.csv

source_name: HEAP mRNA library, Ago2Halo/+ mESCs


title: HEAP miRNA library, Ago2Halo/+ mESCs, biological rep 1, technical rep 1

description:
KIM_4-WT1-miRNA-5_IGO_07657_D_11_S1
mESCs_mirna_counts.csv


title: HEAP mRNA library, Ago2Halo/+ mESCs, biological rep 2, technical rep 2

description:
LIZ_5-WT2-mRNA-6_IGO_07657_D_15_S14
processed data file: mESC_peaks.csv


title: HEAP mRNA library, Ago2Halo/+ mESCs, biological rep 2, technical rep 1

description:
KIM_5-WT2-mRNA-6_IGO_07657_D_15_S14
processed data file: mESC_peaks.csv


title: HEAP mRNA library, Ago2Halo/+ mESCs, biological rep 3, technical rep 1

description:
KIM_6-WT3-mRNA-6_IGO_07657_D_16_S16
processed data file: mESC_peaks.csv


title: RNA-seq, KP clone 1-3 expressing mutant T6B-YFP

description:
processed data file: KP_T6B_counts_DEseq.csv
mut_0_24_1_4_IGO_09793_B_7_S33

data_processing:
RNA-seq reads were aligned to the standard mouse genome (mm10) using STAR 2.5.3a.
Aligned reads were counted at each gene locus using the GENCODE annotation vM22.
Differential gene expression analysis was performed using DESeq2 v1.20.0.
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing differential gene expression analysis results and gene counts

source_name: KP clone expressing mutant T6B-YFP

growth_protocol: Mouse KP lung adenocarcinoma cells were cultivated in Advanced DMEM/F12 containing 5% FBS, HEPES, GlutaMax and penicillin/streptomycin.

extract_protocol:
Total RNAs were extracted from cells using TRIzol Reagent following the manufacturer's instructions , treated with DNase and precipitated with isopropanol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 1µg of total RNA with an RNA integrity number varying from 9-10 underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).

treatment_protocol: Cells were treated with 1000 ng/mL Doxycycline for 48 hours to induce T6B-YFP expression prior to RNA isolation.

value: KRasG12D; p53-null

value: Mouse KRasG12D; p53-null lung adenocarcinoma cell line

value: transduced with retrovirus expressing a doxycycline inducible mutant T6B-YFP fusion protein


title: RNA-seq, KP clone 1-4 expressing mutant T6B-YFP

description:
processed data file: KP_T6B_counts_DEseq.csv
mut_0_24_1_7_IGO_09793_B_8_S34


title: RNA-seq, KP clone 1-2 expressing mutant T6B-YFP

description:
processed data file: KP_T6B_counts_DEseq.csv
mut_0_24_1_2_IGO_09793_B_6_S32


title: HEAP mRNA library, Ago2Halo/+ mESCs, biological rep 1, technical rep 1

description:
KIM_4-WT1-mRNA-6_IGO_07657_D_14_S15
processed data file: mESC_peaks.csv


title: HEAP mRNA library, Ago2Halo/+ mESCs, lefty2 mutant biological rep 1

description:
6-ES-Mut1-mRNA_IGO_08827_B_6_S12
The predicted miR-291-3p binding site on the 3'UTR of the Lefty2 mRNA was mutated using CRISPR-Cas9-mediated homologous recombination
processed data file: mESC_lefty2mut_peaks.csv

value: Ago2Halo/+; Lefty2 mut1


title: Patient_12_cancer

source_name: ESCC tumor tissue

value: cancer


title: RNA-seq, KP clone 1-2 expressing wild-type T6B-YFP

description:
processed data file: KP_T6B_counts_DEseq.csv
wt_0_24_1_2_IGO_09793_B_2_S28

source_name: KP clone expressing wild-type T6B-YFP

value: transduced with retrovirus expressing a doxycycline inducible wild-type T6B-YFP fusion protein


title: RNA-seq, KP clone 1-3 expressing wild-type T6B-YFP

description:
processed data file: KP_T6B_counts_DEseq.csv
wt_0_24_1_4_IGO_09793_B_3_S29


title: HEAP miRNA library, Ago2Halo/+ mESCs, biological rep 2, technical rep 2

description:
LIZ_5-WT2-miRNA-5_IGO_07657_D_12_S2
mESCs_mirna_counts.csv

value: mouse embryonic stem cells (mESCs)


title: RNA-seq, KP clone 1-1 expressing wild-type T6B-YFP

description:
processed data file: KP_T6B_counts_DEseq.csv
wt_0_24_1_1_IGO_09793_B_1_S27


title: HEAP mRNA library, Ago2Halo/+ mESCs, lefty2 mutant biological rep 2

description:
7-ES-Mut2-mRNA_IGO_08827_B_7_S11
The predicted miR-291-3p binding site on the 3'UTR of the Lefty2 mRNA was mutated using CRISPR-Cas9-mediated homologous recombination
processed data file: mESC_lefty2mut_peaks.csv

value: Ago2Halo/+; Lefty2 mut2


title: T3

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

data_processing:
Sequencing was carried out using the Illumina HiSeq 4000 according to the manufacturer’s instructions. Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequence quality was examined using the FastQC software. The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software (v2.0.4). The transcript abundances for each sample was estimated with StringTie (v1.2.3), and the FPKM value for gene and transcript level were calculated with R package Ballgown(v2.6.0). The differentially expressed genes and transcripts were filtered using R package Ballgown.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs

source_name: T, MCF12A cells

extract_protocol:
RNA was harvested using Trizol and standard RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocol

value: epithelial breast cell line MCF-12A

tag: agent


title: T2


title: T1


title: T5


title: T4


title: HEAP mRNA library, Ago2Halo/+ mESCs, biological rep 1, technical rep 2

description:
LIZ_4-WT1-mRNA-6_IGO_07657_D_14_S15
processed data file: mESC_peaks.csv


title: T6


title: C4

source_name: C, MCF12A cells

value: control


title: RNA-seq, KP clone 1-1 expressing mutant T6B-YFP

description:
processed data file: KP_T6B_counts_DEseq.csv
mut_0_24_1_1_IGO_09793_B_5_S31


title: C5


title: C3


title: C1


title: C2


title: R3’ subset in the synovium_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: R3’ subset in the synovium

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10

source_name: R3’ subset in the synovium

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) according to the manufacturer's instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: inflammatory monocyte cells


title: R2’ subset in the synovium_rep3

description: R2’ subset in the synovium

source_name: R2’ subset in the synovium


title: R3’ subset in the synovium_rep1

description: R3’ subset in the synovium


title: RNA-seq, KP clone 1-4 expressing wild-type T6B-YFP

description:
processed data file: KP_T6B_counts_DEseq.csv
wt_0_24_1_7_IGO_09793_B_4_S30


title: C6


title: R3’ subset in the synovium_rep2

description: R3’ subset in the synovium


title: R2’ subset in the synovium_rep2

description: R2’ subset in the synovium


title: R2’ subset in the synovium_rep1

description: R2’ subset in the synovium


title: R1 subset in the blood_rep3

description: R1 subset in the blood

source_name: R1 subset in the blood


title: R1 subset in the blood_rep2

description: R1 subset in the blood


title: R1 subset in the blood_rep1

description: R1 subset in the blood


title: RNASEQ-Upf1-KO-2

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

data_processing:
trimming with cutadapt
rRNA depletion with Bowtie
aligment with TopHat2
For differential expression : counts were realized on the exons with FeatureCounts and normalized using DESeq2
Genome_build: hg38 human
Supplementary_files_format_and_content: Text file contain raw counts realized on the exons with FeatureCounts

source_name: colon cancer cell line

growth_protocol: Maintained in McCoy medium (Invitrogen) supplemented with 10% fetal calf serum, 100 mg/ml streptomycin and 100 U/ml penicillin at 37°C under 5% CO2 atmosphere

extract_protocol:
Ribosome Profiling was performed as described in Baudin-Baillieu et al, 2016 and total RNA was purified by hot acid phenol extraction
cDNA library from 100 ng RNA was prepared by the Imagif plateform (Institut de Biologie Intégrative de la Cellule, Gif sur Yvette, France), using the TruSeq Small RNA Sample Prep Kit with 3’ sRNA Adapter (Illumina) according to the manufacturer’s protocol. RNA integrity and quality was verified using Bioanalyzer Small RNA Analysis kit (Agilent). Sequencing was performed at the genomic plateform of the Institut de Biologie de l’École Normale Supérieure (Paris, France) on an Illumina Nextseq 500 and with a single-read 75 cycle runs. Four sequencing libraries were prepared from purified RPFs and total RNA, for each biological replicate of eRF3-depleted, Upf1-depleted and control cells. A minimum of 7 108 reads were achieved for bioinformatics analysis.

