title: Def_ATACseq_rep2

description: Genome-wide library of transposed fragments

data_processing:
Library Strategy: ATAC-seq
Mapping : bowtie -m 2 --maxIns 350, mm9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig : un-normalised coverage of filtered fragments (reconstructed, duplicate-filtered fragments : see above),  density of alignments in a moving 300 bp window with an increment of 30  bp

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).


title: Def_ATACseq_rep3

status: Public on May 06 2021

type: SRA

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Fetal Liver

growth_protocol: Primary Primitive Erythroblasts: Primary primitive erythroblasts were derived from yolk sacs at embryonic day 10.5 (E10.5). A total of ~1x106 erythroblasts were obtained from each single embryo. Definitive Erythroid Cells: Definitive erythroid cells were obtained from a well-established fetal liver culture system (Drissen et al. 2005). Fetal livers were dissected from E12.5 mouse embryos, and the dissociated cell suspension was expanded for 5–7 d in Stempro (Invitrogen) supplemented with Epo (1 U/ml), SCF (50 ng/ml) and dexamethasone (1 μM). After expansion of the cultures, mature red blood cells were removed by negative selection for Ter119 using anti-Ter119 magnetic beads (Miltenyi Biotec), to obtain a population of erythroid precursors, which was then purified by CD44 positive cell sorting before being placed into expansion media to recover for 6 hours.  mES Cell line: ES cell lines were maintained in BHK-21 GMEM (Invitrogen) supplemented with 10% foetal calf serum (Gibco), 100 U/ml Penicillin/Streptomycin (Invitrogen), 2mM Glutamine (Invitrogen), 1mM Sodium Pyruvate (Invitrogen), 1x MEM Non-essential amino acids (Invitrogen). 0.1mM 2-mercaptoethanol (Invitrogen) 1000U/ml LIF (ESGRO) on 0.1% gelatin coated plates. Cells were passaged every 2 days.

treatment_protocol: Definitive Erythroid Cells: Cultures were switched to medium containing a high Epo concentration (5 U/ml) to induce differentiation into mature erythroid cells and harvested after 24 hours. mES Cell line: Cells were resuspended by treatment with 0.05% trypsin/EDTA (Invitrogen) for 2 minutes at 37ºC, before washing with growth media and fixation.

tag: cell type

value: Cultured fetal liver cells

tag: strain


title: Prim_ATACseq_rep2

source_name: Primitive Erythroid

value: Erythrocytes from E10.5 mice


title: FL_Enhancer_capture_rep3

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
Distal_Element_Interacting.txt

data_processing:
Library strategy: Capture-C
Library Strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 1 maintaining strict read order, mm9
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: mm9
Supplementary_files_format_and_content: Promoter_Interacting.txt: Custom combined data format (chrom \t start \t stop \t sample_gene \t sample_gene \t etc...)
Supplementary_files_format_and_content: Distal_Element_Interacting.txt: Custom combined data format (chrom \t start \t stop \t sample_gene \t sample_gene \t etc...)

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
1-5ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

tag: genes analysed


title: Prim_ATACseq_rep3


title: Prim_ATACseq_rep1


title: 1013_C

city: Durham

first: Rachel

middle: A

last: Johnston

state: NC

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
Reads were trimmed with Trim Galore (Krueger, 2015) to remove adapter sequence and base pairs with Phred score < 20 from the ends of reads, keeping only reads ≥ 20 basepairs long after trimming.
Trimmed reads were mapped to the dog genome (canfam3.1) using two-pass mapping with STAR (Dobin et al., 2013). Only uniquely mapped reads were retained.
Gene expression was quantified using HT-Seq (Anders et al., 2014) with the “union” mode using the Canis_familiaris.CanFam3.1.94.gtf file from Ensembl.
Genome_build: canfam3.1
Supplementary_files_format_and_content: allwolfcounts.txt is a tab delimited text file showing the output from HTseq, which provides the number of reads mapping to each gene for each RNA-Seq sample/library.

molecule: polyA RNA

organism: Canis lupus

source_name: primary epidermal keratinocytes from ear punch

growth_protocol: Primary wolf epithelial keratinocytes were grown with 3T3 feeder cells in FAD medium: 1:1 DMEM:F12 base media [ThermoFisher Scientific] + 5% BCS + 0.4 ug/ml hydrocortisone + 10 ng/ml epidermal growth factor (EGF) + 1% Penicillin-Streptomycin [ThermoFisher Scientific] + 10 uM ROCK inhibitor Y-27632 [Cayman Chemical, Ann Arbor, MI, USA].

extract_protocol:
Trizol Plus RNA Purification Kit with DNAse treatment (RNAse-Free DNAse Set, Ambion) and column cleanup (PureLink RNA Mini Kit, Invitrogen)
Half-reactions of the TruSeq RNA Sample Preparation Kit (Illumina)

treatment_protocol: polyI:C experiment: Keratinocytes were plated at 1.5E4 cells per well of a 12-well plate with 3T3 feeder cells in FAD medium. When cells were at ca. 30% confluence, they were switched to a low-serum medium (FAD + 0.5% BCS) without RI and incubated for 24 hours. Cells were then treated with 1 ug/ml polyI:C (Sigma-Aldrich) or vehicle control (sterile, endotoxin-free water) for 24 hours. CDV experiment: Keratinocytes were plated in duplicate on 24-well plates at 8E4 cells per well in FAD + 5% BCS + RI, without feeder cells. After a 24 hour incubation, the medium was changed to FAD + 0.5% BCS. After an additional 24 hours, cells were infected with CDV at an MOI of 100 TCID50/ml (or were provided medium in same volume, as control). Cells were collected 5 days post-infection.

tag: cbd103 genotype

value: yy

tag: estimated age

value: pup

tag: cell culture treatment

value: null control

tag: cell culture experiment

value: CDV experiment


title: 1013_CDV

value: canine distemper virus


title: Def_ATACseq_rep1


title: 16366_C

value: yB

value: 5+ years


title: 16361_CDV

value: 3-4 years


title: 16366_CDV


title: 16371_CDV


title: 16370_C

value: ~8 years


title: 16371_C


title: 16361_C


title: 16370_CDV


title: 1005F_CDV


title: Def_ATACseq_rep4


title: 15071_Het_PIC2

source_name: immortalized epidermal keratinocytes from ear punch

value: polyI:C experiment_immortalized


title: 15071_Het_C2


title: 1005F_C


title: 15071_Imm_PIC1


title: 15071_Imm_C2


title: 15071_Het_C1


title: 15071_Het_PIC1


title: 15071_Imm_C1


title: 1013MC

value: polyI:C experiment


title: 16361P


title: 993MP


title: 16370P


title: 1013MP


title: 16370C


title: 16361C


title: 993MC


title: ISG-KO A549-ACE2 cells IFN treated and sorted for SARS-CoV-2 infection

city: PARIS 15

first: Artem

last: Baidaliuk

address: 25-28 rue Dr. Roux

country: France

institute: Institut Pasteur

description: ISG CRISPR/Cas9 knockout sgRNA region

data_processing:
library strategy: PCR amplicon sequencing
Reads were demultiplexed using bcl2fastq Conversion Software v2.20 (Illumina) and fastx_toolkit v0.0.13.
Sequencing adapters were removed using cutadapt v1.9.1.
The reference library was built using bowtie2 v2.2.9.
Read mapping was performed with bowtie2 allowing 1 seed mismatch in --local mode and samtools v1.9.
Genome_build: Reference sequences sgRNA_multifasta_map_ref.fasta
Supplementary_files_format_and_content: Read count table provided in read_count_table.txt is composed of the following columns sgRNA, gene, Lib_isg_ctrl (showing a total number of reads mapping to sgRNA sequence in the non-infected sample), Lib_isg_sort (showing a total number of reads mapping to sgRNA sequence in the infected sample).

organism: Homo sapiens

source_name: lung epithelial cells A549-ACE2

growth_protocol: A549-ACE2 (ATCC #CCL-185) were grown in DMEM (Gibco #31966021) supplemented with 10% FBS (Gibco #A3160801), and penicillin/streptomycin (100 U/mL and 100 µg/mL, Gibco # 15140122). Blasticidin (10 µg/mL, Sigma-Aldrich #SBR00022-10ML) was added for selection of A549-ACE2. All cells were maintained at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Sorted and control (non-infected, not IFN-treated) cells were centrifugated (20 min, 2,000g) and resuspended in lysis buffer (NaCI 300 mM, SDS 0.1%, EDTA 10 mM, EGTA 20 mM, Tris 10 mM) supplemented with 1% Proteinase K (Qiagen #19133) and 1% RNAse A/T1 (ThermoFisher #EN0551) and incubated overnight at 65°C. Two consecutive phenol-chloroform (Sigma #P3803-100ML) extractions were performed and DNA was recovered by ethanol precipitation.
Nested PCR was performed using the Herculase II Fusion DNA Polymerase (Agilent, #600679). PCR1 products were purified using QIAquick PCR Purification kit (Qiagen #28104). PCR2 products were purified using Agencourt AMPure XP Beads (Beckman Coulter Life Sciences #A63880). DNA concentration was determined using Qubit dsDNA HS Assay Kit (Thermo Fisher #Q32854) and adjusted to 2 nM prior to sequencing.

treatment_protocol: To generate ISG KO library cells, 36x10^6 A549-ACE2 cells were seeded in 6 well plates (10^6 cells per well) 24h before transduction. For each well, 100 µL of concentrated lentivector was diluted in 500 µL of serum-free DMEM, supplemented with 10 µg/mL of DEAE dextran (Sigma #D9885). After 48h, transduced cells were selected by puromycin treatment for 20 days (1 µg/mL ; Sigma #P8833). 4x10^7 A549-ACE2 cells were treated with IFN (200U/mL). 16h later, cells were infected at a MOI of 1 in serum-free media complemented with TPCK-trypsin and IFN alpha (200 U/mL). After 90 min, the viral inoculum was removed and cells were maintained in DMEM containing 5% FBS and IFN (200 U/mL). After 24h, cells were harvested and fixed for 15 min in Formalin 1%. Fixed cells were washed in cold FACS buffer containing PBS, 2% Bovine Serum Albumin (Sigma-Aldrich #A2153-100G), 2 mM EDTA (Invitrogen #15575-038) and 0.1% Saponin (Sigma-Aldrich #S7900-100G). Cells were incubated for 30 min at 4°C under rotation with primary antibody diluted in FACS buffer. Incubation with the secondary antibody was performed during 30 min at 4°C under rotation. Stained cells were resuspended in cold sorting buffer containing PBS, 2% FBS, 25 mM Hepes (Sigma-Aldrich #H0887-100ML) and 5 mM EDTA. Infected cells were sorted on a BD FACS Aria Fusion.

