title: H1-TKO cells - cheRNA - rep3

extract_protocol:
40x106 mES cells were lysed in 800 uL ice-cold Lysis Buffer A (10 mM Tris pH 7.5, 0.1% NP-40, 150 mM NaCl) for 5 minutes on ice. Nuclei were collected by sucrose cushion centrifugation (24% sucrose in lysis buffer A), rinsed with ice-cold PBS + 1mM EDTA, and resuspended in 500uL ice-cold Glycerol Buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol). Nuclei were lysed by adding one volume of ice-cold Lysis Buffer B (10 mM HEPES pH 7.6, 1mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3M NaCl, 1M urea, 1% NP-40) and kept on ice for 10 minutes, with periodic vigorous shaking. Insoluble chromatin was sedimented by centrifugation at 15000g and 4ÂºC for 2 minutes, rinsed twice with cold PBS + 1mM EDTA, and resuspended in 100 uL PBS. At this point, 10 pg of an in vitro transcribed luciferase RNA was added to both the nucleoplasmic and chromatin samples as a spike-in control. RNAs were purified using TRIzolTM, following manufacturerâ€™s instructions
Before library preparation, ribosomal RNA was depleted from the samples by a treatment with Ribo-Zero rRNA Removal Kit (Illumina). Libraries were generated using TruSeq Stranded Total RNA Library Prep (Illumina), and sequenced by 1x75 single reads

value: cheRNA


title: WT mES, ChrMeRIP rep1

status: Public on Sep 13 2022

type: SRA

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

country: Spain

institute: CBMSO(CSIC/UAM)

description:
WT-mES_ChrMeRIP_IP_Watson.bw
WT-mES_ChrMeRIP_IP_Crick.bw

library_source: transcriptomic

data_processing:
Raw reads were aligned to mm10 genome using TopHat2 (for RNA samples) or BWA mem (for DNA samples), using standard parameters
Low score alignments were filtered using samtools view
bigwig files were generated with bedtools genomeCoverageBed
Differential expression analysis was carried out with DEseq2
Mnase data combing was performed with NucWave
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for coverage files for each experiment, and a bed file containing a list of differential transcripts in H1-TKO cells

molecule: total RNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells were grown in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Biosera), 1x non-essential aminoacids (Gibco), 1mM sodium piruvate (Gibco), 2mM L-glutamine (Gibco), 50 uM B-mercaptoethanol (Gibco), 103 U/mL LIF (ESGRO), 100 U/mL penicillin (Invitrogen) and 100 ug/mL streptomycin (Invitrogen), at 37ºC and 5% CO2

extract_protocol:
RNA fragmentation and meRIP were performed as described in Dominissini et al. (2013) and Zeng et al. (2018), with the following modifications. Aliquots containing 2 g of CheRNAs in 18L of DEPC H2O were fragmented by incubation with 2 L of 100 uL Tris pH 7, 100 uL ZnCl2 1M, 800 uL DEPC water, at 70ºC for 8 minutes, and reactions were stopped by adding 2 L of 0.5M EDTA. A total of 50 g of pooled fragmented CheRNAs were incubated with 5 g of anti-m6A antibodies (Synaptic Systems) previously bound to A/G protein agarose beads (SantaCruz) in IP buffer (10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% Igepal CA-630), and supplemented with RiboLockTM (Thermo Scientific), during 6 hours at 4ºC. Beads were washed three times with IP buffer, meRNAs were eluted in elution buffer (10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% Igepal CA-630, 6.67mM m6A) and purified through RNeasy columns (Qiagen) following the manufacturers protocol
TruSeq Stranded total RNA, Libraries 1x75 reads

tag: cell type

value: Embryonic stem cells

tag: genotype

value: WT

tag: merip antibody

value: anti-m6A, Synaptic Systems (202003)

tag: molecule subtype

value: chromatin enriched RNA


title: H1-TKO cells - cheRNA - rep1

data_processing:
Raw reads were aligned to mm10 genome using TopHat2 (for RNA samples) or BWA mem (for DNA samples), using standard parameters
Low score alignments were filtered using samtools view
bigwig files were generated with bedtools genomeCoverageBed
Differential expression analysis was carried out with DEseq2
Mnase data combing was performed with NucWave
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for coverage files for each experiment,  and a bed file containing a list of differential transcripts in H1-TKO cells

source_name: H1-TKO cells

value: Histone H1 triple KO


title: H1-TKO cells - cheRNA - rep2


title: mES WT cells - cheRNA - rep3

source_name: mES WT cells


title: MELA_0334 Tumour

type: genomic

city: Herston

first: Felicity

last: Newell

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer Medical Research Institute

hyb_protocol: Illumina protocol

scan_protocol: iScan Illumina

data_processing:
2021
The raw data in the form of IDAT files for 144 samples were imported filtered and normalized using the ChAMP package implemented in R .  Probes were primarily filtered out if detection p-value > 0.01 or there were fewer than three beads in 5% or more of samples.  A β-mixture quantile normalisation (BMIQ) was performed to account for probe type 1 and type 2 biases, followed by a quantile normalisation.  Further filtering was performed to remove probes if they were located in non-CpG sites, X and Y chromosomes, single nucleotide polymorphism-related polymorphisms and probes that map to multiple locations.

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumour

label_protocol: Illumina protocol

growth_protocol: not applicable

extract_protocol: All prep DNA/RNA/miRNA Universal kit

treatment_protocol: not applicable

tag: tissue

value: melanoma tumour


title: H1-TKO cells - Mnase - rep2

library_source: genomic

extract_protocol:
Cells were washed twice with PBS, and crosslinked by a 10 minutes incubation with PBS + 1% formaldehyde at room temperature. Crosslinking reactions were stopped by the addition of 125 mM glycine and additional rocking for 5 minutes. Cells were collected by scrapping in 2 mL ice-cold PBS + protease inhibitors (10 uM leupeptin, 100 uM PMSF, 1uM pepstatin, 2 ug/mL aprotinin), collected by centrifugation at 180g for 5 minutes at 4oC, resuspended in Homogenization Buffer (10 mM Tris pH 7.4, 1mM EDTA, 0.1mM EGTA, 15 mM NaCl, 50 mM KCl, 0.15mM spermine, 0.5 mM spermidine, 0.2% NP-40, 5% sucrose) at a concentration of 2x106 cells/mL and incubated on ice for 3 minutes. Nuclei were then placed on top of a 3.5 mL sucrose cushion (Homogenization Buffer + 10% sucrose), and centrifuged for 20 minutes at 900g and 4oC. The nuclei pellet was resuspended in ice-cold Wash Buffer (10mM Tris pH 7.4, 15mM NaCl, 50 mM KCl, 0.15 mM spermine, 0.5 mM spermidine, 8.5% sucrose) at a concentration of 2x106 nuclei/mL, and divided in 1 mL aliquots. Two of these aliquots were treated with 0 and 600 units of MNase (Thermo Fisher) after adding 1mM CaCl2 for 6 minutes at 25oC. Enzymatic reactions were stopped by adding 9mM EDTA and 3.5 mM EGTA and placing the samples at 4oC.Next, samples were purified and those treated with 600 units of MNase loaded in a 1.2% agarose gel. The fragments corresponding to the mononucleosomal fraction (around 150 bp) were sliced from the agarose gel and purified using a Speedtools PCR Clean Up Kit (Biotools) following manufacturerâ€™s instructions
Libraries were generated with the NEBNext DNA Library Prep Kit (New England Biolabs) and sequenced by 2x75 paired-end reads


title: mES WT cells - cheRNA - rep2


title: MELA_0057 Tumour


title: MELA_0026 Tumour


title: E4.5 Blastocyst

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.1) used for cell barcode and UMI counting
STAR (v2.7.1a) used for mouse reference genome (mm10) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Genome_build: mm10
Supplementary_files_format_and_content: tsv files include UMI counts for each cell barcode and genes

molecule: polyA RNA

source_name: B6C3F1 mouse

growth_protocol:
Before incorporation into embryoids, the ES cells were maintained in DMEM medium supplemented with 15% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 50 U/ml penicillin-streptomycin, 0.1 mM 2-mercaptoethanol, 0.4 μM PD0325901, 3 μM CHIR99021 and 4 ng/ml Lif on gelatine coated culture plates.
XTE cells were  maintained Fibronectin-coated plates in XTE medium (N2B27 supplemented with 3 μM CHIR99021, 50 ng/ml BMP4, 25 ng/ml Fgf4,1 μg/ml Heparin and 20 ng/ml Activin).

extract_protocol:
Embryoids or E4.5 embryos were dissociated to single cells using TrypLE (Gibco) and 6000 cells were used for library preparation.
Single cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions using BD Rhapsody WTA Reagent kit (BD)

treatment_protocol: Embryoids were generated by seeding ES cells (10,000 cells) and XTEs (50,000-80,000) in an AggreWell™400 plates (StemCell Technologies) for 48 h and then the aggregates were transferred to cell repellent plates for 48 h to facilitate cavitation and formation of embryoids.

tag: strain

value: whole embryo


title: MELA_0072 Tumour


title: mES WT cells - cheRNA - rep1


title: MELA_0279 Tumour


title: H1-TKO cells - Ttseq -rep1

extract_protocol:
4-thiouridine (4sU) was added to sub-confluent cell cultures at a final concentration of 1 mM for 10 min before cell harvest. Cells were lysed directly on a plate with 5 ml of TRIzol (Invitrogen), total RNA was isolated following manufacturerÂ´s protocol and sonicated by two pulses of 30 seconds in a Bioruptor instrument. A total of 100 ug of sonicated RNA per cell line was used for biotinylation and purification of 4sU-labeled nascent RNAs. Biotinylation reactions consisted of total RNA and EZ-Link HPDP-Biotin dissolved in dimethylformamide (DMF) and were performed in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) for 2 h with rotation at RT. Unbound Biotin-HPDP was removed by chloroform/isoamylalcohol (24:1) extraction in MaXtract tubes (Qiagen). RNA was precipitated with 10th volume of 5M NaCl and 1 volume of isopropanol. Following one wash in 80% ethanol, the RNA pellet was left to dry and resuspended in 100 uL RNase-free water. Biotinylated RNA was purified using uMacs Streptavidin kit, eluted twice using 100 mM DTT and recovered using RNeasy MinElute Cleanup column (Qiagen) according to instructions
cDNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturerâ€™s instructions. Libraries were pooled and sequenced by 2x75 single-reads

value: Nascent RNA


title: Healthy brain microvessels 3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description:
pooled from 2 males
Healthy_3

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Davis et al., Kraken: A set of tools for quality control and analysis of high-throughput sequence data). Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.62. Only genes with a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: hg38
Supplementary_files_format_and_content: library size normalized counts per sample

source_name: brain microvessels

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
200ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry and 1x75bp single end setup.

