title: H10A_Control_1


title: G8A_Control_1

status: Public on Mar 06 2019

type: SRA

city: Stanford

first: Sabina

last: Kanton

state: CA

address: 318 Campus Drive

department: Psychiatry and Behavioral Sciences

country: USA

institute: Stanford University

description:
dissected cerebral organoid
Data_Fat4_Dchs1_805cells.csv

library_source: transcriptomic

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers for SmartSeq2 data (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.). Cellranger (v 2.1.0) was used for basecalling for 10X data.
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.). For 10X data, demultiplexing was performed using Cellranger (v 2.1.0).
or SmartSeq2 data, reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.9. For 10X data, alignment to GRCh38 was performed using Cellranger (v 2.1.0).
For SmartSeq2 data, Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1. For 10X data, gene count matrix was computed using Cellranger (v 2.1.0)
For 10X data, barcode is found in R1 from bp 1-16 and UMI is found in bp 17-26.
Genome_build: GRCh38.77
Supplementary_files_format_and_content: For SmartSeq2 data, data frame including sample name, gene ID, and FPKM values for each single cell. For 10X data, log transformed and normalized gene expression values as computed by Seurat (v 2.3.0) with gene IDs and cell barcode information for Dchs1 and Ctrl cells used in further analysis.

molecule: polyA RNA

organism: Homo sapiens

source_name: iPSC Control

growth_protocol: Cerebral organoids were generated according to Lancaster et al. (Nature Protocols, 2014). Neurons were differentiated according to Boyer et al. (Current Prot Stem Cell Biol, 2012, PMID:22872424).

extract_protocol:
Single cells from dissociated organoids were sorted into 96 well plates using FACS and cDNA was obtained using SmartSeq2 protocol (Picelli et al., Nature Protocols, 2014). Neurons from 2d culture were encapsulated into droplets and cDNA was generated using 10X Genomics single cell 3' v2 kit.
Libraries for SmartSeq2 data were generated using the NexteraXT kit. Libraries from 2d cultured neurons were generated using the 10X Genomics 3' Single Cell v2 kit.

treatment_protocol: Dissected regions of organoids were dissociated into single cell suspensions using Papain-based (Neural tissue dissociation kit, Miltenyi Biotec) dissociation with intermittend triturations. Cell suspensions underwent several filtering (30um, 20um) and washing steps (using HBSS). Neuronal cells in 2D culture.  were brought into single cell suspension using 1% (v/v) Accutase (Sigma) in DPBS/EDTA  (0.5 mM, Gibco, Invitrogen)

tag: Stage

value: 51 days

tag: tissue

value: Control organoid 1

tag: scrna-seq protocol


title: G9A_Control_1


title: G5A_Control_1


title: G6A_Control_1


title: G11A_Control_1


title: F9A_Control_1


title: F4A_Control_1


title: G12A_Control_1


title: F6A_Control_1


title: F7A_Control_1


title: F3A_Control_1


title: C11B_Control_2

value: Control organoid 2


title: Sca-1-CD45+ rep 1

type: RNA

city: Adelaide

first: Peter

middle: James

last: Psaltis

state: South Australia

address: North Terrace

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

description: Biological Replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The log-2 of the gene expression data was normalised using the non-linear normalisation fastlo
To assess differential expression between groups of interest, the LIMMA package in R was utilised to implement the empirical Bayes method of Smyth to shrink the gene-wise sample variances towards a common value.  The false discovery rate (FDR 44), which is the expected proportion of false discoveries amongst the rejected hypotheses, was also calculated.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: aortic adventitia

label_protocol: High-quality samples were labelled according to instructions for the Illumina Direct Hyb labelling method (San Diego, CA, USA).

extract_protocol: Total RNA was isolated and purified immediately using an RNeasy® Plus Mini Kit (Qiagen, Germany), as per manufacturer's instructions. The quality of all total RNA samples was assessed according to manufacturer’s instructions for the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: strain

tag: age

value: 12 weeks

value: aortic adventitia


title: F1A_Control_1


title: F11A_Control_1


title: H6A_Control_1


title: H4A_Control_1


title: H7A_Control_1


title: F10A_Control_1


title: H11A_Control_1


title: E5A_Control_1


title: E4A_Control_1


title: E7A_Control_1


title: E6A_Control_1


title: G3A_Control_1


title: E3A_Control_1


title: E2A_Control_1


title: E1A_Control_1


title: E11A_Control_1


title: E10A_Control_1


title: E12A_Control_1


title: D9A_Control_1


title: D8A_Control_1


title: D7A_Control_1


title: D6A_Control_1


title: D4A_Control_1


title: D5A_Control_1


title: D3A_Control_1


title: C6A_Control_1


title: D10A_Control_1


title: B2A_Control_1


title: B3A_Control_1


title: C3A_Control_1


title: C8A_Control_1


title: C11A_Control_1


title: B1A_Control_1


title: E8A_Control_1


title: C10A_Control_1


title: B8A_Control_1


title: C7A_Control_1


title: B9A_Control_1


title: B11A_Control_1


title: D2A_Control_1


title: B5A_Control_1


title: C12A_Control_1


title: C1A_Control_1


title: C5A_Control_1


title: A5A_Control_1


title: A2A_Control_1


title: B10A_Control_1


title: A4A_Control_1


title: H9B_Control_3b

value: 55 days

value: Control organoid 3


title: H8B_Control_3b


title: H7B_Control_3b


title: B6A_Control_1


title: A8A_Control_1


title: H5B_Control_3b


title: H4B_Control_3b


title: A9A_Control_1


title: H11B_Control_3b


title: G9B_Control_3b


title: G8B_Control_3b


title: H3B_Control_3b


title: G6B_Control_3b


title: H6B_Control_3b


title: G3B_Control_3b


title: G2B_Control_3b


title: H10B_Control_3b


title: G12B_Control_3b


title: G1B_Control_3b


title: G11B_Control_3b


title: G4B_Control_3b


title: H12B_Control_3b


title: G10B_Control_3b


title: G5B_Control_3b


title: F9B_Control_3b


title: F7B_Control_3b


title: F6B_Control_3b


title: F5B_Control_3b


title: F4B_Control_3b


title: H1B_Control_3b


title: G7B_Control_3b


title: F1B_Control_3b


title: H2B_Control_3b


title: F3B_Control_3b


title: F12B_Control_3b


title: F10B_Control_3b


title: E8B_Control_3b


title: E9B_Control_3b


title: E5B_Control_3b


title: E3B_Control_3b


title: E2B_Control_3b


title: F8B_Control_3b


title: E6B_Control_3b


title: E12B_Control_3b


title: E11B_Control_3b


title: D9B_Control_3b


title: D8B_Control_3b


title: E10B_Control_3b


title: E1B_Control_3b


title: E4B_Control_3b


title: D4B_Control_3b


title: D2B_Control_3b


title: D7B_Control_3b


title: D3B_Control_3b


title: D5B_Control_3b


title: D6B_Control_3b


title: WT2

city: New York

first: Christopher

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

description:
WT_vs_Mdxmtr.deseq.counts.txt
WT_vs_Mdxmtr.deseq.txt

data_processing:
Quality assessment and fold change calculations were performed in BaseSpace (Illumina).
Sequencing data was quality checked using FastQC, aligned to the reference genome (mm10, UCSC, Santa Cruz, CA, USA) with the STAR software package.
Differential expression based on fragments per kilobase of transcript per million mapped reads was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2

