title: ST_DL_End_2

value: Moneymaker


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B8_ad012

status: Public on Sep 29 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACA,PL,ILA

tag: Sex

value: male

tag: age

tag: strain


title: noCre_hemisphere_PrD_4

city: Zurich

first: Claudia

last: Scheckel

state: NY

address: Schmelzbergstrasse 12

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital Zurich

description: GeneCounts.txt

library_source: transcriptomic

data_processing:
Library strategy: Ribo-seq
filtering (min:0-13:20,mean:14-39:20)
clipping of 3'linker sequence (GTGTCAGTCACTTCCAGCGG)
collapsing of exact sequences
removal of 5'linker (14nt)
alignment with STAR
Genome_build: Ensembl GRCm38.p5
Supplementary_files_format_and_content: Txt file containing uniquely and unambigously mapped reads per gene (column 3 of GeneCounts output of STAR)

molecule: total RNA

source_name: hemisphere

growth_protocol: Dissected flash-frozen brain regions or hemispheres from control or prion diseased mice

extract_protocol:
Partial RNase digestion (MNase treatment) and isolation of ribosome protected fragments (GFP immunoprecipitation followed by ultracentrifugation)
CIP treatment, 3'linker ligation, reverse transcription, circularization and PCR ampflication

treatment_protocol: Intraperitoneal inoculation of non-infectious brain homogenate or prions

tag: cre driver

tag: time point

tag: treatment

tag: gender

value: unknown

tag: multiplex index

value: TAGC


title: ST_DL_End_1

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

data_processing:
Clean reads were mapped to the reference genome tomato SL4.0 using SALMON to calculate gene expression level
Genome_build: SL4.0
Supplementary_files_format_and_content: tab-delimited text file with count values for every gene and every sample

organism: Solanum lycopersicum

growth_protocol: Plants were grown under controlled greenhouse conditions in 10 L pots containing substrate (Irish peat, perlite, coconut fiber; 50/40/10; v/v/v), watered with a nutrient solution and supplemented with 16 h of 250 µmol m2 s-1 light. The day and night temperatures were maintained at > 23°C/20°C. Breaker fruits (i.e 63 DAF) were excised and transfered to growth chambers for 7 days under 4 different environments : standard temperature (ST, 23°C days/ 20°C night) + high light (HL, 16h 300µE) ; standard temperature (ST) + dim light (DL, 16h 25µE); high temperature (HT, 32°C day/26°C night) + high light (HL) or high temperature (HT) + dim light (DL).

extract_protocol:
Total RNAs were extracted from the frozen grinded seed tissues using the NucleoSpin® RNA Plant and Fungi kit (Macherey-Nagel, Düren, Germany), according to the manufacturer instructions (protocol 5.1) without the incubation step at 56°C using the following recommended sample type: alfalfa seed for embryo and potato tuber for the endosperm
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 20M reads of 50bp per sample

treatment_protocol: Seeds were manually extracted from the equatorial section of the fruit. The embryo and endosperm were hand-dissected, immediately frozen in liquid nitrogen and stored at -80°C prior to RNA isolation.

tag: genotype

tag: age (daf)

tag: temperature

value: Standard temperature

tag: light

value: Dim light

tag: tissue

value: endosperm


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B8_ad001


title: noCre_hemisphere_PrD_3C

description: GeneCounts.txt

value: AGCT


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B8_ad007


title: ST_HL_Em_4

source_name: Standard temperature_High light_embryo

value: High light

value: embryo


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B8_ad010


title: ST_HL_Em_3


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B8_ad006


title: ST_HL_Em_2


title: DKMR15_I_CD5KO_unstim_rep2

city: Marseille

first: Rudy

last: AUSSEL

address: Parc Scientifique et Technologique de Luminy

institute: CIML

description:
Sample 15
SAMP1_to_SAMP36_featureCounts_table

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
fastq files were aligned to mouse reference genome GRCm38 using STAR aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VST function in the DESeq2 package in R
Differentially expressed genes (³1-fold and £5% false discovery rate) were identified by linear modeling using the DESeq2 package
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files with counts for each Sample from featureCounts

extract_protocol:
Total RNA  was extracted by using RNeasy mini plus kit (QIAGEN)
RNA-Seq libraries were generated from 250 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Purified naïve CD4+ T cells were stimulated with plate-bound anti-CD3 (3 microgram/mL) plus anti-CD28 (1 microgram/mL) for 4 h and 20 h. Total RNA of untreated samples was extracted immediately after purification.

tag: background strain

value: untreated

value: lymph nodes and spleens

tag: cell type

value: CD4+ T cells from lymph nodes and spleens


title: ST_HL_Em_1


title: noCre_hemisphere_PrD_6

description: GeneCounts.txt

value: TACG


title: noCre_hemisphere_PrD_11

description: GeneCounts.txt

value: M


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B8_ad002


title: ST_DL_Em_3

source_name: Standard temperature_Dim light_embryo


title: ST_DL_Em_2


title: noCre_hemisphere_PrD_17

description: GeneCounts.txt

value: GCTA


title: noCre_cortex_PrD_16

description: GeneCounts.txt

source_name: cortex

value: ATCG


title: noCre_cortex_PrD_13

description: GeneCounts.txt


title: ST_DL_Em_1

value: Moneymaker


title: GFAP_terminal_PrD_3

description: GeneCounts.txt

value: GFAP

value: prions


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B7_ad001

value: ACA,PL,ILA

value: male


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B7_ad012


title: HapXAM, rep3

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

country: China

institute: Zhejiang University

description:
Replicate 3 of library HapXAM.
processed data file: WT-BbHapX_Conidiation.xlsx

data_processing:
Illumina Hiseq X Ten used for sequencing.
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with Cufflinks software.
Screening of differentially expressed genes in paired library of WT/∆BbHapX. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build: Beauveria bassiana ARSEF 2860; The reference genome has the accession NO. of ADAH00000000. GenBank assembly accession NO. is GCA_000280675.1.
Supplementary_files_format_and_content: WT-BbHapX_Conidiation.xlsx: Excel file includes Gene ID, mean FPKM values, log2(fold change), FDR-value and gene description for the paired sample.

organism: Beauveria bassiana ARSEF 2860

source_name: DBbHapX

growth_protocol: Conidia suspension (100 ul, 5X10^6 conidia ml-1) of WT and ΔBbHapX of Beauveria bassiana were inoculated on the SDA plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar), and incubated at 25 °C for 3 days.

extract_protocol:
Resultant mycelia of each strain were ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were harvested from the culture plates.

tag: strain/background

value: ARSEF 2860

tag: genotype/variation

value: <delta>BbHapX

value: Mycelia

value: 3 days


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B7_ad007

tag: brain region

tag: Sex


title: noCre_hemisphere_PrD_3B

description: GeneCounts.txt

value: unknown

value: TAGC


title: GFAP_terminal_PrD_2

description: GeneCounts.txt

value: F


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B7_ad010

tag: age

tag: strain


title: HapXAM, rep2

description:
Replicate 2 of library HapXAM.
processed data file: WT-BbHapX_Conidiation.xlsx

tag: time point


title: noCre_hemisphere_PrD_20

description: GeneCounts.txt

tag: cre driver

tag: treatment


title: CEMBA190117_6A_1_CEMBA190117_6A_2_C3_ad002


title: GFAP_terminal_PrD_1

description: GeneCounts.txt

tag: gender

tag: multiplex index


title: HapXAM, rep1

description:
Replicate 1 of library HapXAM.
processed data file: WT-BbHapX_Conidiation.xlsx


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B7_ad006


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B8_ad004


title: GFAP_terminal_ctrl_3

description: GeneCounts.txt

value: non-infectious brain homogenate

value: CGAT


title: WTAM, rep3

description:
Replicate 3 of library WTAM.
processed data file: WT-BbHapX_Conidiation.xlsx

source_name: WT

value: WT


title: GFAP_terminal_ctrl_2

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B7_ad004


title: WTAM, rep2

description:
Replicate 2 of library WTAM.
processed data file: WT-BbHapX_Conidiation.xlsx


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B7_ad002


title: WTAM, rep1

description:
Replicate 1 of library WTAM.
processed data file: WT-BbHapX_Conidiation.xlsx


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B7_ad008


title: GFAP_8wpi_PrD_3

description: GeneCounts.txt

value: M

value: GCTA


title: GFAP_8wpi_PrD_2

description: GeneCounts.txt

value: ATCG


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B6_ad012


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B6_ad001


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B6_ad007


title: GFAP_8wpi_PrD_1

description: GeneCounts.txt

value: GFAP

value: GATC


title: GFAP_8wpi_ctrl_3

description: GeneCounts.txt


title: GFAP_8wpi_ctrl_2

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B6_ad010

value: ACA,PL,ILA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B6_ad006

value: male


title: GFAP_8wpi_ctrl_1

description: GeneCounts.txt

value: CTAG


title: GFAP_4wpi_PrD_3

description: GeneCounts.txt

value: prions

value: TCGA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B6_ad002


title: 3d_4RNA_RPE

city: Irvine

first: Les

last: Kallestad

address: 829 Health Sciences Rd

department: Ophthalmology

institute: University of California Irvine

data_processing:
trimmomatic
piccard tools mark duplicates
macs2
STAR
Rsubread
edgeR
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma Separated Value

source_name: RPE

extract_protocol:
Fresh retina and RPE tissues were harvested from photosensitive Abca4-/-Rdh8-/- mice according to published protocols. Under a dissecting microscope, spring scissors were used to puncture the eye and remove the cornea, iris, and lens. The remaining eyecup had 4 radial incisions made every 90 degrees, resulting in a flat and open eye cup. The retina was then gently removed using curved tweezers and placed in a 1.5 ml microcentrifuge tube containing RNAlater (Qiagen, Hilden, Germany). The RPE-containing eyecup was placed in a 1.5 ml microcentrifuge tube containing RNAprotect (Qiagen). The second eye was processed identically and pooled with the first eye from the same mouse. Total RNA from RPE cells was isolated using the simultaneous RPE cell isolation and RNA stabilization (SRIRS) method. Briefly, the tube containing RNAprotect with the 2 pooled RPE/choroid eyecups was agitated after 10 min and collected at 20 min at RT.  After the second agitation the eyecups (choroid) were removed, with dissociated RPE cells remaining in solution. Retina and RPE samples in RNAlater and RNAprotect, respectively, were stored at 4° C for up to one week.
 Illumina TruSeq Stranded mRNA Library, ATAC-Seq library preparation, Illumina Nextera DNA library prep kit