tag: tissue

value: human colon cancer cell line

value: HCT116 (ATCC CCL-247)


title: RNASEQ-eRF3-KO-2


title: RNASEQ-eRF3-KO-1


title: RNASEQ-WT-2


title: RNASEQ-WT-1


title: RIBOSEQ-Upf1-KO-2

data_processing:
Library strategy: Ribo-Seq
trimming with cutadapt
rRNA depletion with Bowtie
aligment with TopHat2
For differential expression : counts were realized on the exons with FeatureCounts and normalized using DESeq2
Genome_build: hg38 human
Supplementary_files_format_and_content: Text file contain raw counts realized on the exons with FeatureCounts


title: RIBOSEQ-Upf1-KO-1


title: U2932-Doxorubicin exposure-2.5ug/mL-2h

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

description: Gene expression data from cell lines of diffuse large B-cell lymphoma with or without doxorubicin exposure

hyb_protocol: Included in the label protocol, see above.

scan_protocol: Gene Chips were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing: Data were analyzed using R version 3.0.2 and several R and Bioconductor packages. The .CEL-files were pre-processed using the Robust Multichip Average procedure (RMA) as implemented in the justRMA function from the Bioconductor package affy.

label: biotin

source_name: Cell line of Diffuse Large B-Cell Lymphoma

label_protocol: Biotinylated cRNA were prepared using the GeneChip 3' IVT Express Kit (#P/N901229, Affymetrix) from 100 ng total RNA using manual P/N702646 Rev.4.

growth_protocol: Cell lines were cultured at 37°C, 95% humidity, and 5% CO2 with RPMI 1640, adequate concentration of fetal bovine serum (10% or 20%), and 1% penicillin/streptomycin.

extract_protocol: Total RNA was purified from cell pellets in Trizol by homogenization and incubating for 5 minutes at RT. 200µl chloroform was added and incubated 2 minutes at RT, the mixture was centrifuged at 12,000 g for 15 minutes at 4°C. The aqueous phase was transferred to a new tube and 100 % ethanol added in 1.25X the volume. Mix well and transfer to mirVANA columns (#1561, Ambion) and follow the manufacturer’s instruction from this point.

treatment_protocol:
No doxorubicin exposure; 0ug/mL; 0h
Cell lines were subjected to gene expression profiling untreated or upon exposure to two distinct drug concentrations (0.00061 μg/mL and 2.5 μg/mL) for 2, 12, and 48 hours.


title: U2932-Doxorubicin exposure-0.00061ug/mL-48h


title: U2932-No doxorubicin exposure-0ug/mL-48h


title: U2932-No doxorubicin exposure-0ug/mL-12h


title: U2932-Doxorubicin exposure-2.5ug/mL-48h


title: U2932-Doxorubicin exposure-0.00061ug/mL-2h


title: U2932-No doxorubicin exposure-0ug/mL-2h


title: RIVA-Doxorubicin exposure-0.00061ug/mL-48h

value: RIVA


title: RNASEQ-Upf1-KO-1


title: SU-DHL-5-No doxorubicin exposure-0ug/mL-0h


title: RIVA-No doxorubicin exposure-0ug/mL-48h


title: RIBOSEQ-eRF3-KO-2


title: U2932-Doxorubicin exposure-2.5ug/mL-12h


title: RIBOSEQ-eRF3-KO-1


title: SU-DHL-5-No doxorubicin exposure-0ug/mL-12h


title: U2932-No doxorubicin exposure-0ug/mL-0h


title: U2932-Doxorubicin exposure-0.00061ug/mL-12h


title: SU-DHL-5-Doxorubicin exposure-0.00061ug/mL-2h


title: SU-DHL-5-Doxorubicin exposure-0.00061ug/mL-12h


title: SU-DHL-5-No doxorubicin exposure-0ug/mL-2h


title: RIBOSEQ-WT-2


title: RIBOSEQ-WT-1


title: SU-DHL-5-Doxorubicin exposure-2.5ug/mL-2h


title: CX3CR1hiLy6Cint subset in situ (single-cell RNA-Seq)

description: CX3CR1hiLy6Cint subset in situ

data_processing:
*R1_001.fastq.gz: technical, cell-barcode, UMI
*R2_001.fastq.gz: Biological, gene read
Sequencing was performed on an Illumina HiSeq 3000 platform using the HiSeq Rapid SBS V2 kit (100 x 2 bp) (Illumina).
Illumina Casava1.8.2 software used for basecalling.
The BD Rhapsody Analysis Pipeline (https://igor.sbgenomics.com/public/apps#jiewho/bd-public-project/bd-rhapsody-analysis-pipeline/) was used to process the sequencing data (fastq files).
The analysis pipeline takes the FASTQ files and a reference file for gene alignment. The pipeline generates molecular counts per cell, read counts per cell, metrics, and an alignment file.Output result files were analyzed and visualized by the BD Data view software (BD BioScience).
Please refer to the BD Single Cell Genomics Bioinformatics PDF document (GMX_BD-Rhapsody-genomics-informatics_UG_EN.pdf) linked to the Series file.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values of usdian molecules per cell; columns are genes; rows are cells with Cell_index and barcode

molecule: polyA RNA

source_name: CX3CR1hiLy6Cint subset in situ

extract_protocol:
CX3CR1hiLy6Cint cells were sorted and targeted single-cell RNA-seq analysis was conducted using BD Rhapsody Single-Cell Analysis System (BD BioScience) following the manufacture’s protocol. In short, the single cell suspension was loaded into a BD Rhapsody cartridge with >200,000 microwells and single cell capture was achieved by random distribution and gravity precipitation.
The bead library was loaded into the microwell cartridge to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell cartridge to hybridize mRNA molecules onto barcoded capture oligos on the beads. Then, these beads were retrieved from the microwell cartridge into a single tube for the subsequent steps of cDNA synthesis, ExoI digestion and multiplex-PCR based library construction. For the library construction, we used the custumized BD Rhapsody Immune Response Panel for mouse (BD BioScience) consisting of primer sets for 404 genes, which contains the following seven genes: Acp5, Atp6v0d2 (NM_175406.3), Atp6v0d2 (NM_175406.3), Ctsk, Foxm1, Itgb3, Nfatc1.


title: RIVA-No doxorubicin exposure-0ug/mL-0h


title: RIVA-Doxorubicin exposure-0.00061ug/mL-2h


title: RIVA-Doxorubicin exposure-2.5ug/mL-2h


title: RIVA-No doxorubicin exposure-0ug/mL-2h


title: NCI-H446-MTA1

city: Beijing

first: Jian

last: Liu

address: Gong Ti  Nan Lu 8#

institute: Beijing Chao-Yang Hospital, Capital Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: cell line NCI-H446

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: NCI-H446 cells were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% penicillin/streptomycin at 37℃ in a humidified incubator with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Control vector or MTA1 overexpression plasmid was transfected into NCI-H446 cells and stable

value: small cell lung carcinoma

value: MTA1-overexpressing cells


title: OCI-Ly7-Doxorubicin exposure-0.00061ug/mL-48h


title: OCI-Ly7-No doxorubicin exposure-0ug/mL-48h


title: NCI-H446-NC

value: control cells


title: RIVA-No doxorubicin exposure-0ug/mL-12h


title: Skin_Dermatomyositis_Negative_4

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

description: Sample name: H1612

hyb_protocol: Incubeted with rotation at 60 RPM for 16 hours at 45C

scan_protocol: Scanned with the Affymetrix® GeneChip Scanner 3000 7G using the Command Console software (Affymetrix®)

data_processing: Data summarized and normalized using the RMA routine as implemented in the oligo R library

label: Biotin

source_name: Skin

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix manual target preparation for genechip ®  whole transcript expression array.

growth_protocol: Not relevant

extract_protocol: Total RNA was extracted from frozen tissue samples using the RNeasy Mini Kit Plus protocol

treatment_protocol: Not relevant

value: Skin

tag: disease

value: Dermatomyositis

tag: serology

value: Negative


title: OCI-Ly7-Doxorubicin exposure-0.00061ug/mL-2h


title: RIVA-Doxorubicin exposure-2.5ug/mL-12h


title: OCI-Ly7-No doxorubicin exposure-0ug/mL-12h


title: Skin_Healthy_Negative_2

description: Sample name: T2

value: Healthy


title: Skin_Dermatomyositis_Tif1

description: Sample name: H1415


title: OCI-Ly7-Doxorubicin exposure-2.5ug/mL-12h


title: OCI-Ly7-Doxorubicin exposure-0.00061ug/mL-12h


title: Skin_Dermatomyositis_Negative_3

description: Sample name: H1511


title: OCI-Ly7-No doxorubicin exposure-0ug/mL-2h


title: Skin_Dermatomyositis_MDA5_3

description: Sample name: H1602


title: RIVA-Doxorubicin exposure-0.00061ug/mL-12h


title: Skin_Healthy_Negative_1

description: Sample name: T1


title: Skin_Dermatomyositis_MDA5_2

description: Sample name: H1508


title: Skin_Healthy_Negative_3

description: Sample name: T3


title: Skin_Healthy_Negative_5

description: Sample name: T6


title: RIVA-Doxorubicin exposure-2.5ug/mL-48h


title: OCI-Ly7-Doxorubicin exposure-2.5ug/mL-2h


title: OCI-Ly7-No doxorubicin exposure-0ug/mL-0h


title: Skin_Healthy_Negative_4

description: Sample name: T4


title: Sb_NM3_mRNA

city: Castanet-Tolosan

first: Christophe

last: Roux

address: Chemin de Borde Rouge

institute: University of Toulouse/CNRS

data_processing:
After quality check using FastQC, adaptor sequences were removed using FASTX-Toolkit.
Reads were mapped with CLC Genomics Workbench 11 (CLC Bio workbench, Qiagen, Aarhus, Denmark) using manufacturer’s recommendations.
Genome_build: Sbicolor_313_v3.1 (McCormick et al., 2017)
Genome_build: Rhiir2-1 (Morin et al., 2019)
Genome_build: Ptrichocarpa_210_v3.0 (Tuskan et al., 2006)
Supplementary_files_format_and_content: Expression values, Unique gene reads, Total gene reads, RPKM

organism: Sorghum bicolor

source_name: Non-mycorrhizal roots of sorghum

growth_protocol: Plants were grown in an autoclaved quartz sand : zeolite substrate (1:1, w:w).