tag: developmental stage

value: adult

value: brain microvessels

tag: disease state

value: Healthy controls


title: MELA_0011 Tumour


title: MELA_0012 Tumour


title: Embryoids

source_name: Embryoids comprised of Lifeact RFPruby ES cells and Gata6H2B:Venus XTE cells

tag: derivation

value: ES cells were derived from established protocols from Lifeact-RFPRuby mice strain. XTE cells were reprogrammed from Gata6-H2B:venus ES cells

value: ES cells and XTE cells


title: MELA_0278 Tumour


title: stool, MG41.01, control turns to NEC, DOL15

city: Pittsburgh

first: David

last: Peters

state: PA

address: 204 Craft Avenue

country: USA

institute: Magee-Womens Research Institute

data_processing:
DNA sequence reads were quality trimmed and adaptor sequences were removed using Trim-Galore.
The reads were aligned to the human refrence sequence using Bismark Bisulfite Read Mapper in paired-end, bowtie2 mode. Any unmapped reads were aligned in single-end, bowtie2 mode.
Read duplicates were removed using Bismark.
Methylation was called on paired-end and single-end files and then merged to determine the methylation status for each CpG site.
DNA methylation signatures were determined using the beta-binomial test implemented in the R packages methylSig and DSS.
Assembly: GRCh38
Supplementary files format and content: Bismark Coverage output merged from PE and SE methylation extractor outputs. <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: stool

extract_protocol:
Snap-frozen specimens were mounted on appropriate embedding molds with clear Optimal Cutting Temperature Embedding Medium and cryostat sectioned at 7 um. These sections were mounted on memebrane slides, stained with toluidine blue and air dried. Tissue DNA was extracted using the Nucleospin Tissue XS Kit. Extracted DNA was quantified by using the KAPA hgDNA Quantification and QC Kit. Stool DNA was extracted using the NucleoSpin DNA Stool, Mini Kit. Human and bacterial DNA content were measured using Femto Human and Femto Bacterial DNA Quantification Kits.
DNA was sheared with Covaris to a size of ~175bp. Libraries were prepared using the KAPA HyperPrep Kit. Libraries were bisulfite converted post-ligation using the EZ DNA Methylation-Direct Kit and amplified 13-15 cycles. Bisulfite-converted DNA libraries underwent targeted capture using the SeqCap Epi CPGiant Enrichment Kit and amplified 10 cycles. Samples were sequenced on a HiSeq with 100 bp paired-end reads to a mean targeted read depth of ~24x.

treatment_protocol: Intestinal tissue samples were procured if resected for NEC or other noninflammatory indications, such as reanastomosis, spontaneous intestinal perforation or anorectal malformation. Resections of intestinal tissue were snap frozen and stored at -80 degrees Celsius until further analysis. Non-NEC tissue samples were healed NEC tissue obtained during surgical reanastomosis. Stool was collected from diapers and identified as being from cases with NEC or premature control infants. The diapers were initially placed at 4 degrees Celsius, transferred to the laboratory within 12-24 h, aliquoted into barcoded tubes and stored at -80 degrees Celsius until processing.

value: stool

value: control turns to NEC

tag: race

value: W

tag: Sex

value: female

tag: dol (days_of_life)_at_sampling

tag: age at_nec_onset

tag: dol at_nec_onset


title: Healthy brain microvessels 1

description:
pooled from 2 females
Healthy_1


title: Healthy brain microvessels 2

description:
pooled from 2 females
Healthy_2


title: stool, MG41.01, control turns to NEC, DOL6


title: MELA_0320 Tumour


title: stool, MG29.01, control turns to NEC, DOL41

value: male


title: stool, MG48.01, control, DOL6

value: control

value: AA


title: Meningitis brain microvessels 4

description:
pooled from 1 male and 1 female
Meningitis_4

value: S. pneumoniae infected


title: MELA_0277 Tumour


title: Healthy brain microvessels 4

description:
pooled from 2 males
Healthy_4


title: Meningitis brain microvessels 3

description:
pooled from 2 males
Meningitis_3


title: MELA_0370 Tumour


title: TRF RE TP20 REP3

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

data_processing:
Alignment to reference assembly mm10 and known splice junctions extracted from the RefSeq database performed using Tuxedo pipeline tophat
Read counting for each gene and normalization to FPKM values  using Tuxedo pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression results FPKM values) of the standard RNAseq analysis are reported in the genes_fpkm.csv file

source_name: liver

extract_protocol:
Total RNA was extracted from liver with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
Library construction was performed according to the Illumina TruSeq Total RNA stranded protocol.  The input quantity for total RNA was 1ug and rRNA was depleted  using ribo-zero rRNA gold removal kit (human/mouse/rat). The rRNA depleted RNA was chemically fragmented for three minutes.  First strand synthesis used random primers and reverse transcriptase to make cDNA.  After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated.  Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip.  The concentrations for the libraries were normalized and then multiplexed together.  The concentration for denaturation was 2nM and the final concentration for clustering was 200pM.  The multiplexed libraries were sequenced by the Genomics High-Throughput Facility at the University of California – Irvine on six lanes using single end 100 cycles chemistry for the HiSeq 4000.   The version of HiSeq control software was HCS 3.4.0.38 with real time analysis software, RTA 2.7.7.

value: C57BL/6J background

tag: age

value: 8-12 weeks

tag: genotype/variation

value: Bmal1 Liver-reconstituted

tag: time of harvest


title: stool, MG45.02, control, DOL16


title: TRF RE TP20 REP2


title: MELA_0413 Tumour

value: melanoma tumour


title: MELA_0369 Tumour


title: stool, MG40.01, control, DOL5


title: Meningitis brain microvessels 2

description:
pooled from 2 females
Meningitis_2

value: adult


title: TRF RE TP20 REP1


title: MELA_0056 Tumour


title: 2

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (ARS1.2) using the miRDeep2 package (version 2.00.8), the miRDeep2 quantifier module was used to quantify all expressed miRNAs in the sequence data, producing read counts for each individual sample.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
Genome_build: ARS1.2
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: Spermatozoa

growth_protocol: Frozen-thawed semen from Holstein Friesian bulls

extract_protocol:
RNA was  precipitated and purified from spermatozoa using trizol according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the NEBNext® Multiplex Small RNA Library Prep kit for Illumina (NEB), following the manufacturer’s instructions.

treatment_protocol: High and Low fertility bulls were selected using an animal adjusted statistical model

tag: fertility status

value: High ferility

value: Spermatozoa

tag: breed

value: Holstein-Friesian

tag: group


title: Meningitis brain microvessels 1

description:
pooled from 2 females
Meningitis_1

value: brain microvessels


title: TRF KO TP20 REP3


title: stool, MG31.01, control, DOL6

value: stool


title: stool, MG39.01, NEC, DOL9

value: NEC


title: stool, MG27.01, NEC, DOL7

value: W


title: TRF KO TP20 REP2


title: MELA_0368 Tumour


title: TRF WT TP20 REP3

value: WT


title: stool, MG15.01, NEC, DOL9

value: female


title: stool, MG25.01, NEC, DOL13

value: male


title: MELA_0275 Tumour


title: TRF KO TP20 REP1


title: TRF WT TP20 REP2


title: RNAseq of mature seeds of Medicago truncatula abi4-2 (NF2525) rep3

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Clean reads were mapped to the reference genome Mt5.0 using Salmon
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Medicago truncatula

source_name: seed

growth_protocol: Plants were grown in a culture room in trays containing a sterile mix of vermiculite at 20°C/19°C, with a 16 h light photoperiod at 200 μmol photons m -²s-².

extract_protocol:
Total RNA was extracted using the NucleoSpin® RNA Plant Plus kit (Macherey-Nagel) according to the manufacturer instructions.
Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 24M reads of 50bp per sample

treatment_protocol: After harvest, seeds were removed from the pods and frozen in LN2 and stored at -80°C until extraction

value: seed

tag: Stage

value: mature

tag: genotype


title: RNAseq of mature seeds of Medicago truncatula abi4-2 (NF2525) rep1

tag: tissue


title: RNAseq of mature seeds of Medicago truncatula abi4-2 (NF2525) rep2


title: RNAseq of mature seeds of Medicago truncatula abi4-1 (NF19813) rep3


title: RNAseq of mature seeds of Medicago truncatula abi4-1 (NF19813) rep1


title: RNAseq of mature seeds of Medicago truncatula abi4-1 (NF19813) rep2


title: MELA_0055 Tumour


title: colon, G80T, NEC

source_name: colon tissue

value: colon tissue


title: MELA_0367 Tumour


title: TRF WT TP20 REP1

tag: strain

value: C57BL/6J background

value: 8-12 weeks


title: MELA_0276 Tumour

value: melanoma tumour


title: stool, MG06.01, NEC, DOL25

tag: disease state


title: TRF RE TP16 REP2

value: Bmal1 Liver-reconstituted


title: colon, G208T, non-NEC

value: non-NEC


title: RNAseq of 24DAP seeds of Medicago truncatula abi4-1 (NF19813) rep2

value: 24 days after pollination


title: TRF RE TP16 REP3


title: TRF RE TP16 REP1


title: colon, G26T, NEC


title: MELA_0332 Tumour


title: MELA_0010 Tumour


title: MELA_0319 Tumour


title: colon, G205T, NEC


title: RNAseq of 13DAP seeds of Medicago truncatula abi4-1 (NF19813) rep3

value: 13 days after pollination


title: TRF KO TP16 REP3


title: colon, G75T, NEC


title: MELA_0164 Tumour


title: MELA_0365 Tumour


title: MELA_0333 Tumour


title: RNAseq of 13DAP seeds of Medicago truncatula abi4-1 (NF19813) rep2


title: colon, G62T, non-NEC


title: RNAseq of 13DAP seeds of Medicago truncatula abi4-1 (NF19813) rep1


title: TRF KO TP16 REP1


title: RNAseq of 24DAP seeds of Medicago truncatula abi4-1 (NF19813) rep3


title: colon, G54T, non-NEC


title: TRF WT TP16 REP3


title: TRF WT TP16 REP2


title: MELA_0364 Tumour


title: MELA_0187 Tumour


title: TRF WT TP16 REP1


title: colon, G11T, non-NEC


title: TRF RE TP12 REP3


title: TRF KO TP16 REP2


title: colon, G49T, non-NEC


title: RNAseq of mature seeds of Medicago truncatula R108 rep1


title: MELA_0274 Tumour


title: colon, G176T, non-NEC


title: MELA_0273 Tumour


title: RNAseq of 24DAP seeds of Medicago truncatula R108 rep3


title: MELA_0008 Tumour


title: TRF RE TP12 REP2


title: colon, G174T, non-NEC


title: MELA_0407 Tumour


title: RNAseq of 24DAP seeds of Medicago truncatula R108 rep2


title: RNAseq of 24DAP seeds of Medicago truncatula R108 rep1


title: colon, G130T, non-NEC


title: TRF RE TP12 REP1


title: RNAseq of mature seeds of Medicago truncatula R108 rep3


title: MELA_0272 Tumour


title: colon, G251T, non-NEC


title: TRF KO TP12 REP3


title: RNAseq of 13DAP seeds of Medicago truncatula R108 rep3


title: RNAseq of mature seeds of Medicago truncatula R108 rep2


title: colon, G173T, NEC


title: RNAseq of 13DAP seeds of Medicago truncatula R108 rep2


title: TRF KO TP12 REP2


title: MELA_0069 Tumour


title: TRF KO TP12 REP1


title: MELA_0007 Tumour


title: colon, G196T, non-NEC


title: colon, G195T, non-NEC


title: TRF WT TP12 REP3


title: RNAseq of 13DAP seeds of Medicago truncatula R108 rep1


title: Tumor Sample 4

city: Teliyarganj, Prayagraj

first: Priyanka

last: Gautam

state: Uttar Pradesh

address: Department of Biotechnology, MNNIT Allahabad

department: Biotechnology

country: India

institute: Motilal Nehru National Institute of Technology

data_processing:
Low quality sequences and adaptor sequences were trimmed using fast (0.20.1)
Alignment of trimmed sequences to GrCh37 were performed using Hisat2 (2.1.0).
Expression estimation was conducted using Feature Counts (2.0.1). Differential expression analysis was performed using DeSeq2 (1.6.3) tool.
Assembly: GrCh37
Supplementary files format and content: Raw counts

source_name: Cancerous Ovarian Tissue

extract_protocol:
RNA was extracted using Trizol method. Total RNA with nuclease free water to final volume of 50µl is used for construction of sequencing library.
For RNA sequencing, sequencing librabries were prepared using NEB#E7490 kit following manufacturer's protocol.