tag: genotype


title: GFAP_terminal_ctrl_1

description: GeneCounts.txt


title: GFAP_4wpi_PrD_1

description: GeneCounts.txt

value: TACG


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B6_ad008


title: GFAP_4wpi_ctrl_3

description: GeneCounts.txt


title: 3d_1RNA_RPE


title: 3d_2RNA_RPE


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B5_ad001


title: GFAP_4wpi_ctrl_2

description: GeneCounts.txt

value: AGCT


title: PV_8wpi_PrD_1

description: GeneCounts.txt

value: PV


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B5_ad007


title: 1d_4RNA_RPE


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B5_ad010


title: GFAP_4wpi_ctrl_1

description: GeneCounts.txt


title: 1d_3RNA_RPE


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B6_ad004


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B5_ad006


title: 1d_2RNA_RPE


title: GFAP_2wpi_PrD_3

description: GeneCounts.txt

value: F

value: TAGC


title: GFAP_4wpi_PrD_2

description: GeneCounts.txt


title: 3D7_Ctrl3_RNA

city: London

first: Moritz

last: Treeck

address: 1 MIdland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
base calling, quality checking, index sorting and generation of initial *cram files performed using the automatic pipelines of the sequencing service of the Wellcome Trust Sanger Institute. All details of the processing are included in the *cram file header.
concatenation of the *cram files from the two lanes of HiSeq2500 run using samtools (v.1.3.1)
generation of *fastq file from *cram files using Picard-tools SamToFastq (v.2.3)
re-alignment of the reads with from *fastq files against the reference genome in a splice-aware manner using hisat2-2.0.0-beta software and generation of *sam files
sorting and indexing of the resulting *sam files using samtools (v.1.3.1)
counting of the reads aligned to each of the Plasmodium genes using htseq-count command from  HTSeq Python library (v. 0.6.1) with  option '-s reverse'  and gff file matching the reference genome, http://plasmodb.org/common/downloads/release-30/PbergheiANKA/gff/data/
Supplementary_files_format_and_content: *.htseq_count files containing the raw read counts for all the genes in Plasmodium falciparum genome
Raw counts were DESeq2 normalised and then tested against linear models of time nested in line and line nested within time
Genome_build: Genome_build: http://plasmodb.org/common/downloads/release-28/Pfalciparum/fasta/data/
Supplementary_files_format_and_content: Raw counts matrix
Supplementary_files_format_and_content: Normalised counts matrix
Supplementary_files_format_and_content: DESeq results file

organism: Plasmodium falciparum

source_name: P.falciparum infected red blood cells

extract_protocol:
Complete RNA was isolated from the samples using Trizol/chloroform extraction followed by isopropanol precipitation and its concentration and integrity was verified using Agilent Bioanalyzer (RNA 6000 Nano kit) and NanoDrop 1000 spectrophotometer.
First strand cDNA synthesis was performed using the SuperScript III First-Strand Synthesis System and a 1:1 mix of Oligo(dT) and random primers (Invitrogen). The DNA-RNA hybrids were purified using Agencourt RNACleanXP beads (Beckman Coulter) and the second cDNA strand was synthetized using a 10 mM dUTP nucleotide mix, DNA Polymerase I (Invitrogen) and RNAseH (NEB) for 2.5 h at 16°C. The long cDNA fragments were purified and fragmented using a Covaris S220 system (duty cycles = 20, intensity = 5, cycles/burst = 200, time = 30s). The ~200 bp long fragments were end-repaired, dA-tailed and ligated to “PCR-free” adapters (Kozarewa et al., 2009) with index tags using NEBNext according to the manufacturer’s instructions. Excess adapters were removed by two rounds of clean-up with 1 volume of Agencourt AMPure XP beads. Final libraries were eluted in 30 μl water, quality-controlled using Agilent Bioanalyzer (High Sensitivity DNA chip) digested with USER enzyme (NEB) and quantified by qPCR.

tag: line

tag: replicate


title: 3d_3RNA_RPE


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B5_ad004


title: 3D7_Ctrl2_RNA


title: FR-2

type: RNA

city: Berkeley

first: Junren

last: Sia

state: California

address: 156 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

hyb_protocol: 2.5 ug of cDNA were hybridized on Mouse Gene 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C

scan_protocol: GeneChip® Scanner 3000

data_processing: CEL files were read into R and then normalized by RMA using the oligo package.

label: biotin

source_name: Neonatal skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

extract_protocol: RNeasy Micro Kit (Qiagen)


title: GFAP_2wpi_PrD_2

description: GeneCounts.txt


title: 1d_1RNA_RPE


title: FR-3


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B5_ad002


title: GFAP_2wpi_PrD_1

description: GeneCounts.txt

value: CGAT


title: FR-1


title: DMSO-2


title: 6h_3RNA_RPE


title: DMSO-3


title: DMSO-1


title: 3D7_Ctrl1_RNA

value: WT


title: GFAP_2wpi_ctrl_3

description: GeneCounts.txt

value: non-infectious brain homogenate


title: 6h_2RNA_RPE


title: GFAP_2wpi_ctrl_2

description: GeneCounts.txt

value: M

value: GCTA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B4_ad012


title: 3D7A_EXPIII_TP1


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B5_ad008


title: 3D7A_EXPIII_TP2


title: 3D7A_EXPII_TP2


title: NB_5RNA_RPE


title: 6h_1RNA_RPE


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B4_ad001


title: NB_4RNA_RPE


title: 3D7A_EXPII_TP1


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B4_ad007


title: GFAP_2wpi_ctrl_1

description: GeneCounts.txt

value: GFAP

value: ATCG


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B4_ad010

value: ACA,PL,ILA


title: GFAP_24wpi_PrD_3

description: GeneCounts.txt


title: GFAP_24wpi_PrD_2

description: GeneCounts.txt


title: GFAP_24wpi_PrD_1

description: GeneCounts.txt


title: NB_2RNA_RPE


title: NB_3RNA_RPE


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B4_ad006

value: male


title: 3D7A_EXPI_TP2


title: 3D7A_EXPI_TP1


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B4_ad002


title: GFAP_24wpi_ctrl_1

description: GeneCounts.txt


title: GFAP_24wpi_ctrl_3

description: GeneCounts.txt


title: 3d_4RNA_Retina

source_name: Retina


title: Eik2_F12_ko_EXPIII_TP1


title: 3d_3RNA_Retina


title: Eik2_F12_ko_EXPII_TP2


title: GFAP_16wpi_PrD_3

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B3_ad012


title: Eik2_F12_ko_EXPIII_TP2


title: GFAP_16wpi_PrD_2

description: GeneCounts.txt

value: CTAG


title: 3d_2RNA_Retina


title: Eik2_F12_ko_EXPII_TP1


title: Eik2_F12_ko_EXPI_TP2


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B3_ad007


title: GFAP_16wpi_PrD_1

description: GeneCounts.txt

value: prions


title: 1d_4RNA_Retina


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B4_ad004


title: 3d_1RNA_Retina


title: GFAP_24wpi_ctrl_2

description: GeneCounts.txt

value: TCGA


title: NB_1RNA_RPE


title: Eik2_F12_ko_EXPI_TP1


title: 1d_3RNA_Retina


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B4_ad008


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B3_ad010


title: Eik2_C3_ko_EXPIII_TP1


title: GFAP_16wpi_ctrl_2

description: GeneCounts.txt

value: GATC


title: GFAP_16wpi_ctrl_3

description: GeneCounts.txt


title: 1d_1RNA_Retina


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B3_ad006


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B3_ad002


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B3_ad004


title: 1d_2RNA_Retina


title: Eik2_C3_ko_EXPII_TP2


title: GFAP_16wpi_ctrl_1

description: GeneCounts.txt


title: 6h_2RNA_Retina


title: Cx3Cr1_terminal_PrD_1

description: GeneCounts.txt

value: terminal


title: Cx3Cr1_terminal_PrD_2

description: GeneCounts.txt


title: Eik2_C3_ko_EXPI_TP2


title: Eik2_C3_ko_EXPIII_TP2


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B3_ad001


title: 6h_1RNA_Retina


title: Eik2_C3_ko_EXPI_TP1


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B2_ad012


title: NB_6RNA_Retina


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B2_ad001


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B3_ad008


title: Cx3Cr1_terminal_ctrl_1

description: GeneCounts.txt


title: NB_5RNA_Retina


title: Cx3Cr1_8wpi_PrD_3

description: GeneCounts.txt


title: Intact embryos from rep2

city: Moscow

first: Evgeny

middle: E

last: Orlov

address: Miklukho-Maklaya 16/10

department: Department of Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemstry, RAS

data_processing:
fastq files were aligned to Xenopus laevis reference genome Xenla9.1 using TopHat2.
Non-normalized counts were obtained using HTseq software.
Statistics of differential expression (siblings vs intacts) were caluclated via DEseq R package.
Genome_build: Xenla9.1
Supplementary_files_format_and_content: tab-delimited statistics of gene differential expression
Supplementary_files_format_and_content: tab-delimited text files with aligned reads per gene

organism: Xenopus laevis

source_name: whole embryos

growth_protocol: Xenopus laevis embryos were obtained, fertilized in vitro and dejellied in 2% cysteine in 0.1xMMR solution. Intact and treated embryos were grown up to late gastrula stage (12.5 NF).

extract_protocol:
The lysates were subjected to total RNA extraction on NucleoSpin (R) RNA columns (Macherey-Nagel). The obtained RNA samples were tested on integrity on Aligent 4200 TapeStation instrument.
For preparation for sequencing, the samples were processed with TruSeq Stranded mRNA Library Prep Kit (Illumina) according to Manufacturer’s protocol. The resulted libraries were tested by qPCR and Aligent 4200 TapeStation.

treatment_protocol: Xenopus twins were obtained via cell separation at two-blastomere stage. The procedure was adopted from (Kageura, Yamana, 1983; Cooke, Webber, 1985).

value: wild-type

value: untreated


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B2_ad010


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B2_ad007


title: Eik2_C3_ko_EXPII_TP1


title: Cx3Cr1_8wpi_PrD_2

description: GeneCounts.txt

value: AGCT


title: 6h_3RNA_Retina


title: NB_4RNA_Retina


title: Intact embryos from rep1


title: Twinned siblings from rep3

value: treated


title: NB_3RNA_Retina


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B2_ad006


title: Cx3Cr1_8wpi_ctrl_3

description: GeneCounts.txt

value: TACG


title: NB_2RNA_Retina


title: Cx3Cr1_terminal_ctrl_2

description: GeneCounts.txt

value: non-infectious brain homogenate

value: F

value: CGAT


title: Twinned siblings from rep2


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B2_ad002


title: NB_1RNA_Retina


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B12_ad012


title: Cx3Cr1_8wpi_ctrl_1

description: GeneCounts.txt

value: M

value: TAGC


title: Cx3Cr1_8wpi_ctrl_2

description: GeneCounts.txt


title: Cx3Cr1_4wpi_PrD_3

description: GeneCounts.txt

value: ATCG


title: Twinned siblings from rep1


title: B6_3ATAC_RPE


title: B6_2ATAC_RPE


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B12_ad008

value: ACA,PL,ILA

value: male


title: NB_2ATAC_RPE


title: Cx3Cr1_4wpi_PrD_2

description: GeneCounts.txt

value: prions


title: Intact embryos from rep3


title: HNP1 cell line  iCLIP negative control

city: Cleveland

first: Briana

last: Prager

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

description: iCLIP negative control

data_processing:
Low-quality bases and adaptor sequences were trimmed using FLEXBAR (v2.5) to remove reads with PHRED quality score < 30. Reads were demultiplexed using the pyCRAC software’s pyBarcodeFilter (v1.2.2.7), and aligned to hg19 using the bwa alignment tool (bwa aln -n 0.06) (v0.7.12-r1039). Paired-end alignments were pooled as previously described to allow downstream analysis without duplicate sequence names (PMID 28349454). For calling sites with truncations, only forward reads were used. Biological duplicates were pooled for analysis using the CTK pipeline (v1.0.8) for identification of CITS sites and CIMS deletion sites (FDR < 0.05). Annotated sites were called using the annotate_bed_file.pl script from MetaPlotR.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files show coverage of YTHDF2 iCLIP libraries, pooled from biological duplicates. bed files contain YTHDF2 iCLIP sites in annotated regions, pooled from biological duplicates.