extract_protocol: Total RNA was extracted from lyophilized extraradical mycelia, root and leaf samples using the RNeasy Plant Mini Kit (Qiagen, Courtaboeuf, France). RNA extracts were DNase treated with the DNA-freeTM Kit, DNase Treatment and Removal Reagents (AMBION® by life technologies). Total RNA was quantified with the Qbit RNA BR Assay kit and purity was estimated using the Nanodrop (ND-1000, Witec, Switzerland).

treatment_protocol: Plants were fertilized once a week with 10 ml Hoagland solution without P, until all plants showed signs of P depletion. From the 22nd week high-P (560 µM) or low-P (28 µM) containing Hoagland solution was applied for 9 weeks.

value: whole root system

tag: symbiotic status

value: non mycorrhizal

tag: treatment

value: Low Phosphate

tag: plant strain

value: Moench, cv Pant-5


title: Sb_NM1_mRNA


title: IP_Ctr4_mRNA

organism: Populus trichocarpa

source_name: Non-mycorrhizal roots of poplar

value: clone 10174


title: IP_Ctr2_mRNA


title: hP_Ctr3_mRNA

value: High Phosphate


title: Sb_NM2_mRNA


title: IPR4_mRNA

organism:
Populus trichocarpa
Rhizophagus irregularis

source_name: Mycorrhizal roots of poplar

value: mycorrhizal

tag: fungal strain


title: NU-DHL-1-No doxorubicin exposure-0ug/mL-2h

tag: cell line


title: Sb-lp-R4_mRNA

organism:
Sorghum bicolor
Rhizophagus irregularis

source_name: Mycorrhizal roots of sorghum


title: hP_Ctr4_mRNA


title: IP_ERM3_mRNA

organism: Rhizophagus irregularis

source_name: Common Mycelial Network connecting a poplar and a sorghum plant

value: Extra Radiacl Mycelium


title: IP_ERM4_mRNA


title: hP_Ctr1_mRNA


title: IPR3_mRNA


title: Sb-lp-R5_mRNA


title: IPR1_mRNA


title: IP_Ctr1_mRNA


title: NU-DHL-1-Doxorubicin exposure-0.00061ug/mL-2h


title: NU-DHL-1-No doxorubicin exposure-0ug/mL-0h


title: hPR4_mRNA


title: IP_ERM2_mRNA


title: NU-DHL-1-Doxorubicin exposure-2.5ug/mL-12h


title: Skin_Dermatomyositis_MDA5_1

description: Sample name: 1


title: NU-DHL-1-Doxorubicin exposure-2.5ug/mL-2h


title: Sb-hp-R6_mRNA


title: FARAGE-No doxorubicin exposure-0ug/mL-2h

value: FARAGE


title: NU-DHL-1-Doxorubicin exposure-0.00061ug/mL-12h


title: FARAGE-Doxorubicin exposure-2.5ug/mL-2h


title: NU-DHL-1-No doxorubicin exposure-0ug/mL-12h


title: FARAGE-Doxorubicin exposure-0.00061ug/mL-2h


title: Skin_Dermatomyositis_Negative_1

description: Sample name: H1112


title: Sb-hp-R4_mRNA


title: hPR2_mRNA


title: hPR3_mRNA


title: hP_ERM2_mRNA


title: hP_ERM3_mRNA


title: Sb-hp-R3_mRNA


title: hP_ERM1_mRNA


title: Sb-lp-R3_mRNA


title: FARAGE-Doxorubicin exposure-0.00061ug/mL-12h


title: FARAGE-Doxorubicin exposure-2.5ug/mL-12h


title: FARAGE-No doxorubicin exposure-0ug/mL-12h


title: B. subtilis incubated for 4h after HHP treatment, biological rep1

status: Public on Oct 26 2019

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

hyb_protocol: Following fragmentation, 1.8~1.9 µg of cDNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip B. subtilis Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450 using GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: CEL files were quantified with Distribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

organism: Bacillus subtilis

label_protocol: The cDNA was purified using MinElute PCR Purification Kit (Qiagen), fragmented into 50~200 bp with DNase I (Takara-Bio, Kyoto, Japan) (0.06 units/μg DNA), labeled with biotin using terminal deoxynucleotidyl transferase (Promega KK, Tokyo, Japan) and GeneChip Labeling Reagent (Affymetrix, Santa Clara, CA, USA).

growth_protocol: B. subtilis TI465 were maintained in Luria-Bertani medium at 37ºC for about 14 h until they reached the stationary phase of cell growth before treatment.

extract_protocol: Total RNA was purified with an Isogen reagent (Nippon gene, Japan).

treatment_protocol: The B. subtilis strain TI465 were grown in NaCl-free L medium (10 g tryptone, 5 g yeast extract, per liter) for 6 h at 37°C with vigorous shaking. Then, the culture was packed into a sterile polyethylene bag that was heat-sealed after exclusion of air bubbles and subjected to HHP treatment (250 MPa) using a Dr. CHEF (Kobe Steel, Kobe, Japan) at 25°C for 10 min as described previously (Inaoka, T., et al., Biosci Biotechnol Biochem 81 (2017) 1235-1240). The rate of increasing and decreasing of pressure was set at 200 MPa/min. The cells treated at 250 MPa were transferred into a recovery medium (NaCl-free L medium) and incubated at 37°C with vigorous shaking for 0h, 2h, or 4h.

tag: strain

tag: genotype/variation

value: trpC2 spoIIAC::kan

value: 37C, 4h incubation after HHP treatment


title: B. subtilis incubated for 4h after HHP treatment, biological rep2


title: B. subtilis incubated for 2h after HHP treatment, biological rep2

value: 37C, 2h incubation after HHP treatment


title: FARAGE-No doxorubicin exposure-0ug/mL-0h


title: B. subtilis incubated for 2h after HHP treatment, biological rep1


title: s346, 2nd sample set (scRNA-seq)

city: PALO ALTO

first: YUAN

last: GUAN

address: 1701 Page Mill Road

institute: Stanford University

data_processing:
Adapter sequences and low-quality bases at the end of the reads were then removed using the Cutadapt software
The reads were then aligned to human exon sequences (Build GRCh38) using STAR
The expression level of each gene for each cell were then quantified using the FeatureCounts tool
Fragments Per Kilobase of Exon Per Million (FPKM) were generated using scater package in R
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited file containing the log2-transformed FPKM values

source_name: PHH

growth_protocol: For production of HO1, iPSCs were dissociated to single cells in buffer with 5 mM EDTA and 10 mM Y-27632 (Santa Cruz Biotechnology, Dallas, Texas), and were re-aggregated in low-cell-adhesion 60 mm dishes (Corning) in endoderm differentiation medium (10e5 cells/dish) containing 10 mM Y-27632. The endoderm differentiation medium consisted of DMEM/F12 + ITS (GIBCO) supplemented with 0.1 mM nonessential amino acids and 1 mM pyruvate. On days 0 to 3, Activin-A (100 ng/ml) and BMP4 (10 ng/ml) were added the definitive endoderm differentiation medium. For endoderm patterning and for the generation of foregut spheroids, Matrigel (BD Biosciences, GFR) was added to RPMI + B27 medium to a final v/v concentration of 2% from days 3 to 9. From days 3 to 6, 50 ng/ml FGF10 (Peprotech) was added to the medium. From days 6 to 9, 10 ng/ml FGF10 and 10 ng/ml BMP4 were added to the medium. After day 9, Matrigel (final 1% v/v concentration) was added to the organoid growth and differentiation medium (HCM, Lonza), which was supplemented with HGF (50 ng/ml), 50-ng/ml oncostatin M and 10 uM Dexamethasone (Sigma, St. Louis MO).  On day 20, the organoids were collected and re-seeded for further differentiation and characterization.

