title: 15_R3_IAA

city: Bethesda

first: Dinah

middle: S.

last: Singer

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

description: HCT116RmAC cells treated with IAA replicate 3

data_processing:
RNA-seq reads were aligned to human reference genome (hg19) with STAR aligner. Raw read counts were obtained using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of sequencing reads for each sample

growth_protocol: The HCT116 RmAC cells were grown in Maccoy's 5A (modified) media (Gibco) supplimented with 10% fetal bovine serum in 37 °C and 7.5% CO2

extract_protocol:
RNA was isolated from WT, RAD21 depleted, BRD4 depleted and BRD4 and RAD21 depleted HCT116 Rad21mAIDmClover cells using the Micro RNeasy-Plus Kit (Qiagen)
Libraries were prepared using  the Illumina TruSeq Stranded mRNA Library Prepaccording to manufacturers' instructions.

treatment_protocol: Depletion of BRD4 by 0.1 uM MZ1 was complete by 4 hours; IAA-induced degradation (500 uM) of RAD21 was complete by 1 hour. Subsequent co-depletion experiments were for 3 hours with 0.1uM MZ1, followed by the addition of 500uM IAA, for a total of 4 hours.

value: human colorectal carcinoma cell line

value: IAA


title: Experiment 1, rRNA depleted, Ervevax, 6hpi, replicate 1

status: Public on Aug 31 2022

type: SRA

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: rRNA depleted total RNA

library_source: transcriptomic

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Sequencing reads were aligned to the hg19 version of the human genome
Reads were then quantified using quasR (Gaidatzis et al, 2015).
For generating the viral genome sequences in the fasta files provided here, sequencing reads were aligned to the rubella virus sequence NC_001545.2 and differences recursively corrected. See JF727654.2 (Ervevax) and JN635289.1 (MA17) for previously available genome sequences.
Genome_build: hg19
Genome_build: Rubella virus NC_001545.2
Supplementary_files_format_and_content: tab-separated values
Supplementary_files_format_and_content: fasta

molecule: total RNA

organism: Homo sapiens

source_name: HUVEC

growth_protocol:
Human umbilical vein cells (HUVEC) from three donors (Promocell) were maintained in Endothelial Cell Growth Medium 2 (Promocell) and supplemented with 10% (v/v) Supplement Mix and 100 units/ml penicillin. The cells were cultivated in a humidified atmosphere with 5% CO2 at 37°C
Viruses were propagated on Vero E6 cells. After 6 days viral supernatant was concentrated by ultrafiltration through a 30 kDa filter and stored at −80°C. For every virus stock, a mock sample from uninfected cells was processed in parallel, which was then used as the mock control for the infections.

extract_protocol:
Illumina Truseq stranded
adapter sequence: GATCGGAAGAGCACACGT
For RNA extraction, medium was removed and cells were lysed in Trizol (Thermo Fisher). Virus stocks were diluted 1:3 in Trizol LS (Thermo Fisher). RNA was extracted using the clean and concentrator kit 25 (Zymo) according to manufacturer's instruction.
RNA-sequencing library were prepared with polyA enrichment, or using the RiboZero kit (Illumina) for rRNA depletion, before continuing with the TruSeq stranded kit (Illumina)
rRNA depleted total RNA
polyA RNA-seq
total RNA from virus stocks

treatment_protocol: Cells were infected with a MOI of 5.

tag: infection

value: yes

tag: rubella virus strain

value: Ervevax

tag: sampling timepoint


title: isogenic control, day 23, rep 1

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Raw sequencing data was trimmed and filtered using fastp 0.19.6
Trimmed reads were aligned and quantified using STAR 2.7.1a
Taxonomic classification of contaminants was performed using Kraken 2.0.9.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited, raw gene counting data. Per sample, with Ensemble gene Ids

source_name: Lis_FX6 clone #7B

growth_protocol: hESC were cultured on Geltrex-coated plates in mTeSR1 medium supplemented with 100 μg/mL Primocin. hESC were passaged using Accutase and medium was supplemented with 5μM ROCK inhibitor Y-27632 for 24 h to increase survival. hESCs were frozen using CryoStem.

extract_protocol:
Total mRNA samples were extracted from hESCs (day 0), at 13 and 23 DIV of their differentiation into cortical neurons, using the mirVana miRNA Isolation Kit according to manufacturer’s protocol. Extraction was performed in three biological experiments.
illumina TruSeq Stranded mRNA Library construction (stranded, polyA enrichment) and RNA sequencing were performed on Illumina NovaSeq 6000, at a commercial laboratory (Macrogen Inc., Europe).

treatment_protocol: hESCs were differentiated into cortical neurons by an accelerated dual SMAD inhibition protocol as previously described by Qi et al., 2017. Briefly, hESCs were plated on Geltrex with mTeSR1 to confluence. From day 0 cells were cultured in KSR media in the presence of small chemical inhibitors of the TGF, SMAD, and Wnt pathways till day 6. From day 2 cells were cultured also in the presence of MEK, FGF and Notch signaling inhibitors to trigger cortical precursors for cortical neuron differentiation. N2/B27 medium was added in increasing 1/3 increment every other day from day 4, until reaching 100% Neurobasal at day 8. The WNT agonist CHIR99021 was added at days 8-15 as it exerted a strong pro-survival effect on cultures. After MACS, cortical neurons were cultured on Poly-L-ornithine hydrobromide/Laminin I/Fibronectin coated wells in NB/B27 supplemented with 1% Pen/Strep, BDNF, dbcAMP and ascorbic acid.

tag: cell line

value: Lis_FX6 clone #7B

tag: cell type

value: neuorns, day 23 of neuronal differentiation

tag: genotype

value: isogenic control

tag: treatment

value: neuronal differentiation


title: MDA134-siCASZ1-pool RNA-seq rep3

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

country: USA

institute: DFCI

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using STAR
For peak calling STAR was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using STAR using the VIPER pipeline

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen). DNA was degraded on columns with DNase I (Qiagen).
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) adapted for use on the Sciclone (Perkin-Elmer) liquid handler.

treatment_protocol: Cells were maintained in their original media and harvested for RNA extraction.

value: MDA_MB134VI breast carcinoma cell line

tag: agent

value: Full Media

tag: genotype/growth protocol

value: MDA134 were transfected with siRNA and cultured for 48-72 hrs


title: 11_RP2_PBS

description: HCT116RmAC cells treated with PBS replicate 2

value: PBS


title: MDA134-siCTR RNA-seq rep3


title: isogenic control, day 13, rep 2

value: day 13 of neuronal differentiation


title: 13_RP1_IAA

description: HCT116RmAC cells treated with IAA replicate 1


title: MDA134-siCASZ1-pool RNA-seq rep2


title: MDA134-siCASZ1-pool RNA-seq rep1


title: MDA134-siCTR RNA-seq rep1


title: actin5C-Gal4>UAS-miR-2b-1 3

city: Gelugor

first: Ghows

last: Azzam

state: Penang

address: 1112 Jalan Persiaran Sains

department: School of Biological Sciences

country: Malaysia

institute: Universiti Sains Malaysia

data_processing:
Galaxy version 22.05.rc1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (parameter- Quality cutoff: 20)
Trimmed sequence reads were mapped to Drosophila melanogaster reference genome assembly (dm6) using RNA STAR (parameters- Length of the genomic sequence around annotated junctions: 36)
Read count extraction and normalization were performed using featureCounts (parameter- Minimum mapping quality per read: 10)
Differential gene expression was performed using edgeR
Assembly: dm6
Supplementary files format and content: Tab-delimited text files with normalized counts for each sample
Supplementary files format and content: Tab-delimited text files with differentially expressed gene with logFC, logCPM, P value and FDR

organism: Drosophila melanogaster

source_name: Adult testes (3-5 Days)

growth_protocol: All fly tocks were maintained at 28˚C and crosses of actin-GAL4 (driver) with w1118 (control) and UAS-miR-2b-1 were made at 28˚C for a maximum gene expression. F1 adult males of the crosses with desired genotype were collected and aged to 3-5 days prior to dissection

extract_protocol:
Adult male testes of actin-GAL4>w1118 (control) and actin-GAL4>UAS-miR-2b-1 were dissected and total RNA was extracted using Trizol and Qiagen RNeasy mini kit. Approximately 2 ug of total RNA was used for the construction of the sequencing libraries
Total RNA was used for cDNA library construction following the protocol supplied with the Truseq™ RNA sample prep Kit (Illumina, San Diego, USA)

tag: tissue

value: Adult testes (3-5 Days)

value: miR-2b-1 overexpression


title: 10_RP1_PBS

description: HCT116RmAC cells treated with PBS replicate 1


title: isogenic control, day 13, rep 1


title: actin5C-Gal4>UAS-miR-2b-1 2


title: actin5C-Gal4>w1118 (Control) 2

value: WT


title: actin5C-Gal4>UAS-miR-2b-1 1


title: actin5C-Gal4>w1118 (Control) 3


title: MDA134-siCASZ1-1 RNA-seq rep3


title: isogenic control, day 0, rep 3

value: hESCs


title: 8_RP2_MZ1_plus_IAA

description: HCT116RmAC cells treated with MZ1+IAA replicate 2

value: human colorectal carcinoma cell line


title: MDA134-siCASZ1-1 RNA-seq rep2


title: actin5C-Gal4>w1118 (Control) 1


title: isogenic control, day 0, rep 2


title: MDA134-siCASZ1-1 RNA-seq rep1


title: 12_R3_PBS

description: HCT116RmAC cells treated with PBS replicate 3


title: isogenic control, day 13, rep 3


title: isogenic control, day 0, rep 1


title: 7_RP1_MZ1_plus_IAA

description: HCT116RmAC cells treated with MZ1+IAA replicate 1


title: E. coli total RNA - nontargeting - rep 2

city: Skolkovo

first: Matvei

last: Kolesnik

address: 3 Nobel str

department: Life Sciences

country: Russia

institute: Skoltech

description: in vitro experiments with E. coli total RNA

data_processing:
Raw RNA sequencing reads were filtered by quality with the simultaneous adapters removal using trimmomatic v. 0.36. The exact parameters of trimmomatic run could be found in raw_data_processing.sh file.
Processed reads were mapped onto reference sequences (RefSeq: NC_000913.3 supplemented with pC002 and pC008 plasmids in case of nontargeting samples and NC_000913.3 supplemented with pC003_RFP_spacer and pC008 plasmids in case of targeting samples) using bowtie2 v. 2.3.4.3 producing corresponding SAM files. In case of the analysis of data obtained from in vitro experiments on isolated E. coli total RNAб reads were mapped only onto the NC_000913.3 sequence. The exact parameters of bowtie2 run could be found in read_mapping.sh file.
For each nucleotide position of each strand of reference sequences the number of 5’ ends of aligned fragments were counted producing corresponding tables (see return_fragment_coords_table.py file for details).
The obtained tables were joined using merge_ends_count_tables.py script. The differences between the numbers of mapped 5’ ends in targeting and nontargeting samples were analyzed using edgeR package v.  3.26.3. The features (here, strand specific nucleotide positions) with low counts were excluded from the analysis. The TMM normalization method implemented in edgeR was applied. Next, the edgeR likelihood ratio test was performed. The obtained p-values were corrected using Benjamini-Hochberg method, and the result tables containing analyzed features with assigned log2FC and adjusted p-values were written to separate files (see TCS_calling.R file for details). The obtained trascript cleavage sites were overlapped with annotated genomic features using GenomicRanges package.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Tab-separated files containing 5' ends counts per each nucleotide position of each strand of reference sequences
Supplementary_files_format_and_content: Tab-separated files containing coordinates of 5' ends of predicted transcript cleavage products, Log2FC and adjusted p-values and coordinates of overlapped genomic features

organism: Escherichia coli

source_name: Total RNA extracted from E. coli

growth_protocol: E. coli cells were grown overnight in LB supplemented with 25 µg/ml chloramphenicol and 100 µg/ml ampicillin. Cell cultures were diluted 1:100 in fresh LB with double selection and grown for 1 hour at 37 °C with continuous shaking. After 1 hour, target expression was induced with 500 ng/ml anhydrotetracyline. Targeting and nontargeting E. coli Δ10LVM cells were also grown under similar conditions for growth assays.

