title: su(Hw)_2-4_BS1

description: Drosophila embryos RNAi, shsu(Hw), replicate 1, 2-4 hours


title: ss_16-18_BS1

status: Public on Jan 05 2023

type: SRA

city: Berkeley

first: Benjamin

middle: Wendell

last: Booth

state: CA

address: 1 Cyclotron Road

department: BioSciences

country: USA

institute: Lawrence Berkeley National Laboratory

description: Drosophila embryos RNAi, shss, replicate 1, 16-18 hours

library_source: transcriptomic

data_processing:
Raw FASTQ files were aligned to the Drosophila melanogaster reference genome (Release 6)  using STAR aligner 2.7.3a  with default settings and up to 20 multiple alignments to produce BAM files.
HTSeq htseq-count v0.12.4 was used to determine read counts overlapping genes.
Differential gene expression in the RNAi experimental samples compared to the mCherry controls was determined using DESeq2 1.24.0.
bigWig files were created using a custom tool called bam2bedgraph to convert bam files into bedgraph files, then UCSC's bedGraphToBigWig to convert the bedgraph files to bigWig format.
Assembly: dm6
Supplementary files format and content: BAM alignment files aligning FASTQ read files to dm6 assembly using STAR 2.7.3a.
Supplementary files format and content: HTSeq htseq-count files produced with HTSeq v0.12.4
Supplementary files format and content: DESeq csv files produced using DESeq2 v1.24.0
Supplementary files format and content: bigWig files produced using custom bam2bedgraph script and UCSC bedGraphToBigWig tool

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
Frozen embryos were homogenized using the Pellet Pestle Cordless Motor (Kimble Cat. No. 749540-0000; Pellet Pestles Sigma Cat. No. Z359947). RNA was extracted from the homogenate using TRIzol Reagent (Thermo Fisher, Cat. No. 15596026), chloroform extraction and isopropanol precipitation.  RNA was resuspended in Nuclease Free Water (Ambion AM9930) and incubated over night before purification using the RNeasy Mini Kit (QIAGEN Cat. No. 74106).  After Qiagen clean up, RNA was quantified using NanoDrop ND1000v 3.5.2.
Libraries for sequencing were made using TruSeq Stranded mRNA Library Prep (llumina 20020594).

tag: tissue

value: embryos

tag: treatment

value: shss

tag: timepoint

value: 16-18 hours


title: ss_16-18_BS2

description: Drosophila embryos RNAi, shss, replicate 2, 16-18 hours


title: ss_12-14_BS2

description: Drosophila embryos RNAi, shss, replicate 2, 12-14 hours

value: 12-14 hours


title: ss_0-1.5_BS2

description: Drosophila embryos RNAi, shss, replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: ss_12-14_BS1

description: Drosophila embryos RNAi, shss, replicate 1, 12-14 hours


title: sens_Sox14_trh_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for sens, Sox14, trh), replicate 2, 16-18 hours


title: ss_0-1.5_BS1

description: Drosophila embryos RNAi, shss, replicate 1, 0-1.5 hours


title: sens_Sox14_trh_mCherry_6-8_BS1

description: Drosophila embryos RNAi, shmCherry (Control for sens, Sox14, trh), replicate 1, 6-8 hours

value: 6-8 hours


title: sens_Sox14_trh_mCherry_6-8_BS2

description: Drosophila embryos RNAi, shmCherry (Control for sens, Sox14, trh), replicate 2, 6-8 hours


title: sens_Sox14_trh_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for sens, Sox14, trh), replicate 1, 0-1.5 hours


title: sens_6-8_BS2

description: Drosophila embryos RNAi, shsens, replicate 2, 6-8 hours

value: shsens


title: sens_16-18_BS2

description: Drosophila embryos RNAi, shsens, replicate 2, 16-18 hours


title: sens_16-18_BS1

description: Drosophila embryos RNAi, shsens, replicate 1, 16-18 hours


title: sens_0-1.5_BS2

description: Drosophila embryos RNAi, shsens, replicate 2, 0-1.5 hours


title: sens_0-1.5_BS1

description: Drosophila embryos RNAi, shsens, replicate 1, 0-1.5 hours


title: sens-2_mCherry_14-16_BS1

description: Drosophila embryos RNAi, shmCherry (Control for sens-2), replicate 1, 14-16 hours

value: shmCherry (Control for sens-2)

value: 14-16 hours


title: sens-2_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for sens-2), replicate 2, 0-1.5 hours


title: sens-2_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for sens-2), replicate 1, 0-1.5 hours


title: sens-2_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for sens-2), replicate 2, 16-18 hours


title: sens_Sox14_trh_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for sens, Sox14, trh), replicate 1, 16-18 hours


title: sens-2_16-18_BS2

description: Drosophila embryos RNAi, shsens-2, replicate 2, 16-18 hours


title: sens-2_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for sens-2), replicate 1, 16-18 hours


title: sens-2_mCherry_14-16_BS2

description: Drosophila embryos RNAi, shmCherry (Control for sens-2), replicate 2, 14-16 hours


title: sens_Sox14_trh_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for sens, Sox14, trh), replicate 2, 0-1.5 hours


title: sens-2_16-18_BS1

description: Drosophila embryos RNAi, shsens-2, replicate 1, 16-18 hours


title: Pancreatic endoderm cells, siControl, Day 14

city: Kyoto

first: Kenji

last: Osafune

address: Shogoin-Kawahara-cho 53

department: Center for iPS Cell Research and Application (CiRA)

country: Japan

institute: Kyoto University

data_processing:
Sequence reads were trimmed and quality-filtered using the Trim Galore! (version 0.6.6), Trimmomatic (version 0.39), and cutadapt (version 3.1) software.
Trimmed sequence reads were mapped to the human GRCh38 genome using STAR (version 2.7.3a).
Reads on annotated genes were counted using featureCounts (version 2.0.1).
Assembly: GRCh38.p13 (hg38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen).
Double-stranded cDNA libraries (RNA-seq libraries) were prepared using a SMART Seq Stranded Kit (TaKaRa) according to the manufacturer’s instructions.

tag: cell line

tag: cell type

value: Induced pluripotent stem cells

tag: genotype

value: WT

value: pancreatic differentiation

tag: time

value: Day 14


title: sens-2_14-16_BS2

description: Drosophila embryos RNAi, shsens-2, replicate 2, 14-16 hours


title: scrt_16-18_BS2

description: Drosophila embryos RNAi, shscrt, replicate 2, 16-18 hours

value: shscrt


title: sens-2_0-1.5_BS1

description: Drosophila embryos RNAi, shsens-2, replicate 1, 0-1.5 hours


title: scrt_16-18_BS1

description: Drosophila embryos RNAi, shscrt, replicate 1, 16-18 hours


title: sens_6-8_BS1

description: Drosophila embryos RNAi, shsens, replicate 1, 6-8 hours


title: scrt_10-12_BS2

description: Drosophila embryos RNAi, shscrt, replicate 2, 10-12 hours

value: 10-12 hours


title: sens-2_0-1.5_BS2

description: Drosophila embryos RNAi, shsens-2, replicate 2, 0-1.5 hours


title: Pancreatic endoderm cells, siHHEX, Day 14

value: HHEX knockdown


title: Posterior foregut cells, Day 10

value: Day 10


title: 2020A84

city: Marseille

first: Frederique

last: Magdinier

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

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

data_processing:
We assessed fastq sequence data quality using FastQC v0.11.5 (Andrews, 2010) and trimmed the reads to remove adapter sequences and low quality bases using Trimmomatic v0.36
Pair end reads were aligned using STAR v2.5.3a  to the GRCh38 human genome release
BAMS index were generated using Sambamba v0.6.6
DEGs and abundance measurements were identified using StringTie v1.3.1c and R package DESeq2 v1.18.1
Assembly: GRCh38 human genome
Supplementary files format and content: tab-delimited text file (.tsv) include RAW counts for each Sample

source_name: Myotubes

growth_protocol: Myoblasts were immortalized with a floxable hTERT cassette. For day-to-day maintenance, human myoblasts were seeded in dishes coated with 0.1% pigskin gelatin in 4:1 Dulbecco modified Eagle medium/Medium 199 supplemented with 15% FBS, 0.02M HEPES, 1.4mg/l vitamin B12, 0.03mg/l ZnSO4, 0.055mg/l dexamethasone, 2.5μg/l hepatocyte growth factor and 10μg/l basic fibroblast growth factor. Myotubes were obtained by full differenciation of myoblasts. Briefly, upon 80 % confluence, myoblasts were switch to DMEM with 2 % Horse serum and left for 10 days. Myotubes differentiation was controled with MF20 IF and measurement of the fusion index.

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

tag: disease

value: telomere 12kb


title: scrt_0-1.5_BS1

description: Drosophila embryos RNAi, shscrt, replicate 1, 0-1.5 hours

value: embryos


title: scrt_0-1.5_BS2

description: Drosophila embryos RNAi, shscrt, replicate 2, 0-1.5 hours


title: 2020A82


title: scro_16-18_BS2

description: Drosophila embryos RNAi, shscro, replicate 2, 16-18 hours

value: shscro

value: 16-18 hours


title: scrt_10-12_BS1

description: Drosophila embryos RNAi, shscrt, replicate 1, 10-12 hours


title: 2020A78

value: telomere 8kb


title: 2020A77


title: 2020A76


title: Smoothmuscle_16

city: Basel

first: Nadim

last: Aizarani

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

description: Library of 92 cells

library_source: transcriptomic single cell

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Assembly: mm10
Supplementary files format and content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

organism: Mus musculus

source_name: dermal smooth muscle cells

extract_protocol:
Vascular smooth muscle cells were isolated from ear skin of C57BL/6J Myh11 GFP mice.
The amplified RNA (aRNA) was reversely transcribed in order to generate libraries for sequencing. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.
CEL-Seq2 (Hasimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)

treatment_protocol: no treatment

tag: strain

value: C57BL/6J Tg Myh11GFP/+ JAX #007745

value: Ear skin

tag: reporter/marker


title: Smoothmuscle_15

description: Library of 92 cells

growth_protocol: Vascular smooth muscle cells were isolated from ear skin of C57BL/6J Myh11 GFP mice.

value: C57BL/6J Tg Myh11GFP/+ JAX #007744


title: sens-2_14-16_BS1

description: Drosophila embryos RNAi, shsens-2, replicate 1, 14-16 hours

value: 14-16 hours


title: scro_12-14_BS2

description: Drosophila embryos RNAi, shscro, replicate 2, 12-14 hours

value: 12-14 hours


title: scro_16-18_BS1

description: Drosophila embryos RNAi, shscro, replicate 1, 16-18 hours


title: ORF_S3

city: Cambridge

first: Julia

last: Joung

state: MA

address: 75 Ames St

institute: Broad Institute

data_processing:
bcl2fastq 2.20.0
Bowtie 1.2.3
RSEM 1.3.1
Assembly: hg38
Supplementary files format and content: Aggregated TPM determined by RSEM for each condition

source_name: 11a induced pluripotent stem cells

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen 74134)
RNA-Seq libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530S)

value: 11a induced pluripotent stem cells

tag: perturbation

value: DYRK1A ORF overexpression

tag: perturbation time

value: 7 days


title: ORF_S1


title: Smoothmuscle_14

description: Library of 92 cells

value: C57BL/6J Tg Myh11GFP/+ JAX #007743


title: 2020A83


title: Smoothmuscle_13

description: Library of 92 cells

value: C57BL/6J Tg Myh11GFP/+ JAX #007742


title: scro_12-14_BS1

description: Drosophila embryos RNAi, shscro, replicate 1, 12-14 hours


title: scro_0-1.5_BS2

description: Drosophila embryos RNAi, shscro, replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: KOsg2_S1