tag: cell line

value: lung epithelial cells

tag: facs

value: sorted

tag: infection

value: infected


title: Control ISG-KO A549-ACE2 cells (not infected with SARS-CoV-2)

description: ISG CRISPR/Cas9 knockout sgRNA region

value: control

value: non-infected


title: 14387P


title: VCAF_Ctrl_3

city: Lund

first: Chris

middle: Denis

last: Madsen

address: Scheelevägen 2

department: Laboratory Medicine

country: Sweden

institute: Lund University

data_processing:
Fastq files were generated with bcl2fastq v.1.8.4 Illumina software. Pseudoalignment and transcript quantification was performed using Kallisto software v0.44.0) against human protein coding genes using GENCODE release 32 (GRCh38.p13) as index. Gene level read counts were generated using the tximport R-package. Differential gene expression analysis was performed using DESeq2 R-package.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited (.tsv) files from kallisto output with sample-specific estimated transcript counts and TPM values. Supplementary file: Tab delimited file with gene-level normalized counts from DESeq2

molecule: total RNA

growth_protocol: Cells were maintained in DMEM high glucose with 10% FBS, 1% Pen-strep, and insulin-tranferrin-selenium supplement, at 37℃, 5% CO2.

extract_protocol:
Cells were harvested 72 hours post-transfection using RNeasy kit (Qiagen) and treated with DNase I.
Library was prepared according to TruSeq® Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E) Modification of “Enrich DNA Fragment” step: from 15 to 13 PCR cycles.

treatment_protocol: Cells were transfected using Dharmafect 4 reagent for siControl (Ctr) and siCCM3 (PDCD10).

value: Human vulval carcinoma-associated fibroblasts, hTERT-immortalised

tag: sirna

value: siControl

tag: genotype/variation


title: 14387C

value: yy


title: siRNA_2

city: Hefei

first: Zubing

last: Cao

state: Anhui

address: 130 changjiang west road

department: Animal Science

country: China

institute: Anhui Agricultural University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: Version GRCh38.p10
Supplementary_files_format_and_content: FPKM

organism: Sus scrofa

source_name: porcine blastocyst_CARM1-siRNA

extract_protocol:
non-injected and CARM1-siRNA injected embryos
The libraries were prepared according to the transcriptome differential expression analysis of the control group and the experimrntal group

value: embryo

value: porcine blastocyst

value: CARM1-siRNA injected


title: siRNA_1


title: VCAF_Ctrl_2


title: 1005FP

value: yB

value: pup


title: 1005FC

value: null control


title: 15071_Imm_PIC2

value: 3-4 years


title: VCAF_Ctrl_1


title: Control_3

source_name: porcine blastocyst_control

value: non-injected control


title: 992MP

value: 6.6 years

value: polyI:C experiment


title: VCAF_CCM_2


title: 992MC


title: 16240P

value: 10+ years


title: VCAF_CCM_3


title: Control_2


title: 16240C


title: 16236P


title: 16236C


title: 16371C


title: siRNA_3


title: 821P

value: 6.7 years


title: Control_1


title: 821C


title: Fstl1_cKO_heart_PCM1_769108_score1

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: left ventricle cardiomyocyte nuclei knockout stressed heart

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq_counts_mouse neonatal_volume_overload.xlsx (Excel file with normalized (DESeq2) count data per gene).

molecule: nuclear RNA

source_name: cardiac tissue left ventricle

growth_protocol: The left ventricle was isolated from 12 day old neonatal mice

extract_protocol:
cardiac nuclei were isolated, stained with PCM1 and sorted by FACS, RNA was isolated with the Rneasy plus micro kit (Quiagen)
Ovation RNA-seq V2, UltraLow V2 kit
RNA-seq, single-read, 50 bp

treatment_protocol: tissue was snap frozen and stored at -80 degree celcius

value: FVB

tag: age

value: 12 days

tag: genotype

tag: fraction

value: nuclear RNA PCM-1+ nuclei

tag: stress

value: left ventricular volume overload

tag: tissue

value: cardiac tissue left ventricle


title: VCAF_CCM_1

tag: cell type

value: Human vulval carcinoma-associated fibroblasts, hTERT-immortalised


title: Fstl1_cKO_heart_PCM1_765401_score1

tag: strain


title: 15070C

value: yy

value: 5-6 years


title: 15070P


title: 16371P

value: yB


title: 16235P

value: 8-10 years


title: Fstl1_cKO_heart_PCM1_765394_score1


title: 16235C

value: null control


title: Fstl1_cKO_heart_PCM1_765385_unstressed

description: left ventricle cardiomyocyte nuclei knockout unstressed heart

value: unstressed


title: Fstl1_het_cKO_PCM1_765386_unstressed

description:
left ventricle cardiomyocyte nuclei knockout unstressed heart
Fstl1_cKO_heart_PCM1_765386_unstressed


title: 996MC

value: 0.6 years


title: 16366P

value: 5+ years


title: 996MP

value: polyI:C experiment


title: 16366C


title: 16230P

value: pup


title: Fstl1_cKO_heart_PCM1_765383_unstressed


title: Fstl1_control_heart_PCM1_769115

description: left ventricle cardiomyocyte nuclei wildtype heart

value: wildtype


title: Fstl1_control_heart_PCM1_769111

value: FVB


title: 910MP


title: 890MP

value: 4.6 years


title: Fstl1_control_heart_PCM1_765388

value: 12 days

value: nuclear RNA PCM-1+ nuclei


title: 910MC


title: 15071P

value: 3-4 years


title: 890MC


title: 15071C


title: 15072P

value: 6-8 years


title: spermatogonia scRNA-seq (Chd4 siRNA)

city: Callaghan

first: Tessa

last: Lord

state: NSW

address: University Dr

country: Australia

institute: University of Newcastle

description: scRNAseq data from undifferentiated spermatogonia transfected with Chd4 siRNA. Three biological replicates were pooled post-transfection to create a single Chd4 knockdown sample for scRNAseq.

data_processing:
Raw base call files were demultiplexed using the 10X Genomics Cell Ranger pipeline (v2.1.0) and aligned to the mouse mm10 transcriptome.
A total of 2 transcriptomes (control and Chd4 knockdown) were merged in R using Seurat
Low quality cell transcriptomes and doublets were assessed within each library and excluded using the following criteria: >1,500 genes and <40,000 UMI counts for Control and >1,500 genes and <40,000 UMI counts for Chd4 knockdown. Filtering based on percent mitochondrial genes detected was conservatively set at <25% for all libraries based on visual inspection of overall distribution and the variability of mitochondrial gene content that occurs based on cell type and proliferation status.
Spermatogonia were isolated from a small number of contaminating feeder cells in the dataset based on Dazl and Ddx4 transcript abundance before the entire dataset was normalized, scaled (“vars.to.regress” included number of genes, number of UMIs, and percent mitochondrial transcripts), and dimensionally reduced using Seurat.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Gene-Cell Matrix filled with Raw Read/Expression Values

source_name: Undifferentiated spermatogonia

growth_protocol: Undifferentiated spermatogonia isolated from adult mouse testes (THY1+ MACS isolation) were maintained on mitomycin treated SNL76/7 mouse embryonic fibroblasts (n=3 biological replicates). Cells were cultured in serum free media supplemented with GDNF and bFGF. Culture media was changed every second day and cells were passaged and placed onto fresh feeder cells once a week.

extract_protocol:
Single cell suspensions of control and Chd4 knockdown spermatogonia were created, and an equal number of cells from each of the 3 biological replicates was combined in single 'control' or 'Chd4 knockdown' tube. Live cells were loaded into a Chromium Controller (10X Genomics, Inc.).
Single-cell cDNA libraries were generated using v2 chemistry according to the manufacturer’s protocol (10X Genomics, Inc.).

treatment_protocol: For transfection, spermatogonia were dislodged from the feeder layer and treated with 2 uL Lipofectamine and 75 pmol siRNA on plastic, for 24 hours.

value: Undifferentiated spermatogonia from primary culture

tag: treatment

value: RNAi with Chd4 siRNA

value: Chd4 knockdown


title: 15067P

tag: cbd103 genotype

value: yB

value: 9-10 years


title: 15072C

value: yy

tag: estimated age

value: null control


title: ATAC-seq old rep3

city: Münster

first: Sara

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
BWA MEM (version 0.7.12) was used to map raw reads
THOR (version 0.1) was used to call and analye differential peaks
Genome_build: GRCm38.81
Supplementary_files_format_and_content: ATACseq.all_peaks.csv containing location, foldchanges and p-values for differential peaks

source_name: hair follicle stem cells

growth_protocol: freshly isolated hair follicle stem cells from mouse

extract_protocol:
Skin pieces were incubated in 0.8% trypsin in PBS for 60 minutes at 37°C. After incubation, the epidermis was manually detached from the dermis, single cell epidermal suspensions where generated by pippeting and collected by centrifugation. Cells were labeled with antibodies against Cd34 and alpha6 integrin, after which Cd34 alpha6 integrin-double positive cells were isolated by flow cytometry. Total RNA was isolated using NucleoSpin RNA Plus kit for RNA seq. For ATAC seq Briefly, nuclei of 50K freshly FACS-sorted single HFSCs were prepared by lysing cells with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0,1% IGEPAL CA-630) for 15 min on ice. Nuclei were then collected by spinning at 6000 g for 10mins at 4°C, resuspended in Tagment DNA Buffer and Tagment DNA Enzyme (TruSight One Kit) and incubated for 30 min at 37°C. Samples were purified with MinElute PCR purification kit (QIAGEN) and PCR-amplified with 10-12 cycles.
Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina) for ATAC seq; Ovation RNA-Seq System V2 (NuGen) followed by subsequent library preparation using the Nextera XT library preparation kit (Illumina) for RNA seq

value: skin

value: HFSCs

value: 24 months


title: 15054P

value: 4-5 years

tag: cell culture treatment

value: polyI:C experiment


title: spermatogonia scRNA-seq (control siRNA)

description: scRNAseq data from undifferentiated spermatogonia transfected with control siRNA. Three biological replicates were pooled post-transfection to create a single control sample for scRNAseq.