extract_protocol:
Total RNA was isolated from cells pelleted at 1 hour post RFP induction. Cell lysis was done using Max Bacterial Enhancement Reagent (Invitrogen) for 4 min and then with TRIzol reagent (Invitrogen) for 5 min. RNA was extracted by chloroform and precipitated with isopropanol. RNA pellets were washed with 70% ethanol and then dissolved in nuclease free water and then treated with Turbo DNA-free kit (Invitrogen).
Total RNA samples were treated with MICROBExpress Bacterial mRNA Enrichment Kit (Invitrogen) for rRNA depletion prior to library preparation. To obtain both primary (5’ PPP) and processed (5’ P/5’ OH) transcripts, RNA samples were treated with RNA 5' Pyrophosphohydrolase (RppH) (NEB) for 30 min at 37C which removes pyrophosphate from 5’ end from triphosphorylated RNA to leave a 5’ monophoshphate RNA. Fragmentation was carried out by sonication using the Covaris protocol to obtain fragments of 200 nt size. T4 PNK (NEB) treatment was done to obtain 5’P ends for adapter ligation during library preparation. Samples were purified using the Zymo Research Oligo Clean and Concentrator kit. Library preparation for RNA sequencing was done using the NEBNext Multiplex Small RNA Library Prep Set for Illumina according to manufacturer’s protocol. BluePippin size selection was done using 2% agarose gel cassette (Sage Science) to select for 100 - 600 bp products. QC at each step was carried out by both Qubit and fragment analyzer. RNA sequencing was performed using Illumina NextSeq High-Output kit 2 × 35 bp paired end read length.

treatment_protocol: Expression of target transcript was induced with 500 ng/ml anhydrotetracyline

tag: strain

value: Escherichia coli C3000


title: 5_RP2_MZ1

description: HCT116RmAC cells treated with MZ1 replicate 2


title: MDA134-shFOXA1-WM-E2-ND RNA-seq rep2

value: Estrogen

value: MDA134 cells with Dox inducible shFOXA1 were maintained in their media in presence of puromicin


title: 9_R3_MZ1_plus_IAA

description: HCT116RmAC cells treated with MZ1+IAA replicate 3


title: 6_R3_MZ1

description: HCT116RmAC cells treated with MZ1 replicate 3


title: MDA134-shFOXA1-WM-E2-ND RNA-seq rep3


title: E. coli total RNA - nontargeting - rep 3


title: E. coli total RNA - nontargeting - rep 1


title: E. coli total RNA - targeting - rep 3


title: MDA134-shFOXA1-WM-E2-DOX RNA-seq rep3

value: Estrogen + Dox

value: MDA134 cells with Dox inducible shFOXA1 were maintained in their media in presence of puromicin and treated with DOX for 3 days


title: E. coli total RNA - targeting - rep 1


title: E. coli total RNA - targeting - rep 2


title: 3_R3_DMSO

description: HCT116RmAC cells treated with DMSO replicate 3

value: DMSO


title: HBMEC, conditioned media treated (Swe22; Feb), P.4 [Swe22_Feb_p4_S24]

city: Seatlle

first: Yu Jung

last: Shin

state: WA

address: 850 Republican st, Brotman 419

department: Bioengineering

institute: University of Washington

description:
GeneCounts.2D.tsv
column O: Swe22_Feb_p4_S24

data_processing:
Image analysis and basecalling was performed using Illumina's Real Time Analysis v3.4.4 software, followed by demultiplexing of indexed reads and generation of FASTQ files with Illumina's bcl2fastq-2.20 software.
Sequenced reads were aligned to iGenome's UCSC hg38 using STAR2 aligner v2.7.7a in the two-pass mode.
STAR2's internal quantification method was used with GENCODE 38 annotations to generate gene-level raw counts
Assembly: hg38
Supplementary files format and content: tab-delimited file containing raw gene counts per sample

source_name: human brain

growth_protocol: Primary human brain endothelial cells were maintained in EGM2-MV media in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina Nextera XT DNA Library Prep Kit (Nextera XT) following manufacturer's protocols.

treatment_protocol:
1) 3 day cultured HBMECs were washed with EBM basal media for 15 minutes to remove the effect of serum. 2) following EBM basal media wash, HBMECs were treated with conditioned media from cortical neurons differentiated from hiPSC harboring swedish mutation (swe22) or hiPSCs of its isogenic control (cvia2)
3) unconditioned media was also used as a control (BNMN media). The unconditioned media is the media that is used to make conditioned media. For contidioned media, we had two batches collected from different hiPSC-CN differentiation. They were designated Dec or Feb based on the month the media was collected. conditioned media was collected by treating the neuron differentiation media (BNMN) on hiPSC-CNs for 72 hours.

value: human brain

value: HBMEC

value: brain endothelial cell

value: Swe22 Feb collected media


title: HBMEC, conditioned media treated (Swe22; Dec), P.4 [Swe22_Dec_p4_S22]

description:
GeneCounts.2D.tsv
column M: Swe22_Dec_p4_S22

value: Swe22 Dec collected media


title: HBMEC, conditioned media treated (Swe22; Dec), P.6 [Swe22_Dec_p6_S23]

description:
GeneCounts.2D.tsv
column N: Swe22_Dec_p6_S23


title: MDA134-shFOXA1-WM-E2-ND RNA-seq rep1

value: MDA_MB134VI breast carcinoma cell line


title: HBMEC, conditioned media treated (CVIA2; Feb), P.6 [CviA2_Feb_p6_S21]

description:
GeneCounts.2D.tsv
column L: CviA2_Feb_p6_S21

value: CVIA2 Feb collected media


title: E. coli Δ10 - nontargeting - rep 3

source_name: Escherichia coli Δ10 cells

value: Escherichia coli {delta}10


title: 14_RP2_IAA

description: HCT116RmAC cells treated with IAA replicate 2

value: IAA


title: 1_RP1_DMSO

description: HCT116RmAC cells treated with DMSO replicate 1


title: HBMEC, conditioned media treated (Swe22; Feb), P.6 [Swe22_Feb_p6_S25]

description:
GeneCounts.2D.tsv
column P: Swe22_Feb_p6_S25

value: WT


title: E. coli Δ10 - nontargeting - rep 2


title: MCF7-WM-E2-batch2 RNA-seq rep2

value: MCF7 breast carcinoma cell line

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days and treated with 10nm E2 for 12hrs


title: HBMEC, conditioned media treated (CVIA2; Feb), P.4 [CviA2_Feb_p4_S20]

description:
GeneCounts.2D.tsv
column K: CviA2_Feb_p4_S20


title: 4_RP1_MZ1

description: HCT116RmAC cells treated with MZ1 replicate 1

value: human colorectal carcinoma cell line


title: T47D-WM-E2-4H RNA-seq rep3

value: T47D breast carcinoma cell line

value: Estrogen 4 hours

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days and treated with 10nm E2 for 4hrs


title: E. coli Δ10 - nontargeting - rep 1


title: HBMEC, conditioned media treated (CVIA2; Dec), P.6 [CviA2_Dec_p6_S19]

description:
GeneCounts.2D.tsv
column J: CviA2_Dec_p6_S19

value: CVIA2 Dec collected media


title: Leukoplakia LP33

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

data_processing:
Sequencing data were aligned to the human reference genome (GRCh38) and processed using CellRanger 2.1.1 (10x Genomics)
The raw gene expression matrix was filtered using the “Seurat” R package (Butler et al., 2018), according to the following criteria: cells with > 200 genes and < 8000 genes, < 10% of mitochondrial gene expression in UMI counts, and genes expressed in > 0.1% cells
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include UMI counts for each cell

molecule: polyA RNA

source_name: Leukoplakia

extract_protocol:
Single cells from the tissues were obtained by using the standard protocols of cell dissociation using a Human Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer's instructions.
Barcoded sequencing libraries were generated using Chromium Single Cell 3' v2 Reagent Kits and sequenced using the HiSeq 4000 platform (Illumina)

tag: subsite

value: oral cavity

tag: disease stage

value: LP

tag: hpv status

value: HPV-


title: E. coli Δ10 - targeting - rep 3


title: Leukoplakia LP17


title: Primary cancer C60

source_name: Primary cancer

value: CA


title: T47D-WM-E2-4H RNA-seq rep2


title: T47D-WM-E2-4H RNA-seq rep1


title: E. coli Δ10 - targeting - rep 2


title: Leukoplakia LP16


title: HBMEC, conditioned media treated (CVIA2; Dec), P.4 [CviA2_Dec_p4_S18]

description:
GeneCounts.2D.tsv
column I: CviA2_Dec_p4_S18

value: human brain

value: HBMEC

value: brain endothelial cell


title: MDA134-shFOXA1-WM-E2-DOX RNA-seq rep2

value: MDA_MB134VI breast carcinoma cell line

value: Estrogen + Dox

value: MDA134 cells with Dox inducible shFOXA1 were maintained in their media in presence of puromicin and treated with DOX for 3 days


title: Leukoplakia LP15


title: 2_RP2_DMSO

description: HCT116RmAC cells treated with DMSO replicate 2

value: DMSO


title: SUM44-WM-E2-4H RNA-seq rep2

value: SUM44PE breast carcinoma cell line


title: E. coli Δ10 - targeting - rep 1

value: Escherichia coli {delta}10


title: HBMEC, unconditioned media treated (BNMN), P.6 [BNMN_p6_S17]

description:
GeneCounts.2D.tsv
column H: BNMN_p6_S17

value: WT

value: BNMN media


title: MDA134-shFOXA1-WM-E2-DOX RNA-seq rep1


title: E. coli C3000 - nontargeting - rep 3

source_name: Escherichia coli C3000 cells

value: Escherichia coli C3000


title: HBMEC, unconditioned media treated (BNMN), P.4 [BNMN_p4_S16]

description:
GeneCounts.2D.tsv
column G: BNMN_p4_S16


title: Lung, CONTROL, biol rep 4 tech rep 4

city: São Paulo

first: Jhonatas

middle: Sirino

last: Monteiro

state: São Paulo

address: 748 Professor Lineu Prestes Ave.

department: Deparment of Biochemistry, Institute of Chemistry

country: Brazil

institute: University of São Paulo

data_processing:
Reads were mapped to the human genome available in the ENSEMBL Database (GRCh38.p13 release 104) using STAR (v.2.7.6a).
Transcript abundance was estimated using RSEM (v1.3.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts, TPM and FPKM values for each technical replicate of each sample

source_name: Lung

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturers protocol followed by a DNAse treatment with Turbo DNAse Kit (Thermo Fisher Scientific) at 37C for 30 min.
Libraries were prepared using Illumina RNA Prep with Enrichment kit, nt, IDT for Illumina DNA/RNA UD Indexes Set A, Tagmentation (Illumina) and Illumina Exome Panel Enrichment Oligos Only (Illumina).

value: Lung

tag: age

tag: Sex

value: female

value: control


title: SUM44-WM-E2-4H RNA-seq rep3

value: Estrogen 4 hours

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days and treated with 10nm E2 for 4hrs


title: E. coli C3000 - nontargeting - rep 2


title: SUM44-WM-E2-4H RNA-seq rep1


title: Non-tumoral surrounding normal tissues N09

source_name: Non-tumoral surrounding normal tissues

value: oropharynx

value: NL

value: HPV-


title: Lung, CONTROL, biol rep 4 tech rep 3


title: MDA134-WM-E2-4H RNA-seq rep3

value: MDA_MB134VI breast carcinoma cell line


title: MDA134-WM-E2-4H RNA-seq rep2


title: E. coli C3000 - nontargeting - rep 1


title: Non-tumoral surrounding normal tissues N08


title: Lung, CONTROL, biol rep 4 tech rep 2


title: Non-tumoral surrounding normal tissues N06

value: oral cavity


title: MDA134-WM-E2-4H RNA-seq rep1


title: Lung, CONTROL, biol rep 3 tech rep 4

value: male


title: Lung, CONTROL, biol rep 4 tech rep 1


title: E. coli C3000 - targeting - rep 2


title: Non-tumoral surrounding normal tissues N46

value: HPV+


title: MCF7-WM-E2-4H RNA-seq rep3

value: MCF7 breast carcinoma cell line


title: E. coli C3000 - targeting - rep 1


title: Non-tumoral surrounding normal tissues N43


title: Lung, CONTROL, biol rep 3 tech rep 3


title: MCF7-WM-E2-4H RNA-seq rep1


title: Lung, CONTROL, biol rep 3 tech rep 2


title: T47D-WM-E2-12H RNA-seq rep3

value: T47D breast carcinoma cell line

value: Estrogen 12 hours

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days and treated with 10nm E2 for 12hrs


title: MCF7-WM-E2-4H RNA-seq rep2


title: Non-tumoral surrounding normal tissues N22


title: Lung, CONTROL, biol rep 2 tech rep 4


title: Non-tumoral surrounding normal tissues N21


title: Non-tumoral surrounding normal tissues N38

value: hypopharynx


title: T47D-WM-E2-12H RNA-seq rep2


title: E. coli C3000 - targeting - rep 3

value: Escherichia coli C3000


title: CSC_rep2

type: RNA

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

hyb_protocol: For miRNA microarray, 100 ng of RNA was hybridized using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.