value: Cancerous Ovarian Tissue

tag: tumor stage

value: IV

tag: histology

value: Adeocarcioma


title: MELA_0204 Tumour


title: MELA_0225 Tumour


title: colon, G149T, non-NEC


title: TRF WT TP12 REP2


title: MELA_0081 Tumour


title: TRF WT TP12 REP1


title: Normal Sample 2

source_name: Normal Ovary Tissue

value: Normal Ovary Tissue

value: Normal


title: RNAseq of 24DAP seeds of Medicago truncatula abi4-1 (NF19813) rep1


title: colon, G52T, NEC

value: NEC


title: Tumor Sample 3


title: colon, G25T, NEC


title: MELA_0271 Tumour


title: MELA_0009 Tumour


title: Normal Sample 1


title: Tumor Sample 2

value: III


title: colon, G19T, non-NEC


title: TRF RE TP8 REP1


title: MELA_0270 Tumour


title: colon, G14T, NEC


title: MELA_0269 Tumour


title: TRF KO TP8 REP3


title: MELA_0268 Tumour


title: ZikV3

city: Philadelphia

first: Sara

last: Cherry

address: 472A Stemmler Hall

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

data_processing:
Raw fastq files were trimmed to remove adapters and low quality reads with bbduk 38.56  using the parameters “ref=/bbmap/resources/adapters.fa ktrim=r k=23 mink=11 hdist=1 minlength=35 tpe tbo qtrim=r trimq=10” (Bushnell).
Transcripts were counted using salmon 0.13.1 in pseudoalignment mode by mapping to Homo sapiens (human) genome assembly GRCh38 (build 94) with the parameters “--validateMappings --rangeFactorizationBins 4 --seqBias –gcBias”.
Transcript counts were collapsed to the gene level using the R package tximport and differential expression was analyzed using DESeq2.
Genome_build: Hg38, build 94
Supplementary_files_format_and_content: quant.sf files are plaintext and show counts per transcript from Salmon
Supplementary_files_format_and_content: csv files show the differential expression output at the gene level from DESeq2

growth_protocol: Human brain microvascular endothelial cells (HBMEC) were maintained in Roswell Park Memorial Institute 1640 medium (RPMI 1640 with L-glutamine, Corning) containing 10% fetal bovine serum (FBS, Hyclone), 10% Nu-Serum (Corning), 1% penicillin/streptomycin (Sigma), 1% sodium pyruvate (Sigma), 1% non-essential amino acids (Sigma), 1% MEM vitamins (Sigma), and 10 mg/mL endothelial cell growth supplement (Corning). Cell lines were confirmed mycoplasma-negative.

extract_protocol:
Cells were then directly lysed in TRIzol and RNA was extracted using the Zymogen RNA Clean and Concentrator Kit with on-column DNase I treatment. RNA quality was measured using the Agilent BioAnalyzer and quantified using the Qubit Fluorescent Quantification System (ThermoFisher Scientific).
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit with ribosomal RNA depletion. Paired-end sequencing with 150bp read-length was performed with the NextSeq 500.

treatment_protocol: HBMEC were either left uninfected (mock) or infected with CHIKV or ZIKV at MOI 5 for 24h

tag: cell type

value: human brain microvascular endothelial cells (HBMEC)

tag: treatment

value: cells harvested at 24hrs post infection with Zika virus (MOI 5)


title: TRF KO TP8 REP2


title: miR-204-3p-mimics - Input DNA

city: Guangzhou

first: Si-Jia

last: Liang

state: Guangdong

address: 74 Zhongshan 2 Rd

department: Pharmacology

country: China

institute: Zhongshan School of Medicine, Sun Yat-Sen University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, using trim_galore version 0.6.4.
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3.
Duplicate reads are removed by Picard version 2.20.7.
Peaks were called using macs2 version 2.2.4.
Assembly: hg38
Supplementary files format and content: Align files; peak text files;

source_name: human monocyte-derived macrophages

growth_protocol: Human peripheral blood mononuclear cells were isolated from healthy volunteer donors by Percoll density gradient centrifugation, and were then differentiated into HMDMs in RPMI-1640 medium supplemented with 10% fetal calf serum, 1% HEPES, 1% penicillin/streptomycin, and 100 ng/ml of macrophage colony-stimulating factor.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the KAPA Hyper Prep Kit (Part# KK8502). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000following the manufacturer's protocols.

treatment_protocol: HMDMs were transfected with miRNA mimics negative control or miRNA-204-3p mimics for 24 h.

tag: cell line

value: human monocyte-derived macrophages

value: transfected with miR-204-3p mimics

tag: chip antibody


title: ZikV2

description: Total RNA Kit with ribosomal RNA depletion


title: MELA_0361 Tumour


title: miR-204-3p-mimics - IP


title: TRF KO TP8 REP1

value: C57BL/6J background

tag: age

value: 8-12 weeks


title: ZikV1


title: MELA_0360 Tumour

value: melanoma tumour


title: TRF WT TP8 REP3

tag: genotype/variation

value: WT


title: ChikV3

value: cells harvested at 24hrs post infection with chikungunya virus (MOI 5)


title: TRF RE TP8 REP2

value: Bmal1 Liver-reconstituted

tag: time of harvest


title: TRF WT TP8 REP2


title: NC-m - IP

value: transfected with mimics negative control


title: ileum, G250T, non-NEC

source_name: ileum tissue

extract_protocol:
Snap-frozen specimens were mounted on appropriate embedding molds with clear Optimal Cutting Temperature Embedding Medium and cryostat sectioned at 7 um. These sections were mounted on memebrane slides, stained with toluidine blue and air dried. Tissue DNA was extracted using the Nucleospin Tissue XS Kit. Extracted DNA was quantified by using the KAPA hgDNA Quantification and QC Kit.
DNA was sheared with Covaris to a size of ~175bp. Libraries were prepared using the KAPA HyperPrep Kit. Libraries were bisulfite converted post-ligation using the EZ DNA Methylation-Direct Kit and amplified 13-15 cycles. Bisulfite-converted DNA libraries underwent targeted capture using the SeqCap Epi CPGiant Enrichment Kit and amplified 10 cycles. Samples were sequenced on a HiSeq with 100 bp paired-end reads to a mean targeted read depth of ~24x.

treatment_protocol: Intestinal tissue samples were procured if resected for NEC or other noninflammatory indications, such as reanastomosis, spontaneous intestinal perforation or anorectal malformation. Resections of intestinal tissue were snap frozen and stored at -80 degrees Celsius until further analysis. Non-NEC tissue samples were healed NEC tissue obtained during surgical reanastomosis.

tag: patient id

value: ileum tissue

value: non-NEC


title: ChikV2


title: MELA_0267 Tumour


title: ileum, G223T, NEC


title: NC-m - input


title: ileum, G230T, NEC


title: Tumor Sample 1

value: Cancerous Ovarian Tissue

value: IIIC

value: Adeocarcioma


title: ChikV1


title: TRF RE TP4 REP3


title: TRF WT TP8 REP1


title: Mock3

value: cells harvested at 24hrs post mock-infection


title: MELA_0005 Tumour


title: ileum, G161T, non-NEC


title: TRF RE TP4 REP2


title: MELA_0003 Tumour


title: Mock2

value: human brain microvascular endothelial cells (HBMEC)


title: TRF RE TP4 REP1


title: Mock1


title: MELA_0048 Tumour


title: MELA_0398 Tumour


title: MELA_0067 Tumour


title: ileum, G34T, non-NEC


title: MELA_0359 Tumour


title: MELA_0266 Tumour


title: ileum, G155T, non-NEC


title: TRF RE TP8 REP3


title: ileum, G152T, non-NEC


title: TRF KO TP4 REP2


title: koRnf31-koAtg5 TNF rep2

city: Boston

first: Kai

middle: W.

last: Wucherpfennig

state: MA

address: 450 Brookline Avenue

department: Department of Cancer Immunology and Virology

institute: Dana-Farber Cancer Institute

data_processing:
The RNA-seq data were analyzed using RSEM, which aligns sequencing reads to the GRCm38 reference genome using STAR and counts the reads in each gene. Differential expression analysis between gene knockout cells and control cells was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: comma-delimited text files include read count values for each Sample

source_name: skin

extract_protocol:
Three biological replicates were used to extract total RNA using the RNeasy Plus Micro Kit (Qiagen #74034) according to the manufacturer’s protocol.
Library preparation and sequencing were performed by Genewiz.

treatment_protocol: B16 ctrl-KO, B16 Rnf31-KO, B16 Atg5-KO, B16 Rnf31/Atg5-dKO tumor cells (5x105/well) were plated in 6-well plates and treated with and without TNFa (2 ng/ml, Peprotech) for 24h.

value: skin

value: melanoma cell line

value: TNFa


title: koRnf31-koAtg5 TNF rep3


title: koRnf31-koAtg5 TNF rep1


title: TRF KO TP4 REP1

value: C57BL/6J background


title: MELA_0002 Tumour


title: TRF WT TP4 REP3

value: 8-12 weeks


title: ileum, G6T, NEC

value: NEC


title: ileum, G154T, NEC


title: MELA_0001 Tumour

value: melanoma tumour


title: koRnf31-koAtg5 Veh rep3

value: Veh


title: koRnf31-koAtg5 Veh rep2


title: MELA_0357 Tumour


title: ileum, H246T, NEC


title: TRF WT TP4 REP1

value: WT


title: MELA_0265 Tumour


title: ileum, G67T, non-NEC


title: ileum, G33T, non-NEC


title: TRF KO TP4 REP3


title: TRF RE TP0 REP3

value: Bmal1 Liver-reconstituted


title: MELA_0312 Tumour


title: ileum, G20T, non-NEC

value: ileum tissue


title: koRnf31-koAtg5 Veh rep1


title: koAtg5 TNF rep3


title: TRF RE TP0 REP2


title: koAtg5 TNF rep2


title: MELA_0318 Tumour


title: koAtg5 TNF rep1


title: ileum, G8T, non-NEC

value: non-NEC


title: ileum, G13T, NEC


title: TRF KO TP0 REP3


title: TRF RE TP0 REP1


title: Morc2aDn H3K9me3 replicate 1 [66612_M2KO_H3K9me3]

city: Vienna

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

data_processing:
ChIP-seq reads were trimmed using Trim Galore v0.6.4 and thereafter aligned to the mm10 reference genome (igenomes) using bowtie v2.4.1. The sorted BAM was filtered to remove reads in blacklisted regions using bedtools v2.29.2 and mm10.blacklist.bed.gz v1, and alignments with a MAPQ score below 10 using samtools v1.9. Duplicated reads were marked and excluded with Picard MarkDuplicates v2.23.3. Sequence alignments were converted to bed format using bedtools, and differential ChIP-seq sites for merged replicates were called using diffReps v1.55.6 with settings --meth gt --window 1000.
Genome_build: mm10
Supplementary_files_format_and_content: sequence alignment in bed format used for differential enrichment analysis

source_name: sorted neuronal nuclei (NeuN+) of the brain

extract_protocol:
Subsequently, nuclei were isolated in nuclear isolation buffer (10 mM Tris-HCl, 50 mM sodium-disulfite, 1% Triton X-100, 10 mM MgCl2, 8.6% sucrose, pH6.5) and centrifuged 5 minutes at 455 g at 4°C. The resulting pellet was washed four times with 900 µl nuclear isolation buffer with centrifugation at 455 g at 4°C. The pelleted nuclei were then resuspended in 1.4 ml of PBS, filtered through a cell strainer and stained with a 1:1000 dilution of the anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated, Millipore MAB377X) for 45 minutes by rotation in the dark at 4°C after adding BSA to a final concentration of 0.1%. After washing in PBS, the stained nuclei were filtered through FACS tubes and sorted on a FACS Aria III (BD) sorter in PBS. After the FACS-sort, the pelleted nuclei were immediately resuspended in ChIP lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1% SDS, pH 8.1). Equal amounts of Bioruptor-sonicated chromatin were diluted 10-fold and precipitated overnight with the H3K9me3 (Abcam ab8898) antibody.
Input DNA was quantified using Quant-iT PicoGreen dsDNA Assay (Thermo Fisher). 1 ng of input DNA was used for library preparation with the Ultra Low Input Library Kit (Qiagen, 180497). The procedure of library preparation was done according to the manual provided by Qiagen with adapter dilution of 1:100. Quality control of the libraries included a fragment analyzer run and qPCR to determine average size and precise concentration. Based on the qPCR values, samples were pooled equimolarly to a concentration of 2.5 nM. The pool was loaded on an Illumina HiSeq2000 flowcell with a concentration of 18 pM and sequenced 50 bp single end.