value: KOsg2 and Cas9 expression


title: GFP S1

value: GFP overexpression


title: GFP S3


title: Lung_old_NaCl_mRNA_SK1.1.162

city: Biberach

first: Sergio

last: Picart-Armada

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

description:
RPKM_685.txt
685_29

data_processing:
Illumina reads were converted to the industry standard FASTQ format and aligned to the mouse reference genome from Ensembl 70 using the STAR v2.5.2a aligner on default settings. For increased alignment accuracy, the STAR genome index was generated to include splice junction annotations with the options ‘—sjdbGTFfile’ and ‘—sjdbOverhang 49’.
The quality of the RNA-Seq samples was verified with FASTQC 0.11.2 and RNASeQC version 1.1.8. The featureCounts tool of the subRead package v1.5.0 was used to quantify the per-gene read counts with the “-s 2” parameter.
Cufflinks v2.2.1  was used to calculate the FPKM values with the following parameters “--max-bundle-frags 1000000000 --max-bundle-length 5000000 --library-type fr-firststrand --no-effective-length-correction --compatible-hits-norm --max-frag-multihits 1”.
The matrix of read counts and were imported into R and per-sample read count normalization factors were calculated using trimmed mean of M-values (TMM) and subsequently normalized using the Bioconductor LIMMA-Voom analysis R package for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: RPKM_685.txt: counts for mRNAs. miRNA_READS_727.txt: counts for microRNAs

source_name: Lung

extract_protocol:
Lung tissue was perfused twice with 10ml 1x PBS (Sigma, city, country) through the right side of the heart entering the pulmonary vasculature. Subsequently, lung was removed from the chest cavity, each lobe was separated and thereafter immediately flash frozen in liquid nitrogen. Lungs were then stored at -80°C until homogenized in 2ml Eppendorf tubes (Eppendorf, Hamburg, Germany) using a TissueLyser LT (Qiagen, Hilden, Germany). Samples remained frozen throughout the entire procedure. Lung powder was generated for next generation sequencing (NGS; 20mg tissue).
Total RNA was isolated using the Qiazol procedure according to manufacturer´s protocol (Qiagen, Hilden, Germany). A total of 20mg tissue was used for RNA isolation. Quality of RNA was assessed by the Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) using the SS RNA Kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Male mice were randomized before the study. Mice were instilled intratracheally (i.t.) under 3-4% isoflurane anesthesia once on day 0. Bleomycin administration was performed in a hanging position with a Vasofix-Braunüle 22G (B.Braun, Melsungen, Germany). Mice were instilled using 0.7 and 0.63 mg/kg of bleomycin sulphate (Merck, Darmstadt, Germany) in saline solution for the young and old mice, respectively. Control mice received saline solution only. Mice were analyzed 21 days after bleomycin administration.

tag: age

value: old

value: NaCl

tag: day

tag: animal id

tag: Sex

value: Male

value: Lung


title: scro_0-1.5_BS1

description: Drosophila embryos RNAi, shscro, replicate 1, 0-1.5 hours

value: embryos

value: shscro


title: Lung_old_Bleo_mRNA_SK1.1.153

description:
RPKM_685.txt
685_28

value: Bleo


title: repo_esn_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for repo, esn), replicate 2, 16-18 hours

value: shmCherry (Control for repo, esn)

value: 16-18 hours


title: KOsg1_S2

value: 11a induced pluripotent stem cells

value: KOsg1 and Cas9 expression


title: Lung_old_NaCl_mRNA_SK1.1.150

description:
RPKM_685.txt
685_27


title: KOsg1_S3

value: 7 days


title: repo_esn_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for repo, esn), replicate 1, 16-18 hours


title: KOsg1_S1


title: NTsg2_S3

value: NTsg2 and Cas9 expression


title: KOsg2_S3


title: GFP S2


title: KOsg2_S2


title: NTsg2_S1


title: NTsg2_S2


title: repo_esn_mCherry_14-16_BS1

description: Drosophila embryos RNAi, shmCherry (Control for repo, esn), replicate 1, 14-16 hours

value: 14-16 hours


title: Lung_old_Bleo_mRNA_SK1.1.130

description:
RPKM_685.txt
685_24


title: Lung_old_NaCl_mRNA_SK1.1.131

description:
RPKM_685.txt
685_25


title: repo_esn_mCherry_14-16_BS2

description: Drosophila embryos RNAi, shmCherry (Control for repo, esn), replicate 2, 14-16 hours


title: NTsg1_S3

value: NTsg1 and Cas9 expression


title: NTsg1_S2


title: NTsg1_S1


title: repo_esn_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for repo, esn), replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: Lung_old_NaCl_mRNA_SK1.1.119

description:
RPKM_685.txt
685_23


title: LHX2_D12_S2

source_name: HUES66 human embryonic stem cells

value: HUES66 human embryonic stem cells

value: LHX2 ORF overexpression

value: 12 days


title: repo_esn_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for repo, esn), replicate 1, 0-1.5 hours


title: ASCL1_D12_S1

value: ASCL1 ORF overexpression


title: LHX2_D7_S1


title: LHX2_D7_S2


title: repo_16-18_BS2

description: Drosophila embryos RNAi, shrepo, replicate 2, 16-18 hours

value: shrepo


title: Lung_old_Bleo_mRNA_SK1.1.114

description:
RPKM_685.txt
685_21

value: old

value: Male

value: Lung


title: ASCL1_D12_S2


title: Lung_old_Bleo_mRNA_SK1.1.105

description:
RPKM_685.txt
685_20

value: Bleo


title: repo_16-18_BS1

description: Drosophila embryos RNAi, shrepo, replicate 1, 16-18 hours

value: embryos

value: 16-18 hours


title: Lung_old_Bleo_mRNA_SK1.1.144

description:
RPKM_685.txt
685_26


title: ASCL1_D7_S2


title: ASCL1_D7_S1


title: Lung_old_NaCl_mRNA_SK1.1.99

description:
RPKM_685.txt
685_19

value: NaCl


title: repo_14-16_BS2

description: Drosophila embryos RNAi, shrepo, replicate 2, 14-16 hours


title: PAX6_D12_S2

value: PAX6 ORF overexpression


title: repo_14-16_BS1

description: Drosophila embryos RNAi, shrepo, replicate 1, 14-16 hours


title: Lung_old_Bleo_mRNA_SK1.1.98

description:
RPKM_685.txt
685_18


title: PAX6_D12_S1


title: PAX6_D7_S1

value: 7 days


title: Lung_old_Bleo_mRNA_SK1.1.92

description:
RPKM_685.txt
685_17


title: LHX2_D12_S1


title: PAX6_D7_S2


title: repo_0-1.5_BS2

description: Drosophila embryos RNAi, shrepo, replicate 2, 0-1.5 hours


title: repo_0-1.5_BS1

description: Drosophila embryos RNAi, shrepo, replicate 1, 0-1.5 hours


title: Lung_old_NaCl_mRNA_SK1.1.89

description:
RPKM_685.txt
685_16


title: NFIB_D7_S2

value: NFIB ORF overexpression


title: NFIB_D12_S1


title: Lung_old_Bleo_mRNA_SK1.1.85

description:
RPKM_685.txt
685_15


title: FOS_D12_S2

value: FOS ORF overexpression


title: NFIB_D7_S1


title: Lung_old_Bleo_mRNA_SK1.1.117

description:
RPKM_685.txt
685_22


title: NFIB_D12_S2


title: FOS_D7_S2


title: Lung_young_Bleo_mRNA_SK1.1.80

description:
RPKM_685.txt
685_14

value: young


title: FOS_D7_S1

value: HUES66 human embryonic stem cells


title: pb_HLH54F_Kah_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for pb, HLH54F, Kah), replicate 2, 16-18 hours

value: shmCherry (Control for pb, HLH54F, Kah)


title: pb_HLH54F_Kah_mCherry_8-10_BS1

description: Drosophila embryos RNAi, shmCherry (Control for pb, HLH54F, Kah), replicate 1, 8-10 hours

value: 8-10 hours


title: Lung_young_NaCl_mRNA_SK1.1.62

description:
RPKM_685.txt
685_12


title: RFX4_D12_S1

value: RFX4 ORF overexpression

value: 12 days


title: RFX4_D12_S2


title: RFX4_D7_S2


title: pb_HLH54F_Kah_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for pb, HLH54F, Kah), replicate 1, 16-18 hours


title: Lung_young_NaCl_mRNA_SK1.1.70

description:
RPKM_685.txt
685_13


title: pb_HLH54F_Kah_mCherry_8-10_BS2

description: Drosophila embryos RNAi, shmCherry (Control for pb, HLH54F, Kah), replicate 2, 8-10 hours


title: pb_HLH54F_Kah_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for pb, HLH54F, Kah), replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: RFX4_D7_S1


title: Lung_young_Bleo_mRNA_SK1.1.56

description:
RPKM_685.txt
685_11

value: Male


title: NFIC_D12_S1

value: NFIC ORF overexpression


title: Lung_young_NaCl_mRNA_SK1.1.49

description:
RPKM_685.txt
685_10

value: Lung


title: pb_HLH54F_Kah_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for pb, HLH54F, Kah), replicate 1, 0-1.5 hours

value: embryos


title: FOS_D12_S1


title: NFIC_D7_S2


title: pb_8-10_BS2

description: Drosophila embryos RNAi, shpb, replicate 2, 8-10 hours

value: shpb


title: NFIC_D7_S1


title: EOMES_D12_S1

value: EOMES ORF overexpression


title: pb_8-10_BS1

description: Drosophila embryos RNAi, shpb, replicate 1, 8-10 hours


title: EOMES_D7_S2


title: EOMES_D12_S2


title: pb_16-18_BS2

description: Drosophila embryos RNAi, shpb, replicate 2, 16-18 hours

value: 16-18 hours


title: ORF_S2

value: 11a induced pluripotent stem cells

value: DYRK1A ORF overexpression

value: 7 days


title: Lung_young_Bleo_mRNA_SK1.1.44

description:
RPKM_685.txt
685_8

value: young

value: Bleo


title: EOMES_D7_S1

value: HUES66 human embryonic stem cells


title: Lung_young_Bleo_mRNA_SK1.1.38

description:
RPKM_685.txt
685_7


title: OTX1_D12_S2

value: OTX1 ORF overexpression


title: Lung_young_Bleo_mRNA_SK1.1.32

description:
RPKM_685.txt
685_6


title: OTX1_D12_S1


title: Lung_young_Bleo_mRNA_SK1.1.28

description:
RPKM_685.txt
685_5


title: Lung_young_Bleo_mRNA_SK1.1.46

description:
RPKM_685.txt
685_9


title: OTX1_D7_S1


title: pb_16-18_BS1

description: Drosophila embryos RNAi, shpb, replicate 1, 16-18 hours


title: GFP_NP_D7_S2

value: GFP overexpression


title: GFP_NP_D12_S1

value: 12 days


title: GFP_NP_D7_S1


title: Lung_young_Bleo_mRNA_SK1.1.22

description:
RPKM_685.txt
685_3


title: pb_0-1.5_BS1

description: Drosophila embryos RNAi, shpb, replicate 1, 0-1.5 hours

value: 0-1.5 hours


title: GFP_mTeSR_D12_S2

value: GFP overexpression in mTeSR


title: Lung_young_NaCl_mRNA_SK1.1.25

description:
RPKM_685.txt
685_4

value: NaCl

value: Male


title: onecut_scro_ss_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for onecut, scro, ss), replicate 2, 16-18 hours

value: embryos


title: GFP_NP_D12_S2


title: pb_0-1.5_BS2

description: Drosophila embryos RNAi, shpb, replicate 2, 0-1.5 hours

value: shpb


title: Lung_young_NaCl_mRNA_SK1.1.16

description:
RPKM_685.txt
685_2

value: Lung


title: GFP_mTeSR_D12_S1


title: GFP_mTeSR_D7_S2


title: onecut_scro_ss_mCherry_12-14_BS2

description: Drosophila embryos RNAi, shmCherry (Control for onecut, scro, ss), replicate 2, 12-14 hours

value: 12-14 hours


title: ChIP_ASCL1_V5

library_source: genomic

data_processing:
bcl2fastq 2.20.0
Bowtie 1.2.3
MACS 1.4.2
Assembly: hg38
Supplementary files format and content: bed files contain peaks called using MACS

molecule: genomic DNA

extract_protocol:
ChIP was performed as described in the methods section of the manuscript
ChIP samples were prepared for NGS with NEBNext Ultra II DNA Library Kit for Illumina

value: ASCL1 V5 ORF expression

tag: antibody

value: V5 antibody pulldown


title: onecut_scro_ss_mCherry_12-14_BS1

description: Drosophila embryos RNAi, shmCherry (Control for onecut, scro, ss), replicate 1, 12-14 hours