scan_protocol: Scanning and image analysis were performed using the Agilent DNA Microarray Scanner (P/N G2565BA) equipped with extended dynamic range (XDR) software, according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Protocol manual. Feature Extraction Software (Version 10.5) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol

data_processing: signal intensities were extracted by Agilent Feature Extraction 10.7.3.1 software. The arrays were quantile normalized. All values lower than 1 were considered below detection and thresholded to 1 and  log2-trasformed. miRNAs not expressed were excluded

source_name: Total RNA from exosomes purified from human GBM CSC culture supernatant

label_protocol: For miRNA microarray, 100 ng of RNA was labeled (Cy3)  using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.

growth_protocol: U373 and U87 cell lines were seeded in growth medium for 48 hours to obtain 80% confluence. Cell plates were then washed twice with PBS and incubated for 24-36 hours in medium supplemented with 10% EV-free FCS. CSC were seeded in medium supplemented with EGF (20 ng/ml), human recombinant bFGF (10 ng/ml) in serum-free medium DMEM/F12 (1:1) to obtain 80-90 % confluence by 48 hours.

extract_protocol: Total RNA was extracted from the pelleted sEVs using the Fatty Tissue RNA Purification Kit (Norgen Biotek, Thorold, ON, Canada), according to manufacturer’s protocol. Before RNA extraction, the sEV preparations were treated with proteinase K followed by RNAse A to avoid contamination by RNA adsorbed to the vesicle external surface.

treatment_protocol: Small EVs (sEVs) were isolated from U373, U87 and CSC cell culture media using differential centrifugation steps. All preparation and centrifugation steps were performed at 4°C. Collected cell media were subjected to a first centrifugation at 300×g for 10 min, followed by a second centrifugation at 2,000×g for 30 min to remove dead cells and apoptotic bodies, and a third centrifugation at 20,000xg to remove residual cell organelles and large vesicles. sEVs were then pelleted from the purified supernatant by ultracentrifugation at 100,000×g for 70 min in 38 ml polycarbonate tubes. These sEV-enriched pellets were resuspended in PBS and ultracentrifuged again as above. The final sEV pellets were used for subsequent applications.

value: CSC

value: GBM primary cancer stem cell (CSC) line


title: Lung, CONTROL, biol rep 3 tech rep 1

value: Lung

value: control


title: Non-tumoral surrounding normal tissues N15


title: Lung, CONTROL, biol rep 2 tech rep 3

value: female


title: U87_rep2

source_name: Total RNA from exosomes purified from human GBM culture supernatant (U87 MG)

value: human glioblastoma (GBM) established cell line


title: T47D-WM-E2-12H RNA-seq rep1


title: Metastatic tumors to lymph nodes LN59

source_name: Metastatic tumors to lymph nodes

value: oropharynx

value: LN


title: CSC_rep1


title: U87_rep1


title: SUM44-WM-E2-12H RNA-seq rep3

value: SUM44PE breast carcinoma cell line


title: Metastatic tumors to lymph nodes LN46


title: U373_rep2

source_name: Total RNA from exosomes purified from human GBM culture supernatant (U373 MG)


title: Lung, CONTROL, biol rep 2 tech rep 2


title: Lung, CONTROL, biol rep 2 tech rep 1


title: Lung, CONTROL, biol rep 1 tech rep 4


title: SUM44-WM-E2-12H RNA-seq rep2


title: SUM44-WM-E2-12H RNA-seq rep1


title: Metastatic tumors to lymph nodes LN22


title: U373_rep1


title: Lung, CONTROL, biol rep 1 tech rep 3


title: MDA134-WM-E2-12H RNA-seq rep3

value: MDA_MB134VI breast carcinoma cell line


title: Primary cancer C09

value: CA

value: HPV-


title: Lung, CONTROL, biol rep 1 tech rep 2


title: MDA134-WM-E2-12H RNA-seq rep2


title: Primary cancer C86

value: HPV+


title: Primary cancer C84


title: MCF7-WM-E2-12H RNA-seq rep3

value: MCF7 breast carcinoma cell line

value: Estrogen 12 hours


title: Lung, CONTROL, biol rep 1 tech rep 1


title: Lung, COVID-19, biol rep 12 tech rep 4


title: PKD_RBC#3

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA in hybridization buffer was hybridized to 8×60 K Whole Salmon Genome Oligo Microarrays (ID 020938, Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 12.1.1.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Oncorhynchus mykiss

label_protocol: 50 ng of RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the Low Input Quick Amp protocol. Yields of cRNA and the dye-incorporation rate were measured.

growth_protocol: Rainbow trout Oncorhynchus mykiss (mean body mass of 120 g) were reared in a commercial inland fish farm, in the South Bohemian region of the Czech Republic. Fish displaying gross signs of PKD such as pale gills, abdominal distension, and lethargy were transported alive to the Institute of Parasitology of the Biology Centre of the Czech Academy of Sciences (České Budějovice, Czech Republic). These fish were compared to an additional 15 naïve SPF fish (mean body mass of 30 g), reared in experimental recirculating systems of the Faculty of Fisheries and Protection of Waters, University of South Bohemia in the Czech Republic.

extract_protocol: RBCs were separated from the whole blood of PKD and SPF rainbow trout. RBCs were washed three times with PBS, then aliquots of 25 × 10E6 cells were pelleted and stored in RNAlater (Sigma-Aldrich, Saint Louis, MO, USA) until further processing

treatment_protocol: Upon arrival, fish were bled from caudal veins using heparinized syringes and needles, and euthanized with clove oil. Upon dissection, for three suspected cases of PKD out of 19 fish studied, we prepared imprints from their swollen kidneys and stained them according to the manufacturer’s instructions with the Kwik–Diff Kit (Richard Allen Scientific, San Diego, CA, USA), consisting of methanol fixation, followed by eosin and methylene blue staining. Light microscopy was used to identify T. bryosalmonae parasites. All fish in the cohort had kidney swelling indices between 3-4 according to the scale and parameters established by Clifton-Hadley et al. (1987) and variable signs of spleen swelling, fibrosis, and of gill and liver pallor.

value: red blood cells

value: juvenile fish of ~ 20 cm

tag: disease state

value: (PKD) diseased individual


title: Primary cancer C08


title: MDA134-WM-E2-12H RNA-seq rep1

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days and treated with 10nm E2 for 12hrs


title: PKD_RBC#2


title: Metastatic tumors to lymph nodes LN38

value: hypopharynx


title: Control_RBC#4

value: Specific pathogen-free


title: PKD_RBC#1


title: PKD_RBC#4


title: Primary cancer C07

value: oral cavity


title: Primary cancer C06


title: Lung, COVID-19, biol rep 12 tech rep 2

value: Lung

value: female

tag: infection


title: MCF7-WM-E2-12H RNA-seq rep2


title: Lung, COVID-19, biol rep 12 tech rep 3


title: T47D-WM RNA-seq rep3

value: T47D breast carcinoma cell line

value: Estrogen Deprived Condition

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days


title: Primary cancer C59

value: oropharynx

value: CA


title: Primary cancer C57

value: HPV+


title: Lung, COVID-19, biol rep 11 tech rep 4


title: MCF7-WM-E2-12H RNA-seq rep1

value: MCF7 breast carcinoma cell line


title: TEKCRIF1_KO 3

city: Daejeon

first: Min Joung

last: Lee

address: Munhwa-ro 266

department: Department of Biochemistry

institute: Chungnam National University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: cerebral microvessels

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: cerebral microvessels

value: tissue

value: knockout


title: Lung, COVID-19, biol rep 12 tech rep 1


title: T47D-WM RNA-seq rep2


title: Lung, COVID-19, biol rep 11 tech rep 3


title: Lung, COVID-19, biol rep 11 tech rep 1


title: T47D-WM RNA-seq rep1


title: Primary cancer C51

value: HPV-


title: Control_RBC#1

value: red blood cells

value: juvenile fish of ~ 20 cm


title: Lung, COVID-19, biol rep 11 tech rep 2


title: TEKCRIF1_KO 2


title: Lung, COVID-19, biol rep 10 tech rep 4

value: male


title: TEKCRIF1_WT 2

value: wild type


title: Control_RBC#2

value: Specific pathogen-free


title: TEKCRIF1_KO 1


title: SUM44-WM RNA-seq rep3

value: SUM44PE breast carcinoma cell line


title: TEKCRIF1_WT 1


title: Control_RBC#3


title: MDA134-WM RNA-seq rep4

value: MDA_MB134VI breast carcinoma cell line


title: Primary cancer C46


title: SUM44-WM RNA-seq rep2

value: Estrogen Deprived Condition


title: Primary cancer C43


title: TEKCRIF1_WT 3


title: SUM44-WM RNA-seq rep1

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days


title: Lung, COVID-19, biol rep 10 tech rep 2

value: Lung


title: Primary cancer C38

value: hypopharynx

value: CA


title: Primary cancer C31

value: oral cavity


title: MDA134-WM RNA-seq rep2


title: Primary cancer C26


title: MDA134-WM RNA-seq rep3


title: Lung, COVID-19, biol rep 9 tech rep 4

value: female


title: PGC-1dMeioLC_Rep2

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

data_processing:
Clean reads were mapped to the Mus musculus mm10 reference genome using Bowtie2 (population) or Hisat2 (a few cells).
Reads were assigned and counted to genes using the RSEM.
The resulting matrix of read counts was then loaded into RStudio (R version 3.4.2), and DESeq2 were used to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: All_TPM.csv. This file contains all samples TPM value of all genes

source_name: PGCs

extract_protocol:
Total RNA was purified using a RNA mini kit (Qiagen)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: For the induced PGCLCs, ESCs or gSCs treated with 1%KSR, 1. ng/ml bFGF and 2ng/ml Activin A for 2 days can form EpiLCs, and further treated with 500 ng/ml BMP4, 100 ng/ml SCF, 50ng/ml EGF and 1000 IU mLif for 4 days to form PGCLCs (1dEBs from 1day of PGCLC induction from EpiLCs).  For E10.5 PGCs, embryonic gonads were dissected from E10.5 embryos and were dissociated by 0.25% TE (Invitrogen), and filtered by 70 μm cell Filter, followed by sorting of PGCs by flow cytometer using anti-integrin-β3 (CD61) antibody and anti-SSEA1 antibody. For 1dMeioLCs, Aggregation of 1 X 104 PGCLCs or E10.5 PGCs with 5-6 X 104 female Actin-GFP E12.5 mice gonadal somatic cells in the wells of a low-cell-binding U-bottom 96-well Lipidure-Coat plate with MF10 medium and 3 μM RA. Cultured for 1 day, 1 day meiocyte-like cells (1dMeioLCs) can be sorted as GFP negative cells by flow cytometer. MF10 medium contains M199 (Sigma) added with 10% FBS, 1 mM L-glutamine and 1% two antibiotics stock, 50 μg/ml Vitamin C (Vc, Sigma) and 10 μM Rocki (Y27632, Rocki inhibitor).