extract_protocol:
Single cells from iPSC (day 0), day 9 HB, and day 30 HO cultures, and PHHs were prepared using the C1 Single-Cell Auto Prep System (Fluidigm, South San Francisco, CA). The captured cells across the 96 wells were manually inspected as a quality control measure to remove empty wells, doublets or debris-containing wells. For quality control (normalization and estimation of technical noise), 0.05 ul of 1:200,000 dilution of External RNA Controls Consortium (ERCC) RNA spike-in Mix1 (Ambion, AM1780) was added to lysis buffer.
High-quality cDNA libraries for single cell transcriptome analysis were prepared using the SMART-Seq v4 Ultra Low RNA Kit for the Fluidigm C1 System (Takara Bio USA, 635025). The size distribution and the concentration of single-cell cDNA were assessed using a Agilent 2100 Bioanalyzer with the high sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, 5067). Sequencing libraries were constructed in 96-well plates using the Nextera XT DNA Sample Preparation kit according to the manufacturer's protocol (Illumina, San Diego, CA, FC-131-1096) with 96 dual barcoded indices (Illumina; FC-131-1002). Library cleanup and pooling was performed using AMPure XP beads (Agencourt Biosciences; A63880). Up to 200 quantified single-cell libraries were pooled, and these were sequenced 150 bp paired-end on one lane of Illumina HiSeq 4000 to a depth of 2.1 million reads per cell.

tag: differentiation stage

value: PHH

tag: cell id at each stage

tag: subject

tag: qc

value: FALSE


title: s341, 2nd sample set (scRNA-seq)

source_name: HB

value: HB

value: TRUE


title: s348, 2nd sample set (scRNA-seq)


title: s344, 2nd sample set (scRNA-seq)


title: s345, 2nd sample set (scRNA-seq)


title: s342, 2nd sample set (scRNA-seq)


title: B. subtilis incubated for 0h after HHP treatment, biological rep2

value: Immediately after HHP treatment


title: s347, 2nd sample set (scRNA-seq)


title: s340, 2nd sample set (scRNA-seq)


title: B. subtilis incubated for 0h after HHP treatment, biological rep1


title: s337, 2nd sample set (scRNA-seq)


title: s335, 2nd sample set (scRNA-seq)


title: s339, 2nd sample set (scRNA-seq)


title: s338, 2nd sample set (scRNA-seq)


title: s336, 2nd sample set (scRNA-seq)


title: s333, 2nd sample set (scRNA-seq)


title: s334, 2nd sample set (scRNA-seq)


title: s332, 2nd sample set (scRNA-seq)

source_name: phLO

value: phLO


title: s330, 2nd sample set (scRNA-seq)


title: s329, 2nd sample set (scRNA-seq)


title: s327, 2nd sample set (scRNA-seq)


title: s328, 2nd sample set (scRNA-seq)


title: s343, 2nd sample set (scRNA-seq)


title: s325, 2nd sample set (scRNA-seq)


title: s326, 2nd sample set (scRNA-seq)


title: s324, 2nd sample set (scRNA-seq)


title: s331, 2nd sample set (scRNA-seq)


title: s323, 2nd sample set (scRNA-seq)


title: s306, 2nd sample set (scRNA-seq)


title: s316, 2nd sample set (scRNA-seq)


title: s321, 2nd sample set (scRNA-seq)


title: s307, 2nd sample set (scRNA-seq)


title: s322, 2nd sample set (scRNA-seq)


title: s319, 2nd sample set (scRNA-seq)


title: s315, 2nd sample set (scRNA-seq)


title: s310, 2nd sample set (scRNA-seq)


title: s308, 2nd sample set (scRNA-seq)


title: s312, 2nd sample set (scRNA-seq)


title: s320, 2nd sample set (scRNA-seq)


title: s309, 2nd sample set (scRNA-seq)


title: s314, 2nd sample set (scRNA-seq)


title: s311, 2nd sample set (scRNA-seq)


title: s313, 2nd sample set (scRNA-seq)


title: s301, 2nd sample set (scRNA-seq)


title: s302, 2nd sample set (scRNA-seq)


title: s304, 2nd sample set (scRNA-seq)


title: s299, 2nd sample set (scRNA-seq)


title: s305, 2nd sample set (scRNA-seq)


title: s303, 2nd sample set (scRNA-seq)


title: s317, 2nd sample set (scRNA-seq)


title: s318, 2nd sample set (scRNA-seq)


title: s298, 2nd sample set (scRNA-seq)


title: s297, 2nd sample set (scRNA-seq)


title: s296, 2nd sample set (scRNA-seq)


title: s295, 2nd sample set (scRNA-seq)


title: s294, 2nd sample set (scRNA-seq)


title: s290, 2nd sample set (scRNA-seq)


title: s293, 2nd sample set (scRNA-seq)


title: s291, 2nd sample set (scRNA-seq)


title: s289, 2nd sample set (scRNA-seq)


title: s292, 2nd sample set (scRNA-seq)


title: s288, 2nd sample set (scRNA-seq)

source_name: iPSC

value: iPSC


title: s286, 2nd sample set (scRNA-seq)


title: s284, 2nd sample set (scRNA-seq)


title: s283, 2nd sample set (scRNA-seq)


title: s285, 2nd sample set (scRNA-seq)


title: s287, 2nd sample set (scRNA-seq)


title: s277, 2nd sample set (scRNA-seq)


title: s282, 2nd sample set (scRNA-seq)


title: s278, 2nd sample set (scRNA-seq)


title: s280, 2nd sample set (scRNA-seq)


title: s279, 2nd sample set (scRNA-seq)


title: s281, 2nd sample set (scRNA-seq)


title: s274, 2nd sample set (scRNA-seq)


title: s275, 2nd sample set (scRNA-seq)


title: s273, 2nd sample set (scRNA-seq)


title: s276, 2nd sample set (scRNA-seq)


title: s300, 2nd sample set (scRNA-seq)


title: s271, 2nd sample set (scRNA-seq)


title: s272, 2nd sample set (scRNA-seq)


title: s269, 2nd sample set (scRNA-seq)


title: s270, 2nd sample set (scRNA-seq)


title: s267, 2nd sample set (scRNA-seq)


title: s268, 2nd sample set (scRNA-seq)


title: s266, 2nd sample set (scRNA-seq)


title: s260, 2nd sample set (scRNA-seq)


title: s259, 2nd sample set (scRNA-seq)


title: s261, 2nd sample set (scRNA-seq)


title: s263, 2nd sample set (scRNA-seq)


title: s262, 2nd sample set (scRNA-seq)


title: s255, 2nd sample set (scRNA-seq)


title: s257, 2nd sample set (scRNA-seq)


title: s258, 2nd sample set (scRNA-seq)


title: s256, 2nd sample set (scRNA-seq)


title: s265, 2nd sample set (scRNA-seq)


title: s254, 2nd sample set (scRNA-seq)


title: s251, 2nd sample set (scRNA-seq)


title: s245, 2nd sample set (scRNA-seq)


title: s250, 2nd sample set (scRNA-seq)


title: s249, 2nd sample set (scRNA-seq)


title: s246, 2nd sample set (scRNA-seq)


title: s252, 2nd sample set (scRNA-seq)


title: s247, 2nd sample set (scRNA-seq)


title: s244, 2nd sample set (scRNA-seq)


title: s243, 2nd sample set (scRNA-seq)


title: s241, 2nd sample set (scRNA-seq)


title: s242, 2nd sample set (scRNA-seq)


title: s240, 2nd sample set (scRNA-seq)


title: s239, 2nd sample set (scRNA-seq)


title: s238, 2nd sample set (scRNA-seq)


title: s237, 2nd sample set (scRNA-seq)


title: s253, 2nd sample set (scRNA-seq)


title: s248, 2nd sample set (scRNA-seq)


title: s234, 2nd sample set (scRNA-seq)


title: s233, 2nd sample set (scRNA-seq)


title: s231, 2nd sample set (scRNA-seq)


title: s226, 2nd sample set (scRNA-seq)


title: s232, 2nd sample set (scRNA-seq)


title: s227, 2nd sample set (scRNA-seq)


title: s229, 2nd sample set (scRNA-seq)


title: s228, 2nd sample set (scRNA-seq)


title: s264, 2nd sample set (scRNA-seq)


title: s224, 2nd sample set (scRNA-seq)


title: s223, 2nd sample set (scRNA-seq)


title: s225, 2nd sample set (scRNA-seq)


title: s222, 2nd sample set (scRNA-seq)


title: s218, 2nd sample set (scRNA-seq)


title: s219, 2nd sample set (scRNA-seq)


title: s217, 2nd sample set (scRNA-seq)


title: s221, 2nd sample set (scRNA-seq)


title: s216, 2nd sample set (scRNA-seq)


title: s215, 2nd sample set (scRNA-seq)