tag: tissue


title: ChIP_ASCL1_Input

value: 7 days

value: Input control


title: OTX1_D7_S2


title: ChIP_PAX6_V5

value: PAX6 V5 ORF expression


title: 171022_reporter_VIM_S3H

data_processing:
library strategy: amplicon
bcl2fastq 2.20.0
custom Python script to determine barcode distribution (see Methods)
Assembly: TF barcode sequences
Supplementary files format and content: Aggregated TF barcode counts determined using custom Python script for each condition

extract_protocol:
genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo D4075)
Libraries were prepared by PCR amplification of TF barcodes using custom primers (see Methods)

value: HUES66 human embryonic stem cells

tag: differentiation protocol

value: overexpression of a library with 90 transcription factors

tag: time point

tag: screen condition

value: VIM reporter sample 3 sorted high bin


title: ChIP_PAX6_Input

tag: cell type


title: 171022_reporter_VIM_S3L

value: VIM reporter sample 3 sorted low bin


title: onecut_scro_ss_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for onecut, scro, ss), replicate 2, 0-1.5 hours

tag: treatment

tag: timepoint

value: 0-1.5 hours


title: ChIP_RFX4_V5

value: RFX4 V5 ORF expression


title: onecut_scro_ss_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for onecut, scro, ss), replicate 1, 16-18 hours

value: 16-18 hours


title: ChIP_NFIB_V5

value: NFIB V5 ORF expression


title: 171022_reporter_VIM_S2H

value: VIM reporter sample 2 sorted high bin


title: 171022_reporter_VIM_S1H

value: VIM reporter sample 1 sorted high bin


title: 2020A81

source_name: Myoblast

growth_protocol: Myoblasts were immortalized with a floxable hTERT cassette. For day-to-day maintenance, human myoblasts were seeded in dishes coated with 0.1% pigskin gelatin in 4:1 Dulbecco modified Eagle medium/Medium 199 supplemented with 15% FBS, 0.02M HEPES, 1.4mg/l vitamin B12, 0.03mg/l ZnSO4, 0.055mg/l dexamethasone, 2.5μg/l hepatocyte growth factor and 10μg/l basic fibroblast growth factor.

value: Myoblast

tag: telomere length

value: telomere 12kb


title: 2020A80


title: ChIP_NFIB_Input


title: onecut_16-18_BS1

description: Drosophila embryos RNAi, shonecut, replicate 1, 16-18 hours

value: embryos

value: shonecut


title: ChIP_RFX4_Input

value: 7 days


title: onecut_12-14_BS2

description: Drosophila embryos RNAi, shonecut, replicate 2, 12-14 hours

value: 12-14 hours


title: 2020A75

value: telomere 8kb


title: 171022_reporter_VIM_S2L

value: HUES66 human embryonic stem cells

value: VIM reporter sample 2 sorted low bin


title: onecut_12-14_BS1

description: Drosophila embryos RNAi, shonecut, replicate 1, 12-14 hours


title: onecut_scro_ss_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for onecut, scro, ss), replicate 1, 0-1.5 hours


title: 2020A74


title: onecut_16-18_BS2

description: Drosophila embryos RNAi, shonecut, replicate 2, 16-18 hours


title: Lung_young_Bleo_mRNA_SK1.1.12

description:
RPKM_685.txt
685_1

value: young

value: Bleo

value: Male

tag: strain

value: Lung


title: onecut_0-1.5_BS2

description: Drosophila embryos RNAi, shonecut, replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: onecut_0-1.5_BS1

description: Drosophila embryos RNAi, shonecut, replicate 1, 0-1.5 hours


title: 171022_reporter_SLC1A3_S3H

value: overexpression of a library with 90 transcription factors

value: SLC1A3 reporter sample 3 sorted high bin


title: 2020A73


title: P97K: CONTROL, Plasma

city: Krakow

first: Paweł

last: Wołkow

address: Kopernika 7c

department: Centre for Medical Genomics - OMICRON

country: Poland

institute: Jagiellonian University Medical College

data_processing:
Basecalls performed using bcl2fastq v2.20.0.422 software.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18 with parameters: -a AGATCGGAAGAGCACACGTCT -e 0.15 -O 10 -m 18 -M 30
Trimmed sequences were mapped to miRBase 22.1, using miRDeep 2.0.1.1 with default parameters.
Normalized values generated from miRDeep software were used for further analysis.
Genome_build: miRBase 22.1
Supplementary_files_format_and_content: tab-delimited text files include raw counts and normalized values for all samples

source_name: Plasma

extract_protocol:
Small RNA was extracted from EVs and from total plasma by using the miRCURY RNA Isolation Kit (Exiqon, Qiagen), according to the manufacturer’s protocol.
Libraries were prepared with NebNext Small RNA Library Prep (NEB), according to the manufacturer’s protocol.

treatment_protocol: Two milliliters of plasma was centrifuged at 3000g for 10 min at RT. The supernatant was filtered through a 0.22-µm syringe membrane filter, and 1.7 ml of the filtrate was used for the isolation of EVs with the miRCURY Exosome Isolation Kit (Exiqon, Qiagen, Aarhus, Denmark) according to the manufacturer’s protocol.

tag: patientid

tag: group

value: CONTROL

value: Plasma


title: P99K: CONTROL, Plasma


title: P98: ALL, Plasma

value: ALL


title: 2020A79

value: Myoblast

value: telomere 12kb


title: kay_16-18_BS2

description: Drosophila embryos RNAi, shkay, replicate 2, 16-18 hours

value: embryos

value: shkay

value: 16-18 hours


title: P95K: CONTROL, Plasma


title: P96K: CONTROL, Plasma


title: P94K: CONTROL, Plasma


title: 171022_reporter_SLC1A3_S3L

value: HUES66 human embryonic stem cells

value: 7 days

value: SLC1A3 reporter sample 3 sorted low bin


title: 171022_reporter_SLC1A3_S2H

value: SLC1A3 reporter sample 2 sorted high bin


title: 171022_reporter_SLC1A3_S2L

value: SLC1A3 reporter sample 2 sorted low bin


title: GFP_mTeSR_D7_S1

tag: perturbation

value: GFP overexpression in mTeSR

tag: perturbation time


title: kay_10-12_BS2

description: Drosophila embryos RNAi, shkay, replicate 2, 10-12 hours

value: 10-12 hours


title: P93K: CONTROL, Plasma


title: P92K: CONTROL, Plasma


title: 171022_reporter_VIM_S1L

value: overexpression of a library with 90 transcription factors

value: VIM reporter sample 1 sorted low bin


title: 171022_reporter_SLC1A3_S1L

value: SLC1A3 reporter sample 1 sorted low bin


title: P88K: CONTROL, Plasma

value: CONTROL

value: Plasma


title: kay_10-12_BS1

description: Drosophila embryos RNAi, shkay, replicate 1, 10-12 hours


title: kay_16-18_BS1

description: Drosophila embryos RNAi, shkay, replicate 1, 16-18 hours


title: 171022_reporter_SLC1A3_S1H

value: SLC1A3 reporter sample 1 sorted high bin


title: P89K: CONTROL, Plasma


title: P87K: CONTROL, Plasma


title: P90K: CONTROL, Plasma


title: FB7

type: genomic

hyb_protocol: processed at diagenode

scan_protocol: processed at diagenode

data_processing:
Raw IDAT files were processed using R package ChAMP. Probes with missing values are removed, samples with more than 10% of probes with a detection p-value of greater than 0.01, probes with a detection p-value of greater than 0.01 in at least one sample and probes for which 5% of samples have a bead count less than 3 are filtered out.  Probes targeting CpG sites that are near SNPs, belong to X/Y chromosomes, or align with multiple locations are filtered out
processed data file includes data normalized with BMIQ

source_name: Fibroblasts

label_protocol: processed at diagenode

extract_protocol: Genomic DNA was extracted using the NucleoSpin Tissue kit (Macherey-Nagel) from two different cell pellets for each sample. A minimum of 500ng was sent to Diagenode services for DNA methylation analysis

value: Fibroblasts

value: active telomerase


title: FB8


title: P86K: CONTROL, Plasma


title: P85K: CONTROL, Plasma


title: P84K: CONTROL, Plasma


title: kay_0-1.5_BS2

description: Drosophila embryos RNAi, shkay, replicate 2, 0-1.5 hours

value: embryos

value: shkay

value: 0-1.5 hours


title: FB6

value: 7 Kb


title: P91K: CONTROL, Plasma


title: FB5


title: P83K: CONTROL, Plasma


title: P80K: CONTROL, Plasma


title: FB4

value: 10 Kb


title: P79K: CONTROL, Plasma


title: gfzf_2-4_BS2

description: Drosophila embryos RNAi, shgfzf, replicate 2, 2-4 hours

value: shgfzf

value: 2-4 hours


title: FB2

value: 15 Kb


title: FB1


title: kay_0-1.5_BS1

description: Drosophila embryos RNAi, shkay, replicate 1, 0-1.5 hours


title: gfzf_0-1.5_BS2

description: Drosophila embryos RNAi, shgfzf, replicate 2, 0-1.5 hours


title: gfzf_16-18_BS2

description: Drosophila embryos RNAi, shgfzf, replicate 2, 16-18 hours

value: 16-18 hours


title: gfzf_16-18_BS1

description: Drosophila embryos RNAi, shgfzf, replicate 1, 16-18 hours


title: P72K: CONTROL, Plasma


title: P74K: CONTROL, Plasma


title: P73K: CONTROL, Plasma


title: P71K: CONTROL, Plasma


title: FB3


title: P75K: CONTROL, Plasma


title: P81K: CONTROL, Plasma


title: MT8

value: Myotubes

value: 6 Kb


title: gfzf_0-1.5_BS1

description: Drosophila embryos RNAi, shgfzf, replicate 1, 0-1.5 hours


title: P70K: CONTROL, Plasma


title: foxo_Sox15_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for foxo, Sox15), replicate 2, 16-18 hours

value: shmCherry (Control for foxo, Sox15)


title: P82K: CONTROL, Plasma

value: CONTROL


title: MT7


title: gfzf_2-4_BS1

description: Drosophila embryos RNAi, shgfzf, replicate 1, 2-4 hours


title: P69K: CONTROL, Plasma

value: Plasma


title: P78K: CONTROL, Plasma


title: P76K: CONTROL, Plasma


title: P77K: CONTROL, Plasma


title: P68K: CONTROL, Plasma


title: MT6

value: 8 Kb


title: foxo_Sox15_mCherry_10-12_BS2

description: Drosophila embryos RNAi, shmCherry (Control for foxo, Sox15), replicate 2, 10-12 hours

value: 10-12 hours


title: MT5


title: P65K: CONTROL, Plasma


title: P64K: CONTROL, Plasma


title: MT4


title: foxo_Sox15_mCherry_10-12_BS1

description: Drosophila embryos RNAi, shmCherry (Control for foxo, Sox15), replicate 1, 10-12 hours


title: MT2

value: 12 Kb


title: P60K: CONTROL, Plasma


title: foxo_Sox15_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for foxo, Sox15), replicate 1, 0-1.5 hours

value: embryos


title: P63K: CONTROL, Plasma


title: P59K: CONTROL, Plasma


title: P62K: CONTROL, Plasma


title: MT1


title: foxo_16-18_BS2

description: Drosophila embryos RNAi, shfoxo, replicate 2, 16-18 hours

value: shfoxo


title: P57K: CONTROL, Plasma


title: foxo_Sox15_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for foxo, Sox15), replicate 1, 16-18 hours


title: foxo_16-18_BS1

description: Drosophila embryos RNAi, shfoxo, replicate 1, 16-18 hours


title: P67K: CONTROL, Plasma


title: P56: ALL, Plasma

value: ALL


title: JR4

source_name: Myoblasts

value: Myoblasts

value: active telomerase


title: foxo_10-12_BS2

description: Drosophila embryos RNAi, shfoxo, replicate 2, 10-12 hours


title: JR3


title: P55: ALL, Plasma


title: P53: ALL, Plasma


title: P66K: CONTROL, Plasma


title: P54: ALL, Plasma


title: JR8

value: 4 Kb


title: P61K: CONTROL, Plasma


title: foxo_10-12_BS1

description: Drosophila embryos RNAi, shfoxo, replicate 1, 10-12 hours


title: P51: ALL, Plasma


title: JR7


title: P58K: CONTROL, Plasma


title: foxo_Sox15_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for foxo, Sox15), replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: P49: ALL, Plasma