value: E10.5 PGCs derived 1 day meiocyte-like cells


title: Lung, COVID-19, biol rep 10 tech rep 1


title: Lung, COVID-19, biol rep 10 tech rep 3


title: E10.5PGC_Rep2

value: E10.5 PGCs


title: Lung, COVID-19, biol rep 9 tech rep 3


title: MCF7-WM RNA-seq rep3

value: MCF7 breast carcinoma cell line


title: Primary cancer C21

value: HPV-


title: Primary cancer C22

value: oropharynx

value: HPV+


title: E10.5PGC_Rep1


title: MCF7-WM RNA-seq rep1


title: Lung, COVID-19, biol rep 9 tech rep 2


title: RT-1dMeioLC_Rep1

source_name: ESC

value: Terc-rescued ESC derived 1 day meiocyte-like cells


title: MDA134-WM RNA-seq rep1


title: PGC-1dMeioLC_Rep1


title: Primary cancer C04


title: MCF7-WM RNA-seq rep2


title: RT-1dMeioLC_Rep2


title: Primary cancer C30


title: Primary cancer C15


title: Lung, COVID-19, biol rep 9 tech rep 1


title: Lung, COVID-19, biol rep 8 tech rep 3

value: male


title: ST-1dMeioLC_Rep1

value: Terc-KO G4 ESC derived 1 day meiocyte-like cells


title: Lung, COVID-19, biol rep 8 tech rep 2


title: T47D-FM RNA-seq rep1

value: T47D breast carcinoma cell line

value: Full Media

value: Ductal and Lobular cells were grown in their own media


title: T_ctrl_24h_3

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) and to the H3N2 genome using STAR (version 2.5.2b, (Dobin and Gingeras, 2015)) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Human genome read counts and virus read counts were combined and raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Genome_build: ENSMBL hg38 release 91
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

extract_protocol:
After infection cells were lysed with TRIzol (Life Technologies) and RNA was isolated by phenol-chloroform followed by isopropanol precipitation.
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer. 1 ug of RNA was used for strand-specific cDNA library construction at Novogene using a NEB directional RNA lib prep kit according to manufacturer’s protocol.
Libraries were sequenced on an Illumina HiSeq 4000 Platform using a paired-end 150 run. 40 M raw reads were generated from each library.

treatment_protocol:
A549 were infected with human H3N2 Pan99 virus MOI 1.Cells were harvested after 4, 8, 24 hpi.
THP1 were infected with human H3N2 Pan99 virus, MOI 0.1. Cells were harvested after 4, 8, 12, 24 hpi.
A549  and THP1 controls were treated identical to infected cells with PBS instead of virus solution.

tag: time pt

value: PBS


title: T_H3N2_12h_3

value: H3N2 influenza A


title: Lung, COVID-19, biol rep 8 tech rep 4

value: Lung


title: T47D-FM RNA-seq rep3

value: Estrogen Deprived Condition

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days


title: T_H3N2_24h_3


title: ST-1dMeioLC_Rep2


title: RT-PGCLC_Rep2

value: Terc-rescued ESC derived PGC-like cells


title: Lung, COVID-19, biol rep 7 tech rep 3


title: SUM44-FM RNA-seq rep1

value: SUM44PE breast carcinoma cell line


title: T47D-FM RNA-seq rep2


title: LT-1dMeioLC_Rep2

value: WT ESC derived 1 day meiocyte-like cells


title: T_ctrl_04h_3


title: T_H3N2_04h_3


title: MDA134-FM RNA-seq rep1

value: MDA_MB134VI breast carcinoma cell line


title: T_H3N2_24h_2


title: SUM44-FM RNA-seq rep3


title: Lung, COVID-19, biol rep 8 tech rep 1


title: LT-1dMeioLC_Rep1


title: T_ctrl_12h_3


title: LT-PGCLC_Rep1

value: WT ESC derived PGC-like cells


title: T_ctrl_24h_2


title: Lung, COVID-19, biol rep 7 tech rep 4


title: SUM44-FM RNA-seq rep2


title: RT-1dEB_Rep2

value: Terc-rescued ESC derived 1 day embryoid bodies


title: T_H3N2_08h_3


title: T_ctrl_08h_3


title: Lung, COVID-19, biol rep 7 tech rep 1


title: ST-PGCLC_Rep1

value: Terc-KO G4 ESC derived PGC-like cells


title: Lung, COVID-19, biol rep 7 tech rep 2

value: male


title: RT-PGCLC_Rep1


title: MDA134-FM RNA-seq rep2


title: RT-1dEB_Rep1


title: MCF7-FM RNA-seq rep1

value: MCF7 breast carcinoma cell line


title: LT-PGCLC_Rep2


title: Lung, COVID-19, biol rep 6 tech rep 4


title: Lung, COVID-19, biol rep 6 tech rep 3


title: MCF7-FM RNA-seq rep3


title: ST-1dEB_Rep2

value: Terc-KO G4 ESC derived 1 day embryoid bodies


title: T_ctrl_12h_2


title: MDA134-FM RNA-seq rep3

value: Full Media


title: T_H3N2_08h_2


title: T_H3N2_12h_2


title: MCF7-FM RNA-seq rep2

value: Ductal and Lobular cells were grown in their own media


title: ST-PGCLC_Rep2


title: Lung, COVID-19, biol rep 6 tech rep 1


title: Lung, COVID-19, biol rep 5 tech rep 2


title: LT-1dEB_Rep2

value: WT ESC derived 1 day embryoid bodies


title: T_H3N2_04h_2

value: H3N2 influenza A


title: MDA134-CDH1-OE-p19-3week-Dox RNA-seq rep2

value: Full Media + DOX

value: MDA134 containing a Dox inducible CDH1 gene were cultured for 3 weeks in presence of Dox


title: Lung, COVID-19, biol rep 6 tech rep 2

value: Lung


title: LT-1dEB_Rep1


title: Lung, COVID-19, biol rep 5 tech rep 4


title: RT-EpiLC_Rep2

value: Terc-rescued ESC derived EpiLCs


title: MDA134-CDH1-OE-p19-ND RNA-seq rep2

value: MDA134 containing a Dox inducible CDH1 gene were cultured for 3 weeks


title: MDA134-CDH1-OE-p19-3day-Dox RNA-seq rep2

value: MDA134 containing a Dox inducible CDH1 gene were cultured for 3 days in presence of Dox


title: T_ctrl_04h_2

value: PBS


title: T_ctrl_08h_2


title: MDA134-CDH1-OE-p19-ND RNA-seq rep1

value: MDA_MB134VI breast carcinoma cell line


title: Lung, COVID-19, biol rep 5 tech rep 3


title: ST-1dEB_Rep1


title: Lung, COVID-19, biol rep 4 tech rep 3


title: MDA134-CDH1-OE-p19-3day-Dox RNA-seq rep1


title: RT-EpiLC_Rep1


title: T_H3N2_12h_1


title: ST-EpiLC_Rep2

value: Terc-KO G4 ESC derived EpiLCs


title: Lung, COVID-19, biol rep 4 tech rep 1


title: Lung, COVID-19, biol rep 5 tech rep 1


title: MDA134-CDH1-OE-p19-3week-Dox RNA-seq rep1


title: T47D-CDH1-KO-FM RNA-seq rep3

value: T47D breast carcinoma cell line

value: T47D cells with CRISPR sgRNAs for CDH1 were maintained in their media in presence of puromicin


title: Lung, COVID-19, biol rep 4 tech rep 4

value: male


title: T47D-CDH1-KO-FM RNA-seq rep1


title: T_ctrl_24h_1


title: T_H3N2_24h_1


title: T_H3N2_08h_1


title: Lung, COVID-19, biol rep 3 tech rep 3


title: T47D-AAVS1-FM RNA-seq rep2

value: T47D cells with CRISPR sgRNAs for AAVS1 were maintained in their media in presence of puromicin


title: T_H3N2_04h_1


title: PGC-1dMeioLC

library_source: genomic

data_processing:
Clean reads were mapAll ATAC-seq reads were first mapped to the mm10 genome. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. ped to the Mus musculus mm10 reference genome using Bowtie2 (population) or Hisat2 (a few cells).
Normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads.
To visualize the ATAC-seq signal in the UCSC genome browser, we extended each read by 250 bp and counted the coverage for each base. The ATAC-seq enrichment was then summed within each 3-kb-window for the entire genome and was compared across different samples.
Pearson correlation was used for all analyses. All the ATAC-seq peaks were called by MACS with the parameters nolambda-nomodel. ATAC-seq peaks that are at least 2.5 kb away from annotated promoters (RefSeq, Ensemble and UCSC Known Gene databases combined) were selected as distal ATAC-seq peaks.
Genome_build: mm10
Supplementary_files_format_and_content: LT-1dEB.bw; ST-1dEB.bw; RT-1dEB.bw; LT-PGCLC.bw; ST-PGCLC.bw; RT-PGCLC.bw; LT-1dMeioLC.bw; ST-1dMeioLC.bw; RT-1dMeioLC.bw; E10.5PGC.bw; PGC-1dMeioLC.bw. These files contain all called peaks in each sample

molecule: genomic DNA

source_name: E10.5 PGCs

extract_protocol:
Cells (500 to 3000 cells per reaction) were centrifuged to remove the supernatant. 20 μl of lysis buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, 0.2% N-P40) was added, followed by pipetting 6-10 times to release the nuclei without purification, and 30 μl reaction buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, 1000 unit Tn5) was mixed on a Vortex for 5 seconds. The reaction was incubated at 37 °C for 20 minutes, followed by addition of 350 μl ERC buffer (MiniElute, Qiagen) to stop the reaction. After DNA purification (MiniElute, Qiagen) and then performing ATAC-seq libraries construction.
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: E10.5 PGCs derived 1 day meiocyte-like cells


title: T47D-CDH1-KO-FM RNA-seq rep2

value: Full Media


title: E10.5 PGC

value: E10.5 PGCs


title: T_ctrl_12h_1


title: Lung, COVID-19, biol rep 2 tech rep 3


title: ST-1dMeioLC

source_name: short telomere

value: Terc-KO G4 ESC derived 1 day meiocyte-like cells


title: LT-EpiLC_Rep2

value: WT ESC derived EpiLCs


title: Lung, COVID-19, biol rep 4 tech rep 2


title: A_ctrl_24h_3


title: T47D-AAVS1-FM RNA-seq rep3


title: A_H3N2_08h_3

value: H3N2 influenza A


title: LT-EpiLC_Rep1


title: T_ctrl_08h_1


title: Lung, COVID-19, biol rep 3 tech rep 2

value: Lung


title: Lung, COVID-19, biol rep 3 tech rep 1


title: MCF7-AAVS1-FM RNA-seq rep2

value: MCF7 breast carcinoma cell line

value: MCF7 cells with CRISPR sgRNAs for AAVS1 were maintained in their media in presence of puromicin


title: T47D-AAVS1-FM RNA-seq rep1


title: MCF7-CDH1-KO-FM RNA-seq rep3

value: MCF7 cells with CRISPR sgRNAs for CDH1 were maintained in their media in presence of puromicin


title: ST-EpiLC_Rep1


title: T_ctrl_04h_1

value: PBS


title: Lung, COVID-19, biol rep 2 tech rep 4


title: Lung, COVID-19, biol rep 1 tech rep 4

value: female


title: ST-PGCLC

value: Terc-KO G4 ESC derived PGC-like cells


title: Lung, COVID-19, biol rep 3 tech rep 4


title: RT-1dMeioLC

source_name: telomere length rescued

value: Terc-rescued ESC derived 1 day meiocyte-like cells


title: LT-PGCLC

source_name: long telomere

value: WT ESC derived PGC-like cells


title: MCF7-CDH1-KO-FM RNA-seq rep2


title: A_H3N2_24h_3


title: Lung, COVID-19, biol rep 2 tech rep 2

value: male


title: RD_shPROX1_samp_4

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

data_processing:
The analysis from the generated FASTQ data was performed using Chipster software (www.chipster.csc.fi) (Kallio et al., 2011).   .
The quality of FASTQ files were assessed with FASTQC, and used as input for alignment to reference genome using HISAT2 (Kim et al., 2015).
Aligned reads per gene were counted with HTseq (Anders et al., 2015) and DEseq2 (Love et al., 2014) was used to anayze differentially expressed genes.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were used and statistical significance of adjusted P-value (FDR) < 0.05 was set as cut off, and the final values were log2 transformed
Genome_build: Homo_sapiens.GRCh38.90 (hg38)
Supplementary_files_format_and_content: raw counts of sequencing reads

source_name: RD cell line

growth_protocol: RD cells were cultured in Dulbecco's Modified Eagle Medium (DMEM high glucose) supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, penicillin (100U/ml) and streptomycin (100U/ml) and maintained at 37ºC in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA from the lysed cells was extracted with Nucleospin RNA II Kit (Macherey-Nagel).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to generate cDNA libraries for next generation sequencing.