source_name: Tibialis anterior muscle

extract_protocol:
RNA was isolated from TA muscles using a miRNEasy kit (Qiagen, Valencia, CA, USA). RNA quality was assessed using a TapeStation (Agilent, Santa Clara, CA, USA) and all samples had a RNA integrity number greater than 9.0. For each sample, 250ng total RNA was delivered to the University of Michigan Sequencing Core for RNA sequencing (RNAseq) analysis. Sample concentrations were normalized, and cDNA pools were created for each sample, and then subsequently tagged with a barcoded oligo adapter to allow for sample specific resolution.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4 months

tag: Sex

value: Male


title: D1B_Control_3b


title: D11B_Control_3b


title: D12B_Control_3b


title: D10B_Control_3b


title: E7B_Control_3b


title: C9B_Control_3b


title: C7B_Control_3b


title: C8B_Control_3b


title: C6B_Control_3b


title: C3B_Control_3b


title: C4B_Control_3b


title: C2B_Control_3b


title: C5B_Control_3b


title: C1B_Control_3b


title: B9B_Control_3b


title: C12B_Control_3b


title: B5B_Control_3b


title: B8B_Control_3b


title: C11B_Control_3b


title: B7B_Control_3b


title: C10B_Control_3b


title: B6B_Control_3b


title: B4B_Control_3b


title: B3B_Control_3b


title: B12B_Control_3b


title: B1B_Control_3b


title: B11B_Control_3b


title: B2B_Control_3b


title: A8B_Control_3b


title: A6B_Control_3b


title: A5B_Control_3b


title: A4B_Control_3b


title: A3B_Control_3b


title: A1B_Control_3b


title: A2B_Control_3b


title: A12B_Control_3b


title: H6A_Dchs1_2

source_name: iPSC Dchs1

value: Dchs1 organoid 2


title: H7A_Dchs1_2


title: H11A_Dchs1_2


title: H2A_Dchs1_2


title: A9B_Control_3b


title: H10A_Dchs1_2


title: G4A_Dchs1_2


title: G6A_Dchs1_2


title: G2A_Dchs1_2


title: H5A_Dchs1_2


title: G5A_Dchs1_2


title: G1A_Dchs1_2


title: H3A_Dchs1_2


title: G11A_Dchs1_2


title: B10B_Control_3b


title: G10A_Dchs1_2


title: A7B_Control_3b


title: F8A_Dchs1_2


title: G3A_Dchs1_2


title: F7A_Dchs1_2


title: F4A_Dchs1_2


title: F5A_Dchs1_2


title: A10B_Control_3b


title: F1A_Dchs1_2


title: A11B_Control_3b


title: F6A_Dchs1_2


title: F3A_Dchs1_2


title: G7A_Dchs1_2


title: F10A_Dchs1_2


title: E7A_Dchs1_2


title: E5A_Dchs1_2


title: E4A_Dchs1_2


title: E6A_Dchs1_2


title: E1A_Dchs1_2


title: E10A_Dchs1_2


title: D6A_Dchs1_2


title: D8A_Dchs1_2


title: D9A_Dchs1_2


title: D4A_Dchs1_2


title: E3A_Dchs1_2


title: E2A_Dchs1_2


title: D3A_Dchs1_2


title: E11A_Dchs1_2


title: D2A_Dchs1_2


title: D5A_Dchs1_2


title: D7A_Dchs1_2


title: D1A_Dchs1_2


title: F12A_Dchs1_2


title: D12A_Dchs1_2


title: D10A_Dchs1_2


title: D11A_Dchs1_2


title: C7A_Dchs1_2


title: C6A_Dchs1_2


title: C9A_Dchs1_2


title: C8A_Dchs1_2


title: E8A_Dchs1_2


title: C4A_Dchs1_2


title: C5A_Dchs1_2


title: E12A_Dchs1_2


title: C1A_Dchs1_2


title: C2A_Dchs1_2


title: C12A_Dchs1_2


title: C3A_Dchs1_2


title: C10A_Dchs1_2


title: C11A_Dchs1_2


title: B4A_Dchs1_2


title: B8A_Dchs1_2


title: B5A_Dchs1_2


title: B9A_Dchs1_2


title: B12A_Dchs1_2


title: B10A_Dchs1_2


title: B3A_Dchs1_2


title: A3A_Dchs1_2


title: A5A_Dchs1_2


title: A12A_Dchs1_2


title: A7A_Dchs1_2


title: A6A_Dchs1_2


title: A10A_Dchs1_2


title: H9B_Fat4_2

source_name: iPSC Fat4

value: Fat4 organoid 2


title: A8A_Dchs1_2


title: A2A_Dchs1_2


title: H5B_Fat4_2


title: H7B_Fat4_2


title: H6B_Fat4_2


title: H8B_Fat4_2


title: H3B_Fat4_2


title: H4B_Fat4_2


title: B1A_Dchs1_2


title: A9A_Dchs1_2


title: H2B_Fat4_2


title: G9B_Fat4_2


title: G8B_Fat4_2


title: H10B_Fat4_2


title: G7B_Fat4_2


title: G6B_Fat4_2


title: G5B_Fat4_2


title: G4B_Fat4_2


title: G2B_Fat4_2


title: F7B_Fat4_2


title: F9B_Fat4_2


title: G11B_Fat4_2


title: F6B_Fat4_2


title: F12B_Fat4_2


title: F1B_Fat4_2


title: F3B_Fat4_2


title: F4B_Fat4_2


title: F10B_Fat4_2


title: F8B_Fat4_2


title: E8B_Fat4_2


title: E6B_Fat4_2


title: E5B_Fat4_2


title: E7B_Fat4_2


title: E4B_Fat4_2


title: F5B_Fat4_2


title: E3B_Fat4_2


title: E12B_Fat4_2


title: E1B_Fat4_2


title: E2B_Fat4_2


title: E11B_Fat4_2


title: E10B_Fat4_2


title: E9B_Fat4_2


title: G3B_Fat4_2


title: D9B_Fat4_2


title: G10B_Fat4_2


title: D7B_Fat4_2


title: D8B_Fat4_2


title: G1B_Fat4_2


title: D6B_Fat4_2


title: D3B_Fat4_2


title: D4B_Fat4_2


title: C9B_Fat4_2


title: D10B_Fat4_2


title: D12B_Fat4_2


title: C7B_Fat4_2


title: C5B_Fat4_2


title: C3B_Fat4_2


title: C2B_Fat4_2


title: C6B_Fat4_2


title: C4B_Fat4_2


title: C8B_Fat4_2


title: B8B_Fat4_2


title: C12B_Fat4_2


title: B5B_Fat4_2


title: B9B_Fat4_2


title: B3B_Fat4_2


title: B6B_Fat4_2