title: P50: ALL, Plasma


title: P52: ALL, Plasma


title: foxo_0-1.5_BS1

description: Drosophila embryos RNAi, shfoxo, replicate 1, 0-1.5 hours


title: MT3

value: 10 Kb


title: P48: ALL, Plasma


title: JR6


title: P46: ALL, Plasma


title: fd59A_caup_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for fd59A, caup), replicate 2, 16-18 hours

value: shmCherry (Control for fd59A, caup)

value: 16-18 hours


title: P45: ALL, Plasma


title: JR5


title: NFIC_D12_S2

value: HUES66 human embryonic stem cells

value: NFIC ORF overexpression

value: 12 days


title: JR4,1


title: P47: ALL, Plasma

value: Plasma


title: foxo_0-1.5_BS2

description: Drosophila embryos RNAi, shfoxo, replicate 2, 0-1.5 hours


title: P43: ALL, Plasma


title: fd59A_caup_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for fd59A, caup), replicate 1, 16-18 hours


title: P41: ALL, Plasma


title: P40: ALL, Plasma


title: fd59A_caup_mCherry_10-12_BS2

description: Drosophila embryos RNAi, shmCherry (Control for fd59A, caup), replicate 2, 10-12 hours


title: JR3,1

value: 6 Kb


title: fd59A_caup_mCherry_10-12_BS1

description: Drosophila embryos RNAi, shmCherry (Control for fd59A, caup), replicate 1, 10-12 hours

value: 10-12 hours


title: JR2

value: 8 Kb


title: P39: ALL, Plasma


title: JR1

value: 12 Kb


title: fd59A_caup_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for fd59A, caup), replicate 2, 0-1.5 hours

value: embryos


title: BMDC, AGF+ DC, AireKO, rep3

city: Kuramoto, Tokushima

first: Minoru

last: Matsumoto

department: Department of Molecular Pathology

institute: Tokushima University Graduate School of Biomedical Sciences

data_processing:
Low-quality parts and adapter sequences were trimmed by fastp (v0.20.0)
Trimmed short reads were mapped to the mm10 genome using STAR (v2.7.3a) with a GTF file from EMBL-EBI (GRCm38.99)
Unmapped reads and reads mapped with low-quality scores (MAPQ < 5) were removed by SAMtools (v1.9)
Duplicated reads were filtered out using Picard Tools (v2.21.1)
Mapped reads on each gene were counted using htseq-count (v0.11.2) with --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
Raw counts were normalized using edgeR package (version 3.38.1) in R programming language
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for all samples
Supplementary files format and content: comma-separated values file includes edgeR normalized abundances for all samples

source_name: bone marrow

extract_protocol:
Lymph nodes were enzymatically digested and then CD45+CD11c+MHCII+ cells were sorted by FACSAria II into tubes containing lysis buffer (QIAGEN, TCL buffer). Bone marrow cells were sorted for B220−CD24+CD11b−/low fraction and B220−CD11c+MHCII+ fraction. Total mRNA was extracted from LNDCs and BMDCs using an RNeasy Mini Kit (Qiagen) following the manufacturers' instructions.
Eluted RNAs were incubated with RT-grade DNase (Nippon Gene) for 10 min at room temperature, followed by purification on an RNeasy column (Qiagen). RNAs were verified quantitatively and qualitatively using an Agilent RNA 6000 Pico Kit run on an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA Integrity Numbers were more than 7. Three independent biological replicates from each genotype were used for RNA-seq analysis. Sequencing libraries were generated from 1.0 ng of total RNA with Ovation SoLo RNA-Seq Systems (NuGEN). The libraries were size-selected with AMPure XP beads (Agilent Technologies) and used for cluster generation on the flow cells. Paired-end 150-bp sequencing was performed with Illumina HiSeq.

value: bone marrow

value: AGF+ dendritic cells

tag: genotype

value: AGF-KI/-

value: male


title: P37: ALL, Plasma

value: ALL


title: P35: ALL, Plasma


title: P36: ALL, Plasma


title: fd59A_16-18_BS2

description: Drosophila embryos RNAi, shfd59A, replicate 2, 16-18 hours


title: P34: ALL, Plasma


title: BMDC, AGF+ DC, AireKO, rep2


title: P33: ALL, Plasma


title: P44: ALL, Plasma


title: P32: ALL, Plasma


title: fd59A_16-18_BS1

description: Drosophila embryos RNAi, shfd59A, replicate 1, 16-18 hours


title: P30: ALL, Plasma


title: BMDC, AGF+ DC, AireKO, rep1


title: P31: ALL, Plasma


title: BMDC, AGF+ DC, rep3

value: AGF-KI/+


title: P29: ALL, Plasma


title: fd59A_10-12_BS1

description: Drosophila embryos RNAi, shfd59A, replicate 1, 10-12 hours


title: P28: ALL, Plasma


title: BMDC, AGF+ DC, rep2


title: P27: ALL, Plasma


title: fd59A_0-1.5_BS2

description: Drosophila embryos RNAi, shfd59A, replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: P25: ALL, Plasma


title: P26: ALL, Plasma


title: fd59A_0-1.5_BS1

description: Drosophila embryos RNAi, shfd59A, replicate 1, 0-1.5 hours


title: BMDC, AGF+ DC, rep1


title: fd59A_caup_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for fd59A, caup), replicate 1, 0-1.5 hours

value: shmCherry (Control for fd59A, caup)


title: P23: ALL, Plasma


title: BMDC, total DC, rep2

value: total dendritic cells


title: BMDC, total DC, rep3


title: P22: ALL, Plasma


title: P21: ALL, Plasma


title: fd59A_10-12_BS2

description: Drosophila embryos RNAi, shfd59A, replicate 2, 10-12 hours


title: esn_16-18_BS2

description: Drosophila embryos RNAi, shesn, replicate 2, 16-18 hours

value: shesn

value: 16-18 hours


title: BMDC, total DC, rep1


title: P18: ALL, Plasma

value: Plasma


title: P19: ALL, Plasma


title: P17: ALL, Plasma


title: esn_14-16_BS2

description: Drosophila embryos RNAi, shesn, replicate 2, 14-16 hours

value: 14-16 hours


title: P15: ALL, Plasma


title: esn_14-16_BS1

description: Drosophila embryos RNAi, shesn, replicate 1, 14-16 hours


title: P16: ALL, Plasma


title: esn_16-18_BS1

description: Drosophila embryos RNAi, shesn, replicate 1, 16-18 hours


title: P24: ALL, Plasma


title: LNDC, AGF- DC, AireKO, rep2

source_name: lymph node

value: lymph node

value: AGF- dendritic cells


title: esn_0-1.5_BS2

description: Drosophila embryos RNAi, shesn, replicate 2, 0-1.5 hours


title: P14: ALL, Plasma


title: P12: ALL, Plasma


title: P20: ALL, Plasma


title: esn_0-1.5_BS1

description: Drosophila embryos RNAi, shesn, replicate 1, 0-1.5 hours


title: P121K: CONTROL, Plasma

value: CONTROL


title: P120K: CONTROL, Plasma


title: LNDC, AGF- DC, rep3


title: LNDC, AGF- DC, rep2


title: P11: ALL, Plasma


title: dmrt99B_6-8_BS1

description: Drosophila embryos RNAi, shdmrt99B, replicate 1, 6-8 hours

value: embryos

value: 6-8 hours


title: LNDC, AGF- DC, AireKO, rep3


title: dmrt99B_6-8_BS2

description: Drosophila embryos RNAi, shdmrt99B, replicate 2, 6-8 hours


title: P118: ALL, Plasma


title: P117K: CONTROL, Plasma


title: P38: ALL, Plasma


title: P116K: CONTROL, Plasma


title: LNDC, AGF+ DC, AireKO, rep3

value: AGF+ dendritic cells


title: dmrt99B_16-18_BS2

description: Drosophila embryos RNAi, shdmrt99B, replicate 2, 16-18 hours


title: P115: ALL, Plasma


title: dmrt99B_16-18_BS1

description: Drosophila embryos RNAi, shdmrt99B, replicate 1, 16-18 hours


title: P13: ALL, Plasma


title: LNDC, AGF- DC, AireKO, rep1

value: AGF-KI/-


title: dmrt99B_0-1.5_BS2

description: Drosophila embryos RNAi, shdmrt99B, replicate 2, 0-1.5 hours


title: LNDC, AGF+ DC, AireKO, rep1

value: male


title: P111: ALL, Plasma

value: ALL


title: LNDC, AGF+ DC, AireKO, rep2


title: P113: ALL, Plasma


title: P112: ALL, Plasma


title: P10: ALL, Plasma


title: dmrt99B_0-1.5_BS1

description: Drosophila embryos RNAi, shdmrt99B, replicate 1, 0-1.5 hours


title: P109K: CONTROL, Plasma


title: LNDC, AGF+ DC, rep2

value: AGF-KI/+


title: LNDC, AGF- DC, rep1


title: P108K: CONTROL, Plasma


title: P107K: CONTROL, Plasma


title: P119K: CONTROL, Plasma


title: dac_6-8_BS2

description: Drosophila embryos RNAi, shdac, replicate 2, 6-8 hours

value: shdac


title: P114K: CONTROL, Plasma


title: dac_6-8_BS1

description: Drosophila embryos RNAi, shdac, replicate 1, 6-8 hours


title: P106K: CONTROL, Plasma


title: P104K: CONTROL, Plasma


title: P105K: CONTROL, Plasma


title: dac_16-18_BS2

description: Drosophila embryos RNAi, shdac, replicate 2, 16-18 hours


title: P103K: CONTROL, Plasma


title: LNDC, AGF+ DC, rep3


title: dac_16-18_BS1

description: Drosophila embryos RNAi, shdac, replicate 1, 16-18 hours


title: 5'-Seq Replicate 4

city: Boston

first: Zlata

last: Gvozdenov

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

description: Random DNA is at ChrXVII from 3911 to 21878 bp.

data_processing:
The reads were aligned with following command: bowtie2 -x sacCer3random_spombe -5 4 -3 16 --no-mixed --no-discordant --dovetail -X 1000 (-5 4 -3 16 was used for 37 nt read length, -5 4 -3 55 was used for 76 nt long reads).
bedtools bamtobed
Bed files were used to compute fragment locations for correctly aligned paired-end reads.
Duplicates based on both read pairs and fragment location were removed from the aligned reads.
5’ isoform location was derived by trimming fragment to obtain first nt position past the 5’ adapter (or the first nucleotide of the insert between the adapters) and by computing 5’ reads per genomic coordinates. Negative control values per genomic coordinate were normalized using internal S. pombe control and subtracted from the MDE treated sample (5’ isoform samples) to obtain true 5’ isoforms.
Assembly: sacCer3 (for spike-in: S. pombe ASM294v2)
Supplementary files format and content: Replicates were analyzed individually (every MDE treated, i.e. de-capped sample has its specific control that comes from the same experiment). Normalized per nucleotide counts were combined into one file, which has 3 columns: chromosome name, position, and counts (separated into two files for two DNA strands; plus bed file aligns to the minus strand, and minus 5seq file aligns to the plus strand).
Library strategy: 5'-Seq

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast were grown in SD his- medium at 30˚C to OD(595)=~0.55.

extract_protocol:
Hot phenol RNA extraction.
1 µg mRNA was obtained from DNased, total RNA (from the strain with random sequence artificial chromosome) via oligo d(T)25 magnetic bead enrichment. RNA was fragmented with NEBNext® Magnesium RNA Fragmentation Module and purified with ethanol precipitation. RNA was dephosphorylated with Quick CIP (NEB), heat inactivated and pre-adenylated 3’ adapter (Jin et al., 2015) was ligated with concentrated T4 RNA Ligase 1 (NEB). Reaction was split in two – mRNA deccaping enzyme (MDE, NEB) was added to one reaction, the other served as a control. 5’ adapter (Jin et al., 2015) was ligated with T4 RNA ligase 2 truncated (NEB), reaction was reverse transcribed, and the library was PCR amplified.