value: RD

value: Rhabdomyosarcoma

tag: knockdown


title: RD_shPROX1_samp_3

tag: cell line


title: RT-1dEB

tag: cell type

value: Terc-rescued ESC derived 1 day embryoid bodies


title: A_ctrl_08h_3


title: Lung, COVID-19, biol rep 1 tech rep 2


title: LT-1dMeioLC

value: WT ESC derived 1 day meiocyte-like cells


title: MCF7-CDH1-KO-FM RNA-seq rep1

value: Full Media


title: A_ctrl_04h_3


title: A_ctrl_24h_2


title: Lung, COVID-19, biol rep 1 tech rep 3


title: A_H3N2_04h_3


title: Lung, COVID-19, biol rep 2 tech rep 1


title: LT-1dEB

value: WT ESC derived 1 day embryoid bodies


title: A_H3N2_24h_2

value: H3N2 influenza A


title: RT-PGCLC

value: Terc-rescued ESC derived PGC-like cells


title: ST-1dEB

value: Terc-KO G4 ESC derived 1 day embryoid bodies


title: SHSY5Y_72h_ASCL1_induction_rep5, RNA-Seq

city: Cambridge

first: Sarah

last: Gillen

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

description: SHSY5Y_ASCL1induced_RNAseq_rawcounts.csv

data_processing:
TrimGalore 0.6.4 for adapter and quality trimming
STAR 2.6.1d alignment to hg19 genome
STAR quant mode reverse to obtain gene counts
DESeq2 1.32.0 for differential expression analysis
Assembly: hg19
Supplementary files format and content: csv files include raw counts and counts per million (CPM) for each sample
Supplementary files format and content: csv files include differential expression outputs from DESeq2 for ASCL1 knockout lines compared to parental

growth_protocol: IMR32 and SH-SY5Y were cultured in DMEM-F12 with GlutaMAX (Gibco) supplemented with 10% FBS (Sigma) and 1% Penicillin-Streptomycin (Sigma).

extract_protocol:
Cells were lysed using RLT buffer and RNA extracted following the RNeasy Protocol Part I (Qiagen)
NEB polyA kit & NEB Ultra II directional RNA kit, 100bp paired end sequencing

value: neuroblastoma cell line

value: dox 5ng/ml

tag: time point

value: 72h induction


title: Lung, COVID-19, biol rep 1 tech rep 1

value: Lung

value: female


title: MCF7-AAVS1-FM RNA-seq rep1

value: MCF7 breast carcinoma cell line

value: MCF7 cells with CRISPR sgRNAs for AAVS1 were maintained in their media in presence of puromicin


title: RD_shPROX1_samp_1


title: Trypanosoma brucei brucei X Trypanosoma brucei gambiense hybrid 181

city: Glasgow

first: Nicola

last: Veitch

address: Bearsden Rd

institute: University of Glasgow

description:
polyA RNA
Digital Gene Expression

data_processing: The processed data files are collated tag sequences and associated tag counts. Tag counts were collated using a custom written script in Perl 5.10.0.

organism: Trypanosoma brucei brucei x Trypanosoma gambiense 181

source_name: Trypanosoma brucei brucei X Trypanosoma brucei gambiense hybrid bloodstream-form

growth_protocol: Bloodstream form hybrids were grown in HMI9 media with 20% fetal bovine serum at 37ºC with 5% CO2 and harvested during mid-log phase (approximately 4,500,000 cells per library).

extract_protocol: Sequence tag preparation was performed with Digital Gene Expression Tag Profile Kit (Illumina) using NlaIII, according to the manufacturer’s instructions.

treatment_protocol: The cells were pelleted at 500 g for 10 mins at 4ºC and immediately re-suspended in RLT buffer (Qiagen RNeasy kit). The cells were disrupted by serial passage through a 26 gauge needle and stored at -80ºC before use. RNA was isolated from the cells using RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase treatment step, to ensure that there was no DNA contamination. The RNA was measured for quantity and quality by Nanodrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer according to the manufacturer’s instructions.

value: Bloodstream-form in vitro

value: Hybrid 181


title: Trypanosoma brucei brucei X Trypanosoma brucei gambiense hybrid 414

description:
polyA RNA
Digital Gene Expression

organism: Trypanosoma brucei brucei x Trypanosoma gambiense 414

value: Hybrid 414


title: A_H3N2_08h_2


title: RD_Control_samp_1

value: RD

value: Rhabdomyosarcoma

value: scrambled shRNA (control)


title: A_ctrl_04h_2

value: PBS


title: RD_Control_samp_4


title: SHSY5Y_72h_ASCL1_induction_rep4, RNA-Seq


title: A_ctrl_08h_2


title: SHSY5Y_72h_ASCL1_induction_rep3, RNA-Seq


title: SHSY5Y_24h_ASCL1_induction_rep4, RNA-Seq

value: 24h induction


title: RD_Control_samp_3


title: RD_shPROX1_samp_2


title: A_H3N2_04h_2

value: H3N2 influenza A


title: SHSY5Y_72h_ASCL1_induction_rep1, RNA-Seq


title: SHSY5Y_72h_ASCL1_induction_rep2, RNA-Seq


title: A_H3N2_04h_1


title: A_H3N2_24h_1


title: A_ctrl_04h_1


title: SHSY5Y_ASCL1_KO2_rep5, RNA-Seq

tag: genotype

value: ASCL1 KO2


title: SHSY5Y_24h_ASCL1_induction_rep5, RNA-Seq

value: neuroblastoma cell line

tag: agent


title: Exp3_Tcell_6hr_star.genome.sorted

city: Bethesda

first: Suman Kumar

last: Vodnala

address: 10 Center Drive

department: Surgery Branch

institute: NCI

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp3_Tcell_6hr

data_processing:
Sample reads were trimmed of adapters and low quality bases using Cutadapt software.
Trimmed reads were aligned to the reference human genome hg38 using STAR
RPKM values were calculated using Cufflinks and compared between samples using Cuffdiff
Genome_build: Samples 1-6 Hg38, Samples 7-18 Hg19
Supplementary_files_format_and_content: Processed data files are tab-delimited text files containing RPKM values for each replicate RNA-Seq measurement

source_name: Human T cells transduced with NY-ESO-1 TCR 6hr tumor interaction

growth_protocol: Cells were grown in culture media.  For co-culture experiments, T cells were added to Mel624 tumor cells in the presence of 160 IU of human recombinant IL-2

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kits according to manufacturers instructions
mRNA samples were processed using Illumina TruSeq Stranded mRNA Library Prep and sequenced using an Illumina HiSeq 4000

treatment_protocol: Mel624 tumor cells were co-cultured with primary human ESO transduced T cells at 1:2 E:T ratio for 0 or 6 hrs, after which each population was sorted by FACS.  sgRNA modified A375 cells were selected with antibiotics for 10 days, after which they were plated overnight in a 6 well dish and collected for RNA extraction after 24 hrs (Samples 1,2,3 are NTsgRNA and 10,11,12 are BIRC2 sgRNA modified A375 cells)

value: Primary human T cell


title: SHSY5Y_24h_ASCL1_induction_rep3, RNA-Seq

value: dox 5ng/ml


title: A_ctrl_08h_1


title: A_H3N2_08h_1


title: SHSY5Y_24h_ASCL1_induction_rep2, RNA-Seq


title: RD_Control_samp_2


title: SHSY5Y_ASCL1_KO2_rep3, RNA-Seq


title: SHSY5Y_24h_ASCL1_induction_rep1, RNA-Seq


title: LM_4

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from the brains of 3 mice.

data_processing:
Illumina bcl2fastq software used for basecalling.
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: LM.tar.gz: Compressed folder containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes; barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.

source_name: Leptomeninges

growth_protocol: Not applicable

extract_protocol:
10x Genomics Chromium single-cell preparation.
NGS Illumina Next Seq.

treatment_protocol: Not applicable

value: 3 months

tag: gender

value: male

value: leptomeninges


title: LM_3

description: RNA was isolated from the brains of 4 mice.

tag: tissue


title: LM_2

tag: strain


title: A_ctrl_24h_1


title: SHSY5Y_ASCL1_KO2_rep4, RNA-Seq


title: SHSY5Y_ASCL1_KO2_rep1, RNA-Seq


title: Exp2_Tcell_6hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp2_Tcell_0hr


title: SHSY5Y_ASCL1_KO1_rep5, RNA-Seq

value: ASCL1 KO1


title: SHSY5Y_ASCL1_KO2_rep2, RNA-Seq


title: LM_1


title: Exp3_Tcell_0hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp3_Tcell_0hr

source_name: Human T cells transduced with NY-ESO-1 TCR 0hr tumor interaction


title: Brain_3

description: RNA was isolated from the brain of 1 mouse.

data_processing:
Illumina bcl2fastq software used for basecalling.
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Brain.tar.gz: Compressed folder containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes; barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.

source_name: Brain

value: 4 months

value: brain


title: Brain_4


title: Exp2_Tcell_0hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp2_Tcell_6hr


title: SHSY5Y_ASCL1_KO1_rep4, RNA-Seq


title: Brain_2


title: Exp1_Tcell_6_hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp1_Tcell_6_hr


title: Exp1_Tcell_0hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp1_Tcell_0hr


title: SHSY5Y_ASCL1_KO1_rep3, RNA-Seq


title: CR_ZT22_REP1

city: Cleveland

first: Roman

last: Kondratov

state: Ohio

address: 2121 Euclid Ave

department: Department of Biological Geological and Environmental Sciences

institute: Cleveland State University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s  1 / 3  instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N  sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the  clean data with high quality.
Paired-end clean reads were aligned to the  reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses  sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped  to this gene.
Assembly: mm10
Supplementary files format and content: FPKM file

source_name: Liver

growth_protocol: Mice were maintained on 12 h light: 12 h dark cycle, the light was on at 7AM (ZT0) and the light was off at 7PM (ZT12). Animals were fed 5008 LabDiet (proteins 26.5%, fat 16.9%, carbohydrates 56.5%). CR mice received 70% of food once per day at ZT14 (2 hours after the light was turned off). Liver tissues were collected across the day and immediately frozen and stored at -80° C. At ZT14, tissues were collected before feeding.

extract_protocol:
Total RNA was extracted from 20 mg of liver tissue using RNeasy Mini Kit (Quagen, 74104) according to manufacturer protocol. RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. After sample quality control, non-directional – polyA enrichment library was prepared using NEBNext Ultra™ II RNA Library Prep Kit for Illumina, and 20M reads (150bp, paired end) per sample were generated on Illumina NovaSeq 6000 platform.
Sequencing libraries were generated using NEBNext® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA)  Library Prep Kit for Illumina® (NEB, USA)  Library Prep Kit for Illumina® (NEB, USA)  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Liver

tag: diet

value: CR

value: Male

tag: time


title: CR_ZT18_REP3


title: CR_ZT14_REP3


title: CR_ZT18_REP2


title: SHSY5Y_ASCL1_KO1_rep2, RNA-Seq


title: CR_ZT22_REP3


title: CR_ZT22_REP2


title: Exp3_Mel624_6hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp3_Mel624_6hr

source_name: Mel624 melanoma cells 6hr after T cell interaction

value: Mel624 melanoma


title: Exp2_Mel624_6hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp2_Mel624_6hr


title: CR_ZT18_REP1


title: MEF_Lmna+/+_replicate_3

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Paired-end reads were trimmed for Nextera transposase adapter sequences using Trimmomatic (v0.32) (PMID: 24695404) in palindrome mode with default settings except ILLUMINACLIP:2:30:10:1:true MINLEN:25.
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) before and after trimming to confirm the removal of any 3’ adapter sequences and the insertion Tn5 motif in the 5’-ends.
Trimmed PE reads were mapped to the hg19 assembly (canonical chromosomes only) using bowtie2 v.2.2.9 (PMID: 22388286) with default settings except -k 2 -X 2000 --no-mixed --no-discordant.
Sorting (SortSam) and labeling duplicates (MarkDuplicates) with Picard tools (v. 2.6.0-27-g915ffa7-SNAPSHOT) (https://broadinstitute.github.io/picard/)
Addition of a NH tag (number of reported alignments)
Filtering to exclude unmapped, multimapping, and mitochondrial reads (samtools view -f 2 -F 4 and custom filter) (PMID: 19505943).
Filtered bam files were converted to bed format using bedtools bamtobed (v2.26.0-92-g88cd6c5) (PMID: 20110278).
Sorted mapped reads were imported into EaSeq version 1.12 (PMID: 26926434) for subsequent analysis and generation of wig-files.
Genome_build: mm10
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (http://easeq.net); Scores represent fragments per kilobasepairs per million reads

source_name: Mouse Embryonic Fibroblasts

growth_protocol: The MEFs (spontaneously immortalized) (Lmna+/+ and Lmna-/-) were grown in Dulbecco modified eagle medium (DMEM), supplemented with 10% fetal bovine serum (FBS) (Gibco BRL), 50 µg/ml streptomycin and 50 units/ml penicillin, under conditions of 37°C, 5% CO2, and 20% oxygen.