title: C1B_Fat4_2


title: C11B_Fat4_2


title: B1B_Fat4_2


title: A7B_Fat4_2


title: A8B_Fat4_2


title: C10B_Fat4_2


title: D1B_Fat4_2


title: A6B_Fat4_2


title: A9B_Fat4_2


title: D5B_Fat4_2


title: A4B_Fat4_2


title: A3B_Fat4_2


title: A1B_Fat4_2


title: A11B_Fat4_2


title: A10B_Fat4_2


title: B7B_Fat4_2


title: H7A_Fat4_3

value: Fat4 organoid 3


title: H5A_Fat4_3


title: H4A_Fat4_3


title: D11B_Fat4_2


title: H8A_Fat4_3


title: G9A_Fat4_3


title: H1A_Fat4_3


title: H2A_Fat4_3


title: H6A_Fat4_3


title: G6A_Fat4_3


title: G3A_Fat4_3


title: G2A_Fat4_3


title: A12B_Fat4_2


title: G10A_Fat4_3


title: G11A_Fat4_3


title: H9A_Fat4_3


title: G1A_Fat4_3


title: G4A_Fat4_3


title: A5B_Fat4_2


title: F7A_Fat4_3


title: F6A_Fat4_3


title: F4A_Fat4_3


title: F3A_Fat4_3


title: F1A_Fat4_3


title: G8A_Fat4_3


title: E9A_Fat4_3


title: E8A_Fat4_3


title: F10A_Fat4_3


title: E7A_Fat4_3


title: G5A_Fat4_3


title: E5A_Fat4_3


title: E4A_Fat4_3


title: E3A_Fat4_3


title: E1A_Fat4_3


title: E6A_Fat4_3


title: E12A_Fat4_3


title: E2A_Fat4_3


title: D9A_Fat4_3


title: D8A_Fat4_3


title: E11A_Fat4_3


title: F8A_Fat4_3


title: F9A_Fat4_3


title: D4A_Fat4_3


title: F5A_Fat4_3


title: D7A_Fat4_3


title: D3A_Fat4_3


title: D2A_Fat4_3


title: D1A_Fat4_3


title: D11A_Fat4_3


title: C9A_Fat4_3


title: D6A_Fat4_3


title: C8A_Fat4_3


title: C7A_Fat4_3


title: C5A_Fat4_3


title: C2A_Fat4_3


title: C4A_Fat4_3


title: E10A_Fat4_3


title: C3A_Fat4_3


title: C11A_Fat4_3


title: C1A_Fat4_3


title: D10A_Fat4_3


title: C10A_Fat4_3


title: D5A_Fat4_3


title: C6A_Fat4_3


title: B8A_Fat4_3


title: B9A_Fat4_3


title: B6A_Fat4_3


title: P0 cortex_ Dyrk1a+/+_Biological replica 3

city: Barcelona

first: Susana

last: de la Luna

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

description:
P0C2W2
Gene expression data from the cerebral cortex of a Dyrk1a+/+ wild type mouse at postnatal day 0

hyb_protocol: After cRNA purification and fragmentation, 15 µg of fragmented cRNA were added to the hybridization mix and used to fill the Affymetrix Mouse GeneChip 430 2.0 Array cartridge. The arrays were hybridized at 60ºC for 16 h with rotation in the Affymetrix GeneChip Hyb Oven 640. The cartridges were washed and marked with streptavidin R-phycoerythrin using the protocol provided by Affymetrix

scan_protocol: the arrays were scanned in an Affymetrix GCS3000 GeneArray Scanner.

data_processing: The images were processed with Microarray Analysis Suite 5.0 (Affymetrix) and cRNA quality was checked (3'/5' ratio of probe sets <1.5, for Gapdh and Actb probes). Raw values obtained from .CEL files were pre-processed using the Robust Multiarray Averaging Method (Irizarry at al, 2003) and the resulting normalized values were used for all subsequent analyses

label: biotin

source_name: P0 cerebral cortex_wild type

label_protocol: Double stranded cDNA was synthesized from 100 ng RNA using the Two Cycle cDNA Synthesis Kit (Affymetrix, Inc.) which incorporates a T7 RNA polymerase promoter, and transcribed in vitro to obtain biotin labeled cRNA, following the kit’s instructions

growth_protocol: Mice were sacrificed by decapitation and cerebral cortices were dissected and stored at -80ºC

extract_protocol: Total RNA was extracted with TriPure Isolation Reagent (Roche). A step of RNA clean-up was performed using RNeasy Mini Kit (Qiagen) and a final step of DNAse treatment was done (DNAse I, Ambion)

treatment_protocol: Frozen samples were homogenized with a Polytron

tag: genotype/variation

tag: developmental stage

value: postnatal day 0

value: cerebral cortex


title: P7 cortex_ Dyrk1a+/-_Biological replica 3

description:
P7C1M2
Gene expression data from the cerebral cortex of a Dyrk1a+/- mutant mouse at postnatal day 7

source_name: P7 cerebral cortex_Dyrk1a+/- mutant

value: postnatal day 7


title: P0 cortex_ Dyrk1a+/+_Biological replica 4

description:
P0C3W2
Gene expression data from the cerebral cortex of a Dyrk1a+/+ wild type mouse at postnatal day 0


title: P7 cortex_ Dyrk1a+/+_Biological replica 4

description:
P7C4W2
Gene expression data from the cerebral cortex of a Dyrk1a+/+ wild type mouse at postnatal day 7

source_name: P7 cerebral cortex_wild type


title: B4A_Fat4_3


title: P0 cortex_ Dyrk1a+/-_Biological replica 2

description:
P0C3M1
Gene expression data from the cerebral cortex of a Dyrk1a+/- mutant mouse at postnatal day 0

source_name: P0 cerebral cortex_Dyrk1a+/- mutant


title: B5A_Fat4_3


title: P0 cortex_ Dyrk1a+/-_Biological replica 3

description:
P0C2M2
Gene expression data from the cerebral cortex of a Dyrk1a+/- mutant mouse at postnatal day 0