title: s213, 2nd sample set (scRNA-seq)


title: s214, 2nd sample set (scRNA-seq)


title: s236, 2nd sample set (scRNA-seq)


title: Skin_Dermatomyositis_Negative_2

description: Sample name: H1406

value: Skin

value: Dermatomyositis

value: Negative


title: s211, 2nd sample set (scRNA-seq)


title: s212, 2nd sample set (scRNA-seq)


title: s210, 2nd sample set (scRNA-seq)


title: s209, 2nd sample set (scRNA-seq)


title: s206, 2nd sample set (scRNA-seq)


title: s230, 2nd sample set (scRNA-seq)


title: s204, 2nd sample set (scRNA-seq)


title: s207, 2nd sample set (scRNA-seq)


title: s205, 2nd sample set (scRNA-seq)


title: s201, 2nd sample set (scRNA-seq)


title: s200, 2nd sample set (scRNA-seq)


title: s198, 2nd sample set (scRNA-seq)


title: s197, 2nd sample set (scRNA-seq)


title: s196, 2nd sample set (scRNA-seq)


title: s194, 2nd sample set (scRNA-seq)


title: s193, 2nd sample set (scRNA-seq)


title: s191, 2nd sample set (scRNA-seq)


title: s192, 2nd sample set (scRNA-seq)


title: s190, 2nd sample set (scRNA-seq)


title: s189, 2nd sample set (scRNA-seq)


title: s188, 2nd sample set (scRNA-seq)


title: s187, 2nd sample set (scRNA-seq)


title: s208, 2nd sample set (scRNA-seq)


title: s184, 2nd sample set (scRNA-seq)


title: s182, 2nd sample set (scRNA-seq)


title: s203, 2nd sample set (scRNA-seq)


title: s183, 2nd sample set (scRNA-seq)


title: s185, 2nd sample set (scRNA-seq)


title: s202, 2nd sample set (scRNA-seq)


title: s199, 2nd sample set (scRNA-seq)


title: s179, 2nd sample set (scRNA-seq)


title: s180, 2nd sample set (scRNA-seq)


title: s195, 2nd sample set (scRNA-seq)


title: s177, 2nd sample set (scRNA-seq)


title: s178, 2nd sample set (scRNA-seq)


title: s181, 2nd sample set (scRNA-seq)


title: s175, 2nd sample set (scRNA-seq)


title: s235, 2nd sample set (scRNA-seq)


title: s176, 2nd sample set (scRNA-seq)


title: s174, 2nd sample set (scRNA-seq)


title: s171, 2nd sample set (scRNA-seq)


title: s172, 2nd sample set (scRNA-seq)


title: s168, 2nd sample set (scRNA-seq)


title: s170, 2nd sample set (scRNA-seq)


title: s169, 2nd sample set (scRNA-seq)


title: s186, 2nd sample set (scRNA-seq)


title: s166, 2nd sample set (scRNA-seq)


title: s162, 2nd sample set (scRNA-seq)


title: s163, 2nd sample set (scRNA-seq)


title: s164, 2nd sample set (scRNA-seq)


title: s160, 2nd sample set (scRNA-seq)


title: s161, 2nd sample set (scRNA-seq)


title: s167, 2nd sample set (scRNA-seq)


title: s158, 2nd sample set (scRNA-seq)


title: s157, 2nd sample set (scRNA-seq)


title: s159, 2nd sample set (scRNA-seq)


title: s154, 2nd sample set (scRNA-seq)


title: s173, 2nd sample set (scRNA-seq)


title: s153, 2nd sample set (scRNA-seq)


title: s151, 2nd sample set (scRNA-seq)


title: s156, 2nd sample set (scRNA-seq)


title: s152, 2nd sample set (scRNA-seq)


title: s150, 2nd sample set (scRNA-seq)


title: s148, 2nd sample set (scRNA-seq)


title: s149, 2nd sample set (scRNA-seq)


title: s147, 2nd sample set (scRNA-seq)


title: s145, 2nd sample set (scRNA-seq)


title: s165, 2nd sample set (scRNA-seq)


title: s146, 2nd sample set (scRNA-seq)


title: s144, 2nd sample set (scRNA-seq)


title: s143, 2nd sample set (scRNA-seq)


title: s142, 2nd sample set (scRNA-seq)


title: s140, 2nd sample set (scRNA-seq)


title: s141, 2nd sample set (scRNA-seq)


title: s139, 2nd sample set (scRNA-seq)


title: s136, 2nd sample set (scRNA-seq)


title: s135, 2nd sample set (scRNA-seq)


title: s155, 2nd sample set (scRNA-seq)


title: s133, 2nd sample set (scRNA-seq)


title: s134, 2nd sample set (scRNA-seq)


title: s132, 2nd sample set (scRNA-seq)


title: s128, 2nd sample set (scRNA-seq)


title: s127, 2nd sample set (scRNA-seq)


title: s125, 2nd sample set (scRNA-seq)


title: s138, 2nd sample set (scRNA-seq)


title: s137, 2nd sample set (scRNA-seq)


title: s131, 2nd sample set (scRNA-seq)


title: s121, 2nd sample set (scRNA-seq)


title: s220, 2nd sample set (scRNA-seq)


title: s130, 2nd sample set (scRNA-seq)


title: s129, 2nd sample set (scRNA-seq)


title: s120, 2nd sample set (scRNA-seq)


title: s118, 2nd sample set (scRNA-seq)


title: s117, 2nd sample set (scRNA-seq)


title: s119, 2nd sample set (scRNA-seq)


title: s115, 2nd sample set (scRNA-seq)


title: s113, 2nd sample set (scRNA-seq)


title: s114, 2nd sample set (scRNA-seq)


title: s111, 2nd sample set (scRNA-seq)


title: s109, 2nd sample set (scRNA-seq)


title: s110, 2nd sample set (scRNA-seq)


title: s126, 2nd sample set (scRNA-seq)


title: s123, 2nd sample set (scRNA-seq)


title: s107, 2nd sample set (scRNA-seq)


title: s108, 2nd sample set (scRNA-seq)


title: s106, 2nd sample set (scRNA-seq)


title: s124, 2nd sample set (scRNA-seq)


title: s104, 2nd sample set (scRNA-seq)


title: s103, 2nd sample set (scRNA-seq)


title: s122, 2nd sample set (scRNA-seq)


title: s102, 2nd sample set (scRNA-seq)


title: s99, 2nd sample set (scRNA-seq)


title: s100, 2nd sample set (scRNA-seq)


title: s101, 2nd sample set (scRNA-seq)


title: s98, 2nd sample set (scRNA-seq)


title: s97, 2nd sample set (scRNA-seq)


title: s95, 2nd sample set (scRNA-seq)


title: s96, 2nd sample set (scRNA-seq)


title: s116, 2nd sample set (scRNA-seq)


title: s94, 2nd sample set (scRNA-seq)


title: s92, 2nd sample set (scRNA-seq)


title: s93, 2nd sample set (scRNA-seq)


title: s112, 2nd sample set (scRNA-seq)


title: s90, 2nd sample set (scRNA-seq)


title: s91, 2nd sample set (scRNA-seq)


title: s89, 2nd sample set (scRNA-seq)


title: s88, 2nd sample set (scRNA-seq)


title: s87, 2nd sample set (scRNA-seq)


title: s105, 2nd sample set (scRNA-seq)


title: s83, 2nd sample set (scRNA-seq)


title: s79, 2nd sample set (scRNA-seq)


title: s81, 2nd sample set (scRNA-seq)


title: s86, 2nd sample set (scRNA-seq)


title: s80, 2nd sample set (scRNA-seq)


title: s85, 2nd sample set (scRNA-seq)


title: s84, 2nd sample set (scRNA-seq)


title: s82, 2nd sample set (scRNA-seq)


title: s74, 2nd sample set (scRNA-seq)


title: s73, 2nd sample set (scRNA-seq)


title: s75, 2nd sample set (scRNA-seq)


title: s78, 2nd sample set (scRNA-seq)


title: s76, 2nd sample set (scRNA-seq)


title: s77, 2nd sample set (scRNA-seq)


title: s69, 2nd sample set (scRNA-seq)


title: s71, 2nd sample set (scRNA-seq)


title: s67, 2nd sample set (scRNA-seq)


title: s70, 2nd sample set (scRNA-seq)


title: s68, 2nd sample set (scRNA-seq)


title: s64, 2nd sample set (scRNA-seq)


title: s63, 2nd sample set (scRNA-seq)


title: s61, 2nd sample set (scRNA-seq)


title: s59, 2nd sample set (scRNA-seq)


title: s60, 2nd sample set (scRNA-seq)


title: s58, 2nd sample set (scRNA-seq)


title: s57, 2nd sample set (scRNA-seq)


title: s53, 2nd sample set (scRNA-seq)


title: s55, 2nd sample set (scRNA-seq)


title: s51, 2nd sample set (scRNA-seq)