organism: Homo sapiens

source_name: Human neuronal progenitor cell

growth_protocol: Cells were cultured as spheres in Neurobasal medium supplemented with B27, L-glutamine, sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF).

extract_protocol:
Crosslinked cell pellets were resuspended in 100 µL of cold 1% SDS + 10mM DTT + 10X Halt protease inhibitor cocktail (Thermo Fisher) solution to dissociate YTHDF2 complexes, and sonicated using a Branson Digital Sonifier Model 450 fitted with 3.125 mm tapered micro tip probe on ice at 10% amplitude (2s ON, 10s OFF cycle, total 20s). The pellet was topped up to 1mL of 1X RIPA buffer (50mM Tris-HCl Ph 7.5, 200mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS), and sonicated again at 10% amplitude (2s ON, 10s OFF cycle, total 20s)
YTHDF2 iCLIP libraries were prepared as previously described (PMID: 27602518) with the following modifications: DNase I (New England Biolabs) and RNase I (Thermo Fisher) was used to digest DNA and RNA in the cell pellet (high RNase I dilution = 1:5, low RNase I dilution = 1:50 or 1:100 depending on cell line). 4 ug of YTHDF2 antibody (Aviva Systems Biology, ARP67917) was used for immunoprecipitation of each 1mg of cell lysate. Equivalent amounts of normal rabbit IgG (Cell Signalling Technology) were used for immunoprecipitation as a negative control. YTHDF2 antibodies or Rabbit IgG were first bound to Pierce Protein A/G Magnetic Beads (Thermo Fisher) in RIPA buffer for 1h at 4 °C. Immunoprecipitation was performed in RIPA buffer at 4 °C overnight. RNA bound to YTHDF2 was ligated to adaptors and purified. SuperScript IV and primers with unique barcodes were used for reverse transcription to tag each replicate. The medium cDNA fraction (80 – 100nt) was extracted by gel purification, and sequenced on the Illumina HiSeq4000 (paired end, 150 bases).

treatment_protocol: Cells were irradiated 150mJ/cm2 at 254nm in a UV crosslinker

tag: cell line

tag: antibody name

value: Normal Rabbit IgG (Cell Signalling Technology #2729)

tag: number of replicates


title: HNP1 cell line YTHDF2 iCLIP rep2

description:
YTHDF2 iCLIP
HNP1_pool.YTHDF2_iCLIP.bedgraph
HNP1_pool.YTHDF2sites.bed

value: YTHDF2 Antibody - C-terminal region (Aviva Systems Biology ARP67917_P050)


title: HNP1 cell line YTHDF2 iCLIP rep1


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B12_ad007


title: Cx3Cr1_4wpi_PrD_1

description: GeneCounts.txt

value: TCGA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B2_ad008


title: 4121 cell line  iCLIP negative control

description: iCLIP negative control

source_name: Patient derived glioblastoma stem cells


title: Cx3Cr1_4wpi_ctrl_3

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B12_ad010


title: NB_1ATAC_RPE


title: 1D_2ATAC_RPE


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B11_ad012


title: 387 cell line  iCLIP negative control

description: iCLIP negative control


title: Cx3Cr1_4wpi_ctrl_2

description: GeneCounts.txt

value: GATC


title: Cx3Cr1_8wpi_PrD_1

description: GeneCounts.txt


title: 1D_1ATAC_RPE


title: 1D_3ATAC_RPE


title: 387 cell line YTHDF2 iCLIP rep2

description:
YTHDF2 iCLIP
387_pool.YTHDF2_iCLIP.bedgraph
387_pool.YTHDF2sites.bed


title: Cx3Cr1_4wpi_ctrl_1

description: GeneCounts.txt

value: CTAG


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B11_ad010


title: Cx3Cr1_2wpi_PrD_3

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B12_ad004


title: 4121 cell line YTHDF2 iCLIP rep2

description:
YTHDF2 iCLIP
4121_pool.YTHDF2_iCLIP.bedgraph
4121_pool.YTHDF2sites.bed


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B12_ad001


title: 6h_3ATAC_RPE


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B12_ad002


title: 6h_2ATAC_RPE


title: 4121 cell line YTHDF2 iCLIP rep1


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B11_ad008


title: 387 cell line YTHDF2 iCLIP rep1


title: Cx3Cr1_2wpi_PrD_1

description: GeneCounts.txt


title: Cx3Cr1_2wpi_PrD_2

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B11_ad007


title: NB_5ATAC_Retina


title: 6h_1ATAC_RPE


title: Cx3Cr1_2wpi_ctrl_3

description: GeneCounts.txt

value: GCTA


title: Nuc-RM95-1

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

description:
RM95
Single nucleus sequencing

data_processing:
Alignment. Cellranger v2.1.1 was used to demultiplex and align sequencing output to a human reference genome. We used a “pre-mRNA” database to align single nuclei to exons as well as introns. Following alignment, nuclei from one patient sample (RM101.1) were removed due to poor quality (low read and gene count).
Extraction of microglial nuclei. Data was processed using the Seurat v3.0.2 package (Butler et al., 2018; Stuart et al., 2019) in R v3.6.1. For each patient, the count matrix was filtered to exclude nuclei with fewer than 100 genes. Counts were normalised for library size, scaled by 10,000 and log-transformed using the natural log. FindVariableFeatures was run using a variance-stabilising transformation (“vst”) to identify the 2,000 most variable genes in each sample.
Data from the 4 patients was then integrated using Seurat’s FindIntegrationAnchors with default parameters, and IntegrateData using 40 principal components (PCs). The dataset consisted of 37,060 nuclei, with a mean read count of 4,305 counts per nucleus, and 1,791 genes per nucleus. Integrated data was scaled (default Seurat parameters). We ran a Principal Components Analysis (PCA), then calculated Uniform Manifold Approximation and Projection (UMAP) embeddings using 40 PCs. We identified clusters using Seurat’s FindNeighbours and FindClusters functions, again using 40 PCs.
Microglial clusters were identified using known markers including P2RY12, CSF1R, CX3CR1, and extracted for downstream analysis.
Pre-processing of microglial nuclei per patient. Microglia from each patient sample were analysed individually as described for all cell types above, with the following modifications: raw counts were filtered to remove genes and counts that were ± 3 standard deviations away from the median value. After normalization, doublets were identified using DoubletFinder v2.0.2 (McGinnis et al., 2019) using 40 PCs, assuming a 7.5% doublet rate. Following removal of doublets, filtering and Seurat normalization were performed again. Data from patients was then integrated and clusters were identified as above. We discarded small clusters than contained markers for microglia as well as other cell types.
Genome_build: hg38 build 95
Supplementary_files_format_and_content: count matrices for each sample

molecule: polyA RNA

source_name: Temporal cortex

extract_protocol:
Brain tissue was sliced on dry ice, then homogenized manually (15 gentle strokes) with 1mL ice-cold  Homogenisation Buffer (HB) with 5µL Rnasin Plus. The homogenate was strained with a 70µm strainer and washed with 1.65mL to a final volume of 2.65mL. 2.65mL of Gradient medium was added (Vf = 5.3mL). To isolate the nuclei, the sample was added to a 4mL 29% cushion using a P1000, and the weight adjusted with HB. The sample was centrifuged in a SW41Ti rotor at 7,700 rpm for 30 minutes at 4°C. The supernatant was removed with a plastic Pasteur pipette, followed by removal of the lower supernatant with P200. Nuclei were resuspended in 200µL of resuspension buffer, transferred to a new tube, washed again with 100-200µL resuspension buffer, and pooled with the previous solution. Clumps were disrupted by pipetting with P200, then filtered through a Falcon tube with 0.35µm strainer. 9µL of sample was mixed with 1µL of propidium iodide (PI) stain, loaded onto a LUNA-FL slide and allowed to settle for 30 seconds. We viewed nuclei with the LUNA-FL Automated cell counter to check numbers and shape.
RNA sequencing was performed using the 10x Genomics Single Cell 3` Reagent Kit (v2) according to manufacturer protocols. cDNA libraries from fresh-frozen nuclei were sequenced on an Illumina HiSeq platform 4000.

value: Female

tag: sample

tag: patient


title: Cx3Cr1_2wpi_ctrl_1

description: GeneCounts.txt


title: Cx3Cr1_2wpi_ctrl_2

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B11_ad006

tag: brain region


title: Nuc-RM77-2

description:
RM77
Single nucleus sequencing

tag: Sex

value: Male


title: Nuc-RM95-2

description:
RM95
Single nucleus sequencing

tag: age


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B11_ad004

tag: strain


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B11_ad002


title: Nuc-RM77-1

description:
RM77
Single nucleus sequencing


title: Cx3Cr1_24wpi_PrD_3

description: GeneCounts.txt

tag: time point


title: 6h_3ATAC_Retina


title: 6h_2ATAC_Retina


title: Nuc-RM102-2

description:
RM102
Single nucleus sequencing


title: Nuc-RM102-1

description:
RM102
Single nucleus sequencing


title: Nuc-RM101-2

description:
RM101
Single nucleus sequencing


title: 6h_1ATAC_Retina


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B10_ad012


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B10_ad010


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B11_ad001


title: Cx3Cr1_24wpi_ctrl_3

description: GeneCounts.txt

tag: cre driver

value: non-infectious brain homogenate

value: AGCT


title: Cx3Cr1_24wpi_PrD_1

description: GeneCounts.txt

tag: treatment

value: CGAT


title: Nuc-RM101-1

description:
RM101
Single nucleus sequencing


title: NB_4ATAC_Retina


title: 3M_3ATAC_Retina


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B10_ad007


title: Cx3Cr1_24wpi_ctrl_2

description: GeneCounts.txt

tag: gender

value: M


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B10_ad006


title: Cx3Cr1_24wpi_ctrl_1

description: GeneCounts.txt

value: F

tag: multiplex index


title: Cx3Cr1_24wpi_PrD_2

description: GeneCounts.txt

value: TAGC


title: Patient3_Paminus

city: Edinburgh

first: Yanick

last: Crow

address: Western General Hospital Campus, Crewe Road

department: MRC Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

data_processing:
Adaptors were trimmed using Cutadapt in paired-end mode discarding reads with less than 20 bases. Resulting paired-end poly(A)+ or poly(A)- sequence reads for each replicate were aligned  to the human genome reference assembly  hg38 using HISAT2 v2.1.0. Read counting was performed using the featureCounts fom subread-1.5.3.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts from featureCounts. ENSEMBL gene level annotation.