extract_protocol:
Nuclei were prepared from 50,000 cells and subjected to tagmentation reaction. DNA was extracted and PCR amplified using Nextera Index primers (FC-121-1011) for paired-end sequencing. DNA was size selected and using Ampure XP magnetic beads. Libraries were quantified using KAPA SYBR FAST qPCR Master mix (KK4932) to determine the optimal number of PCR cycles. After running the remaining number of PCR cycles, libraries were purified with Ampure XP beads (with size slection). Libraries were quantified by running 1 μl of each sample on Bioanalyzer High Sensitivity DNA Chip.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (FC-121-1030, FC-121-1011). In all, 2 nM of all libraries were pooled and 1.5 pM were analyzed on Illumina NextSeq500 (500/550 High Output v2 Kit—150 cycles).

treatment_protocol: The MEFs were not treated prior to ATAC seq processing

value: Lmna+/+

tag: replicate


title: CR_ZT14_REP2


title: MEF_Lmna+/+_replicate_4


title: SHSY5Y_parental_rep5, RNA-Seq

value: parental


title: CR_ZT14_REP1


title: SHSY5Y_ASCL1_KO1_rep1, RNA-Seq


title: Exp1_Mel624_6_hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp1_Mel624_6_hr


title: MEF_Lmna+/+_replicate_2


title: Exp3_Mel624_0hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp3_Mel624_0hr

source_name: Mel624 melanoma cells 0 hr after T cell interaction


title: Brain_1

tag: age


title: SHSY5Y_parental_rep4, RNA-Seq


title: MEF_Lmna+/+_replicate_1


title: SHSY5Y_parental_rep3, RNA-Seq


title: CR_ZT10_REP3

tag: Sex


title: 12_sgB_Veh_3

description:
NTsgRNA_BIRC2KO_RNAseq_RPKM
X12_sgB_Veh_3

source_name: A375 cells transduced with Cas9 and BIRC2 sgRNA

value: A375 melanoma


title: CR_ZT10_REP2


title: MEF_Lmna-/-_replicate_4

value: Lmna-/-


title: Exp1_Mel624_0hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp1_Mel624_0hr

source_name: Mel624 melanoma cells 0hr after T cell interaction


title: SHSY5Y_parental_rep2, RNA-Seq

value: neuroblastoma cell line


title: DNA mehtylation of human stomach (S150TN)

type: genomic

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

hyb_protocol: Standard Illumina Protocol

scan_protocol: The array was scanned with an iScan System

data_processing: The data were analyzed using GenomeStudio Methylation Module Software.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted by standard phenol/chloroform method, and was quantified using a Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).

value: Non-cancerous mucosae


title: DNA mehtylation of human stomach (S162TN)


title: CR_ZT6_REP3


title: CR_ZT10_REP1


title: MEF_Lmna-/-_replicate_3


title: MEF_Lmna-/-_replicate_1


title: IMR32_ASCL1_KO2_rep5, RNA-Seq

value: ASCL1 KO2


title: Exp2_Mel624_0hr_star.genome.sorted

description:
Kishton_RNAseq_Mel624_NYESOTcell_RPKMvalues
Exp2_Mel624_0hr

source_name: Mel624 melanoma cells 0 hr after  T cell interaction


title: DNA mehtylation of human stomach (S152TN)


title: DNA mehtylation of human stomach (S151TN)


title: SHSY5Y_parental_rep1, RNA-Seq


title: MEF_Lmna-/-_replicate_2


title: IMR32_ASCL1_KO2_rep4, RNA-Seq


title: 3_HKO_Veh_3

description:
NTsgRNA_BIRC2KO_RNAseq_RPKM
X3_HKO_Veh_3

source_name: A375 cells transduced with Cas9 and non-targeting sgRNA


title: DNA mehtylation of human stomach (S154TN)


title: DNA mehtylation of human stomach (S141TN)


title: 10_sgB_Veh_1

description:
NTsgRNA_BIRC2KO_RNAseq_RPKM
X10_sgB_Veh_1


title: DNA mehtylation of human stomach (S137TN)


title: CR_ZT6_REP2


title: DNA mehtylation of human stomach (S131TN)


title: CR_ZT6_REP1


title: DNA mehtylation of human stomach (S124TN)


title: 2_HKO_Veh_2

description:
NTsgRNA_BIRC2KO_RNAseq_RPKM
X2_HKO_Veh_2


title: Rpl10a_LOF_RNA_Rep3

city: Stanford

first: Maria

last: Barna

state: California

address: 279 Campus Drive, Beckman Center B309

institute: Stanford University

description:
ribo_cds_rna_total_counts.csv
LOF_23_BC5

data_processing:
For analysis pre-processing, UMI-tools was used to extract sample barcodes and UMIs. Reads were demultiplexed, sample barcodes were removed, and reads were quality filtered (fastq_quality_filter -Q33 -q 20 -p 70) using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
The 3’ adapter sequence CTGTAGGCACCATCAAT was removed using cutadapt, and the 5’ end of each read was then removed using fastx_trimmer from FASTX-Toolkit. Raw files included have been preprocessed up to this point.
To remove reads that aligned to rRNA, tRNA, and snRNAs, reads were first aligned to these sequences using bowtie2 (bowtie2 parameters: -L 18) and subsequently discarded. Filtered reads that did not align to rRNA/tRNA/snRNAs were then aligned using bowtie2 (bowtie2 parameters: --norc -L 18) to an GRCm38/mm10 transcriptome reference derived from UCSC/GENCODE VM20 knownCanonical annotations filtered for high confidence transcripts that contain at least one of the following: a Uniprot ID, a RefSeq ID, or an Entrez ID.
PCR duplicates were then removed using UMI-tools. (Note 9 base UMI is in description of each read in FASTQ files)
Ribosome protected fragments (RPFs) were then parsed for uniquely aligned reads, separated into read length groups, and ribosome A site positions were determined by offsetting the distance of the 5’ end of each read to canonical start sites in each length group and adding 4 nucleotides. RNA-Seq reads were also parsed for uniquely aligned reads and were assigned to the center of each read. RPFs and RNA-Seq reads were then counted using the transcriptome annotations detailed above.
Reads aligning to the CDS (with the first 15 codons and last 5 codons removed) were used for RPF libraries, and reads aligning to the entire transcript were used for RNA-Seq libraries.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Counts aligning to CDS (with the first 15 codons and last 5 codons removed) for ribosome protected fragments; counts aligning to entire transcript for RNA-Seq

source_name: E8.5 mouse embryo

growth_protocol: Embryos were harvested at E8.5

extract_protocol:
Whole E8.5 embryos were dissected in cold HBSS with 100 µg/mL cycloheximide and each embryo lysed for 30 minutes at 4℃ in 215 µL lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 8% glycerol, 1% Triton X-100, 100 μg/ml cycloheximide, 20 U/ml Turbo DNAse (Thermo Scientific, AM2238), and Complete Protease Inhibitor EDTA-free (Sigma-Aldrich, 11836170001)).  Lysates were sequentially centrifuged at 1300g for 5 minutes at 4℃ and then 10,000g for 10 minutes at 4℃.  70 µL of the clarified lysate was taken as the RNA input sample for RNA-seq and mixed with 55 µL water and 375 TRIzol LS (Thermo Scientific) and stored at -80C for subsequent RNA extraction.  The remaining lysate was treated with 0.5 μg RNase A (Thermo Scientific, AM2271) and 300 U RNase T1 (Thermo Scientific, EN0541) for 30 minutes at room temperature with gentle rocking. These RNases were chosen to prevent degradation of the ribosome in the small amount of material present in a single E8.5 embryo.  RNase activity was stopped by addition of 100 U SUPERase RNase Inhibitor (Thermo Scientific, AM2694). Ribosomes were enriched by sucrose cushion (1 M sucrose in lysis buffer containing 20 U/mL SUPERase RNase Inhibitor), and centrifuging in a TLA 120.2 rotor (Beckman) at 70,000 rpm for 4 hours at 4°C. The ribosome pellet containing the ribosome-protected Ribo-Seq library was resuspended in 500 μL TRIzol.
Total RNA and ribosome footprints were extracted using the Direct-zol Micro Kit (Zymo) followed by DNase digest with TURBO DNase at 37℃ for 30 minutes.  DNase was removed using the RNA Clean and Concentrator 5 kit (Zymo).  The total RNA and ribosome-protected footprint samples were depleted of rRNA using Ribo-Zero Gold from the TruSeq Stranded Total RNA Library Prep Gold (Illumina 20020598) following manufacturer’s instructions.  The samples were then purified with the RNA Clean & Concentrator 5 kit (Zymo) with the modifications that 2 volumes of RNA Binding Buffer and 4.5 volumes of ethanol were added to ribosome footprinting samples to purify small RNAs and 1 volume of RNA Binding Buffer and 1 volume of ethanol was added to total RNA samples to isolate RNA > 200 nt.  Total RNA samples were then diluted to 100 µL with 5 mM Tris-HCl pH 7.5, mixed with 100 µL of 2x alkaline fragmentation buffer (100 mM Na2CO3 pH 9.2, 2 mM EDTA), and incubated at 95℃ for 20 minutes to partially fragment the RNA.  The reaction was halted with 440 μL STOP Buffer (70 μL 3 M sodium acetate (NaOAc) pH 5.5, 2 μL Glycoblue, and 370 μL nuclease free water) and precipitated with isopropanol overnight at -80°C.  Fragmented total RNA and ribosome-protected footprints were size-selected by running on a 15% tris-borate-EDTA (TBE)-urea polyacrylamide gel with 20/100 ladder (IDT 51-05-15-02) to identify the 30-70 nucleotide region (for total RNA) or the oNTI199 and oNTI265 oligos to demarcate the 28-34 nucleotide region (for ribosome-protected fragments).  Gel slices were crushed and incubated at room temperature overnight in 400 μL RNA extraction buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.25% SDS), and the RNA precipitated with isopropanol. Samples were then 3’dephosphorylated by denaturing at 65°C for 5 minutes and incubating with 1 μL 10x T4 PNK Buffer, 1 μL SUPERase Inhibitor, 1 μL 10 U/μL T4 PNK (NEB M0201S) in a 10 µL reaction at 37°C for 1 hour followed by heat inactivation at 65°C for 20 minutes. Samples were then incubated with 0.5 μL of 50 μM Universal miRNA Cloning Linker (NEB S1315S), denatured at 65°C for 5 minutes, and mixed with 1 μL T4 RNA Ligase 2, truncated KQ (NEB M0373S), 1 μL 10x buffer, 6 μL 50% PEG 8000, and 1.5 μL water for 4.5 hours at 25°C. Free adaptor was then removed by addition of 1 μL 10 U/μL 5’-Deadenylase (NEB M0331S), 1 μL 10 U/μL RecJ Exonuclease (Lucigen/Epicentre, RJ411250), and 1 μL 20 U/μL SUPERase Inhibitor and incubation at 30℃ for 1 hour. Samples were then purified using Zymo RNA Clean and Concentrator 5 columns using the protocol above to preserve small RNAs (100 μL sample, 200 μL RNA binding buffer, 450 μL 100% ethanol).  Each 10 μL sample was then incubated with 2 μL of 1.25 μM reverse transcription primers containing sample barcodes and unique molecular identifiers and denatured at 65°C for 5 minutes, followed by reverse transcription by SuperScript III (Thermo Fisher, 18080-044) in a 20 μL reaction incubated at 25℃ for 5 minutes followed by 48°C for 40 minutes. RNA was then hydrolyzed by adding 2.2 μL of 1 N NaOH and incubating for 20 minutes at 98°C. Samples were then purified using Zymo RNA Clean & Concentrator 5 kit (100 μL sample, 200 μL RNA binding buffer, 450 μL 100% ethanol) and run on a 10% TBE-urea polyacrylamide gel. cDNA was gel extracted using DNA extraction buffer (300 mM NaCl, 10 mM Tris-HCl pH 8, 1 mM EDTA, 0.1% SDS) overnight and precipitated with isopropanol at -80°C overnight. Samples were then circularized with CircLigase (Illumina, CL4115K) in a 20 μL reaction (15 μL cDNA, 2 μL 10x CircLigase Buffer, 1 μL 1 mM ATP, 1 μL MnCl2, 1 μL CircLigase) for 12 hours at 60°C followed by a 10-minute heat inactivation at 80℃.  Samples were purified using Zymo RNA Clean & Concentrator 5 columns (100 μL sample, 200 μL RNA binding buffer, 450 μL 100% ethanol) and eluted with 12 μL 10 mM Tris-HCl pH 8. 1 μL of library was used for PCR amplification with Phusion High-Fidelity DNA Polymerase (Thermo Fisher F530S) (98°C 30 seconds, 98°C 10 seconds, 65°C 10 seconds, 72°C 5 seconds) for 10 cycles.  PCR product was run on native 8% TBE polyacrylamide gels, extracted overnight using DNA extraction buffer, and isopropanol precipitated for at least 2 hours at -80°C. Sample concentration and quality was determined by running on the Agilent 2100 Bioanalyzer (High-Sensitivity DNA) by the Stanford Protein and Nucleic Acid (PAN) Facility both before and after library pooling. Libraries were sequenced by the Stanford Functional Genomics Facility (SFGF) on the Illumina NextSeq 500 (1x75nt).