title: 5'-Seq Replicate 5


title: P101K: CONTROL, Plasma


title: dac_0-1.5_BS2

description: Drosophila embryos RNAi, shdac, replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: 5'-Seq Replicate 2


title: 5'-Seq Replicate 3


title: dac_0-1.5_BS1

description: Drosophila embryos RNAi, shdac, replicate 1, 0-1.5 hours


title: P102K: CONTROL, Plasma


title: P110K: CONTROL, Plasma


title: P100K: CONTROL, Plasma


title: LNDC, AGF+ DC, rep1


title: P07: ALL, Plasma


title: caup_16-18_BS2

description: Drosophila embryos RNAi, shcaup, replicate 2, 16-18 hours

value: shcaup


title: P08: ALL, Plasma


title: MNase-Seq Control 4

description:
Random DNA is at ChrXVII from 3911 to 21878 bp.
MNase_control_fragment_location.bed

data_processing:
bowtie2 --no-mixed --no-discordant --no-dovetail --no-contain --no-overlap
bedtools bamtobed
Bed files were used to compute fragment locations for correctly aligned paired-end reads.
Assembly: sacCer3
Supplementary files format and content: After checking the replicates, all fastq files were unified (into one R1 and one R2 file). Paired-end read derived MNase-Seq fragments (MNase_fragment_location.bed for chromatin, and MNase_control_fragment_location.bed for naked DNA) have 3 columns: chromosome name, start location and end location. Midpoints derived for the chromatin fragments (MNase_midpoint_list.bed) have 3 columns: chromosome name, nt location, and number of midpoints per nt location. MNase midpoints per 10 bp sliding window (MNase_midpoint_10bp_sliding_window_chrXVIInorm_copy_number.bed) have 4 columns: chromosome name, start, end, and the count of midpoints per sliding window. In the later one, ChrXVII copy number were adjusted to allow comparison with genomic data.

extract_protocol:
Mononucleosomes and genomic DNA digestion product corresponding to mononucleosomal-sized DNA were excised from the agarose gel.
Library preparation was performed as described in Wong et al., 2013 with the following exception: 1 μg gel-excised mononucleosomal DNA/control DNA was used as the starting material.
TrueSeq combinatorial dual sequencing primers (Illumina) were used for library ligation and amplification; the library was amplified for 12 cycles.

treatment_protocol: Nucleosomal DNA was obtained following the protocol described by Rando, 2010 with the modifications: crosslinked spheroplasts stemming from 100 ml culture were treated with 1600 U MNase (Worthington Biochemical Corporation) for 1-1.5 h at 37 ˚C. A control DNA was obtained by MNase-treatment of genomic DNA from the same experiment (genomic DNA isolated from formaldehyde-crosslinked spheroplasts).

tag: fraction

value: naked DNA (control)


title: MNase-Seq Control 3


title: P06: ALL, Plasma


title: P04: ALL, Plasma


title: caup_16-18_BS1

description: Drosophila embryos RNAi, shcaup, replicate 1, 16-18 hours

value: 16-18 hours


title: P03: ALL, Plasma

value: Plasma


title: caup_10-12_BS2

description: Drosophila embryos RNAi, shcaup, replicate 2, 10-12 hours

value: 10-12 hours


title: P02: ALL, Plasma


title: MNase-Seq Control 2


title: P05: ALL, Plasma


title: MNase-Seq Control 1


title: P09: ALL, Plasma


title: caup_10-12_BS1

description: Drosophila embryos RNAi, shcaup, replicate 1, 10-12 hours


title: P01: ALL, Plasma


title: E99K: CONTROL, Plasma exosomes

source_name: Plasma exosomes

value: Plasma exosomes


title: caup_0-1.5_BS2

description: Drosophila embryos RNAi, shcaup, replicate 2, 0-1.5 hours


title: E95K: CONTROL, Plasma exosomes


title: MNase-Seq Replicate 3

description:
Random DNA is at ChrXVII from 3911 to 21878 bp.
MNase_fragment_location.bed
MNase_midpoint_list.bed
MNase_midpoint_10bp_sliding_window_chrXVIInorm_copy_number.bed

value: chromatin


title: E98: ALL, Plasma exosomes


title: E96K: CONTROL, Plasma exosomes

value: CONTROL


title: E97K: CONTROL, Plasma exosomes


title: MNase-Seq Replicate 1


title: caup_0-1.5_BS1

description: Drosophila embryos RNAi, shcaup, replicate 1, 0-1.5 hours

value: embryos


title: cad_2-4_BS2

description: Drosophila embryos RNAi, shcad, replicate 2, 2-4 hours

value: shcad

value: 2-4 hours


title: E92K: CONTROL, Plasma exosomes


title: 190712_media_Lentivirus

description: Other (lentivirus RNA)

library_source: other

data_processing:
bcl2fastq 2.20.0
custom Python script to determine barcode distribution (see Methods)
Assembly: TF barcode sequences
Supplementary files format and content: Aggregated TF barcode counts determined using custom Python script for each condition
Library strategy: amplicon

molecule: other

organism: Lentivirus

source_name: Lentivirus library

extract_protocol:
Lentivirus RNA was extracted using the QIAmp Viral RNA Mini Kit (Qiagen 52906). Genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo D4075)
Lentivirus RNA was reverse transcribed using the qScript Flex cDNA Kit (VWR 95049-100) with a custom primer (see Methods). Libraries were prepared by PCR amplification of TF barcodes using custom primers (see Methods)

value: Lentivirus library


title: E94K: CONTROL, Plasma exosomes


title: E93K: CONTROL, Plasma exosomes


title: E91K: CONTROL, Plasma exosomes


title: cad_2-4_BS1

description: Drosophila embryos RNAi, shcad, replicate 1, 2-4 hours


title: E89K: CONTROL, Plasma exosomes


title: cad_16-18_BS2

description: Drosophila embryos RNAi, shcad, replicate 2, 16-18 hours


title: cad_16-18_BS1

description: Drosophila embryos RNAi, shcad, replicate 1, 16-18 hours


title: E90K: CONTROL, Plasma exosomes


title: E87K: CONTROL, Plasma exosomes


title: E88K: CONTROL, Plasma exosomes


title: cad_0-1.5_BS2

description: Drosophila embryos RNAi, shcad, replicate 2, 0-1.5 hours


title: E85K: CONTROL, Plasma exosomes


title: E86K: CONTROL, Plasma exosomes


title: E83K: CONTROL, Plasma exosomes


title: cad_0-1.5_BS1

description: Drosophila embryos RNAi, shcad, replicate 1, 0-1.5 hours


title: E82K: CONTROL, Plasma exosomes


title: E84K: CONTROL, Plasma exosomes


title: E81K: CONTROL, Plasma exosomes


title: E80K: CONTROL, Plasma exosomes


title: bsh_ERR_Xbp1_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for bsh, ERR, Xbp1), replicate 2, 16-18 hours

value: shmCherry (Control for bsh, ERR, Xbp1)


title: bsh_ERR_Xbp1_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for bsh, ERR, Xbp1), replicate 1, 16-18 hours


title: bsh_ERR_Xbp1_mCherry_10-12_BS2

description: Drosophila embryos RNAi, shmCherry (Control for bsh, ERR, Xbp1), replicate 2, 10-12 hours


title: E79K: CONTROL, Plasma exosomes


title: E78K: CONTROL, Plasma exosomes


title: E77K: CONTROL, Plasma exosomes


title: bsh_ERR_Xbp1_mCherry_10-12_BS1

description: Drosophila embryos RNAi, shmCherry (Control for bsh, ERR, Xbp1), replicate 1, 10-12 hours


title: E76K: CONTROL, Plasma exosomes


title: E74K: CONTROL, Plasma exosomes


title: E72K: CONTROL, Plasma exosomes


title: bsh_ERR_Xbp1_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for bsh, ERR, Xbp1), replicate 2, 0-1.5 hours


title: MNase-Seq Replicate 2


title: E73K: CONTROL, Plasma exosomes


title: E71K: CONTROL, Plasma exosomes


title: bsh_16-18_BS2

description: Drosophila embryos RNAi, shbsh, replicate 2, 16-18 hours

value: shbsh


title: E70K: CONTROL, Plasma exosomes


title: E69K: CONTROL, Plasma exosomes


title: bsh_16-18_BS1

description: Drosophila embryos RNAi, shbsh, replicate 1, 16-18 hours


title: bsh_10-12_BS2

description: Drosophila embryos RNAi, shbsh, replicate 2, 10-12 hours


title: E68K: CONTROL, Plasma exosomes


title: bsh_10-12_BS1

description: Drosophila embryos RNAi, shbsh, replicate 1, 10-12 hours


title: E66K: CONTROL, Plasma exosomes


title: E64K: CONTROL, Plasma exosomes


title: E62K: CONTROL, Plasma exosomes


title: bsh_0-1.5_BS2

description: Drosophila embryos RNAi, shbsh, replicate 2, 0-1.5 hours


title: E61K: CONTROL, Plasma exosomes


title: 9-9_KO_Exp

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

description:
Gibbs_RNAseq_NormalizedCounts_human.txt
Gibbs_RNAseq_NormalizedCounts_STM.txt

data_processing:
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were ≥20nt after trimming were kept for further analysis.
Reads were mapped to human genome reference combining the GRCh38v93 and transcriptome  with Salmonella enterica serovar Typhi strain Ty2 ASM754v1 genome.  STAR software was used to align reads to reference genome. Reads were kept for subsequent analysis if they mapped to a single genomic location. Gene counts were measured using the featureCounts. Only genes that had at least 10 reads in any given library were used in subsequent analysis.Normalization and differential expression within each species was carried out using the DESeq2 under R statistical programming environment.
Assembly: GRCh38v93, Salmonella enterica serovar Typhi strain Ty2 ASM754v1
Supplementary files format and content: Gibbs_RNAseq_NormalizedCounts_human.txt: Reads mapped to human GRCh38v93, DESeq2 normlized counts, tab-delimited txt file
Supplementary files format and content: Gibbs_RNAseq_NormalizedCounts_STM.txt: Reads mapped to Salmonella enterica serovar Typhi strain Ty2 ASM754v1, DESeq2 normlized counts, tab-delimited txt file

source_name: peripheral blood

growth_protocol: Overnight stationary cultures in Miller LB were sub-cultured 1:33 and grown for 160 minutes at 37°C and 250 rpm to reach SPI-1 inducing late-log phase (an OD600 of 0.8–1.1 for S. Typhi).  2e7 THP-1 cells were plated at 1×106 cells/mL in complete RPMI one hour before infection in 24-well non-TC plates. THP-1s were infected at an MOI 10. To kill the extracellular bacteria, gentamicin was added one hour post infection (hpi) at 50 mg/mL and then diluted to 15 mg/mL at 2 hpi.

extract_protocol:
After sorting, RNA was immediately isolated from collected cells using mirVana miRNA Isolation Kit’s total RNA protocol (ThermoFisher #AM1560). Prior to extraction, samples in RNAlater were diluted 3x with PBS, spun down at 5,000 xg, and aspirated to remove RNAlater. After resuspending cells in the kit’s L/B buffer, samples were vortexed for 60 sec to ensure lysis of Salmonella. Following total RNA extraction, gDNA was removed with 4 U TURBO DNase (ThermoFisher #AM2238) per μg of RNA and then purified with RNeasy MinElute cleanup kit (Qiagen #74204). In the gDNA-free RNA, the relative human to bacterial mRNA ratio was determined by RT-qPCR measurement of human ACTB and S. Typhi rpoD. In brief, 150ng of RNA was reverse transcribed with iScript cDNA synthesis kit (Bio-Rad #1708891) and 1:5 dilution of this cDNA was analyzed using iTaq Universal SYBR Green Supermix (Bio-Rad #1725124) and primers listed in Table S3 on a QuantStudio 3 System (ThermoFisher). This ratio was used to combine uninfected THP-1 mRNA and late-log S. Typhi inoculum mRNA for the control samples following Westermann & Vogel’s approach
mRNA was isolated and sequenced at Duke Sequencing and Genomic Technologies (SGT). cDNA library with depleted rRNA was followed with Illumina Standard Total RNA Prep using Ribo-Zero Plus (Illumina #20037135).

treatment_protocol: WT THP-1 cells and MCLON2 -/- THP-1 KO cells were infected with S. Typhi under "Exp" condition,  or spiked-in with RNA from late log phase S. Typhi for "Ctrl" condition.