value: RNAi with control (non-targeted) siRNA

value: Control


title: 1014MC

value: yearling

tag: cell culture experiment


title: 15054C


title: 15067C


title: 15062C

value: pup


title: 15062P


title: ATAC-seq old rep1


title: RNA old rep2

data_processing:
STAR (version 2.5.2b)  was used to map reads
featureCounts (version v1.6.2) was used to estimate gene counts
DEseq2 (version 1.22.2) was used to calculate pairwise differential gene expression
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: normalized_annotated_counts_all.results.csv containing annotated DEseq2 results


title: 16230C


title: RNA young rep3

description: normalized_annotated_counts_all.results.csv

value: 6 months


title: RNA old rep1


title: ATAC-seq young rep4


title: RNA young rep2


title: ATAC-seq young rep2


title: ATAC-seq old rep4


title: RNA young rep1


title: ATAC-seq young rep1


title: ATAC-seq old rep2


title: ATAC-seq young rep3


title: 1014MP


title: RNA old rep3


title: human monocyte-derived langerhans cells donor 1

city: Montpellier cedex 5

first: Fabien

middle: P

last: Blanchet

address: 1919 route de Mende

institute: IRIM - CNRS UMR9004

description: MoLC

data_processing:
RNA-seq libraries were sequenced on an Illumina HiSeq 2500 machine with base calling by CASAVA software version 1.8.2.
Trimmomatic software (version 0.33) was used to trim raw single-ended reads which were then aligned to human genome (hg19 / GRC37, UCSC) using Bowtie (version 2.2.5).
TopHat (version 2.0.14) was used to analyse the mapping results and identify splice junctions between exons
The mapped reads counting was performed with Cufﬂinks (version 2.2.1) and reported as “fragments per kilobase of transcript per million fragments mapped” or FPKM.
The Cuffmerge option from Cufflinks program was used to merge identified transcript pieces to full length  transcripts and to annotate the transcripts accordingly.
Merged transcripts  from two or more samples / conditions were compared using Cuffdiff to determine the differential expression  levels at transcript and gene level including a measure of significance between samples / conditions
Genome_build: Human Genome hg19 / GRC37, UCSC. Annotation reference: Gencode v19, Ensembl 75
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each condition

source_name: monocyte-derived langerhans cells

growth_protocol: MoDC were obtained from CD14+ human primary blood monocytes upon 5-7 days incubation with 500 U/ml GM-CSF, 500 U/ml IL-4 in IMDM medium supplemented with 10% FBS, 100 U/ml penicillin, 100 mg/ml streptomycin and 2 mM L-glutamine. For MoLC, 10 ng/ml TGF-b was added in the medium

extract_protocol:
Total RNA was isolated from 4x10^6 human monocyte-derived cells (MoDC, MoLC and MoDC+TGF-b) with TRIzol-chloroform (Invitrogen) precipitation, according to manufacturer’s recommendation, and cleaned up with RNeasy mini kit (Qiagen).
mRNA were enriched by poly-A purification, then fragmented and reverse transcribed. Adapters were ligated to random primed cDNA and adapter-specific PCR amplification was performed. Samples were barcoded and size selected to generate 50 base-pair single-end read cDNA libraries for Illumina sequencing

treatment_protocol: MoDC differentiated as above were also treated with 20 ng/ml TGF-b in the defined condition MoDC + TGF-b.

value: Human blood

tag: source cell type

value: Human blood primary monocyte

tag: derived cell type

value: monocyte-derived langerhans cells

value: IL-4/GM-CSF/TGF-beta 5-7 days

tag: donor


title: TGF-beta-treated human monocyte-derived Dendritic cells donor 2

description: MoDC+TGF-b

source_name: monocyte-derived Dendritic cells

value: monocyte-derived Dendritic cells

value: IL-4/GM-CSF 5-7 days then TGF-beta for 24h


title: human monocyte-derived langerhans cells donor 2

description: MoLC


title: TGF-beta-treated human monocyte-derived Dendritic cells donor 3

description: MoDC+TGF-b


title: TGF-beta-treated human monocyte-derived Dendritic cells donor 1

description: MoDC+TGF-b


title: human monocyte-derived Dendritic cells donor 3

description: MoDC

value: IL-4/GM-CSF 5-7 days


title: human monocyte-derived Dendritic cells donor 2

description: MoDC


title: ctrl-6m_5

type: RNA

city: Regensburg

first: Alexander

last: Scheiter

state: Bavaria

address: Franz-Josef-Strauss Allee 11

department: Institute of Pathology

institute: University of Regensburg

description: E685 EV

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Cy3, Biotin

source_name: normal liver

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: C57BL/6J x 129Sv

value: normal liver

tag: injected with

value: empty vector


title: ctrl-6m_3

description: E607 EV


title: Control_hmsc

city: Harbin

first: Yue

last: CHEN

state: Heilongjiang

address: 92 Xidazhi St, Nangang

institute: Harbin Institute of Technology, China

description:
C
without drug treated, in vitro culture 21 days

data_processing:
Libraries are sequenced via BGISEQ-500
Adapter and low-quality bases below a quality score of 15 were trimmed from raw RNA-Seq reads. After trimming, reads with less than 20 bp were further removed. The remaining reads were aligned to human reference genome hg38 via STAR software (version 2.5.3a)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Count values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Mesenchymal Stem Cells

growth_protocol: The cells were cultured in human bone marrow mesenchymal stem cell medium (Cyagen Biosciences, Cat#: HUXMA-90011) according to the manufacturer’s instructions.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols.

treatment_protocol: Metformin (100 μM), oltipraz (20 μM) , rapamycin (10 nM) and vitamin C (280 μM) were used to treat MSC as indicted.

tag: Stage

tag: group

value: control

value: Mesenchymal Stem Cells

tag: drug


title: VC_hmsc

description:
VC
drug treated 21 days

value: drug treated

value: vitamin C


title: E545K-5m_3

description: E322 E545K

source_name: liver tumor

value: liver tumor

tag: age

value: PIK3CA E545K


title: human monocyte-derived langerhans cells donor 3

description: MoLC


title: E545K-3m_5

description: E728 E545K

source_name: liver preneoplasia

value: liver preneoplasia


title: ctrl-3m_4

description: E813 EV


title: ctrl-6m_2

description: E606 EV


title: ctrl-6m_1

description: E605 EV


title: ctrl-3m_1

description: E671 EV


title: E545K-5m_2

description: E304 E545K


title: E545K-5m_5

description: E716 E545K


title: ctrl-6m_4

description: E684 EV


title: E545K-5m_1

description: E297 E545K


title: E545K-5m_4

description: E320 E545K


title: E545K-3m_3

description: E324 E545K


title: E545K-3m_4

description: E727 E545K


title: Oltipraz_hmsc

description:
O
drug treated 21 days

value: oltipraz


title: ctrl-3m_2

description: E672 EV


title: S5_nonlesional_IL1 [5F-AR12]

city: Guangzhou

first: Jin

last: Xu

state: Guandong

address: No. 135 Xingang Xilu

department: School of Life Sciences

institute: Sun Yat-Sen University

data_processing:
Basecalls performed using  CASAVA v1.8.2
The raw sequence reads were mapped to human reference genome (hg38) using STAR with parameters  "--sjdbO  verhang 100 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --  outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --sjdbScore 1  --readFilesCommand zca  t  --runMode   alignReads   --genomeLoad LoadAndKeep  --limitBAMsortRAM 10000000000 ".
Read pairs, which aligned concordantly to the genome were counted according to the annotation from UCSC(gencode.v27.annotation.gtf) using htseq-count
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts  for each Sample, sample ordered by 1-5

growth_protocol: All samples were bisected and cultured at 37°C in 5% CO2 for 24 hours in 1mL of Cornification media (DMEM/F12 (Sigma-Aldrich Cat#D6421,Missouri), 90mM Adenine, 0.94M CaCl, 10nM Triiodothyronine, 1x-ITS (Gibco Cat#51500056,New York), 100x Antibiotic/Antimycotic (Gibco Cat#15240062, New York), 2% heat-inactivated FBS(Gibco Cat#10082139, New York), 1x Glutamax (Gibco Cat#35050061, New York), 0.01mg/ml Getamicin (Gibco Cat#15750060, New York) in one well of a 24-well plate (VWR Cat#10062-896, Pennyslvannia).

extract_protocol:
After 24 hours, the explants were preserved in RNAlater (Ambion Cat# AM7022) for RNA sequencing, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: For IL-1β treatment group, 50ng/mL of IL-1β (eBiosciences Cat # BMS331, San Diego), was used to stimulate the explant for 24 hours.

tag: subject age

value: facial skin

tag: tissue type

value: non-lesional human skin

value: 50ng/mL IL-1β


title: S5_nonlesional_no Tx [5E-AR7]

source_name: nonlesional_no Tx

tag: tissue

value: none (no treatment)


title: ctrl-3m_3

description: E811 EV

tag: strain


title: Metformin_hmsc

description:
Met
drug treated 21 days

tag: cell type

value: metformin


title: Rapamycin_hmsc

description:
Rapa
drug treated 21 days

value: rapamycin


title: S5_rosacea_no Tx [5A-AR2]

source_name: rosacea_no Tx

value: lesional papulopustular rosacea human skin

tag: treatment


title: H1047R-12m_1

description: E285 H1047R

value: C57BL/6J x 129Sv

value: PIK3CA H1047R


title: S4_nonlesional_IL1 [4F-AR27]


title: E545K-3m_1

description: E306 E545K


title: S4_nonlesional_no Tx [4E-AR25]


title: H1047R-3m_4

description: E675 H1047R


title: NDI 106

city: Zaragoza

first: Alberto

last: Cebollada

state: Aragón

address: C/ San Juan Bosco, 13

country: Spain

institute: Instituto Aragonés de Ciencias de la Salud

description: NDI 106

data_processing:
Ion Torrent S5XL platform software used for basecalling.
Sequenced reads were trimmed for barcodes and PCR primer sequences, mapped to GRCh37/hg19 whole genome usingthe Torrent MApping Program (TMAP v5.2.22) with parameters (soft clipping off, maximum mismatch and open gap penalties, gap extension penalty 10, minimum alignment length 135, "unique best hit and stage1 map4")
Relevant HERVW loci were identified by unbiased read mapping, verified as HERVW loci using the RepeatMasker program (GRCh37.p5 version of the human genome database), which uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI)[23].
For each sample, the number of reads corresponding to individual HERVW copies listed was calculated, as well as the cumulative error rate.
Relative frequencies were calculated as the number of reads mapping to an individual HERVW ENV element relative to the total number of reads.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include HERVW loci analyzed; percentage of reads per locus for each Sample; all samples combined in 1 file

source_name: PBMC

extract_protocol:
PBMC were purified, lyzed using Trizol reagent. RNA was prepared using in house standard methods, ThermoScriptTM RT-PCR System (11146-024, ThermoFisher) was used to synthesized cDNA with random hexamer primers. An HERVW amplicon was amplified using published primers (DOI: 10.1016/j.jviromet.2009.05.024)
Library preparation and sequencing was carried out using the workflow and kits approved for IonTorrent technology (Beckman Coulter, Thermofisher, Kapa/Roche).