treatment_protocol: For neuron-specific ChIP, freshly isolated brains were homogenized in PBS, cross-linked at a final concentration of 1% formaldehyde for 10 minutes at room temperature and treated with glycine at a final concentration of 125 mM.

value: brain

value: Morc2afl/fl Nestin-Cre+

value: adult

value: H3K9me3 (Abcam, ab8898)


title: TRF WT TP4 REP2


title: Morc2aDn H3K9me3 replicate 1 [66611_M2KO_H3K9me3]


title: WRKY63 nV input

city: New Taipei City

first: FU-YU

last: HUNG

address: Singyi Rd. 17ave. 9s 8th 2F

country: Taiwan

institute: RIKEN

data_processing:
The raw sequence data were processed using the Illumina sequence data analysis pipeline GAPipeline 1.3.2. CLC workbench was then employed to map the reads to the Arabidopsis genome (TAIR10).
To determine the correlation between biological repeats, Pearson correlation was computed using R statistical software on normalized signal intensity for ChIP binding peaks. The alignments were first converted to Wiggle (WIG) files. The data were then imported into the Integrated Genome Viewer (IGV) for visualization.
Genome_build: TAIR 10
Supplementary_files_format_and_content: bigwig files

organism: Arabidopsis thaliana

source_name: 10 days old plants

growth_protocol: The transgenic Arabidopsis seedlings were grown under Long-day conditions at 22°C and harvested after 10 days then treated without vernalization or 4 weeks of vernalization.

extract_protocol:
2 ng of DNA from ChIP was pooled to ensure that there are enough starting DNA for library construction. Two biological replicates were prepared and sequenced for each ChIP-seq experiment. The ChIP DNA was first tested by qRT-PCR and then used to prepare ChIP-seq libraries.
End repair, adaptor ligation, and amplification were carried out using the NEB Genomic DNA Sample Prep kit according to the manufacturer's protocol.

tag: ecotype

value: without vernalization


title: WRKY63 +V input

source_name: 10 days old plants with Vernalization

value: with vernalization


title: koAtg5 Veh rep2

value: skin

value: melanoma cell line


title: TRF KO TP0 REP1

value: C57BL/6J background


title: TRF KO TP0 REP2

value: 8-12 weeks


title: koAtg5 Veh rep1


title: WRKY63 nV GFP-IP

value: anti-GFP antibody (ab290)


title: Mphosph8Dn H3K9me3 replicate 2 [66596_M8KO_H3K9me3]

value: Mphosph8fl/fl Nestin-Cre+


title: koRnf31 TNFa rep3

value: TNFa


title: Mphosph8Dn H3K9me3 replicate 3 [66609_M8KO_H3K9me3]


title: TRF WT TP0 REP 3

value: WT


title: Mphosph8Dn H3K9me3 replicate 1 [66592_M8KO_H3K9me3]


title: TRF WT TP0 REP 2


title: koRnf31 TNFa rep2


title: WRKY63 +V GFP-IP


title: G93A treated by spermidine

city: Seoul

first: Hoon

last: Ryu

state: Seoul

address: Seoul

department: Brain Science Institute

country: South Korea

institute: Korea Institute of Science and Technology

data_processing:
Raw reads were aligned to the mouse genome (GRCm38, mm10) according to the STAR as an accurate alignment tool for high-throughput RNA-seq data
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Group

source_name: Spinal cord

extract_protocol: The spinal cord was snap-frozen on dry ice and total RNA was extracted immediately from the lumbar portion using RNeasy Lipid Tissue Mini-kit (Quiagen Inc., Valencia, CA, USA).

treatment_protocol: The mice was treated with spermidine or PBS foor 30 days at 4 times a week.

value: Spinal cord

value: ALS (G93A) transgenic mice

value: Spermidine treatment

value: Day 30


title: TRF WT TP0 REP 1


title: G93A vehicle


title: koRnf31 TNFa rep1


title: control H3K9me3 replicate 2 [66595_WT_H3K9me3]

value: brain

value: control


title: koAtg5 Veh rep3

value: Veh


title: control H3K9me3 replicate 1 [66591_WT_H3K9me3]

value: adult

value: H3K9me3 (Abcam, ab8898)


title: WT treated by spermidine


title: koRnf31 Veh rep3

value: skin


title: koRnf31 Veh rep2

value: melanoma cell line


title: input [66590_input]


title: WT vehicle


title: koRnf31 Veh rep1


title: Control TNFa rep2


title: Control TNFa rep3


title: control H3K9me3 replicate 3 [66608_WT_H3K9me3]


title: AL KO TP20 REP1

value: C57BL/6J background


title: AL KO TP20 REP3

value: 8-12 weeks


title: AL KO TP20 REP2


title: MV_2

city: Beijing

first: Jiangping

last: Song

address: 167A Beilishi Road, Xi Cheng District

institute: State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
For 10x data, Cell Ranger 6.1.2 was used to quantify gene expression leve with human reference version GRCh38.
The output of Cell Ranger filtered gene expression matrix were analyzed by R software (Version 3.6.1) with the Seurat package (Version 3.2.0).
Before the downstream analysis, low-quality cells were excluded and retained the high-quality single-cell data that met the following criterial: 1) cell with the number of detected genes was greater than 200 and less than 4000; 2) cell with the percentage of gene derived from the mitochondrial genome less than 10%; 3) HBB negative.
After removal of low-quality cells, the gene expression matrices were normalized by the NormalizeData function in Seurat.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Cardiac valve

extract_protocol:
Valve leaflets were collected in 10 mL DMEM (Gibco, 11885084) containing 10% fetal bovine serum (Gibco, 10091148) on ice. Samples were washed by PBS to remove the remaining blood cells and then cut into small pieces. These small pieces were washed by PBS again and digested in HBSS (Corning, 21-022-CV) containing 1.2 U/mL Dispase II (Sigma, D4693-1G) and 2 mg/mL Collagenase, Type 1 (Worthington, LS004194) at 37 °C for 30 minutes, followed by gently shaking. The single-cell suspension was filtered with a 40 μm cell strainer and collected by centrifugation at 400g, 4 °C for 5 minutes. The supernatant was discarded, and the cell pellets were resuspended in 1 mL DMEM containing 10% cold fetal bovine serum. These steps were repeated 1 time. The supernatant was discarded, and the cell pellets were resuspended in 1 mL ACK lysing buffer (Gibco, A1049201) and incubated for 5 minutes at room temperature. The resulting suspension was further diluted to 10x the initial volume with cold PBS, and centrifuged at 400g, 4 °C for 5 minutes. The cell precipitate was resuspended in 500 uL cold DMEM containing 10% fetal bovine serum and use immediately.
Single-cell suspensions were processed through the 10x Genomics Chromium System (10x Genomics, Pleasanton, CA, USA), followed by the construction of 3’ gene expression v3.1 libraries and sequencing on an Illumina Noveseq6000 sequencer. Briefly, cells (>90% viability), reagents, gel beads, and partitioning oil are loaded onto 10x Chromium Chip B. Ideally, each individual cell is wrapped with an oil drop that contains gel beads and reagents. This creates an independent reaction space for each cell called gel bead in emulsion (GEM). The primers provided by the gel bead contain a sequencing primer, barcode, UMI, and poly (dT) sequence. The cell in the GEM is lysed, and incubation of the GEM produces barcoded, full-length cDNA from poly-adenylated mRNA. Next, all cDNAs are pooled together, and the steps of general library construction are performed including amplification, fragmentation, end repair, adapter ligation, and sample index PCR (98 °C for 45 seconds; [98 °C for 20 seconds, 67 °C for 30 seconds, and 72 °C for 1 minute] x 14 cycles; 72 °C for 1 minute). The libraries were then sequenced using Illumina Noveseq6000 by CapitalBio Technology (Beijing, China).

value: Cardiac valve

tag: patient diagnosis

value: end-stage heart failure

value: Cardiac valve cell


title: MV_3

description: 10x Genomics


title: AL WT TP20 REP3

value: WT


title: AL RE TP20 REP1

value: Bmal1 Liver-reconstituted


title: d28

city: Illkirch-Graffenstaden

last: Moreno Fortuno

state: Bas Rhin

address: 1 Rue Laurent Fries

institute: INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE

description: library was sequenced twice to obtain enough sequencing depth

data_processing:
low quality reads were removed and adaptor sequences were trimed with Trim Galore (v0.5.0)
reads were mapped to reference genome with Bowtie 2(v2.2.9)
Peaks were called using MACS2 (v2.1.1) and annotated using the HOMER program annotatePeaks.pl (v4.10.3)
The overlapping peaks across different samples were merged using BEDTools (v2.30.0), counting the reads located in each merged peak using featureCounts (v1.6.3)
Differentially binding regions were identified by DESeq2 (v1.30.1)
Assembly: Saccharomyces cerevisiae genome assembly R64 (sacCer3)
Supplementary files format and content: ATACseq_merged_peaks_raw_counts.txt: txt file containing the raw counts in each sample for every peak detected by MACS2
Supplementary files format and content: ATACseq_merged_peaks_ID.txt: txt file containing information relative to all the peaks detected by MACS2, like chromosomal coordinates, its gene annotation and the distance to the nearest TSS.
Supplementary files format and content: ATACseq_merged_peaks_normalized_counts.txt: txt file cotaining the normalized counts in each sample for every peak detected by MACS2

organism: Saccharomyces cerevisiae

source_name: evolved WP35 yeast cells, Day28

growth_protocol: Yeast cells were grown in Synthetic complete media + 0.1% mannose for 22h at 30°C in a shaking-incubator (225rpm) in a volume of 10ml; then the cells were transferred  to 10ml of fresh synthetic complete media containing 0.1% mannose and 0.2% galactose as carbon sources and grown in the shaker-incubator for another 24h

extract_protocol:
5 million yeast cells were pelleted by centrigugation (2min/4600rpm) and the cell wall was digested with Zymolyase100T
ATAC-seq libraries were generated as detailed in Hendrickson et al., 2018, using the Illumina Tagment DNA TDE1 Enzyme Kit for genomic DNA tagmentation. Then the libraries were amplified using the NEBNext Hi-Fidelity 2X PCR Master Mix and the primers descriven in Buenrostro et al., 2013, and the product was size-purified by Ampure XP magnetic beads.