value: peripheral blood

tag: cell line

value: THP-1 cell line

value: human monocytic cell line

value: Total RNA from THP-1 cells infected with S. Typhi


title: 9-9_WT_Ctrl

value: WT

value: Total RNA from THP-1 cells with spike-in of RNA from late-log S. Typhi


title: 9-9_WT_Exp


title: E75K: CONTROL, Plasma exosomes


title: bsh_0-1.5_BS1

description: Drosophila embryos RNAi, shbsh, replicate 1, 0-1.5 hours

value: 0-1.5 hours


title: E60K: CONTROL, Plasma exosomes


title: E57K: CONTROL, Plasma exosomes


title: E59K: CONTROL, Plasma exosomes


title: 9-9_KO_Ctrl


title: 9-4_WT_Exp


title: E56: ALL, Plasma exosomes

value: ALL


title: Xbp1_16-18_BS1

description: Drosophila embryos RNAi, shXbp1, replicate 1, 16-18 hours

value: 16-18 hours


title: E67K: CONTROL, Plasma exosomes

value: Plasma exosomes


title: bsh_ERR_Xbp1_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for bsh, ERR, Xbp1), replicate 1, 0-1.5 hours


title: 9-4_WT_Ctrl


title: Xbp1_10-12_BS2

description: Drosophila embryos RNAi, shXbp1, replicate 2, 10-12 hours

value: 10-12 hours


title: Xbp1_16-18_BS2

description: Drosophila embryos RNAi, shXbp1, replicate 2, 16-18 hours

value: embryos


title: E58K: CONTROL, Plasma exosomes

value: CONTROL


title: E55: ALL, Plasma exosomes


title: E65K: CONTROL, Plasma exosomes


title: E54: ALL, Plasma exosomes


title: 9-4_KO_Exp


title: E53: ALL, Plasma exosomes


title: E52: ALL, Plasma exosomes


title: E63K: CONTROL, Plasma exosomes


title: 9-4_KO_Ctrl


title: E51: ALL, Plasma exosomes


title: E50: ALL, Plasma exosomes


title: Xbp1_0-1.5_BS2

description: Drosophila embryos RNAi, shXbp1, replicate 2, 0-1.5 hours


title: E48: ALL, Plasma exosomes


title: 9-1_WT_Exp


title: Xbp1_0-1.5_BS1

description: Drosophila embryos RNAi, shXbp1, replicate 1, 0-1.5 hours


title: E47: ALL, Plasma exosomes


title: TfAP-2_scrt_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for TfAP-2, scrt), replicate 2, 16-18 hours

value: shmCherry (Control for TfAP-2, scrt)


title: E46: ALL, Plasma exosomes


title: 9-1_WT_Ctrl


title: 9-1 KO_Exp


title: E45: ALL, Plasma exosomes


title: TfAP-2_scrt_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for TfAP-2, scrt), replicate 1, 16-18 hours


title: 9-1 KO_Ctrl


title: E43: ALL, Plasma exosomes


title: E41: ALL, Plasma exosomes


title: E44: ALL, Plasma exosomes


title: TfAP-2_scrt_mCherry_10-12_BS1

description: Drosophila embryos RNAi, shmCherry (Control for TfAP-2, scrt), replicate 1, 10-12 hours


title: E40: ALL, Plasma exosomes


title: V_20

city: Cardiff

first: Frank

last: Wessely

address: Maindy Road

department: UK DRI

country: United Kingdom

institute: Cardiff University

data_processing:
CellRanger (v6.1.1, 10X Genomics) was used to map raw sequencing reads to the reference genome based on Ensembl v106 (generated according to the build steps of refdata-gex-GRCh38-2020-A available from 10X Genomics). The Cell Ranger count option --include-introns was used to count intronic reads. The filtered feature-barcode matrices from Cell Ranger count were used as input to downstream processing by the Seurat R package.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 from Cell Ranger count output containing gene-cell barcode matrices in HDF5 format

source_name: Brain frontal cortex

extract_protocol:
1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment.  On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce.  The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations.  Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension.  Nuclei were purified using FACS prior to 10x loading.
Library preparation was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).

value: Brain frontal cortex

value: vascular

tag: donor id

tag: Sex

value: M

tag: age

tag: disease

value: AD

tag: braak tangle

value: V

tag: apoe

tag: pmi

tag: ph cerebellum

tag: brain weight


title: V_19

tag: tissue

value: CT

value: II


title: E39: ALL, Plasma exosomes

tag: patientid


title: Xbp1_10-12_BS1

description: Drosophila embryos RNAi, shXbp1, replicate 1, 10-12 hours

source_name: embryos

tag: treatment

tag: timepoint


title: E37: ALL, Plasma exosomes

tag: group


title: E38: ALL, Plasma exosomes


title: V_18

value: F


title: TfAP-2_scrt_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for TfAP-2, scrt), replicate 2, 0-1.5 hours


title: E36: ALL, Plasma exosomes


title: E49: ALL, Plasma exosomes


title: E34: ALL, Plasma exosomes


title: V_17


title: E33: ALL, Plasma exosomes


title: TfAP-2_16-18_BS2

description: Drosophila embryos RNAi, shTfAP-2, replicate 2, 16-18 hours


title: TfAP-2_16-18_BS1

description: Drosophila embryos RNAi, shTfAP-2, replicate 1, 16-18 hours


title: E31: ALL, Plasma exosomes


title: E32: ALL, Plasma exosomes


title: V_15


title: TfAP-2_scrt_mCherry_10-12_BS2

description: Drosophila embryos RNAi, shmCherry (Control for TfAP-2, scrt), replicate 2, 10-12 hours


title: E30: ALL, Plasma exosomes


title: E29: ALL, Plasma exosomes


title: TfAP-2_10-12_BS2

description: Drosophila embryos RNAi, shTfAP-2, replicate 2, 10-12 hours


title: E28: ALL, Plasma exosomes


title: V_14


title: E27: ALL, Plasma exosomes


title: V_13


title: E26: ALL, Plasma exosomes


title: TfAP-2_10-12_BS1

description: Drosophila embryos RNAi, shTfAP-2, replicate 1, 10-12 hours


title: E25: ALL, Plasma exosomes


title: TfAP-2_0-1.5_BS2

description: Drosophila embryos RNAi, shTfAP-2, replicate 2, 0-1.5 hours


title: E35: ALL, Plasma exosomes


title: V_12


title: Sox15_16-18_BS2

description: Drosophila embryos RNAi, shSox15, replicate 2, 16-18 hours


title: E22: ALL, Plasma exosomes


title: E23: ALL, Plasma exosomes


title: E21: ALL, Plasma exosomes


title: E20: ALL, Plasma exosomes


title: TfAP-2_0-1.5_BS1

description: Drosophila embryos RNAi, shTfAP-2, replicate 1, 0-1.5 hours


title: V_11

value: I


title: V_16

value: VI


title: E18: ALL, Plasma exosomes

value: ALL


title: Sox15_10-12_BS2

description: Drosophila embryos RNAi, shSox15, replicate 2, 10-12 hours


title: V_10


title: TfAP-2_scrt_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for TfAP-2, scrt), replicate 1, 0-1.5 hours

value: 0-1.5 hours


title: E17: ALL, Plasma exosomes

value: Plasma exosomes


title: V_09


title: E16: ALL, Plasma exosomes


title: E24: ALL, Plasma exosomes


title: Sox15_10-12_BS1

description: Drosophila embryos RNAi, shSox15, replicate 1, 10-12 hours

value: 10-12 hours


title: E15: ALL, Plasma exosomes


title: E13: ALL, Plasma exosomes


title: E12: ALL, Plasma exosomes


title: Sox15_0-1.5_BS1

description: Drosophila embryos RNAi, shSox15, replicate 1, 0-1.5 hours

value: embryos


title: E121K: CONTROL, Plasma exosomes

value: CONTROL


title: V_06


title: E120K: CONTROL, Plasma exosomes


title: V_07


title: V_05


title: Sox15_16-18_BS1

description: Drosophila embryos RNAi, shSox15, replicate 1, 16-18 hours

value: 16-18 hours


title: Sox14_6-8_BS2

description: Drosophila embryos RNAi, shSox14, replicate 2, 6-8 hours

value: 6-8 hours


title: E19: ALL, Plasma exosomes


title: E11: ALL, Plasma exosomes


title: E119K: CONTROL, Plasma exosomes


title: V_04

value: Brain frontal cortex

value: vascular


title: V_03

value: M


title: E116K: CONTROL, Plasma exosomes


title: E115: ALL, Plasma exosomes


title: V_02

value: AD

value: V


title: E14: ALL, Plasma exosomes


title: E114K: CONTROL, Plasma exosomes


title: E113: ALL, Plasma exosomes


title: Sox15_0-1.5_BS2

description: Drosophila embryos RNAi, shSox15, replicate 2, 0-1.5 hours


title: V_01

value: CT

value: III


title: E112: ALL, Plasma exosomes


title: V_08


title: E111: ALL, Plasma exosomes


title: P_20

value: parenchyma


title: E118: ALL, Plasma exosomes


title: E110K: CONTROL, Plasma exosomes


title: Sox14_0-1.5_BS2

description: Drosophila embryos RNAi, shSox14, replicate 2, 0-1.5 hours


title: Sox14_0-1.5_BS1

description: Drosophila embryos RNAi, shSox14, replicate 1, 0-1.5 hours


title: Sox14_16-18_BS2

description: Drosophila embryos RNAi, shSox14, replicate 2, 16-18 hours


title: Sox14_16-18_BS1

description: Drosophila embryos RNAi, shSox14, replicate 1, 16-18 hours


title: E109K: CONTROL, Plasma exosomes


title: E10: ALL, Plasma exosomes


title: P_18

value: F


title: E107K: CONTROL, Plasma exosomes


title: E108K: CONTROL, Plasma exosomes


title: Sox14_6-8_BS1

description: Drosophila embryos RNAi, shSox14, replicate 1, 6-8 hours


title: Sox102F_16-18_BS2

description: Drosophila embryos RNAi, shSox102F, replicate 2, 16-18 hours


title: Sox102F_16-18_BS1

description: Drosophila embryos RNAi, shSox102F, replicate 1, 16-18 hours


title: E104K: CONTROL, Plasma exosomes


title: P_17

value: II


title: P_16

value: VI


title: P_19


title: E105K: CONTROL, Plasma exosomes

value: Plasma exosomes


title: E102K: CONTROL, Plasma exosomes


title: P_15


title: E117K: CONTROL, Plasma exosomes


title: Sox102F_12-14_BS1

description: Drosophila embryos RNAi, shSox102F, replicate 1, 12-14 hours

value: 12-14 hours


title: Sox102F_0-1.5_BS2

description: Drosophila embryos RNAi, shSox102F, replicate 2, 0-1.5 hours

value: embryos

value: 0-1.5 hours


title: P_14


title: E101K: CONTROL, Plasma exosomes

value: CONTROL


title: Pdp1_16-18_BS1

description: Drosophila embryos RNAi, shPdp1, replicate 1, 16-18 hours

value: 16-18 hours


title: E04: ALL, Plasma exosomes

value: ALL


title: E09: ALL, Plasma exosomes


title: E08: ALL, Plasma exosomes


title: Sox102F_0-1.5_BS1

description: Drosophila embryos RNAi, shSox102F, replicate 1, 0-1.5 hours


title: E03: ALL, Plasma exosomes


title: E07: ALL, Plasma exosomes


title: Sox102F_12-14_BS2

description: Drosophila embryos RNAi, shSox102F, replicate 2, 12-14 hours


title: P_11

value: Brain frontal cortex

value: I


title: P_12

value: M

value: AD


title: E103K: CONTROL, Plasma exosomes


title: P_13

value: CT


title: E02: ALL, Plasma exosomes


title: E100K: CONTROL, Plasma exosomes


title: E06: ALL, Plasma exosomes


title: Pdp1_16-18_BS2

description: Drosophila embryos RNAi, shPdp1, replicate 2, 16-18 hours


title: P_09


title: E05: ALL, Plasma exosomes


title: Pdp1_14-16_BS2

description: Drosophila embryos RNAi, shPdp1, replicate 2, 14-16 hours

value: 14-16 hours


title: Pdp1_14-16_BS1

description: Drosophila embryos RNAi, shPdp1, replicate 1, 14-16 hours


title: E01: ALL, Plasma exosomes


title: Pdp1_0-1.5_BS2

description: Drosophila embryos RNAi, shPdp1, replicate 2, 0-1.5 hours


title: P_10

value: parenchyma

value: V


title: NSC Setd5 +/- #3

city: Milan

first: Edoardo

middle: Niccolò

last: Bellini

state: Lombardia

address: Via Olgettina 58

department: Neuroscience

country: Italy

institute: San Raffaele Hospital

data_processing:
Fastq files, after adaptors trimming using Trimmomatic (Bolger et al, 2014), were aligned to the mm10 mouse reference genomes using Bowtie2 (Langmead & Salzberg, 2012). Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and GSEA (Huang et al., 2009), respectively. Statistical and downstream bioinformatics analysis were performed within the R environment.
Assembly: mm10
Supplementary files format and content: Normalize count matrix

source_name: NSCs

growth_protocol: Cells were cultured in Neural inducing medium (NIM) composed of: DMEM/F12 (Sigma-Aldrich) supplemented with Hormon Mix (DMEM/F12, 0,6% Glucose (Sigma-Aldrich) (30%), Insulin (Sigma-Aldrich) 250µg/ml, putrescin powder (Sigma-Aldrich) 97µg/ml, apotransferrin powder (Sigma Aldrich), sodium selenite 0,3µM, progesterone 0,2µM), 1mg/ml penicillin/streptomycin (Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich), 0,66% Glucose (30% in phosphate buffer salt (PBS) (Euroclone)), Heparin 4µg/ml, 10 ng/ml bFGF (basic fibroblast growth factor) (ThermoFisher Scientific) and 10 ng/ml EGF (epithelial growth factor) (10 ng/ml) (ThermoFisher Scientific). To culture NSCs in adhesion, cells were seeded in coverslips coated with 1:100 Matrigel. For high oxygen culture, cells were cultured in an incubator with 21% oxygen concentration.