tag: pathology

value: Non-diseased individual

value: PBMC


title: NDI 104

description: NDI 104


title: H1047R-3m_3

description: E422 H1047R


title: NDI 99

description: NDI 99


title: S4_rosacea_no Tx [4A-AR20]


title: S3_nonlesional_IL1 [3F-AR11]


title: S3_nonlesional_no Tx [3E-AR10]


title: NDI 98

description: NDI 98


title: CIS 114

description: CIS 114

value: Clinical isolated syndrome (CIS)


title: CIS 73

description: CIS 73


title: S3_rosacea_no Tx [3A-AR1]


title: RNA-Seq P1_rep1

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Raw sequencing data was processed via the Cell Ranger pipeline (10xGenomics, version 2.0.1) to generate a count matrix from the bcl files.
Genome_build: mm10 (GRCm38.84)
Supplementary_files_format_and_content: Unfiltered feature-barcode matrices HDF5

source_name: mouse brain cortex

extract_protocol:
For single cell RNA seq, tissue pieces were processed to obtain single cell suspension using papain digestion (15-30 minutes according to embryo age) (Papain dissociation kit, Worthington). We followed the protocol as per the provider’s instructions.  After dissociation and concentration, cells were resuspended in BSA 0.04% in PBS, at a concentration of 800-1200 cells/uliter. Cells were counted in a hemocytometer chamber and immediately processed for single cell GEM formation (10x Genomics, single cell RNA sequencing 3’, Chromium V2 or V3 for Fezf2 experiments).
For single cell RNA seq we loaded the 10x chips aiming to recover 7,000–10,000 cells.cDNA amplification and library construction were done following 10xGenomics instructions. For the complete wild type developmental atlas we generated Chromium V2 libraries, while Chromium V3 was used for all Fezf2 experiments. Libraries were quantified in BioAnalyzer and sequenced in HiSeq or NovaSeq illumina platforms.
single cell RNA sequencing 3’, Chromium V2 or V3

treatment_protocol: For embryos E14.5 or younger we dissected the head, for older animals we isolated the brains. Dissection was performed in Hybernate E (Brainbits). The tissue was then embedded in 3% low melting agarose at 35-37C. Once the agarose solidified, the tissue was sectioned in 250um thick sections in a vibratome in iced Hybernate E. Sections were transferred to another plate and the prospective somatosensory cortex was dissected and meninges removed. For the earliest time points (E11.5 and E12.5) the prospective somatosensory cortex (medio-lateral region) was dissected without prior sectioning. Tissue was kept in cold buffers and on ice all time. RNAse free technique was used for handling. Cortical tissue from 4 animals was pulled together for each timepoint. For the Fezf2 experiments, samples were directly dissected from the cortex and processed individually, till genotype confirmation, when we combined samples from embryos with the same genotype. We genotyped embryos through PCR and qPCR on DNA extracted quickly from tail clips (QuickExtract DNA Extraction Solution, Lucigen), and through B-galactosidase detection assays.

value: somatosensory cortex

tag: developmental stage

tag: genotype

value: wild type

tag: chromium single cell 3' solution chemistry


title: H1047R-3m_2

description: E356 H1047R


title: CIS 70

description: CIS 70


title: RNA-Seq E18_5_rep2


title: RNA-Seq P1_rep2


title: H1047R-6m_1

description: E350 H1047R


title: S2_nonlesional_IL1 [2F-AR19]


title: NDI 102

description: NDI 102


title: S2_nonlesional_no Tx [2E-AR18]


title: RNA-Seq E18_5_rep1


title: RNA-Seq E16_5


title: S2_rosacea_no Tx [2A-AR13]


title: CIS 58

description: CIS 58


title: CIS 49

description: CIS 49


title: S1_nonlesional_IL1 [1F-AR12]


title: S1_nonlesional_no Tx [1E-AR7]


title: RNA-Seq E14_5


title: RNA-Seq E15_5


title: RNA-Seq E13_5


title: WT_NH4_rep2

data_processing:
Mapping: STAR --runThreadN 4 --outFilterMultimapNmax 1
Duplicate removal: samtools rmdup
Genome_build: Aspnd5rm
Supplementary_files_format_and_content: bigwig: forward reads (deeptools) - bamCoverage -p4 --binSize 1 --normalizeUsingRPKM --filterRNAstrand forward
Supplementary_files_format_and_content: bigwig: reverse reads (deeptools) - bamCoverage -p4 --binSize 1 --normalizeUsingRPKM --filterRNAstrand reverse

organism: Aspergillus nidulans

source_name: ANM Liquid culture

growth_protocol: Wild type (MH1) mycelia grown for 16 h in supplemented liquid Aspergillus Nitrogen-free Minimal media (ANM) pH 6.5, containing 1% (w/v) glucose as sole carbon source and 10 mM ammonium, glutamine or alanine.

extract_protocol:
Mycelia were strained and blotted dry before snap freezing in liquid nitrogen. Samples were stored at -80ºC for up to 12 months.
Total RNA was isolated by grinding mycelia under liquid nitrogen and subsequent addition to RNA extraction buffer (7.0 M Urea, 100 mM Tris-HCl pH 8.0, 10 mM EDTA, 1.0% sodium dodecyl sulfate) followed by two phenol-chloroform-isoamylalcohol extractions and one chloroform extraction (Sambrook and Russell, 2001). RNA was precipitated in 3M ammonium acetate and 50% isopropanol, resuspended in DEPC-H2O, and re-precipitated overnight in 4M lithium chloride at -20ºC. RNA quality was determined by visualization after electrophoretic separation in a 1.2% agarose gel containing 1.1% formaldehyde run in 1x MOPS buffer (20 mM MOPS pH 7.0, 5 mM sodium acetate, 1 mM EDTA). RQ1 DNase (Promega) treatment of RNA followed the manufacturer’s instructions.
RNA was indexed with the TruSeq Stranded Total RNA Sample Prep Kit (Illumina) and fragmented to 180-bp. Libraries were sequenced using 50-bp single-end reads on the Illumina Hi-Seq 2500 platform

value: Mycelia

tag: nitrogen sources

value: 10 mM Ammonium Tartrate


title: H1047R-3m_1

description: E355 H1047R

value: liver preneoplasia


title: S1_rosacea_no Tx [1A-AR2]

value: facial skin


title: WT_NH4_rep1


title: RNA-Seq E12_5


title: WT_Gln_rep3

value: 10 mM Glutamine


title: WIBR3 CDK8/19i (dataset 2)

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

description: WIBR3 CDK8/19i

data_processing:
Alignment software: STAR version 2.3.0ewith default parameters and annotated genome with UCSC hg19 gtf
Sam to BAM and sorting: sambamba version 0.6.7
Read counts: Rsubread version 1.30.9 with in built annotation hg19 and default parameters
Count normalization: DESeq2 version 1.20.0 function "counts" with normalization parameter=TRUE
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix of normalized counts with the DESeq2 function "counts" and normalization parameter = TRUE

source_name: pluripotent stem cell line

growth_protocol: Human PSC (H1, D2#2, D2#4, CB5, WIBR3) were maintained in conventional primed conditions, specifically, by culture on growth factor-reduced phenol red-free matrigel (BD Biosciences #356231) with mTeSR (Stem Cell Technologies). Cultures were passage every 5-7 days manually using either 2mg/ml dispase (Gibco), 0,5 μM EDTA/1xPBS, or accutase (Gibco).

extract_protocol:
Total RNA was extracted from cells on column by RNeasy kit with DNA digestion following provider’s recommendations (Qiagen #74104, #79254),
total RNA with RIN numbers in the range 9.0 to 10 (Agilent 2100 Bioanalyzer), were used. For library construction 10 ng of total RNA samples were processed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) by following manufacturer instructions. Resulting cDNA was sheared on a S220 Focused-ultrasonicator (Covaris) and subsequently processed with the ""NEBNext Ultra II DNA Library Prep Kit for Illumina"" (NEB #E7645). Briefly, oligo(dT)-primed reverse transcription was performed in presence of a template switching oligonucleotide, double stranded cDNA was produced by 11 cycles of PCR and submitted to acoustic shearing. Fragments were processed through subsequent enzymatic treatments of end repair, dA-tailing, and ligation to Illumina adapters. Adapter-ligated libraries were completed by limited-cycle PCR (8 cycles).
The resulting directional cDNA libraries were sequenced for 50 bases in a single-read format, instrument: Illumina HiSeq2500. Primary data processing: Image analysis, per-cycle base-calling and quality score assignment was performed with Illumina Real Time Analysis software.

treatment_protocol: Human PSC were cultured in two media conditions. Standard primed conditions ("Primed" = mTeSR media with FGF2 and TGFb1, feeder-free, on matrigel); or, including additional media supplementation with recombinant human LIF (20 ng/ml) and CDK8/19-small molecule inhibitor at 0,4 mM (= "CDK8/19i").

tag: condition


title: WT_Gln_rep2


title: WIBR3 Primed (dataset 2)

description: WIBR3 Primed

value: Primed


title: CB5 CDK8/19i (dataset 2)

description: CB5 CDK8/19i


title: Post-infection replicate 2

first: Nicholas

last: Heaton

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
Raw fastq files were mapped and statistical analysis was performed using the MaGEck pipeline (li, et al, 2014).
Supplementary_files_format_and_content: Un-normalized mapped read count.

growth_protocol: Cells were grown under standard laboratory conditions and stably transfected with CRISPR components.

extract_protocol:
Genomic DNA was extracted, and PCR for the sgRNA sequences was performed.
Illumina adaptors and barcodes were incorporated into the PCR primers.
PCR amplified libraries were generated with independent barcodes to allow multiplexing.  High amounts of PhiX DNA were included in the sequencing run, as low diversity libraries were expected.

treatment_protocol: Cells were transduced with sgRNA lentivirus and subsequently infected with hCoV-229E.