value: yeast cells

value: W303 MATalpha HO::HIS3::pGAL1-YFP

value: Synthetic complete media + 0.1% mannose + 0.2% galactose

tag: time


title: d28p

tag: genotype


title: Control TNFa rep1

tag: tissue

value: TNFa


title: AL RE TP20 REP3

tag: strain


title: Control Veh rep3


title: d10p

source_name: evolved WP35 yeast cells, Day10


title: AL RE TP20 REP2


title: AL WT TP20 REP2


title: AL WT TP20 REP1


title: TV_3

description: 10x Genomics


title: TV_4

description: 10x Genomics


title: d10


title: d7c

source_name: evolved WP35 yeast cells, Day7


title: TV_2

description: 10x Genomics


title: MV_1

description: 10x Genomics


title: TV_5

description: 10x Genomics


title: Colon tumor organoid, Psen1 KO, EGF, rep3

city: Erlangen

first: Reyes

last: Gamez-Belmonte

state: Bayern

address: Hartmanstraße, 14

department: Medizin 1

institute: Universitätsklinikum Erlangen

data_processing:
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR mapper with default parameters
Read count extraction was performed using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts values for each Sample

source_name: Colon tumor organoid

growth_protocol: Intestinal tumors from Psen1flox and Psen1ΔIEC Apcmin/+ mice were digested with collagenase D  and Dispase II. Cells were resuspended in Matrigel  and cultured in Advanced DMEM/F12 medium supplemented with glutamine (2mM), HEPES (10mM) and N-acetylcystein (1mM); Penicillin-Streptomycin (100U/mL and 100µg/mL), B27 5x and EGF (50ng/mL).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: All tumor organoids were incubated at 37°C in 5% CO2. Tumor organoids were cultured in growth medium for 72h in the presence or not of EGF (50ng/mL)

value: Colon tumor organoid

value: Psen1 KO

value: EGF


title: d7a


title: AL RE TP16 REP2

source_name: liver


title: AL RE TP16 REP1


title: d3p

source_name: evolved WP35 yeast cells, Day3


title: Colon tumor organoid, Psen1 KO, EGF, rep2


title: PV_5

description: 10x Genomics


title: Colon tumor organoid, Psen1 KO, EGF, rep1


title: TV_1

description: 10x Genomics


title: Control Veh rep2

value: Veh


title: PV_4

description: 10x Genomics


title: d3


title: d0c

source_name: WP35 yeast cells, Day0


title: AL KO TP16 REP3


title: Colon tumor organoid, Psen1 KO, H2O, rep2


title: Colon tumor organoid, Psen1 KO, H2O, rep3


title: AL KO TP16 REP2


title: AL RE TP16 REP3


title: AL KO TP16 REP1


title: PV_2

description: 10x Genomics


title: AL WT TP16 REP3


title: Control Veh rep1

value: skin


title: Colon tumor organoid, Psen1 KO, H2O, rep1


title: d0b


title: Colon tumor organoid, WT, EGF, rep3


title: AL WT TP16 REP2


title: AV_5

description: 10x Genomics


title: AV_4

description: 10x Genomics


title: Colon tumor organoid, WT, EGF, rep2


title: AL WT TP16 REP1


title: PV_3

description: 10x Genomics


title: Colon tumor organoid, WT, H2O, rep3


title: Colon tumor organoid, WT, EGF, rep1


title: AL RE TP12 REP2


title: AV_3

description: 10x Genomics


title: AL RE TP12 REP3


title: AV_1

description: 10x Genomics


title: AL KO TP12 REP3


title: AL RE TP12 REP1


title: Colon tumor organoid, WT, H2O, rep2


title: AL KO TP12 REP2


title: control replicate 5 [WT-66533]

data_processing:
RNA-seq reads were trimmed using trim-galore v0.5.0, and reads mapping to abundant sequences included in the iGenomes UCSC GRCm38 reference (mouse rDNA, mouse mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were aligned to the mouse genome (Ensembl GRCm38 release 94) using star v2.6.0c, and reads in genes were counted with featureCounts (subread v1.6.2) and TEcounts v2.0.3.
Differential gene expression analysis on raw counts of genes or genes plus repeat elements was performed using DESeq2 v1.18.1, and gene set over-representation analysis was performed with clusterprofiler 3.6.0 in R v3.4.1.
Genome_build: UCSC GRCm38
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts

extract_protocol:
Freshly isolated brains were homogenized in nuclear isolation buffer (10 mM Tris-HCl, 50 mM sodium-disulfite, 1% Triton X-100, 10 mM MgCl2, 8.6% sucrose, pH6.5) and centrifuged 5 minutes at 455 g at 4°C. The resulting pellet was washed four times with 900 µl nuclear isolation buffer with centrifugation at 455 g at 4°C. The pelleted nuclei were then resuspended in 1.4 ml of PBS, filtered through a cell strainer and stained with a 1:1000 dilution of the anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated, Millipore MAB377X) for 45 minutes by rotation in the dark at 4°C after adding BSA to a final concentration of 0.1%. After washing in PBS, the stained nuclei were filtered through FACS tubes, sorted on a FACS Aria III (BD) sorter in PBS, pelleted 5 minutes at 590 g at 4°C and the pellet was immediately used for RNA isolation with TRIzol reagent (Invitrogen). Total RNA was isolated according to the manufacturer's instructions.
cDNA libraries for each of the samples were generated from total RNA using the NEB PolyA enrichment Kit following the manufacturer’s instructions.

value: brain

value: Morc2afl/fl Nestin-Cre-

value: adult


title: Colon tumor organoid, WT, H2O, rep1


title: Morc2a∆n replicate 2 [M2KO-66534]

value: Morc2afl/fl Nestin-Cre+


title: Morc2a∆n replicate 1 [M2KO-66532]


title: AL KO TP12 REP1

value: C57BL/6J background

value: 8-12 weeks


title: PV_1

description: 10x Genomics

value: Cardiac valve

value: end-stage heart failure

value: Cardiac valve cell


title: AL WT TP12 REP3

value: WT


title: Mphosph8∆n replicate 2 [M8KO-66530]

value: Mphosph8fl/fl Nestin-Cre+


title: AL WT TP12 REP2


title: Mphosph8∆n replicate 3 [M8KO-66531]


title: AL RE TP8 REP3

value: Bmal1 Liver-reconstituted


title: Mphosph8∆n replicate 1 [M8KO-66529]


title: AL WT TP12 REP1


title: AL RE TP8 REP2


title: control replicate 4 [WT-66528]


title: AV_2

description: 10x Genomics


title: control replicate 2 [WT-66526]

value: Mphosph8fl/fl Nestin-Cre-


title: AL KO TP8 REP2


title: control replicate 1 [WT-66525]


title: AL KO TP8 REP1


title: control replicate 3 [WT-66527]


title: Mphosph8∆n replicate 3 [M8KO-36397]

source_name: Mphosph8∆n_whole brain

extract_protocol:
Brains were isolated and homogenized in TRIzol reagent (Invitrogen). Total RNA was isolated according to the manufacturer's instructions.
cDNA libraries for each of the samples were generated from total RNA using the NEB PolyA enrichment Kit following the manufacturer’s instructions.

tag: strain background

value: whole brain

value: postnatal day 14


title: AL KO TP8 REP3


title: AL WT TP8 REP3


title: Mphosph8∆n replicate 1 [M8KO-36395]


title: AL WT TP8 REP2


title: Mphosph8∆n replicate 2 [M8KO-36396]


title: control replicate 2 [M8KO.HET-36393]

source_name: control_whole brain

value: Mphosph8fl/+ Nestin-Cre+


title: control replicate 3 [M8KO.HET-36394]


title: Lungs, Ad14p1 infected hamster 3

city: Boise

first: Jay

middle: Ryan

last: Radke

state: ID

address: 500 W. Fort St

institute: IVREF

data_processing:
fastq files were imported into CLC Genomics Workbench and reads were trimmed.
mapped to Syrian hamster genome (BCM_Maur_2.0 (GCF_017639785.1)
Differential expression determined between Ad14 and Ad14p1 infected samples with CLC Genomics
Assembly: BCM_Maur_2.0 (GCF_017639785.1)
Supplementary files format and content: tab-delimited text files include TPM and RPKMs

organism: Mesocricetus auratus

source_name: Left lobe of lung

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using KAPA mRNA HyperPrep and indexes were added for Illumina Sequencing, according to the manufacturer’s instructions.

treatment_protocol: Hamsters were infected with 5x10^9 genomes of Ad14 or Ad14p1 via intratracheal installation and infection was allowed to proceed for 5 days

value: Left lobe of lung

value: wild-type

tag: infection


title: Lungs, Ad14p1 infected hamster 4


title: Lungs, Ad14 infected hamster 4


title: AL RE TP4 REP2

extract_protocol:
Total RNA was extracted from liver with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
Library construction was performed according to the Illumina TruSeq Total RNA stranded protocol.  The input quantity for total RNA was 1ug and rRNA was depleted  using ribo-zero rRNA gold removal kit (human/mouse/rat). The rRNA depleted RNA was chemically fragmented for three minutes.  First strand synthesis used random primers and reverse transcriptase to make cDNA.  After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated.  Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip.  The concentrations for the libraries were normalized and then multiplexed together.  The concentration for denaturation was 2nM and the final concentration for clustering was 200pM.  The multiplexed libraries were sequenced by the Genomics High-Throughput Facility at the University of California – Irvine on six lanes using single end 100 cycles chemistry for the HiSeq 4000.   The version of HiSeq control software was HCS 3.4.0.38 with real time analysis software, RTA 2.7.7.


title: Lungs, Ad14p1 infected hamster 2


title: Lungs, Ad14p1 infected hamster 1


title: AL RE TP4 REP1


title: AL WT TP8 REP1


title: ZT18 sample 0 run FGC2190

first: Garret

middle: A.

last: FitzGerald

address: 3400 Civic Center Boulevard

description: 10x Genomics

data_processing:
mm10
Assembly: Tab-separated values files and matrix files

source_name: Whole aorta

extract_protocol:
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

treatment_protocol: Freshly dissected whole aortas from C57BL6 mice were rinsed with ice-cold PRMI1640 to remove blood residue. Aortic cells isolation was performed by incubation of tissue with enzyme digestion buffer (PRMI1640 medium containing DNase, 120U/mL, Liberase, 4U/mL and hyaluronidase, 60U/mL)  at 37 °C for 40 min. Isolated cell suspension was filtered through a 40 um cell filter to remove undigested tissue, and enzymatic digestion was stopped by resuspending the cells in PRMI1640 medium+ 10% FBS. Cells were washed 2X with FACS buffer (DPBS+ FBS 2%+ EDTA 5mM+ HEPES 20mM+ sodium pyruvate 1mM) and resuspended in DMEM/F12 +10% FBS for cell viability test using trypan blue.