title: s56, 2nd sample set (scRNA-seq)


title: s52, 2nd sample set (scRNA-seq)


title: s72, 2nd sample set (scRNA-seq)


title: s54, 2nd sample set (scRNA-seq)


title: s49, 2nd sample set (scRNA-seq)


title: s50, 2nd sample set (scRNA-seq)


title: s65, 2nd sample set (scRNA-seq)


title: s46, 2nd sample set (scRNA-seq)


title: s44, 2nd sample set (scRNA-seq)


title: s43, 2nd sample set (scRNA-seq)


title: s39, 2nd sample set (scRNA-seq)


title: s47, 2nd sample set (scRNA-seq)


title: s62, 2nd sample set (scRNA-seq)


title: s48, 2nd sample set (scRNA-seq)


title: s45, 2nd sample set (scRNA-seq)


title: s42, 2nd sample set (scRNA-seq)


title: s40, 2nd sample set (scRNA-seq)


title: s66, 2nd sample set (scRNA-seq)


title: s41, 2nd sample set (scRNA-seq)


title: s37, 2nd sample set (scRNA-seq)


title: s38, 2nd sample set (scRNA-seq)


title: s36, 2nd sample set (scRNA-seq)


title: s34, 2nd sample set (scRNA-seq)


title: s33, 2nd sample set (scRNA-seq)


title: s31, 2nd sample set (scRNA-seq)


title: s30, 2nd sample set (scRNA-seq)


title: s29, 2nd sample set (scRNA-seq)


title: s27, 2nd sample set (scRNA-seq)


title: s28, 2nd sample set (scRNA-seq)


title: s25, 2nd sample set (scRNA-seq)


title: s26, 2nd sample set (scRNA-seq)


title: s24, 2nd sample set (scRNA-seq)


title: s23, 2nd sample set (scRNA-seq)


title: s22, 2nd sample set (scRNA-seq)


title: s21, 2nd sample set (scRNA-seq)


title: s19, 2nd sample set (scRNA-seq)


title: s35, 2nd sample set (scRNA-seq)


title: s17, 2nd sample set (scRNA-seq)


title: s14, 2nd sample set (scRNA-seq)


title: s9, 2nd sample set (scRNA-seq)


title: s15, 2nd sample set (scRNA-seq)


title: s18, 2nd sample set (scRNA-seq)


title: s6, 2nd sample set (scRNA-seq)


title: s32, 2nd sample set (scRNA-seq)


title: s20, 2nd sample set (scRNA-seq)


title: s7, 2nd sample set (scRNA-seq)


title: s10, 2nd sample set (scRNA-seq)


title: s11, 2nd sample set (scRNA-seq)


title: s13, 2nd sample set (scRNA-seq)


title: s4, 2nd sample set (scRNA-seq)


title: s12, 2nd sample set (scRNA-seq)


title: s2, 2nd sample set (scRNA-seq)


title: S123, 1st sample set (scRNA-seq)


title: s1, 2nd sample set (scRNA-seq)


title: S89, 1st sample set (scRNA-seq)

source_name: GM

value: GM


title: S72, 1st sample set (scRNA-seq)


title: S55, 1st sample set (scRNA-seq)


title: s8, 2nd sample set (scRNA-seq)


title: S38, 1st sample set (scRNA-seq)


title: S157, 1st sample set (scRNA-seq)


title: S106, 1st sample set (scRNA-seq)

source_name: DM

value: DM


title: S4, 1st sample set (scRNA-seq)


title: S191, 1st sample set (scRNA-seq)


title: S21, 1st sample set (scRNA-seq)


title: S140, 1st sample set (scRNA-seq)


title: S125, 1st sample set (scRNA-seq)


title: S91, 1st sample set (scRNA-seq)


title: S74, 1st sample set (scRNA-seq)


title: S208, 1st sample set (scRNA-seq)


title: S40, 1st sample set (scRNA-seq)


title: S176, 1st sample set (scRNA-seq)


title: s5, 2nd sample set (scRNA-seq)


title: S142, 1st sample set (scRNA-seq)


title: S57, 1st sample set (scRNA-seq)


title: S108, 1st sample set (scRNA-seq)


title: S159, 1st sample set (scRNA-seq)


title: S6, 1st sample set (scRNA-seq)


title: S193, 1st sample set (scRNA-seq)


title: S120, 1st sample set (scRNA-seq)


title: S35, 1st sample set (scRNA-seq)


title: S69, 1st sample set (scRNA-seq)


title: S86, 1st sample set (scRNA-seq)


title: S23, 1st sample set (scRNA-seq)


title: S210, 1st sample set (scRNA-seq)


title: S174, 1st sample set (scRNA-seq)


title: S171, 1st sample set (scRNA-seq)


title: S52, 1st sample set (scRNA-seq)


title: S154, 1st sample set (scRNA-seq)


title: S137, 1st sample set (scRNA-seq)


title: S1, 1st sample set (scRNA-seq)


title: S188, 1st sample set (scRNA-seq)


title: S18, 1st sample set (scRNA-seq)


title: S131, 1st sample set (scRNA-seq)


title: S80, 1st sample set (scRNA-seq)


title: S205, 1st sample set (scRNA-seq)


title: S63, 1st sample set (scRNA-seq)


title: S97, 1st sample set (scRNA-seq)


title: S46, 1st sample set (scRNA-seq)


title: S182, 1st sample set (scRNA-seq)


title: S12, 1st sample set (scRNA-seq)


title: S165, 1st sample set (scRNA-seq)


title: S199, 1st sample set (scRNA-seq)


title: S148, 1st sample set (scRNA-seq)


title: S114, 1st sample set (scRNA-seq)


title: S29, 1st sample set (scRNA-seq)


title: S216, 1st sample set (scRNA-seq)


title: S67, 1st sample set (scRNA-seq)


title: S84, 1st sample set (scRNA-seq)


title: S186, 1st sample set (scRNA-seq)


title: S101, 1st sample set (scRNA-seq)


title: S50, 1st sample set (scRNA-seq)


title: S103, 1st sample set (scRNA-seq)


title: S152, 1st sample set (scRNA-seq)


title: S169, 1st sample set (scRNA-seq)


title: S16, 1st sample set (scRNA-seq)


title: S118, 1st sample set (scRNA-seq)


title: S203, 1st sample set (scRNA-seq)


title: S33, 1st sample set (scRNA-seq)


title: S220, 1st sample set (scRNA-seq)

value: LIVER


title: S124, 1st sample set (scRNA-seq)


title: S73, 1st sample set (scRNA-seq)


title: S56, 1st sample set (scRNA-seq)


title: S175, 1st sample set (scRNA-seq)


title: S158, 1st sample set (scRNA-seq)


title: S135, 1st sample set (scRNA-seq)


title: S141, 1st sample set (scRNA-seq)


title: S5, 1st sample set (scRNA-seq)


title: S192, 1st sample set (scRNA-seq)


title: S107, 1st sample set (scRNA-seq)


title: S22, 1st sample set (scRNA-seq)


title: S47, 1st sample set (scRNA-seq)


title: CBM Mesenchymal rep6

city: Farmington

first: Peter

last: Maye

state: Connecticut

address: 263 Farmington Avenue

department: Reconstructive Sciences

institute: UConn Health

description: ribosomal RNA depleted total RNA

data_processing:
Illumina RTA 2.4.11 is used for base calling
FASTQC 0.11.7 and MultiQC are used to access the quality of the reads. Sickle is used to trim low quality reads
RNASTAR version 2.5.3a is used as the alignment tool.
htseq_count function from HTSeq 0.9.1 is used to measure the abundance of each feature
DESeq2 version 1.20.0 is used to normalize the counts and generate differentially expressed feature list from the abundance count. Pathway prediction analysis is carried out through Gene ontology (PANTHER Overrepresentation Test (Released 20181010) and Annotation Version and Release Date: GO Ontology database  Released 2018-10-08). Pathway prediction was also carried out using Ingenuity Pathway Analysis tool (Build version: 470319M, Content version: 42012434 (Release Date: 2017-12-07)) from Qiagen.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: Day 7 bone marrow stromal cultures

growth_protocol: Bone marrow stromal cultures were grown in vitro for 7 days in MEM-alpha with 10% FBS and 1% Penstrep

extract_protocol:
RNA was extracted using Direct-zol RNA Miniprep Plus kit from Zymo. Ribosomal RNA was depleted with the help of RiboGone-Mammalian from Takara Biosciences.
Illumina compatible libraries were generated using SMARTer Stranded RNA-Seq Kit from Takara Biosciences and paired end sequencing was performed using the NextSeq sequencing kit i.e. NextSeq® 500/550 High Output Kit v2 (150 cycles)

treatment_protocol: Prior to extraction of RNA, hematopoietic and mesenchymal cells were sorted based on the cell surface markers CD45 and Sca1 with the help of FACS. CD45+Sca1+ were considered hematopoietic cells and CD45-Sca1+ were considered mesenchymal cells.