tag: cell line


title: Unselected replicate 2


title: WT_Ala_rep3

value: 10 mM Alanine


title: D2#4 CDK8/19i (dataset 2)

description: D2#4 CDK8/19i


title: CB5 Primed (dataset 2)

description: CB5 Primed


title: Post-infection replicate 1


title: WT_Ala_rep2


title: WT_Ala_rep1


title: Unselected replicate 1


title: D2#4 Primed (dataset 2)

description: D2#4 Primed


title: WT_NH4_rep3


title: slam_Nanos2TAGTAG_5_1440min

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

institute: Queen Mary University of London

description:
SLAM-seq, Nanos2TAGTAG, line 5, 1440min
OTHER – SLAM-Seq
half_life_EXP.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.27
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name

source_name: Spermatogonial stem cell lines (SSCs)

growth_protocol: see sample characteristics

extract_protocol:
SSCs were depleted from feeders and RNA was extracted with Trizol. These steps were performed in the dark, until the IAA treatment.
SLAM-seq libraries were prepared by using the Lexogen SLAMseq Kinetics Kit – Catabolic Kinetics Module and the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, following the manufacturer’s’ instructions.


title: Forelimb, E10

city: Paris

first: Estelle

last: Hirsinger

address: 9 quai Saint Bernard

department: LBD

institute: IBPS

data_processing:
Sequence analysis with Cell Ranger Single Cell Software Suite 3.0.2 by 10X Genomics
Raw base call files were demultiplexed with the cellranger mkfastq pipeline into library specific FASTQ files.
The FASTQ files for each library were then processed independently with the cellranger count pipeline.
This pipeline used STAR to align cDNA reads to the Gallus gallus genome (Sequence: GRCg6a, Gallus gallus reference).
Genome_build: GRCg6ar95
Supplementary_files_format_and_content: For each sample, set of 3 files in format 10X (list of cell barcodes, list of genes and expression matrix (raw counts))

organism: Gallus gallus

source_name: Limb

extract_protocol:
Forelimbs from 2 different E4 embryos, 3 different E6 embryos and 3 different E10 embryos were dissected and dissociated by collagenase and mechanical treatments. 5000 cells per conditions were loaded into the 10X Chromium Chip with the Single Cell 3’ Reagent Kit v3 according to the manufacturer’s protocol. Samples were pooled together at each developmental stage (E4 (N=2), E6 (N=3) and E10 (N=3)) before making the libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: Forelimb

value: Embryonic day 10


title: VTA, Female, Saline SF2---VTA

city: Richmond

first: Peter

last: Hamilton

state: VA

address: 1217 E Marshall St

department: Anatomy and Neurobiology

institute: Virginia Commonwealth University

description:
VTA, Female, Saline
Ribosomal depeted RNA isolate

data_processing:
Mapping sequence reads to the reference genome: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus Rnor6.0 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Extracting gene hit counts: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Differential gene expression analysis: After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the drug treated and saline treated groups of samples within sex and brain region was performed.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: uniqe gene hit counts

organism: Rattus norvegicus

source_name: microdissected ventral tegmental area

growth_protocol: In lieu of the final choice session (2:00 P.M. ±1h), rats were rapidly decapitated without anesthesia, brains were sectioned into 1 mm coronal slices using sex-specific brain matrices (Zivic Instruments: Pittsburgh, PA; Male: BSRLS001-1; Female: BSRLA001-1), and bilateral tissue punches were collected from the nucleus accumbens (NAc; 12 gauge; internal diameter 2.16 mm) and ventral tegmental area (VTA; 16 gauge; internal diameter 1.19 mm). Tissue was frozen on dry ice and stored at -80℃.

extract_protocol:
RNA was extracted and purified (RNeasy, Qiagen) according to manufacturer’s instructions. Total RNA was quantified with the Qubit RNA HS Assay Kit (Thermo Fisher). RNA quality control assays were performed on the TapeStation 4200 (Agilent), and the RNA Integrity Number (RIN) for all samples (±S.E.M.) ranged from 8.0 to 9.2 (mean value 8.7±0.05).
Ribosomal RNA depletion and library preparation (Illumina Ribo-Zero)
2x150 paired-end reads on an Illumina sequencing platform (HiSeq 2500) with a sequencing depth of ~22M reads per sample (mean value 22±0.03M).

value: Sprague Dawley

value: Saline

tag: Sex

value: Female


title: slam_Nanos2TAGTAG_5_540min

description:
SLAM-seq, Nanos2TAGTAG, line 5, 540min
OTHER – SLAM-Seq
half_life_EXP.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.26
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: D2#2 CDK8/19i (dataset 2)

description: D2#2 CDK8/19i


title: slam_Nanos2TAGTAG_5_120min

description:
SLAM-seq, Nanos2TAGTAG, line 5, 120min
OTHER – SLAM-Seq
half_life_EXP.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.25
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: Forelimb, E6

value: Embryonic day 6


title: VTA, Male, Saline SM3---VTA

description:
VTA, Male, Saline
Ribosomal depeted RNA isolate

value: Male


title: VTA, Female, Saline SF1---VTA


title: RNA-Seq E11_5


title: WT_Gln_rep1

city: Headington

first: Damien

last: Downes

address: John Radcliffe Hospital

institute: The University of Oxford


title: D2#2 Primed (dataset 2)

description: D2#2 Primed


title: Forelimb, E4

value: Embryonic day 4


title: slam_Nanos2TAG+_4_1440min

description:
SLAM-seq, Nanos2TAG+, line 4, 1440min
OTHER – SLAM-Seq
half_life_CTL.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.24
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: H1 Primed (dataset 2)

description: H1 Primed


title: slam_Nanos2TAG+_4_540min

description:
SLAM-seq, Nanos2TAG+, line 4, 540min
OTHER – SLAM-Seq
half_life_CTL.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.23
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: MED12-KO BRCA2 iKO rep2

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

data_processing:
Raw mRNA sequence reads were pre-processed using Cutadapt (v1.15) to remove bases with quality scores < 20 and adapter sequences, followed by alignment of clean RNA-seq reads to GRCh38.83 with STAR (v2.5.3a). Uniquely-mapped reads overlapping genes were counted by HTseq-count with default parameter using annotation from ENSEMBL v83.
Genome_build: RNA-seq: GRCh38.83
Supplementary_files_format_and_content: Merged file: tab-delimited text files include raw read counts for each Sample

source_name: Human embryonic kidney 293A

growth_protocol: All the cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum. For the cells with BRCA2 inducible depletion, Doxycycline (1 ug/mL; Sigma) and IAA (500 uM; Fisher Scientific) were added to the medium and maintained for 2 days to induce BRCA2 degradation as BRCA2 iKO.

extract_protocol:
Cells were collected and total RNA was extracted using an RNeasy Mini Kit (QIAGEN; #74104) according to the manufacturer’s instructions.
The library was prepared using an Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: F

value: fetus

tag: genotype/variation

value: MED12 KO BRCA2 iKO


title: VTA, Female, Fentanyl L7---VTA

description:
VTA, Female, Fentanyl
Ribosomal depeted RNA isolate

value: Fentantyl


title: slam_Nanos2TAG+_4_120min

description:
SLAM-seq, Nanos2TAG+, line 4, 120min
OTHER – SLAM-Seq
half_life_CTL.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.22
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: MED12-KO BRCA2 iKO rep1


title: VTA, Female, Fentanyl L2---VTA


title: CCNC-KO BRCA2 iKO rep2

value: CCNC KO BRCA2 iKO


title: 3BWCT3 bravo-2 Rep3

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

institute: Center for Research in Agricultural Genomics (CRAG)

data_processing:
Adaptor sequences were removed using cutadapt.
The mapping of the reads to the genome was done with STAR.
Quantification of the reads was done with RSEM. Araport11 were used as transcripts of reference and TAIR10 as reference genome.
In R studio, genes with 0 counts in all samples were removed. NOIseq was used for the bias detection, correction and normalization. ARSyNseq was used for batch effect correction. Genes with low number of counts (cpm<4) were filtered.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include TPM and FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: Primary root

growth_protocol: Arabidopsis seeds were surface sterilized with 35% sodium hypochlorite followed by 5 washes with distilled sterile water. To synchronize germination seeds were vernalized for 2 to 3 days at 4oC in darkness. Seeds were grown in vertically oriented 120x120 mm plates containing half-strength Murashige and Skoog (MS) medium without sucrose, supplemented with vitamins (0.5MS-) and 0.8% plant agar. Plates were sealed with Micropore tape. Seeds were grown under long day conditions (16 hours light and 8 hours dark) at 22oC and 60% relative humidity for all the experiments.

extract_protocol:
The protocol is described in Clark et al., 2018.
cDNA libraries were prepared from the extracted RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and Low Input Library Preparation Kit (Clontech laboratories).

value: Seedling

value: 5 days

value: Quiescent Center (QC) cells


title: VTA, Male, Saline SM1---VTA


title: VTA, Female, Fentanyl L1---VTA


title: 2BWCT2 bravo-2 Rep2


title: CCNC-KO BRCA2 iKO rep1


title: 1BWCT2 - bravo-2 Rep1


title: slam_Nanos2TAGTAG_5_540min rep2

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.20
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: H1 CDK8/19i (dataset 2)

description: H1 CDK8/19i


title: 4WCT1 - WT Rep3

value: wild type


title: slam_Nanos2TAGTAG_5_120min rep2

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.19
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: BRCA2 iKO rep2

value: BRCA2 iKO


title: 3WCT1 - WT Rep2


title: VTA, Male, Fentanyl N2---VTA

description:
VTA, Male, Fentanyl
Ribosomal depeted RNA isolate


title: BRCA2 iKO rep1


title: slam_Nanos2TAG+_4_1440min rep1

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.18
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: 1WCT3 - WT Rep1


title: VTA, Male, Fentanyl N1---VTA


title: MED12-KO rep2

value: MED12 KO


title: NAc, Female, Saline SF4---NAc

description:
NAc, Female, Saline
Ribosomal depeted RNA isolate

source_name: microdissected nucleus accumbens

value: Sprague Dawley


title: slam_Nanos2TAGTAG_5_1440min rep2

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.21
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: slam_Nanos2TAG+_4_540min rep1