source_name: skin

growth_protocol: Primary fibroblasts were maintained at 3%O2, in DMEM supplemented by 10% FBS

extract_protocol:
Transcripts remaining after an initial selection for polyadenylated RNA were ribo-depleted, and both poly(A)+ and poly(A)- fractions then sequenced
Libraries  were  prepared  from 100ng  of  3 total-RNA  samplesusing  the NEBNEXT  Ultra  II Directional RNA Library Prep kit(New England Biolabs#E7760) according to a protocol provided by the manufacturer. Libraries were barcoded using NEBNext Multiplex Oligos for Illumina Set 4(NEB, #E7730S)

tag: cell type

value: Primary Fibroblasts

tag: fraction

value: polyA minus

tag: disease state

value: patient


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B10_ad004

value: ACA,PL,ILA

value: male


title: 3H_3ATAC_Retina

tag: genotype


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B10_ad002


title: 3M_1ATAC_Retina


title: B6_1ATAC_RPE


title: Control3_Paminus

value: control


title: 3H_2ATAC_Retina


title: Patient1_Paminus


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B1_ad012


title: 3H_1ATAC_Retina


title: Cx3Cr1_16wpi_PrD_1

description: GeneCounts.txt

value: prions

value: GATC


title: 1M_3ATAC_Retina


title: Control2_Paminus


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B1_ad007


title: Control1_Paminus


title: Cx3Cr1_16wpi_ctrl_2

description: GeneCounts.txt

value: CTAG


title: 3M_2ATAC_Retina


title: Cx3Cr1_16wpi_ctrl_3

description: GeneCounts.txt

value: GCTA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B1_ad010


title: Cx3Cr1_16wpi_ctrl_1

description: GeneCounts.txt


title: Patient2_Paminus


title: 1M_1ATAC_Retina


title: Cx3Cr1_16wpi_PrD_3

description: GeneCounts.txt


title: Patient2_Paplus

value: polyA plus


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B1_ad006


title: CamKIIa_terminal_PrD_hippocampus_3

description: GeneCounts.txt

source_name: hippocampus

value: CamKIIa

value: terminal


title: Cx3Cr1_16wpi_PrD_2

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B1_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: 1H_2ATAC_Retina


title: CamKIIa_terminal_PrD_hippocampus_2

description: GeneCounts.txt

value: TACG


title: Patient3_Paplus


title: Control3_Paplus


title: 1H_1ATAC_Retina


title: 1M_2ATAC_Retina


title: CamKIIa_terminal_PrD_hippocampus_1

description: GeneCounts.txt

value: M

value: TCGA


title: 1H_3ATAC_Retina


title: Control2_Paplus


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B1_ad008


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A9_ad012


title: CamKIIa_terminal_PrD_cortex_2

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A9_ad001


title: CEMBA190117_6A_1_CEMBA190117_6A_2_B1_ad001


title: A673_TCF4_ChIPSeq

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

data_processing:
For ChIP-seq data, raw reads were aligned to hg19 reference genome using bowtie 2 aligner (version 2.3.4.3) followed by removal of PCR duplicates with Picard MarkDuplicates. ChIP-seq peaks were called using MACS (Model-Based Analysis of ChIP-seq, version 2.1.2) with default parameters.
Reads were extended in the 5’ to 3’ direction by the estimated fragment length and normalized at -log10 of the Poisson p-value of IP file compared to expected background counts by MACS2 bdgcmp command.
BigWig files were generated by bedGraphToBigWig tool (https://genome.ucsc.edu/) and visualized in Integrative Genomics Viewer (http://software.broadinstitute.org/software/igv/). Motif identification and comparison were performed with HOMER using findMotifsGenome program.
For RNAseq data, we aligned 150bp paired-end reads to hg19 (UCSC) genome using HISAT2 (version 2.0.4) and counted reads with htseq-count program (version 0.11.2). Differentially expressed genes were identified by DESeq2 package with adjusted P value < 0.1 and absolute log2 (Fold change) > 0.5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads.
Supplementary_files_format_and_content: narrowPeak files
Supplementary_files_format_and_content: *DEG.txt: Tab-delimited text files

source_name: Ewing sarcoma cell line

growth_protocol: A673 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 mg/ml streptomycin, and kept in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
RNAs were isolated using miRNeasy RNA isolation kit (Qiagen). RNA sequencing libraries were prepared using TruSeq Library Prep Kit (Illumina) according to the manufacturer’s protocol, and were sequenced on HiSeq sequencer (Illumina).
A673 cell lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with following antibody: Anti-KLF15 (Proteintech, 66185-1-Ig), anti-TCF4 (Abcam, ab223073), anti-NKX2-2 (Proteintech, 13013-1-AP). Immunoprecipitated DNA was extracted with the Min-Elute PCR purification kit (Qiagen), followed by DNA library preparation using standard Illumina protocol and sequencing on HiSeq 4000 platform (Illumina).

tag: cell line

value: Ewing sarcoma cell line

tag: chip antibody


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A9_ad006


title: CamKIIa_terminal_ctrl_hippocampus_3

description: GeneCounts.txt

value: non-infectious brain homogenate


title: Patient1_Paplus

value: Primary Fibroblasts


title: NB_2ATAC_Retina


title: NB_3ATAC_Retina


title: NB_1ATAC_Retina


title: Control1_Paplus


title: WT_3ATAC_Retina


title: CamKIIa_terminal_ctrl_hippocampus_2

description: GeneCounts.txt

value: F

value: CGAT


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A9_ad002

value: ACA,PL,ILA

value: male


title: A673_KLF15_ChIPSeq


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A9_ad004


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A9_ad008


title: CamKIIa_terminal_ctrl_cortex_2

description: GeneCounts.txt

value: ATCG


title: WT_2ATAC_Retina


title: CamKIIa_terminal_ctrl_hippocampus_1

description: GeneCounts.txt

value: AGCT


title: CamKIIa_terminal_PrD_cortex_1

description: GeneCounts.txt

value: prions


title: CamKIIa_terminal_ctrl_cortex_1

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A8_ad001


title: CamKIIa_8wpi_PrD_hippocampus_3

description: GeneCounts.txt


title: 1X OS 96h replicate 3

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

data_processing:
Raw sequence reads were cleaned for adapter sequences using cutadapt with default parameters.
The trimmed reads were mapped to the Monodelphis domestica reference genome (MonDom5) using TopHat2, allowing for a base-pair mismatch value of 6.
Prior to calculating raw count values with the Subread package featureCounts, 51reads aligned to mitochondrial genes and ribosomal RNA were removed.
Genome_build: MonDom5
Supplementary_files_format_and_content: Raw Reads, csv

organism: Monodelphis domestica

source_name: kidney cells (RRID:CVCL_0472)

growth_protocol: OK cells (RRID:CVCL_0472) were plated on permeable supports in DMEM/F12 medium (Sigma D6421) with 10% FBS (Atlanta Biologicals) and 5 mM GlutaMAX (Gibco).

extract_protocol:
Cells were collected using Accutase (BD Biosciences) and RNA was extracted using the Ambion PureLink RNA mini kit (ThermoFisher) at 12, 48, and 96 h after transferring cells to OSS and at 0, 48, and 96 h from cells maintained under static conditions. RNA from three experiments was combined to create each sample, and three independent samples were sequenced for each time point.
Library preparation was performed using the TruSEQ Stranded Total RNA Sample Preparation Kit (Illumina) according to manufacturer’s instructions.
Following removal of ribosomal RNA, the remaining RNA was fragmented for 8 min, followed by reverse transcription performed. Double stranded cDNA was subjected to 3’ adenylation and ligation of sequencing adapters. Sequencing was carried out on a NextSeq 500 (Illumina) to generate 75 bp paired-end reads.

treatment_protocol: The following day (t = 0 h), a subset of the filters were transferred to an orbital platform shaker rotating at 146 rpm (OSS) in incubation continued.

value: Opossum Kidney (OK) Cells

tag: stress

value: orbital shear stress

tag: time


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A8_ad007

tag: brain region


title: A673_NKX2-2_ChIPSeq


title: 1X OS 96h replicate 2


title: CamKIIa_8wpi_PrD_hippocampus_2

description: GeneCounts.txt

value: CamKIIa


title: CamKIIa_8wpi_PrD_hippocampus_1

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A8_ad010

tag: Sex


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A8_ad006

tag: age


title: A549 CTC

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

country: South Korea

institute: National Cancer Center

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes Read_Count values, FPKM values, TPM values for each Sample

source_name: A549 lung cancer cells with sphere culture condition

extract_protocol:
RNAs were extracted from the Lung cell lines of Homo Sapiens. Poly(A) mRNA using the Illumina TruSeq RNA Sample Prep Kit, according to the manufacturer’s instructions.
Libraries were prepared using Illumina TruSeq mRNA Sample Prep kit, according to the manufacturer's protocol.

tag: tissue

value: Lung

value: sphere culture condition


title: 1X OS 48h replicate 3


title: 1X OS 96h replicate 1


title: WT_1ATAC_Retina


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A8_ad004

tag: strain


title: CamKIIa_8wpi_PrD_cortex_3

description: GeneCounts.txt

source_name: cortex

tag: cre driver

tag: time point

value: CTAG


title: CamKIIa_8wpi_PrD_cortex_2

description: GeneCounts.txt

tag: treatment

tag: gender

value: GATC


title: A549 2D

source_name: A549 lung cancer cells (2D)

value: 2-dimensionally cultured


title: 1X OS 48h replicate 2

tag: cell type


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A8_ad012


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A8_ad002


title: 1X OS 48h replicate 1


title: CamKIIa_8wpi_PrD_cortex_1

description: GeneCounts.txt

value: M

tag: multiplex index

value: TAGC


title: H460 (3rd)

source_name: H460 lung cancer cells (2D)


title: CamKIIa_8wpi_ctrl_hippocampus_3

description: GeneCounts.txt

value: non-infectious brain homogenate

value: F

value: TCGA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A8_ad008

value: ACA,PL,ILA

value: male


title: 1X OS 12h replicate 3


title: 45 min incubation in egg white filtrate at 45°C or 0 min incubation in egg white filtrate

city: Rennes

first: Florence

last: Baron

address: 65 rue de Saint Brieuc

institute: Agrocampus Ouest

description: Mean of 3 biological replicates and 2 technical replicates of S. Enteritidis exposed to egg-white filtrate  for 45min compared to a reference (0 min of incubation, i.e. S. Enteritidis washed with egg-white filtrate)

hyb_protocol: The microarray, containing 3971 ORFs (representing 94.4% of S. Enteritidis gene composition) (NC_011294.1), was designed using Agilent’s e-array software (https:\\earray.chem.agilent.com\earray\). The custom oligonucleotide microarray was manufactured by Agilent Technologies using an 8x15K format and included each probe in duplicate. Microarray hybridization and data analysis were performed by the Pasteur Institute (Transcriptome and Epigenome Platform PF2, Paris, France). S. Enteritidis exposed to egg-white filtrate for 45 min was compared to a reference (0 min of incubation, i.e. S. Enteritidis washed with egg-white filtrate). For each time point, three arrays were hybridized with three independent biological replicates in duplicate (giving three biological replicates and two technical replicates). Cy3 and Cy5 dye-swap design was included in order to reduce dye specific effects.