title: P7 cortex_ Dyrk1a+/+_Biological replica 3

description:
P7C1W2
Gene expression data from the cerebral cortex of a Dyrk1a+/+ wild type mouse at postnatal day 7


title: P7 cortex_ Dyrk1a+/-_Biological replica 1

description:
P7C1M1
Gene expression data from the cerebral cortex of a Dyrk1a+/- mutant mouse at postnatal day 7


title: P7 cortex_ Dyrk1a+/+_Biological replica 1

description:
P7C1W1
Gene expression data from the cerebral cortex of a Dyrk1a+/+ wild type mouse at postnatal day 7


title: Utrecht_diffSSc_8

city: Utrecht

first: Nila

middle: Hendrika

last: Servaas

address: Lundlaan 6

department: Laboratory for translational immunology

country: Netherlands

institute: UMC Utrecht

data_processing:
Real-time base calling on the HiSeq 2000 sequencer (Illumina)
Quality filtering according to the Illumina pipeline
After quality filtering according to the BGI pipeline, reads were aligned to the GrCh37 reference human genome (Genome Reference consortium) and the H. sapiens transcriptome (Ensembl) using SOAPaligner/SOAP2 (yu S Bioinformatics 2009)
Summed exon read counts per gene were calculated using HTSeq-count.
A filter was applied to exclude all genes with a mean reads per kilobase per million mapped reads (RPKM) lower than 0.1
Genome_build: GrCh37
Supplementary_files_format_and_content: Reads per kilobase per million mapped reads (RPKM)

source_name: CD14+ monocytes

extract_protocol:
Human CD14+ monocytes were purified from heparinised whole blood of SSc patients and matched healthy donors after centrifugation over Ficoll-Paque gradient. Briefly, CD14+ monocytes were purified from PBMCs using the anti-CD14 microbeads (Miltenyi Biotec), on the autoMACs Pro Separator (Miltenyi Biotec) according to manufacturer’s protocol. Cells were lysed in RLTplus buffer (Qiagen) containing 1% (v/v) beta-mercaptoethanol (Sigma). Total RNA was purified with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. DNAse treatment (RNAse Free DNase I set, Qiagen) on column was performed.
RNA-Seq library preparation was accomplished using the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA, USA).

tag: cell type

value: CD14+ monocytes

value: Peripheral blood

tag: cohort

value: Utrecht - definite SSc

tag: disease state

value: diffuse systemic sclerosis


title: Utrecht_diffSSc_9


title: B3A_Fat4_3


title: P0 cortex_ Dyrk1a+/+_Biological replica 1

description:
P0C2W1
Gene expression data from the cerebral cortex of a Dyrk1a+/+ wild type mouse at postnatal day 0


title: P0 cortex_ Dyrk1a+/-_Biological replica 1

description:
P0C2M1
Gene expression data from the cerebral cortex of a Dyrk1a+/- mutant mouse at postnatal day 0


title: Utrecht_diffSSc_5


title: P7 cortex_ Dyrk1a+/+_Biological replica 2

description:
P7C4W1
Gene expression data from the cerebral cortex of a Dyrk1a+/+ wild type mouse at postnatal day 7


title: Utrecht_diffSSc_4


title: P0 cortex_ Dyrk1a+/+_Biological replica 2

description:
P0C3W1
Gene expression data from the cerebral cortex of a Dyrk1a+/+ wild type mouse at postnatal day 0


title: P0 cortex_ Dyrk1a+/-_Biological replica 4

description:
P0C3M2
Gene expression data from the cerebral cortex of a Dyrk1a+/- mutant mouse at postnatal day 0


title: P7 cortex_ Dyrk1a+/-_Biological replica 2

description:
P7C4M1
Gene expression data from the cerebral cortex of a Dyrk1a+/- mutant mouse at postnatal day 7


title: P7 cortex_ Dyrk1a+/-_Biological replica 4

description:
P7C4M2
Gene expression data from the cerebral cortex of a Dyrk1a+/- mutant mouse at postnatal day 7