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.17
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: MED12-KO rep1


title: Hindgut tissue of healthy fetal rats 9 on GD16 (N16_3)

city: Shenyang

first: Yu Zuo

last: Bai

state: Liaoning Province

address: No. 36 Sanhao Street

description:
N16_3
Hindgut tissue of fetal rat
circ.expression.annot.txt

data_processing:
Illumina HiSeq 4000 software used for basecalling.
The efficiency of experimental ribosome RNA removal is affected by the species and sample quality. Therefore, the Bowtie2 short read alignment tool was used to map the reads to the ribosomal RNA (rRNA) database.
The rRNA-mapped reads were removed, followed by mapping to the reference genome using TopHat2 (version 2.1.1).
After alignment with the reference genome, the reads that could be mapped to the genome were discarded, and the unmapped reads were collected for circRNA identification. The 20-mers from both ends of the unmapped reads were extracted and aligned to the reference genome to identify unique anchor positions within the splice site. Anchored reads that aligned in the reversed orientation (head to tail) indicated circRNA splicing and were subsequently subjected to find_circ to identify circRNAs. The circRNAs were blast searched against circBase for annotation. Those that could not be annotated were considered novel circRNAs.
To quantify the circRNAs, back-spliced junction reads were scaled to reads per million mapped reads (RPM) according to the following formula: RPM = 106C/N, where C is the number of back-spliced junction reads that uniquely aligned to a circRNA and N is the total number of back-spliced junction reads.
Genome_build: Ensembl release 94 Rnor 6.0
Supplementary_files_format_and_content: circ.expression.annot.txt: Tab-delimited text file contains abundance measurements (counts, rpm).
Supplementary_files_format_and_content: circ_candidates.fa: FASTA file contains assembly results.

source_name: hindgut

growth_protocol: Mature female Wistar rats (number: 18; age: 7–8 weeks old; body weight: 230–280 g) were acquired from the Experimental Animal Center, Shengjing Hospital of China Medical University (Shenyang, China). The Key Laboratory of the Health Ministry for Congenital Malformations (Shenyang, China) provided a specific pathogen-free animal laboratory (room temperature: 22 ± 2°C; humidity: 55 ± 5%; 12-h light/12-h dark cycle; free access to water and food) for rodents. In total, 9 pregnant rats were gavage-fed a single dose of 125 mg/kg 1% ETU (Sigma-Aldrich; Merck Millipore, Darmstadt, Germany) on GD10, and the remaining pregnant rats received the same dose of saline without ETU as a control.

extract_protocol:
Total RNAs were extracted from the hindgut tissue using TRIzol reagent. Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Illumina HiSeqTM 4000

tag: diagnosis

value: Healthy

value: Hindgut

value: Gestational day 16


title: slam_Nanos2TAG+_4_120min rep1

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.16
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: Hindgut tissue of healthy fetal rats 8 on GD16 (N16_2)

institute: Shengjing Hospital of China Medical University

description:
N16_2
Hindgut tissue of fetal rat
circ.expression.annot.txt


title: CCNC-KO rep2

tag: age

value: CCNC KO


title: VTA, Male, Fentanyl N3---VTA

value: Male


title: slam_Nanos2TAGTAG_5_60mi

description:
SLAM-seq, Nanos2TAGTAG, line 5, 60min
OTHER – SLAM-Seq
half_life_EXP.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.15
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: NAc, Female, Saline SF1---NAc

value: Saline

value: Female


title: Hindgut tissue of healthy fetal rats 7 on GD16 (N16_1)

description:
N16_1
Hindgut tissue of fetal rat
circ.expression.annot.txt


title: WT rep2

value: F

value: fetus


title: NAc, Male, Saline SM4---NAc

description:
NAc, Male, Saline
Ribosomal depeted RNA isolate


title: slam_Nanos2TAGTAG_5_30min rep2

description:
SLAM-seq, Nanos2TAGTAG, line 5, 30min
OTHER – SLAM-Seq
half_life_EXP.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.14
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: Hindgut tissue of healthy fetal rats 6 on GD15 (N15_3)

description:
N15_3
Hindgut tissue of fetal rat
circ.expression.annot.txt

value: Gestational day 15


title: slam_Nanos2TAGTAG_5_0min rep2

description:
SLAM-seq, Nanos2TAGTAG, line 5, 0min
OTHER – SLAM-Seq
half_life_EXP.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.13
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: human monocyte-derived Dendritic cells donor 1

description: MoDC

data_processing:
RNA-seq libraries were sequenced on an Illumina HiSeq 2500 machine with base calling by CASAVA software version 1.8.2.
Trimmomatic software (version 0.33) was used to trim raw single-ended reads which were then aligned to human genome (hg19 / GRC37, UCSC) using Bowtie (version 2.2.5).
TopHat (version 2.0.14) was used to analyse the mapping results and identify splice junctions between exons
The mapped reads counting was performed with Cufﬂinks (version 2.2.1) and reported as “fragments per kilobase of transcript per million fragments mapped” or FPKM.
The Cuffmerge option from Cufflinks program was used to merge identified transcript pieces to full length  transcripts and to annotate the transcripts accordingly.
Merged transcripts  from two or more samples / conditions were compared using Cuffdiff to determine the differential expression  levels at transcript and gene level including a measure of significance between samples / conditions
Genome_build: Human Genome hg19 / GRC37, UCSC. Annotation reference: Gencode v19, Ensembl 75
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each condition

source_name: monocyte-derived Dendritic cells

value: Human blood

tag: source cell type

value: Human blood primary monocyte

tag: derived cell type

value: monocyte-derived Dendritic cells

value: IL-4/GM-CSF 5-7 days

tag: donor


title: NAc, Male, Saline SM3---NAc

data_processing:
Mapping sequence reads to the reference genome: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus Rnor6.0 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Extracting gene hit counts: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Differential gene expression analysis: After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the drug treated and saline treated groups of samples within sex and brain region was performed.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: uniqe gene hit counts

tag: strain


title: Hindgut tissue of healthy fetal rats 5 on GD15 (N15_2)

description:
N15_2
Hindgut tissue of fetal rat
circ.expression.annot.txt

tag: tissue


title: slam_Nanos2TAG+_4_60min rep2

description:
SLAM-seq, Nanos2TAG+, line 4, 60min
OTHER – SLAM-Seq
half_life_CTL.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.12
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: Hindgut tissue of healthy fetal rats 4 on GD15 (N15_1)

description:
N15_1
Hindgut tissue of fetal rat
circ.expression.annot.txt


title: NAc, Female, Saline SF2---NAc

tag: treatment


title: NAc, Female, Fentanyl L8---NAc

description:
NAc, Female, Fentanyl
Ribosomal depeted RNA isolate

value: Fentantyl


title: NAc, Male, Saline SM1---NAc


title: slam_Nanos2TAG+_4_30min rep2

description:
SLAM-seq, Nanos2TAG+, line 4, 30min
OTHER – SLAM-Seq
half_life_CTL.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.11
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: Hindgut tissue of healthy fetal rats 3 on GD14 (N14_3)

description:
N14_3
Hindgut tissue of fetal rat
circ.expression.annot.txt

value: Gestational day 14


title: E545K-3m_2

description: E307 E545K

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

value: C57BL/6J x 129Sv

value: liver preneoplasia

tag: injected with

value: PIK3CA E545K


title: RPE23_2

city: Sevilla

first: Lorena

last: Buono

state: Sevilla

address: Carretera de Utrera km 1

institute: CABD

data_processing:
Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0
The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1
Genome_build: danRer10
Supplementary_files_format_and_content: txt file including the FPKM values for all genes in each eye domain

organism: Danio rerio

source_name: sorted RPE cells

growth_protocol: Zebrafish embryos were raised in E3 medium at 28 °C

extract_protocol:
Total RNA was extracted by TRIzol (Invitrogen) following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse-free (Ambion).
Ribo-Zero® rRNA Removal Kit (Illumina)

treatment_protocol: Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever, 2012

tag: cell type

value: sorted RPE cells

tag: developmental stage

value: 23 hpf

tag: transgenic line


title: slam_Nanos2TAGTAG_5_60min rep1

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.9
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name

tag: genotype


title: slam_Nanos2TAG+_4_0min rep2

description:
SLAM-seq, Nanos2TAG+, line 4, 0min
OTHER – SLAM-Seq
half_life_CTL.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.10
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: CCNC-KO rep1

data_processing:
Raw mRNA sequence reads were pre-processed using Cutadapt (v1.15) to remove bases with quality scores < 20 and adapter sequences, followed by alignment of clean RNA-seq reads to GRCh38.83 with STAR (v2.5.3a). Uniquely-mapped reads overlapping genes were counted by HTseq-count with default parameter using annotation from ENSEMBL v83.
Genome_build: RNA-seq: GRCh38.83
Supplementary_files_format_and_content: Merged file: tab-delimited text files include raw read counts for each Sample

value: CCNC KO


title: NAc, Female, Fentanyl L7---NAc

value: Sprague Dawley


title: RPE23_1


title: Hindgut tissue of healthy fetal rats 1 on GD14 (N14_1)

description:
N14_1
Hindgut tissue of fetal rat
circ.expression.annot.txt

value: Healthy

value: Hindgut


title: NAc, Female, Fentanyl L2---NAc

value: Female


title: WT rep1

value: F

value: fetus

value: wild type


title: NAc, Female, Fentanyl L1---NAc


title: Hindgut tissue of healthy fetal rats 2 on GD14 (N14_2)

description:
N14_2
Hindgut tissue of fetal rat
circ.expression.annot.txt


title: slam_Nanos2TAGTAG_5_30min rep1

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.8
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: Hindgut tissue with ETU-induced ARMs 9 on GD16 (A16_3)

description:
A16_3
Hindgut tissue of fetal rat
circ.expression.annot.txt

value: Ethylenethiourea (ETU)-induced anorectal malformations (ARMs)

value: Gestational day 16


title: RPE18_2

value: 18 hpf


title: NAc, Male, Fentanyl N7---NAc

description:
NAc, Male, Fentanyl
Ribosomal depeted RNA isolate

value: Fentantyl

value: Male


title: slam_Nanos2TAG+_4_60min rep1

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.6
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: NAc, Male, Fentanyl N3---NAc


title: Hindgut tissue with ETU-induced ARMs 8 on GD16 (A16_2)

description:
A16_2
Hindgut tissue of fetal rat
circ.expression.annot.txt


title: RPE23_3


title: RPE18_1


title: NR23_3

source_name: sorted neural retinal cells

value: sorted neural retinal cells


title: slam_Nanos2TAG+_4_30min rep1

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.5
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: Hindgut tissue with ETU-induced ARMs 7 on GD16 (A16_1)

description:
A16_1
Hindgut tissue of fetal rat
circ.expression.annot.txt

data_processing:
Illumina HiSeq 4000 software used for basecalling.
The efficiency of experimental ribosome RNA removal is affected by the species and sample quality. Therefore, the Bowtie2 short read alignment tool was used to map the reads to the ribosomal RNA (rRNA) database.
The rRNA-mapped reads were removed, followed by mapping to the reference genome using TopHat2 (version 2.1.1).
After alignment with the reference genome, the reads that could be mapped to the genome were discarded, and the unmapped reads were collected for circRNA identification. The 20-mers from both ends of the unmapped reads were extracted and aligned to the reference genome to identify unique anchor positions within the splice site. Anchored reads that aligned in the reversed orientation (head to tail) indicated circRNA splicing and were subsequently subjected to find_circ to identify circRNAs. The circRNAs were blast searched against circBase for annotation. Those that could not be annotated were considered novel circRNAs.
To quantify the circRNAs, back-spliced junction reads were scaled to reads per million mapped reads (RPM) according to the following formula: RPM = 106C/N, where C is the number of back-spliced junction reads that uniquely aligned to a circRNA and N is the total number of back-spliced junction reads.
Genome_build: Ensembl release 94 Rnor 6.0
Supplementary_files_format_and_content: circ.expression.annot.txt: Tab-delimited text file contains abundance measurements (counts, rpm).
Supplementary_files_format_and_content: circ_candidates.fa: FASTA file contains assembly results.