scan_protocol: Images of the microarrays were scanned using an Axon 4000a scanner (Axon, Instruments, CA, USA) and intensity data were extracted using the GenepixPro 6.1 software.

data_processing:
Raw microarray data were first normalized using the LOWESS (Locally Weighted Scatter Plot Smoother) regression option in the R software suite, version 2.10.1 (http://www.r-project.org/), to correct for dye-bias within the array, followed by median normalization to normalize across all arrays.
Changes in gene expression upon incubation in egg-white filtrate compared to the control were recorded as log2 fold differences. Statistical significance was estimated with a moderated t-test using the LIMMA package (Smyth 2004) of the R software suite (version 2.10.1). The adjustment of raw p-values was then performed to account for multiple comparisons, using the method of Benjamini and Yekutieli (BY) (Benjamini and Yekutieli, 2001)
Genes that exhibited ≥2.0 fold changes in expression (with respect to the control) and P≤0.05 were considered as differentially regulated.

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: 0 min incubation in egg white filtrate  at 45°C or 45min incubation in egg white filtrate  at 45°C

label_protocol: The resultant total RNA (500 ng of each sample) was reverse transcribed and labeled using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, Life Technologies, Courtaboeuf, France) according to the protocol provided by the manufacturer, except that the hexamer solution was replaced with the pdN6 hexamer solution (Roche Diagnostics, Meylan, France).

extract_protocol: After incubation, cells were centrifuged at 10,000 x g at 4 °C for 5 min, pellets were immediately frozen in liquid nitrogen and stored at -80 °C. After defrosting on ice, cells were disrupted by treatment with TE (Tris-HCl 10 mM pH7, EDTA 1 mM) buffer, containing 20 mg/mL lysozyme, for 30 min at 37 °C followed by mechanical lysis with zirconium beads using a FastPrep-24 instrument (MP Biomedicals, Illkirch, France) with two cycles of 30 s at 30 Hz interspaced with 30 s cooling periods. Total RNA was then isolated by phenol-chloroform extraction. The evaluation of RNA quantity and quality was assessed spectrophotometrically by measuring the ultraviolet absorbance profile (NanoDrop, NanoDrop Technologies, Inc., Rockland, Wilmington, DE, USA) at 230, 260 and 280 nm. For the microarray experiment, additional analysis for RNA integrity was performed using a RNA 6000 Nano LabChip kit (2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA, USA; (Mueller et al., 2000). The RNA samples were then DNase treated using a DNA-free kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions. Quantification of the RNA and any contamination by proteins was again assessed using a NanoDrop ND-1000 and RNA integrity again confirmed using a 2100 Bioanalyzer.

treatment_protocol: After propagation in tryptic soy broth, bacterial suspensions were centrifuged at 5,600 x g and 15 °C for 7 min, and cells were washed three times with egg-white filtrate. The final pellet was resuspended in the original volume of egg-white filtrate and was used to inoculate egg-white filtrate at a final concentration of 7.3 ± 0.2 log10 cfu/mL. Cells were incubated for 45 min at 45 °C.


title: H460 PR (2nd)

source_name: Lung cancer cells survived after paclitaxel treatment

value: survived after paclitaxel treatment


title: CamKIIa_8wpi_ctrl_hippocampus_2

description: GeneCounts.txt

value: GCTA


title: 1X OS 12h replicate 2

value: Opossum Kidney (OK) Cells


title: FGF2, biological rep1

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Command Console (AGCC 3.1, Affymetrix®) and Expression Console (EE 1.1, Affymetrix®). Partek Genomics Suite v6.10 was used to generate the RMA values.

organism: Rattus norvegicus

source_name: Adult hippocampal NSPCs grown in FGF2

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Adult rat hippocampal neural stem and progenitor cells (NSPCs) were grown in N2 medium, DMEM/F-12 (1:1), adding N2 Supplement (1x) (Gibco). NSPCs were expanded as neurospheres with 10 ng/mL of fibroblast growth factor 2 (FGF-2) (PeproTech).

extract_protocol: The isolation, characterization and culturing of adult rat hippocampal neural stem and progenitor cells (NSPCs) used in this study have been described in Palmer, T. D., Takahashi, J. & Gage, F. H. The adult rat hippocampus contains primordial neural stem cells. Mol. Cell. Neurosci. 8, 389–-404 (1997).

treatment_protocol: In the proliferation condition, cells were grown in 10ng/mL of FGF2 for four days in vitro. In the quiescence condition, cells were grown in 10ng/mL of FGF2 and 50ng/mL of bone morphogenetic protein 4 (BMP4) (PeproTech) for four days in vitro.

value: neural stem and progenitor cells

tag: phenotype

value: proliferating


title: FGF2, biological rep2


title: CamKIIa_8wpi_ctrl_hippocampus_1

description: GeneCounts.txt

value: CamKIIa

value: AGCT


title: CamKIIa_8wpi_ctrl_cortex_3

description: GeneCounts.txt


title: H460 DR

source_name: H460 lung cancer cells survived after doxorubicin treatment

value: Lung

value: survived after doxorubicin treatment


title: FGF2+BMP4, biological rep2

source_name: Adult hippocampal NSPCs grown in FGF2+BMP4

value: quiescent


title: FGF2+BMP4, biological rep3


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A7_ad010

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: H460 (2nd)

value: 2-dimensionally cultured


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A7_ad001


title: FGF2, biological rep3


title: CamKIIa_8wpi_ctrl_cortex_2

city: Zurich

first: Claudia

last: Scheckel

address: Schmelzbergstrasse 12

institute: University Hospital Zurich

description: GeneCounts.txt

data_processing:
Library strategy: Ribo-seq
filtering (min:0-13:20,mean:14-39:20)
clipping of 3'linker sequence (GTGTCAGTCACTTCCAGCGG)
collapsing of exact sequences
removal of 5'linker (14nt)
alignment with STAR
Genome_build: Ensembl GRCm38.p5
Supplementary_files_format_and_content: Txt file containing uniquely and unambigously mapped reads per gene (column 3 of GeneCounts output of STAR)

extract_protocol:
Partial RNase digestion (MNase treatment) and isolation of ribosome protected fragments (GFP immunoprecipitation followed by ultracentrifugation)
CIP treatment, 3'linker ligation, reverse transcription, circularization and PCR ampflication

value: CTAG


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A7_ad006


title: 1X OS 12h replicate 1

value: orbital shear stress


title: Static 96h replicate 3

value: Static


title: H460 CR

source_name: H460 lung cancer cells survived after cisplatin treatment

value: survived after cisplatin treatment


title: H460 PR (1st)

source_name: H460 lung cancer cells survived after paclitaxel treatment


title: Static 96h replicate 2


title: FGF2+BMP4, biological rep1


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A7_ad004

value: ACA,PL,ILA


title: CamKIIa_8wpi_ctrl_cortex_1

description: GeneCounts.txt

value: non-infectious brain homogenate

value: M

value: CGAT


title: Static 96h replicate 1

value: Opossum Kidney (OK) Cells


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A7_ad012

value: male


title: H460 (1st)


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A7_ad008


title: Static 48h replicate 3


title: CamKIIa_4wpi_PrD_hippocampus_2

description: GeneCounts.txt

value: prions

value: F


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A6_ad001


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A6_ad010


title: Static 48h replicate 1


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A6_ad008


title: Static 48h replicate 2


title: CamKIIa_4wpi_PrD_cortex_1

description: GeneCounts.txt

value: CamKIIa

value: TCGA


title: CamKIIa_4wpi_PrD_hippocampus_1

description: GeneCounts.txt

value: TACG


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A6_ad007


title: Static 0h replicate 3


title: CamKIIa_4wpi_PrD_cortex_2

description: GeneCounts.txt

value: GATC


title: Static 0h replicate 1


title: CamKIIa_4wpi_PrD_cortex_3

description: GeneCounts.txt

value: AGCT


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A6_ad006


title: H460 CTC

source_name: H460 lung cancer cells with sphere culture condition

value: Lung

value: sphere culture condition


title: CamKIIa_4wpi_ctrl_hippocampus_3

description: GeneCounts.txt

value: TAGC


title: J2_gGII.4_24h

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

description: enteroid harvested 24 hrs after infection with gamma irradiated GII.4

data_processing:
Reads were trimmed with TrimGalore!
Trimmed reads were aligned to GRCh38 using HISAT2
Aligned reads were quantified using featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma separated files containg read counts for each sample

source_name: jejunum

growth_protocol: Two jejunal HIE cultures (J2 and J11) were grown and infected with GII.4[P31] (Sydney 2012 variant: TCH12-580 strain) as previously described (Ettayebi et al., Science, 2016; Zou et al., Methods Mol Biol., 2019).

extract_protocol:
RNA were extracted from 5-day differentiated, mock-inoculated monolayers at 3 hpi, and from GII.4- or gGII.4-inoculated monolayers at 6, 10 and 24 hpi using Qiagen RNeasy mini Kit (Qiagen).
The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent Santa Clara, CA). Paired-end sequencing (100 bp) was performed on an IlluminaHiSeq 2500. Sequencing was performed with ribosomal RNA depletion, 100-bp paired reads (2X100) with 30 million paired end reads for a total of 60 million reads per RNA sample.

treatment_protocol: We performed RNA-Seq analysis on two differentiated jejunal human intestinal enteroid lines (J2 and J11), inoculated with mock, gamma-irradiated GII.4 or infectious GII.4 at high MOI infection (1.8x10^8 genome equivalents/well).