value: Rpl10a LOF/LOF

tag: molecule

value: rRNA depleted total RNA


title: 1_HKO_Veh_1

description:
NTsgRNA_BIRC2KO_RNAseq_RPKM
X1_HKO_Veh_1


title: IMR32_ASCL1_KO2_rep1, RNA-Seq


title: IMR32_ASCL1_KO2_rep3, RNA-Seq


title: IMR32_ASCL1_KO2_rep2, RNA-Seq


title: Rpl10a_LOF_RNA_Rep2

description:
ribo_cds_rna_total_counts.csv
LOF_21_BC3


title: CR_ZT2_REP3


title: Rpl10a_LOF_RNA_Rep1

description:
ribo_cds_rna_total_counts.csv
LOF_14_BC4


title: 11_sgB_Veh_2

description:
NTsgRNA_BIRC2KO_RNAseq_RPKM
X11_sgB_Veh_2


title: IMR32_ASCL1_KO1_rep4, RNA-Seq


title: AL_ZT22_REP2

value: AL


title: IMR32_ASCL1_KO1_rep3, RNA-Seq

value: ASCL1 KO1


title: Rpl10a_WT_RNA_Rep3

description:
ribo_cds_rna_total_counts.csv
WT_6_BC1


title: CR_ZT2_REP2


title: Rpl10a_LOF_Ribo_Rep3

description:
ribo_cds_rna_total_counts.csv
LOF_23_BC1

data_processing:
Library strategy: Ribo-seq
For analysis pre-processing, UMI-tools was used to extract sample barcodes and UMIs. Reads were demultiplexed, sample barcodes were removed, and reads were quality filtered (fastq_quality_filter -Q33 -q 20 -p 70) using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
The 3’ adapter sequence CTGTAGGCACCATCAAT was removed using cutadapt, and the 5’ end of each read was then removed using fastx_trimmer from FASTX-Toolkit. Raw files included have been preprocessed up to this point.
To remove reads that aligned to rRNA, tRNA, and snRNAs, reads were first aligned to these sequences using bowtie2 (bowtie2 parameters: -L 18) and subsequently discarded. Filtered reads that did not align to rRNA/tRNA/snRNAs were then aligned using bowtie2 (bowtie2 parameters: --norc -L 18) to an GRCm38/mm10 transcriptome reference derived from UCSC/GENCODE VM20 knownCanonical annotations filtered for high confidence transcripts that contain at least one of the following: a Uniprot ID, a RefSeq ID, or an Entrez ID.
PCR duplicates were then removed using UMI-tools. (Note 9 base UMI is in description of each read in FASTQ files)
Ribosome protected fragments (RPFs) were then parsed for uniquely aligned reads, separated into read length groups, and ribosome A site positions were determined by offsetting the distance of the 5’ end of each read to canonical start sites in each length group and adding 4 nucleotides. RNA-Seq reads were also parsed for uniquely aligned reads and were assigned to the center of each read. RPFs and RNA-Seq reads were then counted using the transcriptome annotations detailed above.
Reads aligning to the CDS (with the first 15 codons and last 5 codons removed) were used for RPF libraries, and reads aligning to the entire transcript were used for RNA-Seq libraries.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Counts aligning to CDS (with the first 15 codons and last 5 codons removed) for ribosome protected fragments; counts aligning to entire transcript for RNA-Seq

value: Ribosome-Protected Fragments (RPFs)


title: CR_ZT2_REP1


title: Rpl10a_WT_RNA_Rep2

description:
ribo_cds_rna_total_counts.csv
WT_19_BC2


title: IMR32_ASCL1_KO1_rep5, RNA-Seq


title: Rpl10a_LOF_Ribo_Rep2

description:
ribo_cds_rna_total_counts.csv
LOF_21_BC8


title: Rpl10a_LOF_Ribo_Rep1

description:
ribo_cds_rna_total_counts.csv
LOF_14_BC11


title: IMR32_parental_rep5, RNA-Seq


title: AL_ZT22_REP1


title: ∆ddl vanS (R334L) cells, replicate 3

city: Boston

first: Boris

middle: R

last: Belitsky

state: MA

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

description: sample 17

data_processing:
Burrows-Wheeler short-read aligner
Custom scripts
DESeq2
Assembly: GCF_000009205.2_ASM920v2
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples

organism: Clostridioides difficile 630

source_name: Clostridioides difficile 630∆erm

growth_protocol: Complex TY medium, exponential growth

extract_protocol:
Cell quenching with 1:1 (vol/vol) solution of ethanol/acetone. RNA isolation using the Direct-zol RNA MiniPrep Plus kit.
Shishkin, A. A., G. Giannoukos, A. Kucukural, D. Ciulla, M. Busby, C. Surka, J. Chen, R. P. Bhattacharyya, R. F. Rudy, M. M. Patel, N. Novod, D. T. Hung, A. Gnirke, M. Garber, M. Guttman and J. Livny (2015). "Simultaneous generation of many RNA-seq libraries in a single reaction." Nat. Methods 12: 323-325.

value: bacterial cell

value: {delta}ddl vanS (R334L)


title: IMR32_ASCL1_KO1_rep2, RNA-Seq


title: IMR32_parental_rep4, RNA-Seq


title: Rpl10a_WT_Ribo_Rep2

description:
ribo_cds_rna_total_counts.csv
WT_19_BC7


title: AL_ZT18_REP3

value: Liver


title: Rpl10a_WT_Ribo_Rep1

description:
ribo_cds_rna_total_counts.csv
WT_16_BC8


title: IMR32_ASCL1_KO1_rep1, RNA-Seq


title: NCI-H358 cells expressing CHST11 vector

city: Taipei

first: Wei-Min

last: Chang

state: Not Applicable

address: 128 Academia Road, Section 2, Nankang,

country: Taiwan

institute: Academia Sinica

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: ATCC

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

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagen RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with antibiotics for two weeks.  Stably transduced cells were use for this experiment.

value: NCI-H358 cells expresses CHST11 vector


title: wild-type cells, replicate 2

description: sample 2

value: wild-type


title: Rpl10a_WT_RNA_Rep1

description:
ribo_cds_rna_total_counts.csv
WT_16_BC3


title: wild-type cells, replicate 1

description: sample 1


title: AL_ZT22_REP3

value: Male


title: A549 cells expressing CHST11 vector

value: A549 cells expresses CHST11 vector


title: A549 cells expressing empty vector

value: A549 cells expresses empty vector


title: ∆ddl vanS (R334L) cells, replicate 1

description: sample 15


title: AL_ZT14_REP2


title: AL_ZT18_REP2


title: AL_ZT18_REP1


title: IMR32_parental_rep1, RNA-Seq

value: parental


title: wild-type cells, replicate 3

description: sample 3


title: NCI-H358 cells expressing empty vector

value: NCI-H358 cells expresses empty vector


title: SHSY5Y_ASCL1_KO2_rep4

description:
SHSY5Y_ATAC_DiffBind.txt
SHSY5Y_ASCL1_KO2_RPGC_mean.bw

data_processing:
TrimGalore 0.6.4 for adapter and quality trimming
Bowtie2 2.4.1 alignment to hg19 genome
Peaks called with MACS2 2.2.7.1 narrowPeak mode
Differential Peaks were determined using DiffBind v2.14.0 with default parameters and summits=200
bigWig files were generated by deeptools with RPGC normalisation and mean of the replicates generated with wiggletools
Assembly: hg19
Supplementary files format and content: narrowPeak files generated from MACS2
Supplementary files format and content: bigwig files are normalised RPGC per sample and the mean average of the 4 replicates
Supplementary files format and content: tables include differential binding outputs from DiffBind for ASCL1 knockout lines compared to parental

growth_protocol: IMR32 and SHSY5Y were cultured in DMEM-F12 with GlutaMAX (Gibco) supplemented with 10% FBS (Sigma) and 1% Penicillin-Streptomycin (Sigma).

extract_protocol:
Cells were lysed using RLT buffer and RNA extracted following the RNeasy Protocol Part I (Qiagen)
libraries were prepared following the exact protocol in Corces et al, Nature Methods 2017, 50bp paired end sequencing

value: neuroblastoma cell line


title: AL_ZT14_REP3


title: dmel head, old, ZT20, rep3

city: Corvallis

first: Rosalyn

middle: M.

last: Fey

state: OR

address: 1500 SW Jefferson Way

institute: Oregon State University

description:
20
adjCountsTable_oldRep3.txt
adjRPMMirReads_oldRep3.txt
adjCountsTable_piRNA_oldRep3.txt
adjRPMtable_piRNA_oldRep3.txt

data_processing:
Reads were quality filtered and sequencing adapters were trimmed using skewer, with parameters set for a minimum quality score of 30 and a minimum read length of 18, using the adapter sequence “TGGAATTCTCGGGTGCCAAGG”.
Reads were aligned to the Drosophila melanogaster genome (BDGP release 6.21/dm6) with Bowtie using the parameters “-l 18 –n 1 -e 50 -a -m 50 -S --best --strata”.
The number of hits to the genome for each read was included by adding NH tags to the output SAM files.
We used a custom Python script to quantify reads by mapping to the miRBase version 22 genome annotation file (release 6). We adjusted reads to account for paralogous microRNAs (which map to multiple places in the genome) by dividing each count by the number of hits to the genome, stored in the NH tags in the SAM file for each sample. Final quantification is in adjusted Reads per Million Mapped MicroRNAs (aRPMMM). We used similar custom Python scripts to quantify reads mapping to piRNAs.
Assembly: dm6.21
Supplementary files format and content: adjCounts tables are replicate-specific tab-delimited text files containing raw counts for each microRNA for each ZT, which have been adjusted to account for paralogous microRNAs.
Supplementary files format and content: adjRPMMirReads tables are replicate-specific tab-delimited text files containing normalized counts for each microRNA in each ZT
Supplementary files format and content: adjCounts_piRNA tables are replicate-specific tab-delimited text files containing raw counts for each piRNA cluster for each ZT, which have been adjusted to account for paralogous clusters
Supplementary files format and content: adjRPM_piRNA tables are replicate-specific tab-delimited text files containing normalized counts for each piRNA cluster in each ZT

source_name: whole heads

extract_protocol:
Each sample of 400 heads was homogenized in TRIzol (Thermo Fisher) with a Kontes handheld motorized pestle following the manufacturer’s instructions. Samples were treated with rDNAse I (Takara) followed by phenol/chloroform extraction. RNA was precipitated with ethanol and sodium acetate.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Library Prep Kit following manufacturer's protocols, with the addition of a DNA block oligo with sequence complimentarity to the Drosophila 30-nt 2S rRNA fragment.