title: Hindgut tissue with ETU-induced ARMs 6 on GD15 (A15_3)

description:
A15_3
Hindgut tissue of fetal rat
circ.expression.annot.txt

value: Gestational day 15


title: NAc, Male, Fentanyl N2---NAc


title: NR23_2


title: slam_Nanos2TAG+_4_0min rep1

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.4
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: Hindgut tissue with ETU-induced ARMs 5 on GD15 (A15_2)

description:
A15_2
Hindgut tissue of fetal rat
circ.expression.annot.txt


title: RPE18_3

value: sorted RPE cells


title: NAc, Male, Fentanyl N1---NAc


title: NR23_1

value: 23 hpf


title: Hindgut tissue with ETU-induced ARMs 4 on GD15 (A15_1)

description:
A15_1
Hindgut tissue of fetal rat
circ.expression.annot.txt


title: NR18_3


title: BS+ET-3

city: Nanning

first: Fareed Uddin

last: Memon

state: Guangxi

address: Department of Clinical Veterinary Medicine, Collage of Animal Sciences and Technology, Guangxi University, Nanning, P.R. China.

department: Clinical Veterinary Medicine

institute: Guangxi University

data_processing:
Quality control: For RNA-seq, the quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to Gallus gallus genome assembly GRCg6a (ftp://ftp.ensembl.org/pub/release-102/fasta/gallus_gallus/dna/Gallus_gallus.GRCg6a.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file: ftp://ftp.ensembl.org/pub/release-102/gtf/gallus_gallus/Gallus_gallus.GRCg6a.102.gtf.gz
DESeq2 (v1.26.0) was applied for the detection of differentially expressed genes (DEGs) with a Padj of < 0.05 and fold change (FC) of > 1.5.
Genome_build: GRCg6a
Supplementary_files_format_and_content: all.sample.gene.count.fpkm.txt: Tab-delimited text file includes count and FPKM values for each Sample.

source_name: Challenged with Eimeria tenella and treated with Bacillus subtilis probiotic

growth_protocol: A total of 63 Chinese native yellow chickens were purchased from a commercial hatchery and reared in 9 coccidia-free cages with free access to feed and water for up to 28 days. Upon arrival, all chicks were weighed and randomly divided into one of three experimental groups with 21 birds in each group. Temperature (32 to 34 °C for 1st week and then decreased by 2°C per week), humidity (60 to 80%) and light (23 h L:1D) were maintained during the entire period of experiment.

extract_protocol:
For the extraction of total RNA from all collected caecum samples, a modified Trizol method was used and the RNA was extracted according to the instructions of Trizol kit manual (B518651-0100, Sangon Biotech co, Ltd, Shanghai, China). The purity of RNA was determined using NanoPhotometer® Spectrophotometer (IMPLEN, CA, USA) and the concentration of total RNA was determined with Qubit® 2.0 Fluorimeter by using Qubit® RNA Assay Kit (Life Technologies, CA, USA). RNA purity and integrity were further measured with Bioanalyzer 2100 system using RNA Nano Assay Kit (Agilent Technologies, CA, USA). The RNA samples those passed the concentration, purity, and integrity tests without any degradation and contamination were used for transcriptome sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 63 chickens were equally divided into one of three treatment groups. The three groups consisted of control negative untreated non-challenged group (NC), positive control untreated challenged group (PC) and B. subtilis-fed challenged group (BS + ET).

tag: breed

value: Chinese native yellow

value: Caecum tissue

value: 28 days

tag: challenge

value: E. tenella sporulated oocysts

value: Bacillus subtilis probiotic


title: mrna_Nanos2TAG+_4

description:
mRNA, Nanos2TAG+, line 4
RNA-Seq
fpkm_tagtag_tagplus_for_cracnorm.txt

data_processing:
sequenced on a HiSeq system
gene pseudocounts were computed by kallisto, assuming mean and sd of the fragment length were 150 and 25, respectively
post-hoc analysis was carried out in R; FPKM values were computed with the fpkm function from the DESeq2 package
table of FPKM values for each gene is provided in a text file.

extract_protocol:
SSCs were depleted from feeders and RNA was extracted with QIAzol reagent following the manufacturer's instructions.
Total RNA was treated with DNAse I and Ribo-depleted. Libraries were generated with SENSE Total RNA-seq Library Prep Kit (Lexogen) following the manufacturer's instructions.


title: slam_Nanos2TAGTAG_5_0min rep1

description:
SLAM-seq, Nanos2TAGTAG, line 5, 0min
OTHER – SLAM-Seq
half_life_EXP.csv

data_processing:
sequenced on a HiSeq system
T-C conversion ratios were computed by slamdunk v0.3.7
post-hoc normalisation of T-C conversion ratios and fitting of simple decaying exponentials to determine transcript half-life were carried out with in-house R-scripts.
half-life values are provided for each gene name


title: NR18_2


title: BS+ET-2


title: Hindgut tissue with ETU-induced ARMs 2 on GD14 (A14_2)

description:
A14_2
Hindgut tissue of fetal rat
circ.expression.annot.txt

value: Hindgut

value: Gestational day 14


title: Hindgut tissue with ETU-induced ARMs 3 on GD14 (A14_3)

description:
A14_3
Hindgut tissue of fetal rat
circ.expression.annot.txt


title: ISG27

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

data_processing:
Fastq files were imported into Partek Flow (Partek Incorporated, Missouri, USA).
Quality analysis and quality control were performed on all reads to assess read quality and to determine the amount of trimming required (both ends: 13 bases 5´and 1 base 3´).
Trimmed reads were aligned against the hg38 genome using the STAR v2.4.1d aligner. Unaligned reads were further processed using Bowtie 2 v2.2.5 aligner.
Aligned reads were combined before quantifying the expression against the ENSEMBL (release 95) database by the Partek Expectation-Maximization algorithm using the counts per million normalization.
Genes with missing values and with a mean expression less than one were filtered out
Genome_build: mmu10
Supplementary_files_format_and_content: txt

source_name: Sca1-ETV6-RUNX1+ Kdm5c-het B-ALL

extract_protocol:
RNA was isolated using Qiagen kit
500 ng total RNA was processed using the TruSeq RNA Sample Preparation v2 Kit (low-throughput protocol; Illumina, San Diego, USA) to prepare the barcoded libraries.
Libraries were validated and quantified using DNA 1000 and high-sensitivity chips on a Bioanalyzer (Agilent, Böblingen, Germany); 7.5 pM denatured libraries were used as input into cBot (Illumina), followed by deep sequencing using HiSeq 2500 (Illumina) for 101 cycles, with an additional seven cycles for index reading.

tag: alteration background

value: Sca1-ETV6-RUNX1+ Kdm5c-het

value: B-ALL

tag: disease state

value: Tumor


title: Hindgut tissue with ETU-induced ARMs 1 on GD14 (A14_1)

description:
A14_1
Hindgut tissue of fetal rat
circ.expression.annot.txt

tag: diagnosis

value: Ethylenethiourea (ETU)-induced anorectal malformations (ARMs)


title: NR18_1

value: 18 hpf


title: PC-3

source_name: Control positive untreated challenged with Eimeria tenella

tag: age


title: ISG26


title: ISG25

source_name: WT T cells

value: WT

value: T cells

value: Control


title: PG_3

source_name: sorted retinal progenitor cells

value: sorted retinal progenitor cells

value: 16 hpf


title: PC-2

value: Chinese native yellow


title: mrna_Nanos2TAGTAG_5

description:
mRNA, Nanos2TAGTAG, line 5
RNA-Seq
fpkm_tagtag_tagplus_for_cracnorm.txt

extract_protocol:
SSCs were depleted from feeders and RNA was extracted with Trizol.
Total RNA was treated with DNAse I and Ribo-depleted. Libraries were generated with SENSE Total RNA-seq Library Prep Kit (Lexogen) following the manufacturer's instructions.


title: PG_2


title: PC-1

value: Caecum tissue


title: PG_1


title: ISG24


title: NC-3

source_name: Control negative untreated non-challenge

value: 28 days


title: ISG23


title: E_NR_2

data_processing:
each file were aligned to the danRer10 zebrafish genome and peaks were called with MACS2 as described in Magri et al., 2019
Genome_build: danRer10
Supplementary_files_format_and_content: bed files reporting genome coordinates for each peak snd its relative raw count value

source_name: sorted Neural Retina cells

extract_protocol:
genomic DNA was tagmented as described in Corces et al., 2016
manufacturer's protocol of NEBNext® High-Fidelity 2X PCR Master Mix (NEB #M0544)

tag: Stage

value: 23 hpf

tag: genotype/variation

value: sorted Neural Retina cells


title: BS+ET-1

value: E. tenella sporulated oocysts

value: Bacillus subtilis probiotic


title: NC-2


title: ISG22


title: D_NR_1


title: ISG21

source_name: WT pro-B cells

value: pro-B cells


title: C_RPE_2

value: sorted RPE cells


title: NC-1


title: ISG20


title: A_RPE_1


title: B_1_Vero-Stx.txt

city: Shinjuku-ku

first: Tsuyoshi

last: Sekizuka

state: Tokyo

address: 1-23-1 Toyama

department: Pathogen Genomics Center

country: Japan

institute: National Institute of Infectious Diseases

description:
GeCKO v2 library B, biological replicate 1, Stx treatment, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibB-normalized-compare.txt
Vero-Stx_GeCKOv2_LibB_mageck-result.sgrna_summary.txt
Vero-Stx_GeCKOv2_LibB_mageck.gene_summary.txt

data_processing:
Illumina RTA1.18.54 software used for basecalling
5' and 3' adapter and low quality trimming using skewer program (version 0.1.126)
Quality filtering (at Phred >= Q20) with split_libraries_fastq.py (version 1.9.1) of QIIME program
Read count of sgRNA using "sort" and "uniq" of unix command program
Reads align to sgRNA of Human GeCKO v2 library A/B
Normalization with following formula; normalized reads per sgRNA = reads per sgRNA / total reads for all sgRNAs in sample x 10^7
Statistic analysis using MAGeCK program (version 0.5.7)
Genome_build: Human GeCKO v2 library A/B
Supplementary_files_format_and_content: tab-delimited text files include raw read count, normalized read count and result of analysis with MAGeCK program.