tag: patient id

value: Jejunal (J2) human intestinal enteroid culture

tag: infection

value: 24 hours post infection


title: J11_GII.4_24h

description: enteroid harvested 24 hrs after infection with GII.4

value: Jejunal (J11) human intestinal enteroid culture


title: J2_GII.4_24h


title: Wild type cells grown in GABA-containing media

city: Jülich

first: Angela

last: Kranz

state: NRW

address: Wilhelm-Johnen-Strasse

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

data_processing:
Processing and mapping of the 10,117,524 single-end sequenced reads was performed with the CLC Genomics Workbench (Qiagen Aarhus A/S).
Reads were trimmed by removing adapter sequences using the Trim Sequences tool and filtered for Phred quality scores <30 .
Trimmed reads (10,052,707) were mapped to the C. glutamicum reference sequence.
Automatic detection of TSSs was done with ReadXplorer  using the following parameters: (i) Only single perfect mappings without errors were considered. (ii) Minimum percentage of coverage increase was set to 100% and minimum number of reads starts to 20. Every possible TSSs for cg0565-cg0568 was manually checked.
Genome_build: BX927147
Supplementary_files_format_and_content: Excel file with results of TSS detection

organism: Corynebacterium glutamicum

source_name: wild type cells

growth_protocol: For determination of the transcriptional start sites in the presence of GABA, three independent cultures (5 ml BHI) were inoculated with a single colony from a fresh agar plate and cultivated at 30°C and 170 rpm over day. The cells were washed two times with saline and used to inoculate the second precultures of 20 ml CGXII medium with 2% (w/v) glucose in a 1:100 dilution. These cultures were cultivated at 30°C and 130 rpm over night. For the main cultures, 50 ml CGXII without ammonium and urea but with 62.5 mM GABA were inoculated with the precultures to an OD600 of 1. The main cultures were incubated at 30°C and 130 rpm and harvested after 6h at an OD600 of 2.5-2.7

extract_protocol:
RNA isolation was performed with the RNeasy-Mini-Kit (Qiagen, Hilden, Germany). For the sequencing RNA of all three cultures was mixed in equal amounts.
Further RNA processing and sequencing was performed by vertis Biotechnologie AG (Freising-Weihenstephan, Germany).

tag: genotype

value: wild type

tag: rna population

value: RNA enriched for Cappable-seq RNA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A7_ad002

source_name: C57BL/6J Male P56 Mouse Brain

value: ACA,PL,ILA


title: J11_gGII.4_10h

description: enteroid harvested 10 hrs after infection with gamma irradiated GII.4

tag: time

value: 10 hours post infection


title: CamKIIa_4wpi_PrD_hippocampus_3

description: GeneCounts.txt

source_name: hippocampus

value: prions

value: M

value: CTAG


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A6_ad012

tag: brain region

value: male


title: J11_GII.4_10h

description: enteroid harvested 10 hrs after infection with GII.4


title: CamKIIa_4wpi_ctrl_hippocampus_2

description: GeneCounts.txt

value: CamKIIa

value: non-infectious brain homogenate

value: GCTA


title: A549 in which HERV2 was excised, clone5, batch2

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description:
polyA RNA
sequence batch2
processed data file: HERV-excised2.matrix.csv

data_processing:
Sequenced reads were trimmed with Trimmomatic.
Sequenced reads were mapped to the human reference genome using STAR.
Mapped reads on respective genetic features were counted using featureCounts.
Genome_build: Hg38
Supplementary_files_format_and_content: Expression read count matrix (csv)

source_name: Lung adenocarcinoma (A549) cells

growth_protocol: F-12K medium with 5.0 µg/mL blasticidin

extract_protocol:
QIAamp RNA Blood Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols. Quality checks, library construction, and sequencing were performed by Novogene (https://en.novogene.com).

tag: cell line

tag: genotype/variation

value: HERV2 excised


title: J11_gGII.4_24h


title: J2_gGII.4_10h


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A6_ad002

tag: Sex

tag: age


title: Static 0h replicate 2

source_name: kidney cells (RRID:CVCL_0472)

value: Opossum Kidney (OK) Cells

tag: stress

value: Static


title: CamKIIa_4wpi_ctrl_hippocampus_1

description: GeneCounts.txt

tag: cre driver

tag: time point

value: ATCG


title: J2_GII.4_10h

value: Jejunal (J2) human intestinal enteroid culture


title: A549 in which HERV2 was excised, clone3, batch2


title: CamKIIa_4wpi_ctrl_cortex_2

description: GeneCounts.txt

source_name: cortex

tag: treatment

tag: gender


title: J11_gGII.4_6h

description: enteroid harvested 6 hrs after infection with gamma irradiated GII.4

tag: cell type

value: Jejunal (J11) human intestinal enteroid culture

value: 6 hours post infection


title: CamKIIa_4wpi_ctrl_cortex_3

description: GeneCounts.txt

tag: multiplex index

value: TCGA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A5_ad004

value: ACA,PL,ILA

tag: strain


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A5_ad002


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A4_ad012


title: CamKIIa_4wpi_ctrl_cortex_1

description: GeneCounts.txt

value: F

value: TACG


title: A549 in which HERV2 was excised, clone1, batch2


title: A549 in which HERV2 was excised, clone2, batch2


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A4_ad001


title: J2_GII.4_6h

description: enteroid harvested 6 hrs after infection with GII.4

tag: patient id

tag: infection


title: A549 with non-target control gRNA, clone 5, batch2

value: Non-target control


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A4_ad007


title: A549 with non-target control gRNA, clone 4, batch2


title: CamKIIa_2wpi_PrD_hippocampus_2

description: GeneCounts.txt

value: prions

value: M

value: TAGC


title: CamKIIa_2wpi_PrD_hippocampus_3

description: GeneCounts.txt

value: CamKIIa

value: AGCT


title: CamKIIa_2wpi_PrD_hippocampus_1

description: GeneCounts.txt

value: CGAT


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A4_ad006

value: male


title: J11_media_3h

description: enteroid harvested 3 hrs after innoculation with media

value: media

value: 3 hours post infection


title: A549 with non-target control gRNA, clone 3, batch2


title: J2_media_3h

value: Jejunal (J2) human intestinal enteroid culture


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A4_ad004


title: CamKIIa_2wpi_PrD_cortex_3

description: GeneCounts.txt

value: GATC


title: A549 in which HERV2 was excised, clone4, batch2

value: HERV2 excised


title: A549 with non-target control gRNA, clone 2, batch2


title: J11_GII.4_6h

value: Jejunal (J11) human intestinal enteroid culture

value: 6 hours post infection


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A4_ad002

value: ACA,PL,ILA


title: J2_gGII.4_6h


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A4_ad008


title: CamKIIa_2wpi_PrD_cortex_2

description: GeneCounts.txt


title: CamKIIa_2wpi_PrD_cortex_1

description: GeneCounts.txt

value: GCTA


title: Pool 2

city: New York

first: Alice

middle: V

last: Easton

address: 430 E 29th St

department: Microbiology

institute: NYU Langone

description: multiplexed sample: all sample metadata including sample barcode is available in the file "sample_metadata.xls"  on the series record.

data_processing:
The *celseq2* analysis method for processing CEL-Seq2 single-cell RNAseq data was performed for two lanes of a paired-end 50 Illumina NovaSeq 6000 run. Per-read per-lane FASTQ files were generated using the bcl2fastq2
Conversion software (v2.2.0) to convert per-cycle BCL base call files outputted by the sequencing instrument into the FASTQ format. For generating the feature-cell UMI count matrix from the multiplexed FASTQ files as input, a global configuration in YAML format was first specified  according to the associated list of CEL-Seq barcodes (6bp in length located 7 bases from the start of Read1) as well as applicable transcriptome annotation information for read alignment to the human reference hg19 and/or mouse reference mm10 using the alignment program Bowtie2 (v2.3.4.1), an experiment table containing relevant metadata (SAMPLE_NAME, CELL_BARCODES_INDEX, R1, R2) was defined, and the *celseq2* software's COUNT_MATRIX    automated pipeline (v0.5.3.3) was run in order to successively demultiplex the 6bp CEL-Seq barcodes from the multiplexed data, map reads of ### human and mouse samples to the associated species reference, and finally generate the matrix of UMI counts for annotated  genomic features.
Genome_build: hg19
Supplementary_files_format_and_content: csv with raw read counts

source_name: Peripheral blood

extract_protocol:
PAXgene RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Peripheral blood

tag: infection status

value: mixed sample (non-demultiplexed)


title: CamKIIa_2wpi_ctrl_hippocampus_3

description: GeneCounts.txt

value: non-infectious brain homogenate

value: M

value: TCGA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A3_ad012

tag: brain region


title: Pool 1


title: CamKIIa_2wpi_ctrl_hippocampus_2

description: GeneCounts.txt

value: CamKIIa


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A3_ad007


title: CamKIIa_2wpi_ctrl_hippocampus_1

description: GeneCounts.txt

value: F

value: CTAG


title: A549_Empty_vector3

description:
PolyA RNA
processed data file: KZFP_OE.expression.matrix.csv

data_processing:
Sequenced reads were trimmed with Trimmomatic.
Sequenced reads were mapped to the human reference genome using STAR.
Mapped reads on respective genetic features were counted using featureCounts.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: KZFP_OE.expression.matrix.csv: Comma-separated text file includes expression read count matrix.

growth_protocol: F-12K medium with 1.0 µg/mL puromycin.

extract_protocol:
QIAamp RNA Blood Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols. Quality checks, library construction, and sequencing were performed by Novogene (https://en.novogene.com).

treatment_protocol: Doxycycline (1.0 µg/mL).

tag: cell line

value: Empty vector overexpression


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A3_ad001

value: male


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A3_ad010


title: A549_Empty_vector1

tag: genotype/variation


title: A549_Empty_vector2


title: CamKIIa_2wpi_ctrl_cortex_2

description: GeneCounts.txt


title: A549 with non-target control gRNA, clone 1, batch2

value: Non-target control


title: A549_ZNF846

value: ZNF846 overexpression


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A3_ad004

tag: Sex


title: CamKIIa_2wpi_ctrl_cortex_1

description: GeneCounts.txt

value: TAGC


title: blood_treated_P71

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

institute: University Medical Center Freiburg

hyb_protocol: 3.8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom S human arrays for 16 h at 45 ° C in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: Data processing was performed using BRB-ArrayTools developed by Dr. Richard Simon and the BRB-ArrayTools Development Team.

source_name: whole blood, patient 71, after 14 days treatment

label_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA). In brief, 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: Relapse remitting MS patients were recruited at the St. Josef Hospital Bochum following inclusion and exclusion criteria of ethic approval from the Ruhr-University Bochum.

extract_protocol: Trizol extraction of whole RNA was performed after manufacturer's instructions.

treatment_protocol: Peripheral blood was drawn in PaxGene tubes (BD) at baseline and after 14 days of treatment. Blood tubes were gently inverted multiple times and allowed to rest for two hours to ensure RNA stability. Samples were frozen on -80°C for subsequent RNA purification.