value: Whole aorta

value: 6-8 weeks old


title: control replicate 1 [M8KO.HET-36392]

first: Maria


title: Lungs, Ad14 infected hamster 2


title: AL KO TP4 REP3


title: AL RE TP8 REP1


title: Lungs, Ad14 infected hamster 1


title: ZT12 sample 0 run FGC2190

description: 10x Genomics


title: Lungs, Ad14 infected hamster 3


title: AL KO TP4 REP2


title: ZT6 sample 0 run FGC2190

description: 10x Genomics


title: AL KO TP4 REP1


title: Lungs, Uninfected hamster 4

value: untreated


title: AL RE TP4 REP3

value: C57BL/6J background


title: ZT0 sample 0 run FGC2190

description: 10x Genomics


title: AL WT TP4 REP3

value: 8-12 weeks


title: Lungs, Uninfected hamster 2


title: ZT18 sample 0 run FGC2171

description: 10x Genomics


title: Jun, Y3

city: Lanzhou

first: Xingdong

last: Wang

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

data_processing:
Clean reads were obtained from the raw data after quality control processing. The 3' adaptors were removed from the clean reads, and the length was screened to retain the sequence with a base length of 18-26nt.
the remaining sequences are aligned with various RNA database sequences (excluding miRNAs), such as mRNA database, Rfam database (including rRNA, tRNA, snRNA, snoRNA, etc.) and RepBase database, and filtered.
the data obtained is effective data, which can be used for subsequent small RNA data analysis.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: normalized counts

organism: Bos grunniens

source_name: yak milk in June

extract_protocol:
Extraction of exosome RNA from yak and Jersey cattle-yak in June and December with reference to the instructions of Norgen 58000 kit.
The experimental procedure was performed according to the standard steps provided by Illumina, including library preparation and sequencing experiments. Small RNA sequencing libraries were prepared using the TruSeq Small RNA Sample PrepKits (Illumina, San Diego, USA) kit. After library preparation, the constructed libraries were sequenced using Illumina instrument with a single-end 1X50bp read length.

value: milk exosomes

value: June


title: Jun, Y2


title: AL WT TP4 REP2

data_processing:
Alignment to reference assembly mm10 and known splice junctions extracted from the RefSeq database performed using Tuxedo pipeline tophat
Read counting for each gene and normalization to FPKM values  using Tuxedo pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression results FPKM values) of the standard RNAseq analysis are reported in the genes_fpkm.csv file


title: ZT12 sample 0 run FGC2171

description: 10x Genomics


title: Dec, Y3

source_name: yak milk in December

value: December


title: Lungs, Uninfected hamster 1


title: ZT0 sample 0 run FGC2171

description: 10x Genomics


title: Dec, Y2


title: AL WT TP4 REP1

value: WT


title: Jun, Y1


title: ZT6 sample 0 run FGC2171

description: 10x Genomics


title: AL RE TP0 REP2


title: AL RE TP0 REP3


title: Dec, Y1


title: AL RE TP0 REP1


title: AL KO TP0 REP3


title: Rag1 KO, Batch 1, Grey Matter

city: Bonn

first: Ozgun

last: Gokce

address: Venusberg-Campus 1/99

institute: UKB-DZNE

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4
Assembly: mm10
Supplementary files format and content: Tab-separated expression matrices of raw counts for each dataset

source_name: Prefrontal Cortex

extract_protocol:
The mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected; grey matter was isolated from the frontal cortex and white matter form optic tract, medial lemniscus and corpus callosum (attached grey matter and choroid plexus were removed carefully) isolated. We developed and established a microglia isolation protocol that prevents ex-vivo transcription and automatizes the mechanical isolation parts using GentleMacs with the Neural Tissue Dissociation Kit (Papain) (Miltenyi Biotec). We added actinomycin D (Act-D, Sigma, No. A1410) to a final concentration of 45 μM into the dissociation solution and enzyme mix to prevent ex-vivo transcription. To collect enough cells for loading onto the 10x Genomics Chromium chip, two gray matter/ white matter tissue samples were combined into one sample. After tissue dissociation, SYTOX Blue negative cells were sorted into a 2 mL Eppendorf tube with 1 mL RPMI+5% FBS. Sorted cells were centrifuge at 300xg for 10min at 4ºC. Cell pellets were resuspended in 0.04% BSA+PBS catching media at a concentration of 700-900 cells per μl.
Single-cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics) chemistry following the manufacturer’s instructions. Sample processing and library preparation was performed according to manufacturer instructions using AMPure beads (Beckman Coulter).

value: Brain cells

value: Prefrontal Cortex

value: 24 months old


title: Zfp2

city: Durham

first: Jeremy

last: Ratiu

state: North Carolina

address: 328 Jones Bldg, Box 3010

department: Immunology

institute: Duke University

data_processing:
Raw reads were demultiplexed, UMI size distributions were determined and cutoff value for minimum UMI collisions (threshold=4) were determined using migec.
Reads were aligned to the mouse TCRa locus and clonotypes assembled and exported using mixcr.
Unweighted V and J-segment usage was determined using VDJtools command CalcSegmentUsage with the argument -u.
Assembly: mm10
Supplementary files format and content: Processed files are .txt files of assembled clonotypes for each sample. Which can be read into VDJtools for analysis.
Library strategy: TCRa-seq

source_name: Zfp335 cKO DP 2

growth_protocol: Mice were maintained under specific pathogen-free conditions

extract_protocol:
DP thymocytes were isolated by FACS sorting. Cells were lysed in trizol and total RNA isolated using the Zymo Direct-zol RNA Microprep kit.
Adopted from Turchaninova et al., Nat Prot, 2016 & Mamedov et al., Front Immunol, 2013

value: Zfp335 cKO

value: DP Thymocyte


title: MLP1_IP_1

city: Sherbrooke

first: Étienne

last: Fafard-Couture

state: Québec

address: 3201 Jean-Mignault

department: Biochemistry and functional genomics

country: Canada

institute: University of Sherbrooke

description: cDNA library generated with TGIRT

data_processing:
library strategy: Thermostable group II intron reverse transcriptases (TGIRT)-seq
Paired-end reads were trimmed using Trimmomatic v0.36 (Bolger et al., 2014), and FastQC v0.11.5 was used to evaluate read quality before and after trimming, as described previously (Fafard-Couture et al., 2021)
Resulting trimmed reads were then aligned stringently (i.e. allowing no mismatch) to the T. thermophila genome assembly version T_Thermophila_MAC_2021 (Stover et al., 2012) (accessible on the Tetrahymena Genome Database at http://www.ciliate.org/system/downloads/1-upd-Genome-assembly.fasta) using STAR v2.6.1a (Dobin and Gingeras, 2016) (with the parameters described previously (Fafard-Couture et al., 2021) and also the following parameter and value: --outFilterMismatchNmax 0. The index needed to align reads to the genome was produced using STAR v2.6.1a as described previously (Fafard-Couture et al., 2021) using the genome assembly described previously and a custom Tetrahymena thermophila annotation (.gtf) file available at https://zenodo.org/record/6391187/files/t_thermophila_complete_2021.gtf . The annotation file was built by converting .gff files (one for protein-coding genes, one for tRNA genes and one for 5s ribosomal RNA genes; these .gff files are available at https://zenodo.org/record/6391187#.YkH9v-fMK3A) into .gtf files and by concatenating these files into one final (.gtf) annotation file using custom bash scripts. This annotation was corrected for embedded genes using CoCo v0.2.5.p1 (Deschamps-Francoeur et al., 2019) with the correct_annotation mode and default parameters.
Counts were attributed to genes and normalized as transcript per million (TPM) as previously described (Fafard-Couture et al., 2021) using CoCo v0.2.5.p1 with the correct_count mode.
Differential expression analysis was performed using DESeq2 (Love et al., 2014) with default parameters and the count output of CoCo correct_count to compare the WT, MLP1 IP and MLP1 partial KO samples.
Assembly: T_Thermophila_MAC_2021 (from the Tetrahymena Genome Database, Stover et al., 2012)
Supplementary files format and content: Excel (.xlsx) file containing the gene id, name, type, isotype and anticodon (for tRNAs only), function (for protein-coding RNAs only) and abundance in each sample (in TPM) for all the genes detected in the TGIRT-Seq. Also shown is the differential expression (DE) analysis results between MLP1 IP vs WT, and KO vs WT comparisons in the form of the log2(fold change), p-value and FDR-adjusted p-values.

organism: Tetrahymena thermophila

source_name: MLP1 immunoprecipitation from WT cells

growth_protocol: For WT and KO samples, liquid cultures were grown to mid-log phase (0.1 - 1 x 10^6 cells/mL) at 30°C shaking at 90 RPM in SPP media (2% proteose peptone, 0.1% yeast extract, 0.2% glucose, 0.003% Fe-EDTA). Cell pellets were harvested by centrifugation for 3 minutes at 1000g. Following two washes in phosphate-buffered saline (PBS), pellets were stored at -80°C. For WT samples destined for the MLP1-immunoprecipitation, T. thermophila cell pellets from 100 mL cultures were collected at log phase (0.1 - 1 x 106 714 cells/mL) and washed twice with 1X PBS.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes followed by quenching with 0.25 M glycine for 5 minutes at room temperature. Cells were washed twice in 1X PBS before lysis in 2 mL buffer A [30 mM Tris-HCl pH 7.4, 150 mM NaCl, 20 mM KCl, 2 mM MgCl2, 0.1% Triton-X100, 1 mM PMSF, 1X PIC, 100U RNase inhibitor] followed by sonication (25% amplification with 15s intervals for 4 minutes). The lysate was clarified by centrifugation at 20,000 g for 45 minutes at 4°C and treated with 10 U TurboDNase. The lysates were pre-cleared using rabbit isotype immunoglobin G (IgG) control-bound Protein G Dynabeads rotating for 1 hour at 4°C. Immunoprecipitations were performed using an affinity purified rabbit anti-MLP1 antibody (ThermoFisher Scientific – Custom Antibodies) and a rabbit IgG control coupled to Protein G Dynabeads rotating 1 hour at 4°C. The Protein G Dynabeads were washed 5 times using buffer A (without PIC, PMSF and RNase inhibitor). Input and eluted RNA was isolated following reverse cross-linking for 45 minutes at 70°C in buffer B [50 mM Tris-HCl pH 7.4, 5 mM EDTA pH 8.0, 10 mM DTT, 1% SDS], followed by Trizol extraction. Then, total (WT and KO) and MLP1-associated RNAs were size-selected (20-300 nucleotides) on a 7 M urea denaturing 10% polyacrylamide gel. RNA was eluted from the gel by overnight rotation in 150 mM sodium acetate, pH 5.1 in 50% phenol:chloroform:isoamylalcohol at 4°C. The aqueous layer was obtained by centrifugation at 20,000g for 10 minutes at 4°C followed by ethanol precipitation overnight at -80°C. The cell pellet was washed once with 70% ethanol, airdried and resuspended in RNase-free H2O.
TGIRT template-switching was used to prepare cDNA libraries using TGIRT-III reverse transcriptase (InGex) as described previously (Fafard-Couture et al., 2021).