extract_protocol:
To perform RNA extraction, cells were seeded in adherent condition (see section 2.1.1) in 15 mm Petrie dish at approximately 60-70 % of confluence and were grown until they reached almost 90% of confluence. Cells were then scraped and pelleted in cold (4°c) and sterile PBS. RNA extraction was performed using RNAeasy mini kit (Qiagen), following manufacturer instruction.
Libraries have been prepared using Tru Seq RNA v2 kit (Illumina) starting from total RNA

value: NSCs

tag: cell type

value: Primary cortical NSCs

tag: genotype

value: Setd5 +/-


title: NSC Setd5 +/- #2

tag: cell line


title: NSC Setd5 +/- #1


title: P_08

tag: fraction

tag: donor id

value: VI


title: NSC WT #3

value: Wild Type


title: Pdp1_0-1.5_BS1

description: Drosophila embryos RNAi, shPdp1, replicate 1, 0-1.5 hours

data_processing:
Raw FASTQ files were aligned to the Drosophila melanogaster reference genome (Release 6)  using STAR aligner 2.7.3a  with default settings and up to 20 multiple alignments to produce BAM files.
HTSeq htseq-count v0.12.4 was used to determine read counts overlapping genes.
Differential gene expression in the RNAi experimental samples compared to the mCherry controls was determined using DESeq2 1.24.0.
bigWig files were created using a custom tool called bam2bedgraph to convert bam files into bedgraph files, then UCSC's bedGraphToBigWig to convert the bedgraph files to bigWig format.
Assembly: dm6
Supplementary files format and content: BAM alignment files aligning FASTQ read files to dm6 assembly using STAR 2.7.3a.
Supplementary files format and content: HTSeq htseq-count files produced with HTSeq v0.12.4
Supplementary files format and content: DESeq csv files produced using DESeq2 v1.24.0
Supplementary files format and content: bigWig files produced using custom bam2bedgraph script and UCSC bedGraphToBigWig tool

extract_protocol:
Frozen embryos were homogenized using the Pellet Pestle Cordless Motor (Kimble Cat. No. 749540-0000; Pellet Pestles Sigma Cat. No. Z359947). RNA was extracted from the homogenate using TRIzol Reagent (Thermo Fisher, Cat. No. 15596026), chloroform extraction and isopropanol precipitation.  RNA was resuspended in Nuclease Free Water (Ambion AM9930) and incubated over night before purification using the RNeasy Mini Kit (QIAGEN Cat. No. 74106).  After Qiagen clean up, RNA was quantified using NanoDrop ND1000v 3.5.2.
Libraries for sequencing were made using TruSeq Stranded mRNA Library Prep (llumina 20020594).

value: embryos

value: 0-1.5 hours


title: P_07

tag: Sex

tag: age

value: II


title: NSC WT #1


title: P_06

value: F

tag: disease

tag: braak tangle


title: NSC WT #2


title: Tumour Taf4KO-APC S3

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

description:
ileum APCd14-induced tumor in Taf4 KO background
rnaseq_taf4_mouse_tumours_results.xlsx
6_M227-M254

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Reads were mapped to reference genome mm9 using STAR v2.5.3a. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 67.
Data normalization and fold-change across conditions computation were performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Assembly: mm10
Supplementary files format and content: Excel file containing normalized (by sequencing depth and gene length) average expression for each condition and log2(fold-change) with adjusted p-values for each DESeq2 comparisons. Mice and organoids data are in two sheets.

source_name: mouse ileum tumour

extract_protocol:
Qiagen RNAeasy mini kit
P2586 : RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: tamoxifen injections at the age of 6-8 weeks

tag: strain

value: mixed genetic background (129SV  and C57Bl/6)

value: adult Intestinal tumor

tag: tag

value: tumoral tissue


title: Kah_8-10_BS2

description: Drosophila embryos RNAi, shKah, replicate 2, 8-10 hours

value: shKah

value: 8-10 hours


title: Tumour APC S1

description:
ileum APCd14-induced tumor in Taf4+/+ background
rnaseq_taf4_mouse_tumours_results.xlsx
1_M250


title: Kah_16-18_BS2

description: Drosophila embryos RNAi, shKah, replicate 2, 16-18 hours

value: 16-18 hours


title: P_05

value: Brain frontal cortex

value: parenchyma

value: CT

tag: apoe

tag: pmi

tag: ph cerebellum

tag: brain weight


title: Tumour APC S2

description:
ileum APCd14-induced tumor in Taf4+/+ background
rnaseq_taf4_mouse_tumours_results.xlsx
2_M91

tag: tissue


title: P_02

value: AD

value: V


title: P_03

value: M


title: WT Saline #2

city: Clermont-Ferrand

first: Fabien

last: Marchand

address: 28 Place Henri Dunant

department: Fundamental and clinical pharmacology of pain

institute: Université Clermont Auvergne, Inserm U1107 NEURO-DOL

description: Sample 14

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the mouse genome (UCSC mm10) with a set of gene model annotations (genes.gtf downloaded from UCSC on August 20 2018 ; GeneIDs come from the NCBI: gene2refseq.gz).
Final read alignments having more than 3 mismatches were discarded. Samtools (v1.5) was used to sort the alignment files. Then, the counting was performed with HTSeq-count (version 0.6.1p1). As the data is from a strand-specific assay, the read has to be mapped to the same strand of the gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw gene counts for every gene (Symbol|NCBI GeneID) and every sample

extract_protocol:
We performed a RNA sequencing analysis of ipsilateral lumbar DRGs (L4-6) from WT-Vehicle, WT-MoArthritis, TrkA/C-KI Vehicle and TrkA/C-KI MoArthritis. n=4 biological sample (n=6 DRGs from 2 mice from the same group pooled per biological sample). Mice were terminally anesthetised and ipsilateral L4-L5-L6 DRGs were quickly harvested, snap frozen in liquid nitrogen and stored at -80°C until use. Total RNA of lumbar DRGs was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was analysed by a parallel capillary electrophoresis instrument (Fragment Analyser, Agilent®) and sent to Montpellier GenomiX platform (MGX, http://www.mgx.cnrs.fr) for RNA sequencing.
RNA-Seq libraries were constructed with the Universal Plus mRNAseq kit from Nugen. 150ng of total RNA were used for the construction of the libraries. Using poly-T oligo attached magnetic beads, total RNA was purified in order to obtain only poly-A mRNA. Following purification, the mRNA is fragmented into small pieces under elevated temperature. The cleaved RNA fragments are reverse-transcribed into first strand cDNA using random hexamer primers, in presence of Actinomycin D. Then, the second strand cDNA was synthesized. These dscDNA had their ends repaired and adapters ligation was performed. The strand that will be sequenced was selected, and then the final products were purified and enriched with 15 cycles of PCR. The final cDNA libraries were validated with a Fragment Analyzer (Agilent) and quantified with a KAPA qPCR kit (Kapa Biosystems, Wilmington, MA). On 3 sequencing lanes of a V4 flowcell, 6 or 7 of the 20 libraries were pooled in equal proportions per lane, denatured with NaOH and diluted to 22 pM before clustering. Cluster formation, primer hybridization and single-end read 50 cycles sequencing were performed on cBot and HiSeq2500 (Illumina, San Diego, CA) respectively.

treatment_protocol: Wild type and knock-in TrkAC mice were injected intraarticulaly with vehicle or complete Freund's adjuvant (CFA) 14 days before DRGs sampling

value: lumbar dorsal roots ganglia

value: Wildtype

tag: disease state

value: control


title: Tumour APC S3

description:
ileum APCd14-induced tumor in Taf4+/+ background
rnaseq_taf4_mouse_tumours_results.xlsx
3_M144


title: WT Saline #3

description: Sample 15


title: Tumour Taf4KO-APC S2

description:
ileum APCd14-induced tumor in Taf4 KO background
rnaseq_taf4_mouse_tumours_results.xlsx
5_M254


title: Tumour Taf4KO-APC S1

description:
ileum APCd14-induced tumor in Taf4 KO background
rnaseq_taf4_mouse_tumours_results.xlsx
4_M227


title: Kah_16-18_BS1

description: Drosophila embryos RNAi, shKah, replicate 1, 16-18 hours

value: embryos

tag: treatment

tag: timepoint


title: P_04

value: VI


title: Kah_0-1.5_BS2

description: Drosophila embryos RNAi, shKah, replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: WT MoAr #3

description: Sample 11

tag: genotype

value: MoArthritis


title: WT Saline #1

description: Sample 13


title: Kah_0-1.5_BS1

description: Drosophila embryos RNAi, shKah, replicate 1, 0-1.5 hours


title: P_01

tag: fraction

value: F

value: III


title: Hr51_6-8_BS2

description: Drosophila embryos RNAi, shHr51, replicate 2, 6-8 hours

value: 6-8 hours


title: Kah_8-10_BS1

description: Drosophila embryos RNAi, shKah, replicate 1, 8-10 hours

value: shKah

value: 8-10 hours


title: WT MoAr #2

description: Sample 10


title: WT Saline #4

description: Sample 16


title: Hr51_6-8_BS1

description: Drosophila embryos RNAi, shHr51, replicate 1, 6-8 hours


title: WT MoAr #1

description: Sample 9

value: Knock-in TrkAC


title: TrkA-C Saline #4

description: Sample 8


title: SMARCA4-WT_ATAC-seq

city: Nanjing

first: Xiangwei

last: Zeng

state: Jiangsu

address: Xianlin avenue

country: China

institute: Nanjing university

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Sequencing reads were aligned to the mm10 reference genome with Bowtie2
Sequencing was performed on Illumina HiseqXten-PE150.
MACS2 (version 2.2.7.1) was used to call peaks
Peak annotation was performed by R package ChIPseeker
Assembly: hg19
Supplementary files format and content: bigWig

source_name: colon

growth_protocol: McCoy's 5 A,10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Fifty thousand cells were collected and centrifuged.
The unfixed nuclei were tagged using tn5 transposase and the resulting library fragments were generated by 12 PCR cycles.