tag: disease status

value: relapse remitting multiple sclerosis (MS)

value: whole blood

value: short chain fatty acid propionate (PA)

value: 14 days

tag: sample type

value: treatment


title: blood_treated_P68

source_name: whole blood, patient 68, after 14 days treatment


title: blood_ctrl_P71

source_name: whole blood, patient 71, prior to treatment

value: baseline

value: control


title: blood_treated_P69

source_name: whole blood, patient 69, after 14 days treatment


title: A549_ZNF808

value: ZNF808 overexpression


title: A549_ZNF8

value: ZNF8 overexpression


title: blood_treated_P67

source_name: whole blood, patient 67, after 14 days treatment


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A3_ad002

value: ACA,PL,ILA

tag: age


title: blood_ctrl_P69

source_name: whole blood, patient 69, prior to treatment

tag: time point


title: CamKIIa_24wpi_PrD_hippocampus_2

description: GeneCounts.txt

tag: cre driver

value: CamKIIa

tag: treatment

value: prions

value: F

value: GCTA


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A3_ad008

value: male


title: CamKIIa_2wpi_ctrl_cortex_3

description: GeneCounts.txt

value: non-infectious brain homogenate

tag: gender

value: AGCT


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A2_ad012


title: blood_ctrl_P67

source_name: whole blood, patient 67, prior to treatment

value: relapse remitting multiple sclerosis (MS)


title: A549_ZNF75D

value: ZNF75D overexpression


title: 428R

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

description: Text file of raw RNA-seq derived counts for genes in the rat genome (ver 6.0) (Ensembl release 89)

data_processing:
The core facility carried out the following conversion and quality control steps on the raw data. Per-cycle base call files were converted to fastq using the bcl2fastq software (v2.17.1.14), library content was checked with the fastq_screen utility (v0.4.2) and fastq file quality was examined using FastQC (0.11.5). After data delivery FastQC (0.11.5) was used to assess quality and trimmotmatic was used to remove contaminating adapter sequences.
Reads were aligned to the rat genome (version 6, Ensembl release 89) and gene counts generated using the R package Rsubread (1.26.1) with the following settings: phredOffset=33, input_format = "gzFASTQ", output_format = 'BAM', output_file = output.files, nthreads=4, nTrim5=12 (for alignment) and isGTFAnnotationFile=TRUE, isPairedEnd=TRUE, strandSpecific=2, nthreads=4 (for counts).
Genes with fewer than 10 reads per million bases we removed before further analysis.
Genome_build: Rattus norvegicus genome version 6, Ensembl 89
Supplementary_files_format_and_content: CSV files generated using edgeR (3.18.1). Gene counts were filtered to remove genes with low counts by identifying the CPM at a count of 10 in line with guidelines published by the edgeR authors (Lun, Chen, Smyth, 2016). The dataset was then normalised using TMM normalisation (Robinson and Oshlack 2010).

source_name: RNA derived from Rattus norvegicus tibialis anterior muscle

extract_protocol:
Total RNA was extracted from muscle using Qiagen RNEasy kit. RNA was quantified using the nanodrop instrument and RNA quality was assesed using the Agilent bioanalyser.
The RNA library was prepared for RNA-sequencin using the Illumina Tru-Seq kit following the manufacturers directions.
RNA-Sequencing was carried out using the Illumina HiSeq 4000 instrument.

treatment_protocol: In vivo electroporation was used to knock out (ko) or knock in (ki) the vitmain D receptor in the tibialis anterior muscle of one hindlimb in rats. VDR-KD groups received VDR shRNA (Table S1) in right leg TAM and scramble shRNA in left leg TAM. VDR-OE groups received pCAGGS-mVDR in right leg TAM, and empty pCAGGS controls in left leg TAM. Immediately following, one HV (900 V/cm, 100 µ-sec pulse), and four LV (90 V/cm, 100 m-sec) pulses were administered across the distal limb via tweezer-electrodes attached to an ECM-830 electroporator (BTX, Holliston, MA). Animals subsequently received a subcutaneous injection of carprofen (50mg/kg), before recovery from anesthesia. RNA-seq was carried out with the contrast of interest being either ko v control limb or ki v control limb.

tag: animal identifier

tag: vdr status

value: IVE VDR knock-out


title: 429R


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A3_ad006

tag: strain


title: CamKIIa_24wpi_PrD_hippocampus_1

description: GeneCounts.txt

value: M

tag: multiplex index

value: GATC


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A2_ad001


title: 428L

value: Sham VDR knock-out


title: A549_ZNF682

value: ZNF682 overexpression


title: CamKIIa_24wpi_PrD_cortex_3

description: GeneCounts.txt

value: TAGC


title: blood_ctrl_P68

source_name: whole blood, patient 68, prior to treatment

tag: tissue

value: whole blood

value: baseline

value: control


title: 427R


title: A549_ZNF669

value: ZNF669 overexpression


title: CamKIIa_24wpi_PrD_cortex_2

description: GeneCounts.txt

value: CamKIIa

value: prions

value: F


title: A549_ZNF611

value: ZNF611 overexpression


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A2_ad007

value: ACA,PL,ILA

value: male


title: CamKIIa_24wpi_PrD_hippocampus_3

description: GeneCounts.txt


title: CamKIIa_24wpi_PrD_cortex_1

description: GeneCounts.txt


title: 427L


title: A549_ZNF610

value: ZNF610 overexpression


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A2_ad010


title: 429L


title: 426R

value: IVE VDR knock-out


title: A549_ZNF605

value: ZNF605 overexpression


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A2_ad004


title: A549_ZNF582

value: ZNF582 overexpression


title: 426L

value: Sham VDR knock-out


title: CamKIIa_24wpi_ctrl_hippocampus_3

description: GeneCounts.txt

value: non-infectious brain homogenate

value: M

value: CTAG


title: CamKIIa_24wpi_ctrl_hippocampus_2

description: GeneCounts.txt

value: CGAT


title: A549_ZNF445

value: ZNF445 overexpression


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A2_ad008


title: 425R


title: CamKIIa_24wpi_ctrl_hippocampus_1

description: GeneCounts.txt

value: ATCG


title: CamKIIa_24wpi_ctrl_cortex_3

description: GeneCounts.txt

value: CamKIIa


title: 425L


title: A549_ZNF440

value: ZNF440 overexpression


title: 424R


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A12_ad012


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A12_ad010


title: CamKIIa_24wpi_ctrl_cortex_2

description: GeneCounts.txt

value: F


title: A549_ZNF419

value: ZNF419 overexpression


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A12_ad008

value: ACA,PL,ILA


title: A549_ZNF44

value: ZNF44 overexpression


title: 424L


title: A549_ZNF33A

value: ZNF33A overexpression


title: A549_ZNF337

value: ZNF337 overexpression


title: 423L


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A12_ad001

value: male


title: A549_ZNF317

value: ZNF317 overexpression


title: CamKIIa_16wpi_PrD_cortex_2

description: GeneCounts.txt

value: prions

value: AGCT


title: A549_ZNF30

value: ZNF30 overexpression


title: 421R

value: IVE VDR knock-in


title: 421L

value: Sham VDR knock-in


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A11_ad012


title: A549_ZNF274

value: ZNF274 overexpression


title: CamKIIa_16wpi_PrD_cortex_1

description: GeneCounts.txt

value: GATC


title: 420R


title: CamKIIa_16wpi_ctrl_hippocampus_3

description: GeneCounts.txt

value: CamKIIa

value: non-infectious brain homogenate

value: GCTA


title: A549_ZNF273

value: ZNF273 overexpression


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A11_ad010

value: ACA,PL,ILA


title: CamKIIa_16wpi_ctrl_hippocampus_2

description: GeneCounts.txt

value: F

value: ATCG


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A12_ad006


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A12_ad007


title: A549_ZNF266

value: ZNF266 overexpression


title: CamKIIa_16wpi_ctrl_hippocampus_1

description: GeneCounts.txt

value: M


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A11_ad007

value: male


title: A549_ZNF26

value: ZNF26 overexpression


title: 419L


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A11_ad006


title: A549_ZNF257

value: ZNF257 overexpression


title: CamKIIa_16wpi_ctrl_cortex_3

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A11_ad004


title: 420L


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A11_ad008


title: CamKIIa_16wpi_ctrl_cortex_2

description: GeneCounts.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A2_ad002


title: A549_ZNF248

value: ZNF248 overexpression


title: 418L


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A11_ad001


title: CamKIIa_16wpi_ctrl_cortex_1

description: GeneCounts.txt

value: TACG


title: A549_ZNF19

value: ZNF19 overexpression


title: 417R

value: IVE VDR knock-in


title: A549_ZNF182

value: ZNF182 overexpression


title: 417L

value: Sham VDR knock-in


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A10_ad012


title: Old HFD 4 RNAseq

first: Donald

middle: K

last: Scott

state: New York

address: 1428 Madison Avenue

department: Diabetes Obesity and Metabolism Institute

institute: MSSM

description:
RNAseq
QC_statistics_to_deliver_old.txt
kallisto_est_count_matrix_old.txt
featureCounts_count_matrix_old.txt
DEseq2_results_HFD_SD_old.txt
HFD1YEAR4

data_processing:
>> RNA-Seq <<
Reads were aligned to the mm10 mouse reference using STAR aligner (v2.4.2a)
Quantification of genes annotated in Gencode vM5 was performed using featureCounts (v1.4.3)
Quantification of transcripts used Kalisto
QC were collected with Picard (v1.83) and RSeQC
Normalization of feature counts and differential expression analysis was done using the DESeq2 package
Genome_build: mm10
Supplementary_files_format_and_content: count and DEseq2 tab-delimited text files
>> Methyl-seq<<
Trim raw reads for quality Package: Trimmomatic Tool: illuminaclip
Map sequencing reads to mm10 Package: BSMAP Tool: BSMAP
Calculate percent methylation at CpGs Package: BSMAP Tool: methratio.py
Split by strand Package: BEDtools Tool: Split
Merge & sort by strand Package: BEDtools Tool: Merge
Remove Duplicates Package: Picard Tool: MarkDuplicates
Merge strands Package: BEDtools Tool: Merge
Filter for properly paired reads Package: Picard Tool: MarkDuplicates
Clip overlapping reads Package: BSMAP Tool: methratio.py
Genome_build: mm10
Supplementary_files_format_and_content: compressed tab-delimited methyl call txt files

source_name: Islets

growth_protocol: C57/BL6J mice

extract_protocol:
Islets were isolated, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA sequencing libraries were prepared using the TruSeqStranded mRNA Library Preparation Kit in accordance with the manufacturer’s instructions (Illumina, Inc., San Diego, CA).