tag: gender

value: female

tag: age

value: 6-8 week old

value: Bone marrow

tag: cell population

value: Mesenchymal

tag: genotype


title: S98, 1st sample set (scRNA-seq)


title: CBM Mesenchymal rep4

description: ribosomal RNA depleted total RNA

tag: tissue


title: S132, 1st sample set (scRNA-seq)


title: S81, 1st sample set (scRNA-seq)


title: CBM Mesenchymal rep5

description: ribosomal RNA depleted total RNA


title: CBM Mesenchymal rep2

description: ribosomal RNA depleted total RNA


title: S209, 1st sample set (scRNA-seq)


title: CBM Mesenchymal rep3

description: ribosomal RNA depleted total RNA


title: S64, 1st sample set (scRNA-seq)


title: WT Mesenchymal rep5

description: ribosomal RNA depleted total RNA

value: wild type


title: WT Mesenchymal rep6

description: ribosomal RNA depleted total RNA


title: S39, 1st sample set (scRNA-seq)


title: S90, 1st sample set (scRNA-seq)


title: S183, 1st sample set (scRNA-seq)


title: S166, 1st sample set (scRNA-seq)


title: WT Mesenchymal rep3

description: ribosomal RNA depleted total RNA


title: WT Mesenchymal rep4

description: ribosomal RNA depleted total RNA


title: S149, 1st sample set (scRNA-seq)


title: S13, 1st sample set (scRNA-seq)


title: WT Mesenchymal rep2

description: ribosomal RNA depleted total RNA


title: WT Mesenchymal rep1

description: ribosomal RNA depleted total RNA


title: S115, 1st sample set (scRNA-seq)


title: S200, 1st sample set (scRNA-seq)


title: CBM Hematopoietic rep6

description: ribosomal RNA depleted total RNA

value: Hematopoietic


title: S30, 1st sample set (scRNA-seq)


title: CBM Hematopoietic rep3

description: ribosomal RNA depleted total RNA


title: S77, 1st sample set (scRNA-seq)


title: CBM Hematopoietic rep2

description: ribosomal RNA depleted total RNA


title: S43, 1st sample set (scRNA-seq)

value: FALSE


title: CBM Hematopoietic rep4

description: ribosomal RNA depleted total RNA


title: CBM Mesenchymal rep1

description: ribosomal RNA depleted total RNA


title: S128, 1st sample set (scRNA-seq)

value: PHH

value: TRUE


title: S217, 1st sample set (scRNA-seq)


title: CBM Hematopoietic rep1

description: ribosomal RNA depleted total RNA


title: S94, 1st sample set (scRNA-seq)


title: WT Hematopoietic rep4

description: ribosomal RNA depleted total RNA


title: S60, 1st sample set (scRNA-seq)

value: phLO


title: WT Hematopoietic rep3

description: ribosomal RNA depleted total RNA


title: S162, 1st sample set (scRNA-seq)

value: HB


title: S179, 1st sample set (scRNA-seq)


title: S145, 1st sample set (scRNA-seq)

value: iPSC


title: WT Hematopoietic rep1

description: ribosomal RNA depleted total RNA


title: CBM Hematopoietic rep5

description: ribosomal RNA depleted total RNA


title: S9, 1st sample set (scRNA-seq)


title: MuSC_d7_Aged_bulkATACseq_Rep4

city: Boston

first: Sundari

last: Chetty

state: MA

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

description: PE ATAC-seq

library_source: genomic

data_processing:
In according with the NextSeq500 analysis, protocol, base calling and quality scoring are performed by an updated implementation of Real-Time Analysis (RTA), called RTA v2
FASTQ reads are processed with the ENCODE-DCC ATAC-seq pipeline, v 1.0
A merged ATAC-seq peak set across samples was generated by applying the bedtools merge command across the sample naive overlap optimal peak sets
Read counts for each peak for each sample were obtained with the bedtools coverage command over the merged ATAC-seq peak set
Technical replicates with pearson correlation < 0.9 across peak CPM values were excluded from analysis
Genome_build: mm10
Supplementary_files_format_and_content: tagAlign files, bigWig files, and peak calls files (narrowPeak) were generated for each technical replicate via the ENCODE ATAC-seq data processing pipeline ()
Reads were aligned to mm10 reference genome using STAR (v 2.5.0a)
Transcript and gene abundance was quantified via RSEM (v 1.3.0)
Technical replicates with pearson correlation < 0.9 across gene TPM values were excluded from analysis
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimeted text file include FPKM, TPM, and expected read count values for each technical replicate

molecule: genomic DNA

source_name: MuSCs, Post-injury Day 7, Aged

extract_protocol:
Hind limb muscles (tibialis anterior and gastrocnemius) of control and experimental mice were dissected using sterile surgical tools,  tissues were minced and transferred into 50 mL conical tubes containing 20 mL of digest solution. Cell sorting was done using a BD FACSAria III Cell Sorter.
Chromatin Accessibility Assay and Sequencing Library Preparation.
At least 10,000 MuSCs were centrifuged at 500xg for 5 min at 4˚C in a fixed angle centrifuge. After removing the supernatant, the cell pellets were re-suspended in 50uL ATAC-Resuspension Buffer (RSB) (500uL 1M Tris-HCl, 100uL 5M NaCl, 150uL 1M MgCl2 in 49.25mL sterile water) with 0.1% NP40, 0.1% tween-20, and 0.01% Digitonin. Samples were pipetted up and down three times to mix, incubated 3 minutes on ice, then diluted in 1mL of ice-cold ATAC-RSB containing 0.1% Tween-20 and centrifuged at 500xg for 10 min at 4˚C to pellet the nuclei. The supernatants were carefully removed and the pellets were re-suspended in 25 µL of transposase reaction mix (12.5 µL 2x TD buffer, 1.25 µL TN5 transposase (Illumina) and 11.25 µL nuclease-free water). Transposase reactions were carried out by incubating samples at 37˚C for 30 min under mild agitation (300 rpm on a Thermo-mixer C, Eppendorf). Once the incubation was completed, sample tubes were placed on ice and the transposed DNA fragments from each sample were purified using a Qiagen MinElute PCR Purification Kit following manufacture’s protocol. Purified DNA fragments were then amplified for 13 cycles using barcoded PCR primers and NEB Next High Fidelity 2x PCR Master Mix (New England Bio Labs) on a thermal cycler. Double concentrated Ampure beads were used to purify transposed DNA amplicons. The molarity of each DNA library was determined (Agilent 2100 Bioanalyzer), pooled into a single tube and sequenced on a NextSeq (Illumina) using 76-bp paired-end reads.
Bulk mRNA Isolation and Sequencing Library Preparation.
MuSCs sorted directly into Trizol were thawed at room temperature, and RNA was extracted using a Qiagen miRNeasy Micro Kit as per manufacturer’s instructions. RNA concentration and integrity were measured with a Nanodrop spectrophotometer (Nanodrop 2000c) and Bioanalyzer (Agilent 2100). 1-10 ng of high-quality RNA (RIN>8) was used to produce cDNA libraries using the SmartSeq v4 protocol (Clontech) as per the manufacturer’s instructions. cDNAs were prepared into sequencing libraries using 150 pg of full-length cDNA amplicons (Nextera XT DNA Library Preparation Kit, Illumina) with dual index barcodes as per manufacturer’s instructions. Barcoded cDNA libraries were pooled into a single tube and sequenced on a NextSeq (Illumina) using 76-bp single-ended reads.

tag: cell type

value: Flow sorted muscle stem cells

value: Aged

tag: timecourse


title: S196, 1st sample set (scRNA-seq)


title: MuSC_d7_Aged_bulkATACseq_Rep3

description: PE ATAC-seq


title: WT Hematopoietic rep6

description: ribosomal RNA depleted total RNA


title: S26, 1st sample set (scRNA-seq)


title: MuSC_d7_Aged_bulkATACseq_Rep1

description: PE ATAC-seq


title: S136, 1st sample set (scRNA-seq)


title: S213, 1st sample set (scRNA-seq)


title: MuSC_d7_Young_bulkATACseq_Rep4

description: PE ATAC-seq

source_name: MuSCs, Post-injury Day 7, Young

value: Young


title: MuSC_d7_Young_bulkATACseq_Rep5

description: PE ATAC-seq


title: WT Hematopoietic rep5

description: ribosomal RNA depleted total RNA


title: MuSC_d7_Young_bulkATACseq_Rep2

description: PE ATAC-seq


title: S85, 1st sample set (scRNA-seq)


title: MuSC_d7_Young_bulkATACseq_Rep3

description: PE ATAC-seq


title: S68, 1st sample set (scRNA-seq)


title: S51, 1st sample set (scRNA-seq)


title: S102, 1st sample set (scRNA-seq)


title: WT Hematopoietic rep2

description: ribosomal RNA depleted total RNA


title: S187, 1st sample set (scRNA-seq)