title: B1A_Fat4_3

description:
dissected cerebral organoid
Data_Fat4_Dchs1_805cells.csv


title: B7A_Fat4_3


title: Utrecht_diffSSc_2


title: Utrecht_diffSSc_7


title: B10A_Fat4_3


title: A9A_Fat4_3


title: A8A_Fat4_3


title: Utrecht_limSSc_11

value: limited systemic sclerosis


title: Utrecht_diffSSc_1


title: A6A_Fat4_3


title: Utrecht_limSSc_10


title: Utrecht_limSSc_9


title: A7A_Fat4_3


title: A5A_Fat4_3


title: Utrecht_limSSc_6


title: Utrecht_limSSc_7


title: A4A_Fat4_3


title: A2A_Fat4_3


title: H9B_Fat4_1

value: 51 days

value: Fat4 organoid 1


title: A1A_Fat4_3

value: 55 days


title: Utrecht_limSSc_5


title: H7B_Fat4_1


title: G9B_Fat4_1


title: H12B_Fat4_1


title: Utrecht_limSSc_2


title: Utrecht_limSSc_3


title: Utrecht_ncSSc_8

value: non-cutaneous systemic sclerosis


title: Utrecht_ncSSc_7


title: G8B_Fat4_1


title: Utrecht_ncSSc_6


title: G7B_Fat4_1


title: Utrecht_limSSc_4


title: Utrecht_ncSSc_5


title: G6B_Fat4_1


title: Utrecht_limSSc_1


title: Utrecht_limSSc_8


title: G5B_Fat4_1


title: G3B_Fat4_1


title: Utrecht_ncSSc_1


title: Utrecht_ncSSc_3


title: G1B_Fat4_1


title: Utrecht_HC_11

value: Healthy donor


title: G2B_Fat4_1


title: G12B_Fat4_1


title: G11B_Fat4_1


title: Utrecht_HC_8


title: Utrecht_HC_10


title: G10B_Fat4_1


title: Utrecht_HC_6


title: F9B_Fat4_1


title: Utrecht_HC_7


title: F8B_Fat4_1


title: F7B_Fat4_1


title: Utrecht_HC_5


title: Utrecht_HC_4


title: Utrecht_HC_2


title: Utrecht_HC_1


title: F5B_Fat4_1


title: F6B_Fat4_1


title: Utrecht_ncSSc_4


title: G7A_Fat4_3


title: F4B_Fat4_1


title: Milan_ncSSc_11

value: Milan - non-fibrotic SSc


title: Milan_ncSSc_12


title: G4B_Fat4_1


title: F3B_Fat4_1


title: Milan_ncSSc_9


title: F1B_Fat4_1


title: F10B_Fat4_1


title: Milan_ncSSc_8


title: Milan_ncSSc_7


title: Milan_ncSSc_5


title: F12B_Fat4_1


title: E9B_Fat4_1


title: E8B_Fat4_1


title: Milan_ncSSc_4


title: E7B_Fat4_1


title: Milan_ncSSc_3


title: E5B_Fat4_1


title: E6B_Fat4_1


title: Milan_eaSSc_12

value: early systemic sclerosis


title: Milan_eaSSc_13


title: E3B_Fat4_1


title: E4B_Fat4_1


title: Milan_eaSSc_10


title: E12B_Fat4_1


title: E1B_Fat4_1


title: Milan_eaSSc_7


title: E11B_Fat4_1


title: E2B_Fat4_1


title: Milan_eaSSc_8


title: Milan_eaSSc_6


title: E10B_Fat4_1


title: Milan_eaSSc_5


title: Milan_eaSSc_2


title: D9B_Fat4_1


title: Milan_eaSSc_1


title: Milan_ncSSc_2


title: D5B_Fat4_1


title: D8B_Fat4_1


title: Milan_ncSSc_1


title: D4B_Fat4_1


title: Milan_RP_2a

value: Raynaud's phenomenon + ANA


title: Milan_RP_3a


title: D6B_Fat4_1


title: Milan_RP_7

value: Raynaud's phenomenon


title: Milan_RP_1a


title: Milan_RP_6


title: Milan_RP_5


title: Milan_eaSSc_9


title: D1B_Fat4_1


title: D12B_Fat4_1


title: D11B_Fat4_1


title: D10B_Fat4_1


title: C9B_Fat4_1


title: Milan_RP_3


title: Milan_eaSSc_3


title: Milan_HC_11


title: D2B_Fat4_1


title: D3B_Fat4_1


title: Milan_RP_1


title: Milan_HC_10


title: Milan_HC_8


title: D7B_Fat4_1


title: C8B_Fat4_1


title: Milan_HC_7


title: C6B_Fat4_1


title: C5B_Fat4_1


title: Milan_HC_4


title: Milan_HC_6


title: C7B_Fat4_1


title: Milan_HC_2


title: C4B_Fat4_1


title: Milan_HC_3


title: C2B_Fat4_1


title: Milan_RP_2


title: C3B_Fat4_1


title: C1B_Fat4_1


title: C11B_Fat4_1


title: C12B_Fat4_1


title: Milan_HC_1


title: C10B_Fat4_1


title: MONO_4h_2

city: Verona

first: Barbara

last: Mariotti

state: Verona

address: strada le grazie 8

department: Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
Reads were mapped onto the Ensembl human transcriptome (version 79) with Tophat and quantified at the gene-level using HTSeq-count (-m union -t exon -i gene_id)
Differential gene expression analysis and gene counts normalization among various samples was performed using DESeq2.
Gene abundance was indicated as variance stabilised data (vsd) caluclated according to the DESeq2 instruction.
Differentially expressed genes were identified using DESeq2 applyinf the LRT test, genes with  an adjusted p-values (padj) lower than 0.05 were considered as differentially expressed
Genome_build: Ensembl genome GrCh38, Ensembl transcriptome version 79
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Excell file containing the gene expression values as FPKM and variance stabilised data (vsd) were calculated according to the DESeq2 instruction.

source_name: Monocytes

growth_protocol: CD14+ monocytes were isolated from buffy coats of healthy donors and manipulated under endotoxin-free conditions. After Ficoll-Plaque gradient centrifugation, CD14+ monocytes were isolated from PBMCs by anti-CD14 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) to reach > 98 % purity.

extract_protocol:
RNA was purified with the RNeasy kit (Qiagen) according to manufacturer's protocol, an on-column DNAse treatment was performed. For each condition, two RNA pools of three donors each one were made. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries for transcriptome analysis were prepared using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA)

treatment_protocol: CD14+ monocytes (3*10^6/mL) were immediatly lysed or cultured in RPMI 1640 + 10% FCS (<0.5 EU/ml)+ 2mM Glu in the presence of 100 ng/mL ultra-pure lipopolysaccharide (LPS, from E. coli strain O111:B4, InvivoGen, San Diego, CA, USA)  for 90min or 4h, and cultured at 37°, 5 % CO2 atmosphere.

tag: agent

value: LPS 100ng/mL

tag: time point

value: 4 hours


title: MONO_T0_2

value: no treatment


title: MONO_T0_1

value: CD14+ monocytes


title: MONO_90m_2

value: 90 minutes


title: MONO_4h_1


title: B8B_Fat4_1


title: B7B_Fat4_1


title: B9B_Fat4_1


title: B5B_Fat4_1


title: MONO_90m_1


title: B4B_Fat4_1


title: HEK293T EXOSC10CAT rep 2 (iCLip-seq)

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

description:
45srDNA.fa
45srDNA.annotation.bed
EXOSC10-CAT.45srDNA.bw
EXOSC10-CAT.hg38.antisense.bw
EXOSC10-CAT.hg38.sense.bw

data_processing:
[Preprocessing - Demultiplex] flexbar --format i1.5 --barcode-trim-end LEFT_TAIL --barcode-keep --pre-trim-phred 30 --min-read-length 28 --adapter-min-overlap 4
[Preprocessing - Collapsing Redundant Reads] nonRedundant reads were collapsed using custom perl scripts
[Preprocessing - Barcode Removal] fastx_trimmer -f 10 -m 20 -z
[Preprocessing - Merge] biological replicate samples were combined to increase coverage
[Alignment] Tophat VN:2.0.14 --max-multihits 1 --library-type fr-firststrand --num-threads 8 --no-novel-juncs --no-coverage-search --no-novel-indels
[Normalization] bigwig files scaled to reads mapped per million
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files are coverage tracks that have been scaled based on reads mapped per million (RPM).

source_name: HEK293T EXOSC10CAT

growth_protocol: HEK293T cell lines were maintained in DMEM with 10% fetal bovine serum at 37 °C and 5% CO2.

extract_protocol:
EXOSC10CAT associated RNA selected by crosslinking and IP. A detailed iCLip protocol can be found by Konig J., Zarnack K., Rot G., Curk T., Kayikci M., Zupan B., Turner D.J., Luscombe N.M. and Ule J. (2011).
EXOSC10CAT associated RNA were prepared using the protocol outlined by Konig J., Zarnack K., Rot G., Curk T., Kayikci M., Zupan B., Turner D.J., Luscombe N.M. and Ule J. (2011).