organism: Chlorocebus sabaeus

source_name: Vero C1008

growth_protocol: Vero C1008 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) with 7.5μg/ml blasticidin. Vero C1008 cells were infected with the pooled lentiviruses to express sgRNAs.

extract_protocol:
Genomic DNA from the frozen cells was purified by the conventional phenol-chloroform method.
First PCR amplification was carried out with 20 cycles using PrimeStar GXL DNA polymerase (Takara, Otsu, Japan) and the following primers (9 forward primers and 1 reverse primer): (Fw) 1stY1R1s0-8: CTACACGACGCTCTTCCGATCT[-/N/NN/NNN/NNNN/NNNNN/NNNNNN/NNNNNNN/NNNNNNNN]TCTTGTGGAAAGGACGAAACACCG (included 0-8 bp random sequence for increasing library complexity); and (Rv) 1stY2as: GCCACTTTTTCAAGTTGATAACGGACTAG. Second PCR amplification was carried out with 10 cycles using the following primers: (Fw) 2nd P5R1s:  AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; and (Rv) 2nd P7Y2as: CAAGCAGAAGACGGCATACGAGAT[CC/TT/AA/GG]GCCACTTTTTCAAGTTGATAACGGACTAG (included barcodes for multiplexing of different samples).
Amplicon sequencing of sgRNA in GeCKO v2.0 library plasmid

treatment_protocol: The sgRNA-expressing cells were treated with 10 ng/ml Stx twice in two weeks.

tag: cell line

value: Vero C1008

value: Stx


title: B_2_Vero-Stx.txt

description:
GeCKO v2 library B, biological replicate 2, Stx treatment, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibB-normalized-compare.txt
Vero-Stx_GeCKOv2_LibB_mageck-result.sgrna_summary.txt
Vero-Stx_GeCKOv2_LibB_mageck.gene_summary.txt


title: A_2_Vero-Stx.txt

description:
GeCKO v2 library A, biological replicate 2, Stx treatment, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibA-normalized-compare.txt
Vero-Stx_GeCKOv2_LibA_mageck-result.sgrna_summary.txt
Vero-Stx_GeCKOv2_LibA_mageck.gene_summary.txt


title: A_1_Vero-Stx.txt

description:
GeCKO v2 library A, biological replicate 1, Stx treatment, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibA-normalized-compare.txt
Vero-Stx_GeCKOv2_LibA_mageck-result.sgrna_summary.txt
Vero-Stx_GeCKOv2_LibA_mageck.gene_summary.txt


title: ISG17

source_name: Pax5-het B-ALL

value: B-ALL

value: Tumor


title: 6D: NOMO-1 Nut-3a+WIP1i #2

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

description: Gene expression data of NOMO-1 cells after 16h of treatment with Nutlin-3a (5 mM) and GSK2830371 (20 mM)

hyb_protocol: Sample hybridization was performed for 16 hours at 45°C according to standard protocol. Washing and staining was performed on an Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned using a GeneChip scanner 3000 (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 (Thermo Fisher Scientific). Normalization was performed using the Signal Space Transformation-Robust multiple-array average normalization method (sst-RMA).

label: biotin

label_protocol: ss-cDNA was prepared from 100 ng total RNA according to the standard protocol (GeneChip® WT PLUS Reagent Kit User Guide, 2018, Thermo Fisher Scientific).

growth_protocol: Cells were cultured in RPM1 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml of penicillin and 100 μg/ml of streptomycin

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

treatment_protocol: Cells were treated with Nutlin-3a or GSK2830371 or the drug combination for 16h before harvesting.

value: acute myeloid leukemia


title: ISG16


title: B_2_control.txt

description:
GeCKO v2 library B, biological replicate 2, control, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibB-normalized-compare.txt
Vero-Stx_GeCKOv2_LibB_mageck-result.sgrna_summary.txt
Vero-Stx_GeCKOv2_LibB_mageck.gene_summary.txt

value: control


title: 320: NOMO-1 Nut-3a+WIP1i #3

source_name: NOMO-1 cells after 16h of treatment with Nutlin-3a (5 mM) and GSK2830371 (20 mM)


title: B_1_control.txt

description:
GeCKO v2 library B, biological replicate 1, control, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibB-normalized-compare.txt
Vero-Stx_GeCKOv2_LibB_mageck-result.sgrna_summary.txt
Vero-Stx_GeCKOv2_LibB_mageck.gene_summary.txt


title: ISG19

value: WT

value: Control


title: ISG15


title: 322: NOMO-1 Nut-3a #3

description: Gene expression data of NOMO-1 cells after 16h of treatment with Nutlin-3a (5 mM)


title: ISG14


title: 5D: NOMO-1 Nut-3a+WIP1i #1


title: 323: NOMO-1 WIP1i #3

description: Gene expression data of NOMO-1 cells after 16h of treatment with GSK2830371 (20 mM)


title: DP WT2

city: Pohang

first: Soeun

last: Kim

address: 77, Cheongam-ro

country: South Korea

institute: POSTECH

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated.
Artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed to reduce biases.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Transcripts are assembled by StringTie with aligned reads, to provide information of known transcripts, novel transcripts, and alternatively spliced transcripts.
Expression profiles are represented as read count and normalization value, based on the transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value is used as a normalization value.
Genome_build: mm10
Supplementary_files_format_and_content: List of differentially expressed genes (DEGs) between WT and CIC-deficient DP cells are presented in data2.xlsx file. KO versus WT fold change, p-value, mean, FPKM and read count for each sample are also shown in data2.xlsx file.

source_name: DP thymocytes

extract_protocol:
The thymus from each mouse was dissected and homogenized into single-cell suspensions for cell sorting. DP thymocytes were sorted by a MoFlo-XDP (Beckman Coulter) on the basis of surface markers of lin-CD4+CD8+TCRlo (Lineage : CD11b, CD11c, CD19, NK1.1, Gr-1, γδTCR, and TER119) and total RNA was extracted with RiboEx (GeneAll, Seoul, Republic of Korea) according to the manufacturer's protocol.
The library for mRNA sequencing was generated using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequencing was performed with NovaSeq 6000 (Illumina).

tag: strain

value: thymus

value: Cicf/f


title: DP WT1

tag: tissue


title: DP KO1


title: ISG18


title: A_2_control.txt

description:
GeCKO v2 library A, biological replicate 2, control, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibA-normalized-compare.txt
Vero-Stx_GeCKOv2_LibA_mageck-result.sgrna_summary.txt
Vero-Stx_GeCKOv2_LibA_mageck.gene_summary.txt

tag: treatment


title: 319: NOMO-1 WIP1i #2

source_name: NOMO-1 cells after 16h of treatment with GSK2830371 (20 mM)


title: DP KO2


title: RNA-Seq P4

data_processing:
Raw sequencing data was processed via the Cell Ranger pipeline (10xGenomics, version 2.0.1) to generate a count matrix from the bcl files.
Genome_build: mm10 (GRCm38.84)
Supplementary_files_format_and_content: filtered feature-barcode matrices HDF5

source_name: mouse brain cortex

extract_protocol:
For single cell RNA seq, tissue pieces were processed to obtain single cell suspension using papain digestion (15-30 minutes according to embryo age) (Papain dissociation kit, Worthington). We followed the protocol as per the provider’s instructions.  After dissociation and concentration, cells were resuspended in BSA 0.04% in PBS, at a concentration of 800-1200 cells/uliter. Cells were counted in a hemocytometer chamber and immediately processed for single cell GEM formation (10x Genomics, single cell RNA sequencing 3’, Chromium V2 or V3 for Fezf2 experiments).
For single cell RNA seq we loaded the 10x chips aiming to recover 7,000–10,000 cells.cDNA amplification and library construction were done following 10xGenomics instructions. For the complete wild type developmental atlas we generated Chromium V2 libraries, while Chromium V3 was used for all Fezf2 experiments. Libraries were quantified in BioAnalyzer and sequenced in HiSeq or NovaSeq illumina platforms.
single cell RNA sequencing 3’, Chromium V2 or V3

treatment_protocol: For embryos E14.5 or younger we dissected the head, for older animals we isolated the brains. Dissection was performed in Hybernate E (Brainbits). The tissue was then embedded in 3% low melting agarose at 35-37C. Once the agarose solidified, the tissue was sectioned in 250um thick sections in a vibratome in iced Hybernate E. Sections were transferred to another plate and the prospective somatosensory cortex was dissected and meninges removed. For the earliest time points (E10.5, E11.5 and E12.5) the prospective somatosensory cortex (medio-lateral region) was dissected without prior sectioning. Tissue was kept in cold buffers and on ice all time. RNAse free technique was used for handling. Cortical tissue from 4 animals was pulled together for each timepoint. For the Fezf2 experiments, samples were directly dissected from the cortex and processed individually, till genotype confirmation, when we combined samples from embryos with the same genotype. We genotyped embryos through PCR and qPCR on DNA extracted quickly from tail clips (QuickExtract DNA Extraction Solution, Lucigen), and through B-galactosidase detection assays.

value: somatosensory cortex

value: wild type

tag: chromium single cell 3' solution chemistry


title: ISG13

source_name: Sca1-ETV6-RUNX1+Pax5-het B-ALL

tag: cell type


title: 6C: NOMO-1 WIP1i #1