value: colon

tag: cell line

tag: cell type

value: Human eukaryotic cells


title: WT MoAr #4

description: Sample 12


title: Hr51_16-18_BS2

description: Drosophila embryos RNAi, shHr51, replicate 2, 16-18 hours

value: 16-18 hours


title: SMARCA4-R1157W_ATAC-seq

tag: SMARCA4-R1157W mutant


title: TrkA-C Saline #2

description: Sample 6


title: TrkA-C Saline #1

description: Sample 5


title: TrkA-C MoAr #4

description: Sample 4


title: TrkA-C MoAr #3

description: Sample 3


title: YCO19_organoid

city: SEOUL

first: hee seung

last: lee

state: --- Select ---

address: SEOUL

country: South Korea

institute: Yonsei University

data_processing:
DNA-seq Image analysis was performed using NovaSeq6000 control Software version 1.3.1, and output base-calling data were de-multiplexed with bcl2fastq version v2.20.0.422, generating fastQC files. Sequencing reads were first mapped/aligned to reference genome hg19 using  the Burrows-Wheeler Aligner (BWA).
Assembly: UCSC hg19
Supplementary files format and content: vcf
Library strategy: whole exome sequencing

source_name: Organoid developed from cholangiocarcinoma epithelial cell

extract_protocol: DNA extract protocol and library construction protocol not provided

value: Tumor organoid

tag: tumor type

value: cholangiocarcinoma


title: Hr51_16-18_BS1

description: Drosophila embryos RNAi, shHr51, replicate 1, 16-18 hours


title: YCO18_organoid


title: YCO15_organoid


title: TrkA-C MoAr #1

description: Sample 1

value: lumbar dorsal roots ganglia


title: TrkA-C MoAr #2

description: Sample 2


title: Hr51_0-1.5_BS2

description: Drosophila embryos RNAi, shHr51, replicate 2, 0-1.5 hours


title: YCO13_organoid


title: Hr51_12-14_BS1

description: Drosophila embryos RNAi, shHr51, replicate 1, 12-14 hours

value: 12-14 hours


title: Hr51_0-1.5_BS1

description: Drosophila embryos RNAi, shHr51, replicate 1, 0-1.5 hours

value: embryos


title: YCO11_organoid


title: YCO10_organoid


title: cytidine 2 (RNA-Seq)

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

data_processing:
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
Transcripts Per kilobase Megabase of library size (TPM) were calculated using DEseq2.0
Assembly: NC_000913.2
Supplementary files format and content: comma-delimited text files include TPM values for each Sample.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Total RNA isolated from E. coli

growth_protocol: E. coli K-12 MG1655 WT was grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, or W2 minimal media with 0.2% glucose and 2 g/L glutamine, cytidine or cytosine.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

tag: nitrogen source

value: cytidine

tag: genotype/variation

value: WT


title: cytosine 2 (RNA-Seq)

value: cytosine


title: Hr3_16-18_BS2

city: Berkeley

first: Benjamin

last: Booth

institute: Lawrence Berkeley National Laboratory

description: Drosophila embryos RNAi, shHr3, replicate 2, 16-18 hours


title: cytosine 1 (RNA-Seq)


title: glutamine 2 (RNA-Seq)

value: glutamine


title: YCO9_organoid


title: TrkA-C Saline #3

description: Sample 7

tag: strain

value: control


title: glutamine 1 (RNA-Seq)


title: E106K: CONTROL, Plasma exosomes

tag: patientid

tag: group

value: CONTROL

value: Plasma exosomes


title: ammonia 2 (RNA-Seq)

value: ammonia


title: Hr51_12-14_BS2

description: Drosophila embryos RNAi, shHr51, replicate 2, 12-14 hours


title: YCO7_organoid


title: RpoD cytosine 2 (ChIP-exo)

description: processed data file: chipexo_rpod_binding.csv

data_processing:
library strategy: ChIP-exo
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity for NtrC, Nac, RpoN and 90% strongest intensity for RpoD were used as background intensity.
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: ASM584v2
Supplementary_files_format_and_content: Comma-delimited text files (peaks) include binding positions and intensity values for each sample.

source_name: Immunoprecipitated DNA

growth_protocol: E. coli K-12 MG1655 WT, NtrC-8myc and Nac-8myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media with 0.2% glucose and 2 g/L glutamine, cytidine or cytosine, or ammonia for nitrogen source.

extract_protocol: ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody

value: anti-RpoD (Neoclone, WP004)


title: YCO8_organoid


title: RpoD cytidine 2 (ChIP-exo)


title: ammonia 1 (RNA-Seq)


title: Hr3_12-14_BS2

description: Drosophila embryos RNAi, shHr3, replicate 2, 12-14 hours


title: YCO6_organoid


title: RpoD cytosine 1 (ChIP-exo)


title: RpoD glutamine 2 (ChIP-exo)


title: RpoD cytidine 1 (ChIP-exo)


title: Hr3_12-14_BS1

description: Drosophila embryos RNAi, shHr3, replicate 1, 12-14 hours


title: Hr3_0-1.5_BS2

description: Drosophila embryos RNAi, shHr3, replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: cytidine 1 (RNA-Seq)


title: RpoD glutamine 1 (ChIP-exo)


title: YCO5_organoid


title: Nac cytosine 2 (ChIP-exo)

description: processed data file: chipexo_nac_binding.csv

value: anti-myc (Santa Cruz Biotech, sc-28207)


title: Hr3_0-1.5_BS1

description: Drosophila embryos RNAi, shHr3, replicate 1, 0-1.5 hours


title: RpoD ammonia 2 (ChIP-exo)


title: RpoD ammonia 1 (ChIP-exo)


title: Nac cytosine 1 (ChIP-exo)


title: YCO4_organoid


title: HLH54F_8-10_BS2

description: Drosophila embryos RNAi, shHLH54F, replicate 2, 8-10 hours

value: 8-10 hours


title: YCO3_organoid

value: Tumor organoid


title: Nac cytidine 1 (ChIP-exo)


title: Nac cytidine 2 (ChIP-exo)


title: Hr3_16-18_BS1

description: Drosophila embryos RNAi, shHr3, replicate 1, 16-18 hours

value: 16-18 hours


title: YCO2_organoid

value: cholangiocarcinoma


title: Nac glutamine 2 (ChIP-exo)


title: HLH54F_8-10_BS1

description: Drosophila embryos RNAi, shHLH54F, replicate 1, 8-10 hours


title: HLH54F_16-18_BS2

description: Drosophila embryos RNAi, shHLH54F, replicate 2, 16-18 hours


title: Nac ammonia 1 (ChIP-exo)


title: RpoN cytosine 2 (ChIP-exo)

description: processed data file: chipexo_rpon_binding.csv

value: anti-RpoN (Neoclone, W0005)


title: Nac glutamine 1 (ChIP-exo)


title: HLH54F_16-18_BS1

description: Drosophila embryos RNAi, shHLH54F, replicate 1, 16-18 hours

value: embryos


title: RpoN cytosine 1 (ChIP-exo)


title: HLH54F_0-1.5_BS2

description: Drosophila embryos RNAi, shHLH54F, replicate 2, 0-1.5 hours


title: Nac ammonia 2 (ChIP-exo)


title: HLH54F_0-1.5_BS1

description: Drosophila embryos RNAi, shHLH54F, replicate 1, 0-1.5 hours


title: RpoN glutamine 2 (ChIP-exo)


title: RpoN cytidine 1 (ChIP-exo)

value: cytidine


title: RpoN glutamine 1 (ChIP-exo)

value: WT


title: RpoN ammonia 2 (ChIP-exo)


title: RpoN cytidine 2 (ChIP-exo)


title: Fer1_Camta_CG10209_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Fer1, Camta, CG10209), replicate 2, 16-18 hours


title: NtrC cytosine 2 (ChIP-exo)

description: processed data file: chipexo_ntrc_binding.csv

value: cytosine


title: RpoN ammonia 1 (ChIP-exo)


title: Fer1_Camta_CG10209_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Fer1, Camta, CG10209), replicate 1, 16-18 hours


title: NtrC cytidine 2 (ChIP-exo)


title: Fer1_Camta_CG10209_mCherry_12-14_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Fer1, Camta, CG10209), replicate 2, 12-14 hours

value: 12-14 hours


title: NtrC cytosine 1 (ChIP-exo)


title: Fer1_Camta_CG10209_mCherry_12-14_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Fer1, Camta, CG10209), replicate 1, 12-14 hours


title: NtrC cytidine 1 (ChIP-exo)


title: NtrC glutamine 2 (ChIP-exo)

value: glutamine


title: Fer1_Camta_CG10209_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for Fer1, Camta, CG10209), replicate 2, 0-1.5 hours


title: 210322_TFmap_S16

description:
TF mapping results for 210322_TFAtlas_S16
library strategy: amplicon

data_processing:
Custom SHARE-seq pipeline
Scanpy v1.7.2
Custom Python script for mapping cells to transcription factor ORFs
Assembly: hg38
Supplementary files format and content: Raw count matrix generated by SHARE-seq pipeline (csv) and annotated processed data generated by Scanpy (h5ad). Map of cells to transcription factor ORFs produced by a custom Python script (csv)

source_name: H1 human embryonic stem cells

extract_protocol:
RNA was extracted using SHARE-seq
single-cell RNA-Seq libraries were prepared using SHARE-seq. Cells were mapped to their respective transcription factor perturbations by PCR amplifying the transcription factor and cell barcodes from the cDNA prior to tagmentation

value: H1 human embryonic stem cells

tag: differentiation protocol

value: overexpression of a library with 3,550 transcription factors

tag: time point

value: 7 days


title: 210322_TFmap_S17

description:
TF mapping results for 210322_TFAtlas_S17
library strategy: amplicon


title: 210322_TFmap_S20

description:
TF mapping results for 210322_TFAtlas_S20
library strategy: amplicon


title: 210322_TFmap_S19

description:
TF mapping results for 210322_TFAtlas_S19
library strategy: amplicon


title: 210322_TFmap_S18

description:
TF mapping results for 210322_TFAtlas_S18
library strategy: amplicon


title: NtrC glutamine 1 (ChIP-exo)


title: NtrC ammonia 2 (ChIP-exo)

value: ammonia


title: NtrC ammonia 1 (ChIP-exo)


title: Fer1_Camta_CG10209_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for Fer1, Camta, CG10209), replicate 1, 0-1.5 hours

tag: tissue

value: 0-1.5 hours


title: 210322_TFmap_S14

description:
TF mapping results for 210322_TFAtlas_S14
library strategy: amplicon


title: 191225_astrocyte_S1L

extract_protocol:
Genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo D4075)
Libraries were prepared by PCR amplification of TF barcodes using custom primers (see Methods)

value: neural progenitors

value: overexpression of a library with 54 transcription factors

tag: screen condition

value: sample 1 sorted low bin


title: Fer1_16-18_BS2

description: Drosophila embryos RNAi, shFer1, replicate 2, 16-18 hours

tag: treatment

tag: timepoint

value: 16-18 hours


title: 191225_astrocyte_S2H

value: sample 2 sorted high bin


title: 191225_astrocyte_S1H

value: sample 1 sorted high bin


title: Fer1_16-18_BS1

description: Drosophila embryos RNAi, shFer1, replicate 1, 16-18 hours

value: embryos


title: Fer1_12-14_BS2

description: Drosophila embryos RNAi, shFer1, replicate 2, 12-14 hours


title: 210322_TFmap_S15

description:
TF mapping results for 210322_TFAtlas_S15
library strategy: amplicon


title: 210322_TFmap_S13

description:
TF mapping results for 210322_TFAtlas_S13
library strategy: amplicon


title: 210322_TFmap_S12

description:
TF mapping results for 210322_TFAtlas_S12
library strategy: amplicon


title: Fer1_12-14_BS1

description: Drosophila embryos RNAi, shFer1, replicate 1, 12-14 hours


title: 190830_cardiomyocyte_Ventricular_S2L

value: cardiomyocytes

value: overexpression of a library with 80 transcription factors

value: 4 weeks

value: ventricular sample 2 sorted low bin


title: 190830_cardiomyocyte_Ventricular_S2H

value: ventricular sample 2 sorted high bin


title: 190830_cardiomyocyte_Ventricular_S1H

value: ventricular sample 1 sorted high bin


title: 190830_cardiomyocyte_Ventricular_S1L

value: ventricular sample 1 sorted low bin


title: 190830_cardiomyocyte_Mature_S2H

value: mature sample 2 sorted high bin


title: 190830_cardiomyocyte_Mature_S1H

value: mature sample 1 sorted high bin


title: 191225_astrocyte_S2L

value: 7 days

value: sample 2 sorted low bin


title: Fer1_0-1.5_BS2

description: Drosophila embryos RNAi, shFer1, replicate 2, 0-1.5 hours

value: 0-1.5 hours


title: 190830_cardiomyocyte_Atrial_S2L

value: atrial sample 2 sorted low bin