value: whole heads

value: female

tag: condition

value: old (55 day)

value: ZT 20


title: dmel head, old, ZT16, rep3

description:
16
adjCountsTable_oldRep3.txt
adjRPMMirReads_oldRep3.txt
adjCountsTable_piRNA_oldRep3.txt
adjRPMtable_piRNA_oldRep3.txt

value: ZT 16


title: ∆ddl vanS (R334L) cells, replicate 2

description: sample 16


title: AL_ZT14_REP1

value: AL


title: IMR32_parental_rep2, RNA-Seq


title: dmel head, old, ZT8, rep3

description:
8
adjCountsTable_oldRep3.txt
adjRPMMirReads_oldRep3.txt
adjCountsTable_piRNA_oldRep3.txt
adjRPMtable_piRNA_oldRep3.txt

value: ZT 8


title: Rpl10a_WT_Ribo_Rep3

description:
ribo_cds_rna_total_counts.csv
WT_6_BC5

value: Ribosome-Protected Fragments (RPFs)


title: SHSY5Y_ASCL1_KO2_rep2

value: ASCL1 KO2


title: AL_ZT10_REP2

value: Liver


title: dmel head, old, ZT12, rep3

description:
12
adjCountsTable_oldRep3.txt
adjRPMMirReads_oldRep3.txt
adjCountsTable_piRNA_oldRep3.txt
adjRPMtable_piRNA_oldRep3.txt

value: ZT 12


title: IMR32_parental_rep3, RNA-Seq


title: SHSY5Y_ASCL1_KO1_rep2

description:
SHSY5Y_ATAC_DiffBind.txt
SHSY5Y_ASCL1_KO1_RPGC_mean.bw

value: ASCL1 KO1


title: SHSY5Y_ASCL1_KO1_rep3


title: AL_ZT10_REP3

value: Male


title: SHSY5Y_ASCL1_KO2_rep3


title: AL_ZT2_REP3


title: AL_ZT2_REP2


title: SHSY5Y_ASCL1_KO2_rep1


title: AL_ZT10_REP1


title: dmel head, old, ZT4, rep3

description:
4
adjCountsTable_oldRep3.txt
adjRPMMirReads_oldRep3.txt
adjCountsTable_piRNA_oldRep3.txt
adjRPMtable_piRNA_oldRep3.txt

value: ZT 4


title: SHSY5Y_ASCL1_KO1_rep1


title: dmel head, old, ZT0, rep3

description:
0
adjCountsTable_oldRep3.txt
adjRPMMirReads_oldRep3.txt
adjCountsTable_piRNA_oldRep3.txt
adjRPMtable_piRNA_oldRep3.txt

value: ZT 0


title: AL_ZT6_REP3


title: SHSY5Y_ASCL1_KO1_rep4


title: dmel head, old, ZT8, rep2

description:
8
adjCountsTable_oldRep2.txt
adjRPMMirReads_oldRep2.txt
adjCountsTable_piRNA_oldRep2.txt
adjRPMtable_piRNA_oldRep2.txt


title: Primary cortical cells, DRB-2hrs, BDNF-1hr, rep3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
polyA RNAs
BDNF_N10

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using FPKM
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2018_1 were also provide

source_name: brain

growth_protocol: primary cortical cells were isolated from embryonic stage 16.5 embryos and maintained for 14 days in culture

extract_protocol:
Cells were lysed using Trizol reagent (Sigma, T9424). Total RNAs were isolated and DNase treated on columns (RNeasy micro kit, Qiagen, 74004) following the manufacturer’s instructions.
Library preparation was performed, starting from 200ng total RNAs, using the TruSeq Stranded mRNA Library Kit (Illumina, 20020595) and the TruSeq RNA UD Indexes (Illumina, 20022371).

treatment_protocol: DRB (50uM), Triptolide (1uM), Bicuculline (20uM), BDNF(50ng/mL)

value: brain

value: Primary cortical cells

value: wild type

tag: treatment

value: DRB-2hrs, BDNF-1hr


title: dmel head, old, ZT4, rep2

description:
4
adjCountsTable_oldRep2.txt
adjRPMMirReads_oldRep2.txt
adjCountsTable_piRNA_oldRep2.txt
adjRPMtable_piRNA_oldRep2.txt

value: whole heads

value: female

value: old (55 day)


title: Primary cortical cells, DRB-2hrs, BDNF-1hr, rep2

description:
polyA RNAs
BDNF_N8


title: AL_ZT6_REP1

value: AL


title: dmel head, old, ZT16, rep2

description:
16
adjCountsTable_oldRep2.txt
adjRPMMirReads_oldRep2.txt
adjCountsTable_piRNA_oldRep2.txt
adjRPMtable_piRNA_oldRep2.txt

value: ZT 16


title: dmel head, old, ZT20, rep2

description:
20
adjCountsTable_oldRep2.txt
adjRPMMirReads_oldRep2.txt
adjCountsTable_piRNA_oldRep2.txt
adjRPMtable_piRNA_oldRep2.txt

value: ZT 20


title: dmel head, old, ZT12, rep2

description:
12
adjCountsTable_oldRep2.txt
adjRPMMirReads_oldRep2.txt
adjCountsTable_piRNA_oldRep2.txt
adjRPMtable_piRNA_oldRep2.txt


title: RNA_ILC3_BATF_ko_3  [3K3_S15]

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10 using Star.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

extract_protocol: Bulk RNA sequencing was performed according to a published Smart-seq2 protocol with minor modification. https://doi.org/10.1038/nprot.2014.006

treatment_protocol: 2000 ILC3s (Lin-CD90.2+KLRG1-) from the small intesine of WT and cKO mice were directly sorted into lysis buffer containing Protector RNase Inhibitor (Roche). Three replicates from each group were subsequently sequenced. 2 ng of purified RNA were used as input for SMART-Seq2 protocol .

tag: strain background

tag: genotype/variation

value: Batffl/flPLZF-Cre+

value: Small intestine


title: AL_ZT2_REP1

value: Liver


title: SHSY5Y_parental_rep4

description:
SHSY5Y_ATAC_DiffBind.txt
SHSY5Y_control_RPGC_mean.bw

tag: cell type

value: neuroblastoma cell line

tag: cell line

value: parental


title: SHSY5Y_parental_rep2

tag: genotype


title: dmel head, old, ZT20, rep1

description:
20
adjCountsTable_oldRep1.txt
adjRPMMirReads_oldRep1.txt
adjCountsTable_piRNA_oldRep1.txt
adjRPMtable_piRNA_oldRep1.txt


title: RNA_ILC3_BATF_ko_2  [3K2_S24]


title: dmel head, old, ZT0, rep2

description:
0
adjCountsTable_oldRep2.txt
adjRPMMirReads_oldRep2.txt
adjCountsTable_piRNA_oldRep2.txt
adjRPMtable_piRNA_oldRep2.txt


title: RNA_ILC3_BATF_ko_1  [3K1_S22]


title: RNA_ILC3_WT_3  [3W3_S10]

value: Batffl/flPLZF-Cre-


title: Primary cortical cells, DRB-2hrs, Bicuculline-1hr, rep3

description:
polyA RNAs
BicS_N10

value: DRB-2hrs, Bicuculline-1hr


title: Primary cortical cells, DRB-2hrs, Bicuculline-1hr, rep2

description:
polyA RNAs
BicS_N8

value: brain


title: Primary cortical cells, DRB-2hrs, BDNF-1hr, rep1

description:
polyA RNAs
BDNF_N7

value: Primary cortical cells


title: AL_ZT6_REP2

value: Male


title: SHSY5Y_parental_rep3


title: SHSY5Y_parental_rep1


title: RNA_ILC3_WT_2  [3W2_S3]


title: Primary cortical cells, DRB-2hrs, Bicuculline-1hr, rep1

description:
polyA RNAs
BicS_N7

value: wild type


title: Primary cortical cells, DRB-2hrs, unstimulated, rep3

description:
polyA RNAs
Ctrl_N10

value: DRB-2hrs, Unstimulated


title: IMR32_ASCL1_KO2_rep2

description:
IMR32_ATAC_DiffBind.txt
IMR32_ASCL1_KO2_RPGC_mean.bw

value: ASCL1 KO2


title: dmel head, old, ZT12, rep1

description:
12
adjCountsTable_oldRep1.txt
adjRPMMirReads_oldRep1.txt
adjCountsTable_piRNA_oldRep1.txt
adjRPMtable_piRNA_oldRep1.txt

value: whole heads

value: female

value: old (55 day)

value: ZT 12


title: IMR32_ASCL1_KO2_rep4


title: dmel head, old, ZT4, rep1

description:
4
adjCountsTable_oldRep1.txt
adjRPMMirReads_oldRep1.txt
adjCountsTable_piRNA_oldRep1.txt
adjRPMtable_piRNA_oldRep1.txt

value: ZT 4


title: dmel head, old, ZT8, rep1

description:
8
adjCountsTable_oldRep1.txt
adjRPMMirReads_oldRep1.txt
adjCountsTable_piRNA_oldRep1.txt
adjRPMtable_piRNA_oldRep1.txt

value: ZT 8


title: IMR32_ASCL1_KO2_rep1


title: RNA_ILC3_WT_1  [3W1_S18]

value: Small intestine


title: dmel head, old ZT0, rep1

description:
0
adjCountsTable_oldRep1.txt
adjRPMMirReads_oldRep1.txt
adjCountsTable_piRNA_oldRep1.txt
adjRPMtable_piRNA_oldRep1.txt

value: ZT 0


title: Primary cortical cells, DRB-2hrs, unstimulated, rep2

description:
polyA RNAs
Ctrl_N8


title: eIF2A_3h_rep4

city: Vancouver

first: Howard

last: Cen

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

data_processing:
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
Alignment was performed using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw counts for each gene.

source_name: MIN6 cells

growth_protocol: MIN6 cells were cultured in Dulbecco’s modified eagle’s medium (Thermo Fisher Scientific) containing 22.2 mM glucose, 100 units/ml penicillin, 100 mg/ml streptomycin and 10% (v/v) FBS.

extract_protocol:
RNA was isolated from cell or islet samples using RNeasy mini kit (Qiagen, #74106) according to manufacturer’s instructions.
tru seq stranded mRNA

treatment_protocol: MIN6 cells were treated with 1 μM thapsigargin for 1 (1h) or 3 (3h) hours or with DMSO vehicle control (0h) in cell culture media

value: MIN6 cells

tag: overexpression

value: thapsigargin


title: dmel head, old, ZT16, rep1

description:
16
adjCountsTable_oldRep1.txt
adjRPMMirReads_oldRep1.txt
adjCountsTable_piRNA_oldRep1.txt
adjRPMtable_piRNA_oldRep1.txt

value: ZT 16


title: IMR32_ASCL1_KO1_rep4

description:
IMR32_ATAC_DiffBind.txt
IMR32_ASCL1_KO1_RPGC_mean.bw

value: neuroblastoma cell line

value: ASCL1 KO1


title: eIF2A_3h_rep3


title: Primary cortical cells, DRB-2hrs, unstimulated, rep1

description:
polyA RNAs
Ctrl_N7

value: brain

value: Primary cortical cells


title: IMR32_ASCL1_KO1_rep3


title: dmel head, young, ZT20, rep3

description:
20
adjCountsTable_youngRep3.txt
adjRPMMirReads_youngRep3.txt
adjCountsTable_piRNA_youngRep3.txt
adjRPMtable_piRNA_youngRep3.txt

value: young (5 day)

value: ZT 20


title: IMR32_ASCL1_KO2_rep3

value: ASCL1 KO2


title: dmel head, young, ZT16, rep3

description:
16
adjCountsTable_youngRep3.txt
adjRPMMirReads_youngRep3.txt
adjCountsTable_piRNA_youngRep3.txt
adjRPMtable_piRNA_youngRep3.txt

value: whole heads

value: female


title: dmel head, young, ZT12, rep3

description:
12
adjCountsTable_youngRep3.txt
adjRPMMirReads_youngRep3.txt
adjCountsTable_piRNA_youngRep3.txt
adjRPMtable_piRNA_youngRep3.txt

value: ZT 12


title: IMR32_ASCL1_KO1_rep2


title: IMR32_ASCL1_KO1_rep1


title: eIF2A_3h_rep1


title: IMR32_parental_rep4

description:
IMR32_ATAC_DiffBind.txt
IMR32_control_RPGC_mean.bw

value: parental


title: dmel head, young, ZT8, rep3

description:
8
adjCountsTable_youngRep3.txt
adjRPMMirReads_youngRep3.txt
adjCountsTable_piRNA_youngRep3.txt
adjRPMtable_piRNA_youngRep3.txt

value: ZT 8


title: eIF2A_1h_rep2


title: IMR32_parental_rep3


title: dmel head, young, ZT4, rep3

description:
4
adjCountsTable_youngRep3.txt
adjRPMMirReads_youngRep3.txt
adjCountsTable_piRNA_youngRep3.txt
adjRPMtable_piRNA_youngRep3.txt

value: ZT 4


title: dmel head, young, ZT0, rep3

description:
0
adjCountsTable_youngRep3.txt
adjRPMMirReads_youngRep3.txt
adjCountsTable_piRNA_youngRep3.txt
adjRPMtable_piRNA_youngRep3.txt

value: ZT 0