tag: cell type/genotype

value: MLP1 IP from wild type cells

tag: molecule type

value: Size-selected RNA


title: Zfp3

source_name: Zfp335 cKO DP 3

tag: cell type


title: KO_2

description: cDNA library generated with TGIRT

source_name: MLP1 partial knockout cells

value: MLP1 partial knockout cells


title: KO_3

description: cDNA library generated with TGIRT


title: AL KO TP0 REP2

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

institute: University of California, Irvine


title: Lungs, Uninfected hamster 3

value: Left lobe of lung

value: wild-type


title: Zfp4

source_name: Zfp335 cKO DP 4


title: MLP1_IP_2

description: cDNA library generated with TGIRT


title: Rag1 KO, Batch 1, White Matter

source_name: White Matter

value: White Matter


title: Zfp1

source_name: Zfp335 cKO DP 1


title: MLP1_IP_3

description: cDNA library generated with TGIRT


title: WT3

source_name: Zfp335 WT DP 3

value: Zfp335 WT


title: AL KO TP0 REP1

source_name: liver

value: C57BL/6J background

value: 8-12 weeks


title: AL WT TP0 REP 3


title: KO_1

description: cDNA library generated with TGIRT


title: WT2

source_name: Zfp335 WT DP 2


title: WT_3

description: cDNA library generated with TGIRT

source_name: Wild type cells

value: Wild type cells


title: Wild type, Batch 1, White Matter


title: WT_2

description: cDNA library generated with TGIRT


title: WT1

source_name: Zfp335 WT DP 1


title: Wild type, Batch 1, Grey Matter


title: WT_1

description: cDNA library generated with TGIRT


title: AL WT TP0 REP 1


title: Wild type, Batch 2, White Matter


title: Wild type, Batch 2, Grey Matter


title: FASTKD1 transgenic heart A

status: Public on Sep 12 2022

city: Columbia

first: Christopher

last: Baines

state: MO

address: 134 Research Park Dr

institute: University of Missouri

data_processing:
The 3' end of the reads were "trimmed" for Illumina adapters, for ambiguous nucleotides (N's), and (because of NextSeq technology) for artificial poly-G (represented as G{100}) using cutadapt version 1.15 (http://dx.doi.org/10.14806/ej.17.1.200)
Trimmed sequence reads were mapped to GrCM38/mm10 using TopHat2 software
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: Heart

extract_protocol:
RNA was harvested by homogenizing the hearts in Trizol foolowed by chlorofom extraction and then ethanol precipitation
RNA libraries for RNA-seq were prepared using Illumina's TruSeq Library Prep Kit

value: Heart

value: FVB/N

tag: Sex

value: M

value: TG

tag: developmental stage

value: Adult (3-months)


title: Non-transgenic heart D

value: NTG


title: Non-transgenic heart B


title: FASTKD1 transgenic heart E


title: FASTKD1 transgenic heart B


title: AL WT TP0 REP 2

tag: age

value: WT


title: Non-transgenic heart A


title: E13 cKO Y rep 2

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

institute: Institute of Science and Technology Austria (IST Austria)

data_processing:
Raw read files were delivered as unaligned BAM and aligned using STAR with parameters: --outFilterMultimapNmax 1, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical and quantMode GeneCounts. STAR index was prepared using genome build GRCm38/mm10 and Gencode M16 annotation.
Downstream analysis of read counts in genes as produced by STAR was performed in R.
We removed samples with a low percentage of uniquely aligned reads (<60%), low absolute number of uniquely aligned reads (<1M) or due to low correlation with biological replicates. For E12.5 we also removed 2 samples due to high level of read counts in Eed deleted region indicating inefficient recombination. Information on which samples were analysed is given in Supplementary MS-Exel file,
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text of read counts in genes as reported by STAR, xlsx file with alignment details and information on sample exclusion

growth_protocol: For embryonic tissue, pregnant females were sacrificed and E12/E13/E16 embryos were collected. For postnatal tissue, mice were sacrificed by decapitation (P0) or cervical dislocation (P4 onwards). Neocortex area was dissected. For MADM cortical bulk sorting, pools of 2-3 individual cortices were used to generate one sample.

extract_protocol:
After cell sorting of E13/E16 and P0 cells, samples were incubated for 30 min at 37 °C and stored at -80°C until further usage. After thawing samples on ice, their total volume was adjusted to 250 µl using RNase-free H2O (Thermo Fisher Scientific) followed by addition of 750 µl Trizol LS (Thermo Fisher Scientific) and inverting five times. After incubating for 5-min at RT, the entire solution was transferred into a MaXtract tube (Qiagen). 200µl microliters chloroform (Sigma-Aldrich) were added. After three times 5sec vortexing and 2min incubation at RT, samples were centrifuged for 2 min with 12,000 rpm at 18 °C. Supernatant was transferred to a new tube and isopropanol (Sigma-Aldrich) was added in a 1:1 ratio. For better visibility of the RNA pellet, 1 µl GlycoBlue (Thermo Fisher Scientific) was added and entire solution was mixed by vortexing 3 × 5sec. Samples were incubated at -20°C for 3 nights to precipitate RNA. Then, samples were centrifuged for 20min with 14,000 rpm at 4 °C. Supernatant was removed and RNA pellet was washed with 70% ethanol, followed by a 5min centrifugation step (14,000 rpm at 4 °C). RNA pellet was resuspended in 12.5 µl RNase-free H2O. RNA quality was analyzed using Bioanalyzer RNA 6000 Pico kit (Agilent) following the manufacturer’s instructions. RNA samples were pipetted into a 96well plate, sealed with AluminumSeal and stored at −80 °C until further use.
Sequencing libraries were prepared following the Smart-Seq v2 protocol (Picelli et al., 2013) using custom reagents (VBCF GmbH) and libraries from a 96-well plate were pooled, diluted and sequenced on a HiSeq 2500 (Illumina)

treatment_protocol: Single-cell suspensions were prepared by using Papain containing l-cysteine and EDTA (vial 2, Worthington), DNase I (vial 3, Worthington), Ovomucoid protease inhibitor (vial 4, Worthington), EBSS (Thermo Fisher Scientific), DMEM/F12 (Thermo Fisher Scientific), FBS and HS. All vials from Worthington kit were reconstituted according to the manufacturer’s instructions using EBSS. The dissected brain area was directly placed into Papain-DNase solution (20 units/ml papain and 1000 units DNase). Enzymatic digestion was performed for 30 min at 37 °C in a shaking water bath. Next, solution 2 (EBSS containing 0.67 mg Ovomucoid protease inhibitor and 166.7 U/ml DNase I) was added, the whole suspension was thoroughly mixed and centrifuged for 5 min at 1000 rpm at RT. Supernatant was removed and cell pellet was resuspended in solution 2. Trituration with p1000 pipette was performed to mechanically dissolve any remaining tissue parts. DMEM/F12 was added to the cell suspension as a washing solution, followed by a centrifugation step of 5 min with 1500 rpm at RT. For MADM bulk sorting, cells were resuspended in media (DMEM/F12 containing 10% FBS and 10% HS) and kept on ice until sorted. Right before sorting, cell suspension was filtered using a 40 µm cell strainer. FACS was performed on a BD FACS Aria III using 100 nozzle and keeping sample and collection devices (0.8 ml PCR tubes) at 4 °C. Duplet exclusion was performed to ensure sorting of true single cells. E12.5 MADM bulk cells were sorted into 4 µl lysis buffer (0.2% Triton X-100, 2U/µl RNase Inhibitor (Clonetech)), while E13.5, E16.5 and P0 MADM bulk samples were sorted into 50µl RNA extraction buffer 10mM EDTA pH 8.0, 30mM EDTA pH 8.0, 1% SDS, 200µm/µl Proteinase K in nuclease-free water).

tag: eed genotype of the mouse

value: cKO

tag: cellular status of eed

tag: color

value: Y


title: E13 het R rep 2

value: het

value: R


title: P0 cKO R rep 2


title: P0 cKO G rep 4

value: G


title: P0 wt G rep 7

value: wt


title: E13 wt Y rep 2


title: FASTKD1 transgenic heart C


title: Subject 52, Severe Sepsis, Day 2

type: RNA

city: Kalyani

first: SAMANWOY

last: MUKHOPADHYAY

state: West Bengal, INDIA

institute: NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS

description: Replicate 1

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs for each sample was hybridized overnight to Human Genome ST 2.0 array in GeneChip hybridization oven 645. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. Then probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using Affymetrix AGCC software (Expression console).

data_processing: The data were analyzed with Microarray using Affymetrix Transcriptome analysis console (GeneChip Human Gene 2.0 ST Array) with Robust Multiarray Average as the normalization method. The data were transformed to log (base 2) scale.

label: Biotin

source_name: Whole blood

label_protocol: Samples were prepared and processed according to Affymetrix protocols (Affymetrix, Inc). The RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc) respectively. For RNA labeling, 200 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 2.0 ST array.

extract_protocol: PAXgene Blood RNA isolation Kit from Qiagen, Hilden, Germany (cat. no. 762164) was used to isolate the RNA from the whole blood according to manufacturer’s instructions.  Spectroscopy was done in Nanodrop-2000 (ND-2000, from Thermo Fisher Scientific,Waltham, Massachusetts, USA) for checking RNA quality and concentration.   Agilent Bioanalyzer RNA nano kit (Agilent RNA 6000 Nano) was used for checking RNA quality.

value: Whole blood

tag: diagnosis

value: Severe Sepsis

tag: time of sample collection

value: 24 hrs

tag: outcome

value: Survived


title: E13 cKO Y rep 1


title: E16 het G rep 5


title: BT474_RNAP2

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
Reads were aligned to the hg19 genome using bowtie 1.1.1,43 with the parameters –all –best –strata -v 2 -m 1 -S
Peak detection was performed using MACS 1.4.244 using -g hs –keep-dup=auto -w -S
Assembly: hg19
Supplementary files format and content: bed file containing peaks

source_name: BT474 cells

growth_protocol: The nononcogenic human primary mammary epithelium cells HME-1 (Clontech, Mountain View, CA) and the breast cancer cell lines BT474, BT-483, HCC-202, HCC-1806, HCC-1954, HCC-1569, MDA-MB-175, MDA-MB-361, MDA-MB-453, SK-BR-3, UACC-812, ZR-75-30, Br-Ca-Mz-01 (http://www.atcc.org) and SUM-185, SUM-190, and SUM-206 (http://www.cancer.med.umich.edu/breast_cell/production) were grown according to the recommendations of the supplier. Twenty-eight breast carcinoma samples were obtained from patients treated at the Institut Paoli-Calmettes (Marseille, France), and corresponded to surgical specimens in case of early-stage disease and/or diagnostic biopsies in case of advanced stage. Their characteristics are summarized in Table 1 and detailed in Table 2. Twenty cases were ERBB2+, whereas eight were ERBB2−. Each patient gave written informed consent and the study was approved by our institutional review board. The following antibodies were purchased from a commercial source: ERBB2 (Santa Cruz, sc-284), Sp1 (Upstate, 07-645), anti-β-tubulin (Abcam, ab11307), immunoglobulin G (IgG) Rabbit (ab171870).

extract_protocol:
BT474 cells were fixed with 1% formaldehyde for 15 minutes, and the cross-linking reaction was stopped by the addition of 125 mM glycine incubating 5 minutes. Cells were washed and lysed in three Lysis Buffers containing 1x Complete Protease Inhibitors Cocktail (Roche) respectively. 1% Triton X-100 was added to the lysate and all lysates were sonicated at 4°C to generate 100 to 300 base pair chromatin fragments. Pretreated mixture of 3 µg of antibody (rabbit polyclonal anti-ERBB2, C18 sc-284 or rabbit polyclonal anti-PolII, N20 sc-899), and protein G-conjugated magnetic Dynabeads (Dynal Biotech, Invitrogen) was added to the supernatant and incubated on a rotating wheel at 4°C for overnight. The immunocomplexes were then washed with RIPA wash buffer (S1) for six times and once with TE containing 50 mM NaCl. The Ab–protein–DNA complexes were eluted twice in 100 µL elution buffer at 65°C for 15 minutes, briefly vortexed every 2 minutes. The combined eluates as well as the input sample (1% of the amount used in the IP procedure) were treated to reverse the crosslink by incubating overnight at 65°C. After Rnase and proteinase K digestion, the DNA fragments were extracted using phenol-chloroform and purified using a Qiagen PCR purification kit.
Library preparation was performed as per Illumina Genome Analyzer II Sample Prer Kit (FC-102-1001)

tag: cell line

value: BT474 cells

value: Breast cancer cell line

value: ChIP antibody:anti-Pol II (N-20), Santa Cruz Biotechnology sc-899, Rabbit polyclonal