treatment_protocol: Transfection of 3xFLAG-EXOSC10CAT expression vector 48 hours before collection

tag: cell line

tag: antibody

value: anti-FLAG M2 magnetic beads) (Sigma Aldrich)

tag: adapter

tag: barcode

value: NNNCCGGNN

tag: treatment

value: HEK293T transiently expressed 3xFLAG-EXOSC10CAT, EXOSC10CAT protein associated RNA

tag: molecule subtype

value: EXOSC10CAT bound RNA


title: HEK293T EXOSC10CAT rep 1 (iCLip-seq)


title: B3B_Fat4_1

tag: Stage

value: 51 days

tag: tissue

value: Fat4 organoid 1

tag: scrna-seq protocol


title: B1B_Fat4_1


title: B12B_Fat4_1


title: B10B_Fat4_1


title: A1B_Fat4_1


title: HLCs_M2_11304_A

city: Tampere

first: Leena

middle: Eloni

last: Viiri

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

data_processing:
Library strategy: GRO-seq
Poor quality reads were filtered using FastX toolkit. For each read a minimum of 97% of the bases were required to exceed phred quality threshold 10
Alignment to reference genome using bowtie1
Sorting and indexing using Samtools sort and index commands
Generation of bedgraph files using bedtools genomecov
Genome_build: hg19
Supplementary_files_format_and_content: Files including suffix .bga are standard bedgraph files which indicate the genome wide coverage at base level resolution

source_name: iPSC

growth_protocol: Hepatocyte-like cells (HLCs) were differentiated by two different methods, slightly modified from protocols published by Si-Tayeb et al. (Hepatology 51, 297–305) and Hay et al. (Stem Cells 26, 894–902).

extract_protocol:
The nuclear run-on was performed as described in (Kaikkonen et al., 2014 Nucleic Acids Res. 42, 12570–12584.)
The library preparation was performed as described in (Kaikkonen et al., 2014 Nucleic Acids Res. 42, 12570–12584.)

value: iPSC-derived HLCs

tag: differentiation method

value: M2 described ortiginally by Hay et al. (Stem Cells 26, 894–902).


title: PHH_A

source_name: liver

value: primary human hepatocyte


title: HLCs_M2_11104_B


title: H8A_Dchs1_1

value: Dchs1 organoid 1


title: HLCs_M2_11304_B


title: PHH_B


title: H7A_Dchs1_1


title: HLCs_M2_11104_A


title: B6B_Fat4_1


title: HEK293T EXOSC10WT rep 1 (iCLip-seq)

description:
45srDNA.fa
45srDNA.annotation.bed
EXOSC10-WT.45srDNA.bw
EXOSC10-WT.hg38.antisense.bw
EXOSC10-WT.hg38.sense.bw

source_name: HEK293T EXOSC10WT

growth_protocol: HEK293T transiently transfected with FLAG-hRRP6 (wild type) were expanded in 15 cm plates to 95% confluency

extract_protocol:
HEK293T were irradiated, lysed and epitope-tagged proteins were purified following protocol from Konig et al. 2011
iCLIP libraries were constructed FLAG-hRRP6 immunoprecipitates following the protocol from Konig et al. 2011
iCLIP library strategy can be found in Konig et al. 2011

value: EXOSC10WT bound RNA


title: HEK293T EXOSC10WT rep 2 (iCLip-seq)

value: transiently transfected with FLAG-hRRP6 (wild type)


title: HLCs_M2_10100_B


title: HLCs_M1_11104_C

value: M1 described originally by Si-Tayeb et al. (Hepatology 51, 297–305).


title: HLCs_M2_10100_A


title: H3A_Dchs1_1


title: H5A_Dchs1_1


title: H6A_Dchs1_1


title: iPSC_11104_B

value: iPSC


title: H4A_Dchs1_1


title: HLCs_M1_11104_B


title: H2A_Dchs1_1


title: H10A_Dchs1_1


title: H11A_Dchs1_1


title: H9A_Dchs1_1


title: G9A_Dchs1_1


title: HLCs_M1_11104_A


title: G8A_Dchs1_1


title: G7A_Dchs1_1


title: G6A_Dchs1_1


title: G5A_Dchs1_1


title: G4A_Dchs1_1


title: G3A_Dchs1_1


title: G2A_Dchs1_1


title: G12A_Dchs1_1


title: G1A_Dchs1_1


title: cdx2low_42

first: Nicolas

last: Rivron

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute / Maastricht University

description:
bulk library
NR3.tsv

data_processing:
Sequencing libraries were mapped with STAR-2.5.3a with default parameters to the ensembl version 93 of the mouse genome, and only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Ensembl version 93 of the mouse genome
Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell

source_name: bulk CDX2-Low TSCs

growth_protocol:
TSCs grown in Tx conditions (Kubaczka, 2014)
[pTSC growth protocol]  TSCs grown in Lt21 conditions (Kubaczka, 2014)
[differentiation protocol ]  TSC plate din Tx conditions. 24 hours media is refreshed with fresh Tx without growth factors.

extract_protocol:
Cells were sorted into 384 well plates. All wells underwent Cel-Seq2 protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genetic background

value: bulk CDX2-Low TSCs

tag: genotype

value: include eGFP knock in bound to the CDX2 coding sequence


title: cdx2low_41

description:
bulk library
NR3.tsv

tag: cell type


title: G11A_Dchs1_1


title: G10A_Dchs1_1


title: Emx1IRES-Cre: Satb2Fl/Fl: 5HT3A-GFP

city: Bethesda

first: Chris

last: McBain

state: Maryland

address: 35 Convent Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: CGE interneurons from Satb2 KO PN

data_processing:
Basecalls performed with Illumina RTA version 1.18.64
Read counts were quanitifed with the 10X Cell Ranger pipeline
I1: UMI
R1: Cell barcode
R2: Biological read
The barcode and UMI sequences appear at the start of the respective reads.
Genome_build: MM10 with GFP sequence appended
Supplementary_files_format_and_content: Comma-separated output file including cell by gene count matrix

source_name: Acute cortical slices

extract_protocol: Library was constructed following Illumina and 10X genomics instructions.

value: brain

tag: region

value: visual cortex

value: CGE-originating interneurons

tag: developmental stage

value: juvenile (p21)


title: 5HT3A-GFP

description: CGE interneurons  from WT PN


title: iPSC_11104_A


title: cdx2low_40

description:
bulk library
NR3.tsv


title: F9A_Dchs1_1


title: cdx2high_38

description:
bulk library
NR3.tsv

source_name: bulk CDX2-High TSCs

value: bulk CDX2-High TSCs


title: cdx2high_39

description:
bulk library
NR3.tsv


title: F8A_Dchs1_1

value: 51 days


title: F7A_Dchs1_1


title: F6A_Dchs1_1


title: PBS_3

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Macrophages of the Meninges Post PBS Treatment - Biological Replicate 3

hyb_protocol: Labeled cRNA were hybridized to these arrays according to the manufacturer’s guidelines (Affymetrix) in blinded interleaved fashion.