treatment_protocol: Male mice 8 weeks or 52 weeks old were put on diets of 41%  or 13.1 % kcal from fat diet for 1 week

tag: age group

value: Old

tag: diet

value: high fat diet

value: Islets

value: 1 year

tag: genotype

value: wild type


title: 418R


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A10_ad010

tag: brain region

value: ACA,PL,ILA


title: A549_ZNF169

tag: cell line

tag: genotype/variation

value: ZNF169 overexpression


title: 416R


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A10_ad008

tag: Sex


title: 416L


title: 422R


title: A549_ZNF141

value: ZNF141 overexpression


title: Old HFD 1 RNAseq

description:
RNAseq
QC_statistics_to_deliver_old.txt
kallisto_est_count_matrix_old.txt
featureCounts_count_matrix_old.txt
DEseq2_results_HFD_SD_old.txt
HFD1YEAR1

tag: age


title: CamKIIa_16wpi_PrD_hippocampus_1

description: GeneCounts.txt

value: CamKIIa

tag: time point

value: prions

value: M

value: GATC


title: A549_ZNF135

value: ZNF135 overexpression


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A10_ad006

value: male


title: Old SD 4 RNAseq

description:
RNAseq
QC_statistics_to_deliver_old.txt
kallisto_est_count_matrix_old.txt
featureCounts_count_matrix_old.txt
DEseq2_results_HFD_SD_old.txt
SD1YEAR4

value: standard diet


title: Mutant strain, CBS_sre1-_rep2

city: Santiago

first: Melissa

last: Gómez

address: Las Palmeras 3425

department: Ciencias Ecológicas

country: Chile

institute: Universidad de Chile

description:
library strategy: ChIP-Exo
none
CBS_sre1-_rep2.bigwig

data_processing:
RNA-seq: The reads were mapped to protein coding genes obtained from the annotation of the genome assembly of the X. dendrorhous included in the BioPoject ID: PRJNA637109, using the RNA-seq analysis tools from the CLC Genomics Workbench 20 software to determine the count data values. Differentially Expressed Genes (DEGs) were estimated using the DESeq2 and edgeR packages of R/Bioconductor using the criteria |log2 fold change| ≥ 1, p-adjusted < 0.05 (DESeq2) or FDR < 0.05 (edgeR), and DEGs common to both analyses (DESeq2 and edgeR) were selected.
ChIP-exo: The reads obtained from Peconic LLC were mapped to the genome assembly of X. dendrorhous included in the BioPoject ID: PRJNA637109, using the aligner Bowtie2 version 2.3.5.1 with default settings for paired end reads. Reads were filtered to retain reads mapped in proper pairs using SAMtools. For the peak calling step, the MACS2 tool was used: the effective genome size was 20 Mb, the peak detection was based in a q-value of 0.05, and the control used for the treatment of BAM files was an IgG BAM file. The intersect function from the BEDtools tool was used to find overlap peaks among the MACS2 output files from each biological replicate. For comparative purposes, the Epigenetics Analysis tools from the CLC Genomics Workbench 20 software was also used for the peak calling step, using a maximum p-value of 0.01. To ensure the generation of a high confidence dataset, in addition to the standard computational analysis, a manual correction of the associated genes up- and downstream of some peaks was included. Additionally, common peaks between each FLAG-tagged strain and the untagged control strain were discarded.
Genome_build: PRJNA637109
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include the counts for each sample. ChIP-exo: Coverage tracks in bigwig format were generated with the bamCoverage tool and visualized with the IGV software. Peak text files include the common peaks of three biological replicas (3BR) of each strain: CBS.FLAG.SRE1N and CBS.cyp61-.FLAG.SRE1, using the peak caller MACS2 (the text file includes all the common peaks) and the peak caller from the CLC Genomics Workbench 20 software (the text file includes only common peaks associated to DEGs).

organism: Phaffia rhodozyma

source_name: Cell pellet

extract_protocol:
For RNA-seq assays, total RNA was extracted and shipped to Macrogen (Macrogen Inc., Seoul, South Korea) for library preparation and sequencing. For the ChIP-exo assays, formaldehyde-cross linked cell pellets were prepared and shipped to Peconic LLC (State College, PA, USA) for the library preparation and sequencing.
Libraries were prepared using Illumina protocols.

tag: parental strain

value: SRE1 deletion

tag: chip antibody

value: Sigma-Aldrich, catalog F3165, SLBT6752


title: Old SD 3 RNAseq

description:
RNAseq
QC_statistics_to_deliver_old.txt
kallisto_est_count_matrix_old.txt
featureCounts_count_matrix_old.txt
DEseq2_results_HFD_SD_old.txt
SD1YEAR3

value: Old


title: A549 with non-target control gRNA, clone 4

description:
PolyA RNA
processed data file: HERV-excised.matrix.csv

data_processing:
Sequenced reads were trimmed with Trimmomatic.
Sequenced reads were mapped to the human reference genome using STAR.
Mapped reads on respective genetic features were counted using featureCounts.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: HERV-excised.matrix.csv: Comma-separated text file includes expression read count matrix.

growth_protocol: F-12K medium with 5.0 µg/mL blasticidin.

value: Non-target control


title: Mutant strain, CBS_sre1-_rep1

description:
library strategy: ChIP-Exo
none
CBS_sre1-_rep1.bigwig


title: Old HFD 3 RNAseq

description:
RNAseq
QC_statistics_to_deliver_old.txt
kallisto_est_count_matrix_old.txt
featureCounts_count_matrix_old.txt
DEseq2_results_HFD_SD_old.txt
HFD1YEAR3

value: high fat diet

value: Islets


title: Old SD 2 RNAseq

description:
RNAseq
QC_statistics_to_deliver_old.txt
kallisto_est_count_matrix_old.txt
featureCounts_count_matrix_old.txt
DEseq2_results_HFD_SD_old.txt
SD1YEAR2

value: 1 year

value: wild type


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A10_ad002

department: Genomic Analysis Laboratory

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

value: ACA,PL,ILA


title: A549 with non-target control gRNA, clone 3


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A10_ad007


title: Mutant strain, CBS_sre1-_rep3

description:
library strategy: ChIP-Exo
none
CBS_sre1-_rep3.bigwig


title: Old SD 1 RNAseq

description:
RNAseq
QC_statistics_to_deliver_old.txt
kallisto_est_count_matrix_old.txt
featureCounts_count_matrix_old.txt
DEseq2_results_HFD_SD_old.txt
SD1YEAR1


title: A549 with non-target control gRNA, clone 2


title: A549 with non-target control gRNA, clone 5


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A10_ad004


title: Mutant strain, CBS_cyp61-_FLAG-SRE1_rep2

description:
library strategy: ChIP-Exo
FLAG epitope fused to Sre1 transcription factor
CBS_cyp61-_FLAG-SRE1_rep2.bigwig
CBS_cyp61-_FLAG-SRE1_3BR_MACS2_allPeaks.txt
CBS_cyp61-_FLAG-SRE1_3BR_CLC_G_W_20_only_DEGs.txt

value: FLAG.Sre1-tagged strain


title: Mutant strain, CBS_cyp61-_FLAG-SRE1_rep1

description:
library strategy: ChIP-Exo
FLAG epitope fused to Sre1 transcription factor
CBS_cyp61-_FLAG-SRE1_rep1.bigwig
CBS_cyp61-_FLAG-SRE1_3BR_MACS2_allPeaks.txt
CBS_cyp61-_FLAG-SRE1_3BR_CLC_G_W_20_only_DEGs.txt


title: Young HFD 3 RNAseq

description:
RNAseq
QC_statistics_to_deliver_young.txt
kallisto_est_count_matrix_young.txt
featureCounts_count_matrix_young.txt
DEseq2_results_HFD_SD_young.txt
HFD1WK3

value: Young

value: 8-10 weeks


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A12_ad004


title: A549 with non-target control gRNA, clone 1


title: A549 in which HERV1 was excised, clone 5

value: HERV1 excised


title: Mutant strain, CBS_cyp61-_FLAG-SRE1_rep3

description:
library strategy: ChIP-Exo
FLAG epitope fused to Sre1 transcription factor
CBS_cyp61-_FLAG-SRE1_rep3.bigwig
CBS_cyp61-_FLAG-SRE1_3BR_MACS2_allPeaks.txt
CBS_cyp61-_FLAG-SRE1_3BR_CLC_G_W_20_only_DEGs.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A1_ad001


title: Young HFD 2 RNAseq

description:
RNAseq
QC_statistics_to_deliver_young.txt
kallisto_est_count_matrix_young.txt
featureCounts_count_matrix_young.txt
DEseq2_results_HFD_SD_young.txt
HFD1WK2


title: Mutant strain, CBS_FLAG-SRE1N_PolII

description:
library strategy: ChIP-Exo
FLAG epitope fused to Sre1 transcription factor
CBS_FLAG-SRE1N_PolII.bigwig


title: Young HFD 1 RNAseq

description:
RNAseq
QC_statistics_to_deliver_young.txt
kallisto_est_count_matrix_young.txt
featureCounts_count_matrix_young.txt
DEseq2_results_HFD_SD_young.txt
HFD1WK1


title: A549 in which HERV1 was excised, clone 4


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A1_ad004


title: Mutant strain, CBS_FLAG-SRE1N_IgG

description:
library strategy: ChIP-Exo
FLAG epitope fused to Sre1 transcription factor
CBS_FLAG-SRE1N_IgG.bigwig


title: A549 in which HERV1 was excised, clone 3


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A1_ad012


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A1_ad002


title: Young RD 2 RNAseq

description:
RNAseq
QC_statistics_to_deliver_young.txt
kallisto_est_count_matrix_young.txt
featureCounts_count_matrix_young.txt
DEseq2_results_HFD_SD_young.txt
SD1WK2


title: Mutant strain, CBS_FLAG-SRE1N_rep2

description:
library strategy: ChIP-Exo
FLAG epitope fused to Sre1 transcription factor
CBS_FLAG-SRE1N_rep2.bigwig
CBS_FLAG-SRE1N_3BR_MACS2_allPeaks.txt
CBS_FLAG-SRE1N_3BR_CLC_G_W_20_only_DEGs.txt


title: Mutant strain, CBS_FLAG-SRE1N_rep3

description:
library strategy: ChIP-Exo
FLAG epitope fused to Sre1 transcription factor
CBS_FLAG-SRE1N_rep3.bigwig
CBS_FLAG-SRE1N_3BR_MACS2_allPeaks.txt
CBS_FLAG-SRE1N_3BR_CLC_G_W_20_only_DEGs.txt


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A1_ad008


title: 422L

description: Text file of raw RNA-seq derived counts for genes in the rat genome (ver 6.0) (Ensembl release 89)

value: Sham VDR knock-in


title: Mutant strain, CBS_FLAG-SRE1N_rep1

description:
library strategy: ChIP-Exo
FLAG epitope fused to Sre1 transcription factor
CBS_FLAG-SRE1N_rep1.bigwig
CBS_FLAG-SRE1N_3BR_MACS2_allPeaks.txt
CBS_FLAG-SRE1N_3BR_CLC_G_W_20_only_DEGs.txt


title: Young RD 1 RNAseq

description:
RNAseq
QC_statistics_to_deliver_young.txt
kallisto_est_count_matrix_young.txt
featureCounts_count_matrix_young.txt
DEseq2_results_HFD_SD_young.txt
SD1WK1


title: A549 in which HERV1 was excised, clone 1

description:
PolyA RNA
processed data file: HERV-excised.matrix.csv


title: CEMBA190117_6A_1_CEMBA190117_6A_2_A1_ad007