title: Non-transgenic heart E

tag: tissue

value: Heart

value: FVB/N

value: M

tag: genotype


title: Subject 52, Severe Sepsis, Day 1

description: Replicate 1

value: 0 hr


title: P0 wt G rep 6

tag: strain


title: Subject 49, Severe Sepsis, Day 2

description: Replicate 1

value: Died


title: Subject 53, Septic Shock, Day 2

description: Replicate 1

value: Septic Shock


title: Subject 50, Septic Shock, Day 2

description: Replicate 1


title: Subject 53, Septic Shock, Day 1

description: Replicate 1


title: Subject 50, Septic Shock, Day 1

description: Replicate 1


title: Subject 32, Severe Sepsis, Day 1_technical replicate

description:
Technical Replicate 1
sample also analyzed on Illumina array

value: F


title: Subject 32, Severe Sepsis, Day 2_technical replicate


title: Subject 49, Severe Sepsis, Day 1

description: Replicate 1


title: P0 het Y rep 2

value: het

value: Y


title: E13 het G rep 7

value: G


title: P0 wt R rep 2

value: wt

value: R


title: P0 cKO G rep 3

value: cKO


title: E16 het G rep 4


title: P0 cKO R rep 1


title: E13 wt Y rep 1


title: E13 het G rep 8


title: P0 cKO G rep 2


title: P0 wt G rep 5


title: P0 wt G rep 4


title: E16 het G rep 2


title: E13 het G rep 6


title: E16 cKO R rep 2


title: P0 het Y rep 1


title: P0 het G rep 9


title: E16 het G rep 3


title: E13 het G rep 5


title: E16 cKO R rep 1


title: E16 het Y rep 2


title: E16 wt R rep 2


title: P0 wt R rep 1


title: E16 het Y rep 1


title: E16 wt G rep 3


title: P0 het G rep 7


title: E13 het G rep 4


title: E16 wt R rep 1


title: E13 cKO R rep 2


title: P0 wt G rep 3


title: E13 het G rep 3


title: E16 wt G rep 2


title: E13 cKO R rep 1


title: P0 wt G rep 1


title: P0 het G rep 6


title: E13 wt R rep 2


title: E13 het Y rep 2


title: E13 het Y rep 1


title: P0 het G rep 8


title: E16 cKO G rep 4


title: P0 het G rep 5


title: E13 het G rep 2


title: E13 cKO G rep 5


title: E13 wt R rep 1


title: P0 het R rep 2


title: E13 het G rep 1


title: P0 wt G rep 2


title: P0 cKO Y rep 2


title: P0 het R rep 1


title: P0 wt Y rep 2


title: E13 wt G rep 4


title: P0 het G rep 4


title: P0 cKO Y rep 1


title: E13 wt G rep 3


title: E16 het R rep 2


title: E13 cKO G rep 4


title: P0 het G rep 3


title: E16 het R rep 1


title: E16 cKO G rep 3


title: P0 wt Y rep 1


title: E13 cKO G rep 3


title: E16 cKO G rep 2


title: E16 wt G rep 1


title: E13 cKO G rep 2


title: E16 wt Y rep 2


title: P0 het G rep 2


title: E13 wt G rep 2


title: E16 het G rep 1


title: P0 cKO G rep 1


title: E16 wt Y rep 1


title: P0 het G rep 1


title: E13 het R rep 1


title: E13 cKO G rep 1


title: E13 wt G rep 1


title: E12 het Y rep 5


title: E12 cKO R rep 1


title: E12 het G rep 8


title: E12 het G rep 9


title: E12 cKO G rep 3


title: E12 cKO G rep 4


title: E12 het G rep 5


title: E12 cKO G rep 5


title: E16 cKO G rep 1


title: E12 het G rep 7


title: E12 cKO Y rep 1


title: E12 cKO G rep 1


title: E12 wt Y rep 5


title: E12 het G rep 4


title: E12 het G rep 6


title: E12 het Y rep 4


title: E12 wt Y rep 4


title: E12 wt G rep 4


title: E12 wt G rep 3


title: E12 wt Y rep 3


title: E12 het G rep 3


title: E12 wt Y rep 1


title: E12 wt Y rep 2


title: E12 wt R rep 1


title: E12 het Y rep 2


title: E12 wt G rep 2


title: E12 cKO G rep 2


title: E12 wt G rep 5


title: E12 het Y rep 3


title: E12 het G rep 1


title: E12 het G rep 2


title: astro mosaic rep6

data_processing:
Raw read files were delivered as unaligned BAM and aligned using STAR with parameters: --outFilterMultimapNmax 1, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical and quantMode GeneCounts. STAR index was prepared using genome build GRCm38/mm10 and Gencode M16 annotation.
Downstream analysis of read counts in genes as produced by STAR was performed in R.
We removed samples based on position on PCA plot or low correlation between biological replicates. Information on which samples were analysed is given in Supplementary MS-Exel file,
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text of read counts in genes as reported by STAR, xlsx file with alignment details and information on sample exclusion

growth_protocol: For postnatal tissue, mice were sacrificed by cervical dislocation. Neocortex area was dissected. For astrocyte sorting, individual animals were used to generate replicates.

extract_protocol: Sequencing libraries were prepared following the Smart-Seq v2 protocol (Picelli et al., 2013) using custom reagents (VBCF GmbH) and libraries from a 96-well plate were pooled, diluted and sequenced on a HiSeq 2500 (Illumina)

treatment_protocol: Single-cell suspensions were prepared by using Papain containing l-cysteine and EDTA (vial 2, Worthington), DNase I (vial 3, Worthington), Ovomucoid protease inhibitor (vial 4, Worthington), EBSS (Thermo Fisher Scientific), DMEM/F12 (Thermo Fisher Scientific), FBS and HS. All vials from Worthington kit were reconstituted according to the manufacturer’s instructions using EBSS. The dissected brain area was directly placed into Papain-DNase solution (20 units/ml papain and 1000 units DNase). Enzymatic digestion was performed for 30 min at 37 °C in a shaking water bath. Next, solution 2 (EBSS containing 0.67 mg Ovomucoid protease inhibitor and 166.7 U/ml DNase I) was added, the whole suspension was thoroughly mixed and centrifuged for 5 min at 1000 rpm at RT. Supernatant was removed and cell pellet was resuspended in solution 2. Trituration with p1000 pipette was performed to mechanically dissolve any remaining tissue parts. DMEM/F12 was added to the cell suspension as a washing solution, followed by a centrifugation step of 5 min with 1500 rpm at RT. For astrocyte sorting, cells were incubated for 25min at 37°C in 100µl LacZ staining reagent (Abcam, diluted 1:50). Reaction was stopped by adding 100µl DMEM/F12 containing 10% FBS and 10% HS. Samples were centrifuged 5 min with 1500 rpm at RT and resuspended in DMEM/F12 containing 10% FBS and 10% HS. Samples were kept in the dark at room temperature until sorting was started. To ensure specificity of LacZ staining, a negative sample was always processed and sorting gates were adjusted accordingly. Right before sorting, cell suspension was filtered using a 40 µm cell strainer. FACS was performed on a BD FACS Aria III using 100 nozzle and keeping sample and collection devices (0.8 ml PCR tubes) at 4 °C. Duplet exclusion was performed to ensure sorting of true single cells. Cells were sorted into 4 µl lysis buffer (0.2% Triton X-100, 2U/µl RNase Inhibitor (Clonetech)).

tag: eed genotype of mouse

tag: color of cell

value: neuro


title: E12 wt G rep 1


title: E12 het Y rep 1


title: astro mosaic rep4

value: astro


title: neuro mosaic rep3


title: astro mosaic rep5


title: astro wt rep3


title: neuro mosaic rep1


title: astro mosaic rep3


title: astro wt rep2


title: astro wt rep4


title: astro mosaic rep2


title: neuro wt rep2


title: astro mosaic rep1


title: neuro mosaic rep2


title: E12 het R rep 1


title: astro wt rep1


title: RPN tumors_1880T1

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing: none provided by the submitter

source_name: Mouse SCLC tumor

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit. Poly-adenylated RNA was enriched from 1ug of RNA with the NEBNext PolyA mRNA Magnetic Isolation Module, incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module.
Up to 10 ng of cDNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 38bp reads.

value: Mouse tumor tissue

value: Rb1fl/flTrp53fl/flNkx2-1fl/fl  (RPN)


title: RP tumors_5090T1

value: Rb1fl/flTrp53fl/fl (RP)


title: RPN tumors_5690T1


title: RP tumors_2606T1


title: RP tumors_4880T1


title: RP tumors_4423T1


title: neuro wt rep1


title: FiTAc-seq for Input of ES5329L FF_2

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 with -k 1 option
ENCODE Blacklist and repeat sequences were removed
Peak signals were generated by MACS2
Bedgraph was converted to bigwig
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
FiTAc-seq has been previously described, briefly, ten 1mm mice tumor tissue cores were used for ChIP profiling. Samples were treated with xylene to remove paraffin and then rehydrated with 100% ethanol for 10 min, 70% ethanol for 10 min, and water for another 10 min. Hydrated tissues were resuspended in 200ul of 1% SDS lysis buffer with 4ul of 50× EDTA-free protease inhibitor cocktail (PIC) and 1ul of 1 M sodium butyrate, then incubated overnight at 65°C with constant agitation at 1,000 r.p.m. The homogenized tissues were sonicated with Bioruptor for 12 cycles of 30 second on and 30 second off at 4°C. The soluble chromatins were subject to ChIP assay as described above. Library preparation and sequencing were done as described above.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.

value: formalin-fixed, paraffin-embedded (FFPE) tissues

value: Rb1fl/flTrp53fl/flNkx2-1fl/fl (RPN)

tag: antibody


title: FiTAc-seq for Input of ES2531L FF_6


title: astro wt rep5

tag: cell type


title: FiTAc-seq for Input of ES5329L FF_1


title: FiTAc-seq for Input of ES2531L FF_2


title: FiTAc-seq for Input of ES2531L FF_3


title: FiTAc-seq for Input of ES5235L FF_5


title: FiTAc-seq for Input of ES5690L FF_1


title: FiTAc-seq for Input of ES5235L FF_1


title: FiTAc-seq for Input of ES2531L FF_1


title: FiTAc-seq for Input of ES2606L WT_3


title: FiTAc-seq for Input of ES2606L WT_1


title: FiTAc-seq for Input of ES5235L FF_2


title: FiTAc-seq for Input of ES5090L WT_1+2


title: FiTAc-seq for Input of ES5090L WT_5


title: FiTAc-seq for Input of ES5090L WT_6


title: FiTAc-seq for Input of ES2606L WT_2


title: FiTAc-seq for Input of ES5090L WT_7


title: FiTAc-seq for Input of ES2606L WT_4


title: FiTAc-seq for H3K27ac of ES5690L FF_1

value: acetyl-histone H3K27  (Abcam, ab4729)


title: FiTAc-seq for Input of ES5090L WT_3


title: RPN tumors_4329T1


title: FiTAc-seq for H3K27ac of ES2531L FF_6


title: FiTAc-seq for Input of ES5090L WT_4


title: RPN tumors_1879T1


title: FiTAc-seq for H3K27ac of ES5329L FF_1


title: FiTAc-seq for H3K27ac of ES5235L FF_2


title: FiTAc-seq for H3K27ac of ES5235L FF_1


title: FiTAc-seq for H3K27ac of ES2531L FF_2


title: FiTAc-seq for H3K27ac of ES2531L FF_1


title: FiTAc-seq for H3K27ac of ES5235L FF_5


title: FiTAc-seq for H3K27ac of ES2531L FF_3


title: FiTAc-seq for H3K27ac of ES2606L WT_4


title: FiTAc-seq for H3K27ac of ES2606L WT_2


title: FiTAc-seq for H3K27ac of ES2606L WT_3


title: FiTAc-seq for H3K27ac of ES5090L WT_5


title: FiTAc-seq for H3K27ac of ES5329L FF_2