scan_protocol: The Scanner 3000 (Affymetrix) was used in conjunction with Affymetrix AGCC software (v4.0) to generate one .CEL file per hybridized cRNA.

data_processing: The Expression Console (Affymetrix) was used to generate 41,345 RMA normalized transcript expression values per .CEL file.

label_protocol: Total RNA was labeled on a sample-by-sample basis according to the manufacturer’s guidelines for use with the Mouse Gene 2.1 ST Array (Affymetrix).

growth_protocol: C57BL/6J (B6) were purchased from The Jackson Laboratory (Bar Harbor, ME).  All mice in this study were handled in accordance with the guidelines set forth by the NIH Animal Care and Use Committee.

extract_protocol: CD206+ macrophages were isolated from PBS or LCMV-infected mice at day 4 post-infection using a FACSAria Digital Cell Sorter (BD). Macrophages were sorted to >95% purity based on the following markers: 7-AAD− Thy1.2−CD45.2+ CD11b+ Gr1− F4/80+ CD206+ and IAb/IEb +. FACS-sorted cells were collected in TRIzol (Invitrogen), and total RNA was extracted using PureLink RNA Micro kits (Life Technologies) per the manufacturer’s instructions.

treatment_protocol: To induce meningitis and subacute meningitis, adult mice at 6–8 weeks of age were infected intracerebrally (i.c.) with 1 × 103 plaque-forming units of LCMV Armstrong clone 53b. Survival was monitored daily. Stocks were prepared by a single passage on BHK-21 cells, and viral titers were determined by plaque formation on Vero cells.

tag: condition

value: PBS-treated


title: PBS_4

description: Macrophages of the Meninges Post PBS Treatment - Biological Replicate 4


title: PBS_1

description: Macrophages of the Meninges Post PBS Treatment - Biological Replicate 1


title: LCMV_3

description: Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 3

value: LCMV-infected


title: LCMV_1

description: Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 1


title: LCMV_4

description: Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 4


title: LCMV_2

description: Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 2


title: PBS_2

description: Macrophages of the Meninges Post PBS Treatment - Biological Replicate 2


title: cdx2high_37

description:
bulk library
NR3.tsv


title: HUB-JF-03 (scRNA-seq)

description: single cell library

source_name: pTS1 pTSCs isolated from blastoids

tag: date sorting

value: pTS1 pTSCs isolated from blastoids

value: include randomly integrated GFP expression cassete


title: HUB-JF-04 (scRNA-seq)

description: single cell library

source_name: newly derived pTSCs

value: newly derived pTSCs


title: F4A_Dchs1_1

source_name: iPSC Dchs1

value: Dchs1 organoid 1


title: JFA-F4GFP-CTR2 (scRNA-seq)

description: single cell library

source_name: F4 TSCs

value: F4 TSCs


title: F3A_Dchs1_1


title: P3 Input Serum Zebularin

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: processed data file not provided, bam file was used to determine barcode representation

library_source: genomic

data_processing:
Demultiplexing and deduplication: Sequencing was performed using 50:8:34 cycles (Read1:Index1:Read2) Illumina bcl2fastq was used to demultiplex paired-end sequencing reads by 8nt index1 read (PCR barcode). NextSeq lanes were merged into single fastq files, creating the primary fastq files. Read1 starts with 6nt UMI and 8nt barcode in the format NNNNNNABCDEFGH. A sample sheet was used with four columns corresponding to sample name, replicate name, barcode sequence, primary fastq name. For each line in the sample sheet, reads matching the barcode sequence were extracted from the primary fastq file, allowing up to two mismatches. Duplicate reads identified by identical first 24nt of read1 were discarded. Read pairs matching parts of the adaptor sequence (SBS3 or T7 promoter) in either read1 or read2 were removed. Demultiplexed and deduplicated reads were written into sample-specific fastq file used for subsequent mapping.
Mapping: Sample-specific paired fastq files were mapped using botwie2 (v2.3.4.3) using --fast parameter to the mouse genome (mm9). Alignments were processed into sorted BAM files with samtools (v1.9). Blacklisted regions were removed from BAM file using BEDTools (v2.27.1). Reads were also mapped to a metagenome of RepBase murine repetitive sequences using botwie2.
Scaling: Input coverage tracks with 1bp resolution in BigWig format were generated from BAM files using deepTools (v3.1.0) bamCoverage and scaled to a reads-per-genome-coverage of one (1xRPGC, also referred to as ‘1x normalization’) using mm9 genome size 2654895218. ChIP coverage tracks were generated from BAM files using deepTools (v3.1.0) bamCoverage. Quantitative scaling amongst samples within each pool was based on their total mapped read counts, as well as the total mapped read counts of the respective input data. One condition in the pool served as a reference (Serum condition, no treatment), which was scaled to 1xRPGC. All other samples were scaled relative to the reference using an explicit scaling factor. The RPGC was calculate by the following formula: ( #mapped[ChIP] / #mapped[Input] ) / ( #mapped[ChIP_Reference] / #mapped[Input_Reference] ).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files are scaled according to MINUTE quantification with respect to the reference of each pool (Serum condition, 1xRPGC)

molecule: genomic DNA

source_name: Embryonic Stem Cell

growth_protocol: Murine embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin-coated dishes.  "Serum" condition: Knockout DMEM (Life Technologies), 2 mM Glutamax (Gibco), 0.1 mM non-essential amino acids (Gibco), 15% ESC-grade fetal bovine serum (FBS) (Gibco), 0.1 mM β-mercaptoethanol, and leukemia inhibitory factor (LIF) (Millipore), "Serum2i" condition: above medium supplemented with 2i; 1 μM MEK inhibitor PD0325901 (Sigma) and 3 μM GSK3 inhibitor CHIR99021 (Sigma). "2i" condition: serum free ESGRO Complete Basal medium (Millipore) with 0.1mM LIF and 2i as described above. For all conditions cells were passaged in 48 h intervals, using accutase (Sigma) for detachment. Cell line was tested for mycoplasma contamination.

extract_protocol:
Cell lysis immediately followed by MNase digestion of native chromatin, T7-adapter ligation, pool-and-split multiplexing, immunoprecipitation and magnetic bead isolation of immunoprecipitated DNA.
Illumnina library preparation by in vitro transcription, reverse transcription and library PCR (see manuscript).

treatment_protocol: Medium was supplemented with 10 μM GSK-J4 (Sigma) for 96 h, 50 μM Zebularin for 96 h or 10 μM EPZ-6438 (BioVision) for 7 days.