title: MuSC_d5_Aged_bulkATACseq_Rep1

description: PE ATAC-seq

source_name: MuSCs, Post-injury Day 5, Aged


title: MuSC_d7_Young_bulkATACseq_Rep1

description: PE ATAC-seq


title: S111, 1st sample set (scRNA-seq)

value: DM


title: MuSC_d5_Aged_bulkATACseq_Rep2

description: PE ATAC-seq


title: MuSC_d5_Young_bulkATACseq_Rep2

description: PE ATAC-seq

source_name: MuSCs, Post-injury Day 5, Young


title: S153, 1st sample set (scRNA-seq)


title: S170, 1st sample set (scRNA-seq)


title: MuSC_d5_Young_bulkATACseq_Rep1

description: PE ATAC-seq


title: s16, 2nd sample set (scRNA-seq)


title: S119, 1st sample set (scRNA-seq)


title: MuSC_d7_Aged_bulkATACseq_Rep2

description: PE ATAC-seq


title: S17, 1st sample set (scRNA-seq)


title: MuSC_d3_Aged_bulkATACseq_Rep3

description: PE ATAC-seq

source_name: MuSCs, Post-injury Day 3, Aged


title: S204, 1st sample set (scRNA-seq)


title: S34, 1st sample set (scRNA-seq)


title: S221, 1st sample set (scRNA-seq)

value: LIVER


title: MuSC_d3_Aged_bulkATACseq_Rep1

description: PE ATAC-seq


title: S75, 1st sample set (scRNA-seq)


title: MuSC_d3_Young_bulkATACseq_Rep3

description: PE ATAC-seq

source_name: MuSCs, Post-injury Day 3, Young


title: S41, 1st sample set (scRNA-seq)


title: S126, 1st sample set (scRNA-seq)


title: MuSC_d1_Aged_bulkATACseq_Rep2

description: PE ATAC-seq

source_name: MuSCs, Post-injury Day 1, Aged


title: S92, 1st sample set (scRNA-seq)

value: GM


title: MuSC_d3_Young_bulkATACseq_Rep2

description: PE ATAC-seq


title: MuSC_d3_Young_bulkATACseq_Rep1

description: PE ATAC-seq


title: S177, 1st sample set (scRNA-seq)


title: S58, 1st sample set (scRNA-seq)


title: MuSC_d1_Aged_bulkATACseq_Rep1

description: PE ATAC-seq


title: MuSC_d1_Young_bulkATACseq_Rep3

description: PE ATAC-seq

source_name: MuSCs, Post-injury Day 1, Young


title: S160, 1st sample set (scRNA-seq)


title: MuSC_d3_Aged_bulkATACseq_Rep4

description: PE ATAC-seq


title: MuSC_d1_Young_bulkATACseq_Rep1

description: PE ATAC-seq


title: MuSC_d1_Young_bulkATACseq_Rep2

description: PE ATAC-seq


title: MuSC_d0_Young_Pax7_Rep1_bulkATAC_Rep3

description: PE ATAC-seq

source_name: MuSCs, Pre-injury, Young, Pax7+


title: S7, 1st sample set (scRNA-seq)


title: S194, 1st sample set (scRNA-seq)


title: S109, 1st sample set (scRNA-seq)


title: S143, 1st sample set (scRNA-seq)


title: MuSC_d0_Young_Pax7_Rep1_bulkATAC_Rep2

description: PE ATAC-seq


title: S24, 1st sample set (scRNA-seq)


title: MuSC_d0_Young_Pax7_Rep1_bulkATAC_Rep1

description: PE ATAC-seq


title: MuSC_d3_Young_bulkATACseq_Rep4

description: PE ATAC-seq


title: MuSC_d3_Aged_bulkATACseq_Rep2

description: PE ATAC-seq


title: S211, 1st sample set (scRNA-seq)


title: S121, 1st sample set (scRNA-seq)


title: S87, 1st sample set (scRNA-seq)


title: MuSC_d0_Aged_bulkATACseq_Rep5

description: PE ATAC-seq

source_name: MuSCs, Pre-injury, Aged


title: S70, 1st sample set (scRNA-seq)


title: S53, 1st sample set (scRNA-seq)


title: S172, 1st sample set (scRNA-seq)


title: MuSC_d0_Aged_bulkATACseq_Rep4

description: PE ATAC-seq


title: S155, 1st sample set (scRNA-seq)


title: S138, 1st sample set (scRNA-seq)


title: MuSC_d0_Aged_bulkATACseq_Rep1

description: PE ATAC-seq


title: MuSC_d0_Young_bulkATACseq_Rep4

description: PE ATAC-seq

source_name: MuSCs, Pre-injury, Young


title: S2, 1st sample set (scRNA-seq)


title: S104, 1st sample set (scRNA-seq)


title: MuSC_d0_Young_bulkATACseq_Rep3

description: PE ATAC-seq


title: S189, 1st sample set (scRNA-seq)


title: MuSC_d0_Aged_bulkATACseq_Rep7

description: PE ATAC-seq


title: MuSC_d0_Young_bulkATACseq_Rep1

description: PE ATAC-seq


title: MuSC_d7_Aged_bulkRNAseq_Rep3

description:
SE RNA-seq
bulkRNAseq.FPKM.tsv
bulkRNAseq.TPM.tsv
bulkRNAseq.expected_count.tsv


title: MuSC_d0_Aged_bulkATACseq_Rep2

description: PE ATAC-seq


title: S19, 1st sample set (scRNA-seq)

source_name: HB


title: MuSC_d7_Aged_bulkRNAseq_Rep2


title: S206, 1st sample set (scRNA-seq)


title: MuSC_d7_Aged_bulkRNAseq_Rep1


title: S36, 1st sample set (scRNA-seq)

source_name: phLO


title: MuSC_d0_Aged_bulkATACseq_Rep6

description: PE ATAC-seq


title: S129, 1st sample set (scRNA-seq)

source_name: PHH


title: MuSC_d0_Aged_bulkATACseq_Rep3

description: PE ATAC-seq


title: S78, 1st sample set (scRNA-seq)

source_name: GM


title: S44, 1st sample set (scRNA-seq)


title: MuSC_d7_Young_bulkRNAseq_Rep3


title: MuSC_d7_Young_bulkRNAseq_Rep1


title: MuSC_d7_Young_bulkRNAseq_Rep4


title: S95, 1st sample set (scRNA-seq)


title: MuSC_d0_Young_bulkATACseq_Rep2

description: PE ATAC-seq


title: S61, 1st sample set (scRNA-seq)


title: MuSC_d7_Young_bulkRNAseq_Rep2


title: S180, 1st sample set (scRNA-seq)


title: S146, 1st sample set (scRNA-seq)

source_name: iPSC


title: S163, 1st sample set (scRNA-seq)


title: MuSC_d7_Aged_bulkRNAseq_Rep4


title: MuSC_d5_Aged_bulkRNAseq_Rep1


title: MuSC_d5_Young_bulkRNAseq_Rep3


title: S10, 1st sample set (scRNA-seq)


title: S112, 1st sample set (scRNA-seq)

source_name: DM


title: MuSC_d5_Young_bulkRNAseq_Rep1


title: MuSC_d5_Aged_bulkRNAseq_Rep2


title: MuSC_d5_Young_bulkRNAseq_Rep2


title: MuSC_d3_Aged_bulkRNAseq_Rep4


title: S27, 1st sample set (scRNA-seq)


title: MuSC_d3_Aged_bulkRNAseq_Rep2


title: MuSC_d3_Aged_bulkRNAseq_Rep1


title: S214, 1st sample set (scRNA-seq)


title: MuSC_d3_Aged_bulkRNAseq_Rep3


title: MuSC_d3_Young_bulkRNAseq_Rep5


title: S127, 1st sample set (scRNA-seq)


title: S42, 1st sample set (scRNA-seq)


title: MuSC_d3_Young_bulkRNAseq_Rep4


title: MuSC_d3_Young_bulkRNAseq_Rep2


title: S76, 1st sample set (scRNA-seq)


title: S178, 1st sample set (scRNA-seq)


title: S59, 1st sample set (scRNA-seq)


title: MuSC_d3_Young_bulkRNAseq_Rep3


title: S93, 1st sample set (scRNA-seq)


title: MuSC_d1_Aged_bulkRNAseq_Rep1


title: S144, 1st sample set (scRNA-seq)


title: S161, 1st sample set (scRNA-seq)


title: MuSC_d1_Young_bulkRNAseq_Rep4


title: S8, 1st sample set (scRNA-seq)


title: MuSC_d1_Young_bulkRNAseq_Rep3


title: MuSC_d1_Young_bulkRNAseq_Rep2


title: S110, 1st sample set (scRNA-seq)


title: S25, 1st sample set (scRNA-seq)


title: S195, 1st sample set (scRNA-seq)


title: MuSC_d1_Young_bulkRNAseq_Rep1


title: S197, 1st sample set (scRNA-seq)


title: S212, 1st sample set (scRNA-seq)