tag: background

value: Serum

value: Input

tag: minute-pool

tag: supplementary file scaling

value: 1x genome coverage


title: F12A_Dchs1_1


title: E9A_Dchs1_1


title: E7A_Dchs1_1


title: F10A_Dchs1_1


title: E8A_Dchs1_1


title: P3 Input Serum EPZ-6438

tag: antibody


title: E6A_Dchs1_1


title: E4A_Dchs1_1


title: F5A_Dchs1_1


title: E5A_Dchs1_1


title: E3A_Dchs1_1


title: P3 H3K27me3-ChIP (07-449) Serum Zebularin

value: Millipore 07-449

value: relative to P3 H3K27me3-ChIP Serum


title: E11A_Dchs1_1


title: E12A_Dchs1_1


title: E2A_Dchs1_1


title: E1A_Dchs1_1


title: D9A_Dchs1_1


title: D8A_Dchs1_1


title: E10A_Dchs1_1


title: F1A_Dchs1_1


title: P3 H3K27me3-ChIP (07-449) 2i


title: P3 H3K27me3-ChIP (CS9733) Serum Zebularin

value: Cell signaling 9733


title: P3 H3K27me3-ChIP (07-449) 2i GSK-J4


title: P3 H3K27me3-ChIP (07-449) 2i EPZ-6438


title: JFA6dDiff2 (scRNA-seq)

description: single cell library

source_name: F4 differentiated TSCs

value: F4 differentiated TSCs


title: D6A_Dchs1_1


title: P3 Input 2i Zebularin


title: D7A_Dchs1_1


title: P3 Input Serum GSK-J4


title: D4A_Dchs1_1


title: D2A_Dchs1_1


title: P3 H3K27me3-ChIP (CS9733) 2i Zebularin


title: D5A_Dchs1_1


title: P3 H3K27me3-ChIP (CS9733) 2i


title: P3 H3K27me3-ChIP (CS9733) 2i GSK-J4


title: D3A_Dchs1_1


title: P3 H3K27me3-ChIP (CS9733) 2i EPZ-6438


title: D1A_Dchs1_1


title: P3 H3K27me3-ChIP (07-449) 2i Zebularin


title: D12A_Dchs1_1


title: D10A_Dchs1_1


title: C8A_Dchs1_1


title: C7A_Dchs1_1


title: C6A_Dchs1_1


title: P3 H3K27me1-ChIP 2i Zebularin

value: Cell signaling 5326S

value: relative to P3 H3K27me1-ChIP Serum


title: C3A_Dchs1_1

value: 51 days


title: C5A_Dchs1_1


title: C4A_Dchs1_1


title: P3 H3K27me1-ChIP 2i GSK-J4


title: P3 H3K27me1-ChIP 2i


title: P2 Input Serum2i

description: contains data from three replicates with different barcodes provided as raw files


title: P2 H3-ChIP Serum

value: Active motif 39763


title: C12A_Dchs1_1


title: C1A_Dchs1_1


title: P2 H3-ChIP Serum2i

value: relative to P2 H3-ChIP Serum


title: P2 Input Serum


title: P2 H3K4me3-ChIP Serum2i

value: Millipore 04-745

value: relative to P2 H3K4me3-ChIP Serum


title: C2A_Dchs1_1


title: B9A_Dchs1_1


title: B8A_Dchs1_1


title: P3 H3K27me1-ChIP Serum Zebularin


title: B7A_Dchs1_1


title: C9A_Dchs1_1


title: P2 H3K27me3-ChIP (C15410195) Serum2i

value: Diagenode C15410195

value: relative to P2 H3K27me3-ChIP Serum


title: D11A_Dchs1_1

value: Dchs1 organoid 1


title: P1 Input Serum

value: Serum


title: B6A_Dchs1_1


title: B5A_Dchs1_1


title: B4A_Dchs1_1


title: P3 H3K27me1-ChIP 2i EPZ-6438


title: P1 H3K4me3-ChIP Serum


title: B1A_Dchs1_1


title: P2 H3K4me3-ChIP Serum


title: P1 H3K27me3-ChIP (C15410195) 2i

value: relative to P1 H3K27me3-ChIP Serum


title: P1 H3K27me3-ChIP (C15410195) Serum

value: 1x genome coverage


title: B12A_Dchs1_1


title: A9A_Dchs1_1


title: P2 H3K27me3-ChIP (C15410195) Serum


title: P1 H3K4me3-ChIP 2i

value: relative to P1 H3K4me3-ChIP Serum


title: A8A_Dchs1_1


title: pkl-1_24h_rep2

city: West Lafayette

first: CHUNZHAO

last: ZHAO

state: Indiana

address: 209 AIRPORT ROAD, APT 5

country: China

institute: Chinese Academy of Science

description: Treatment with 4 ºC for 24 h

data_processing:
The reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2 with default parameter
Genome_build: TAIR10
Supplementary_files_format_and_content: Mapped read counts of each gene were generated by the cuffnorm command and the differentially expressed genes were analyzed using cuffdiff in Cufflinks.

organism: Arabidopsis thaliana

source_name: pkl-1 24h rep2

extract_protocol: The 10-day-old wild type and pkl-1 seedlings treated with 4 ºC for 0, 3, and 24 h using TRIzol reagent (Life Technologies). The total RNAs were sent to Core Facility for Genomics of Shanghai Center for Plant Stress Biology (PSC) for transcriptome sequencing by Illumina HiSeq2500.

tag: treatment

value: 4 C for 24 h


title: B10A_Dchs1_1


title: pkl-1_3h_rep2

description: Treatment with 4 ºC for 3 h

source_name: pkl-1 3h rep2

value: 4 C for 3 h


title: pkl-1_24h_rep3

description: Treatment with 4 ºC for 24 h

source_name: pkl-1 24h rep3


title: pkl-1_3h_rep3

description: Treatment with 4 ºC for 3 h

source_name: pkl-1 3h rep3


title: A7A_Dchs1_1


title: A6A_Dchs1_1


title: A5A_Dchs1_1


title: pkl-1_3h_rep1

description: Treatment with 4 ºC for 3 h

source_name: pkl-1 3h rep1


title: pkl-1_0h_rep3

description: Treatment with 4 ºC for 0 h

source_name: pkl-1 0h rep3

value: 4 C for 0 h


title: P1 Input 2i

value: Input


title: pkl-1_0h_rep2

description: Treatment with 4 ºC for 0 h

source_name: pkl-1 0h rep2


title: A3A_Dchs1_1


title: A4A_Dchs1_1


title: B3A_Dchs1_1


title: pkl-1_0h_rep1

description: Treatment with 4 ºC for 0 h

source_name: pkl-1 0h rep1


title: A2A_Dchs1_1


title: Col-0_24h_rep3

description: Treatment with 4 ºC for 24 h

source_name: Col-0 24h rep3


title: Col-0_24h_rep2

description: Treatment with 4 ºC for 24 h

source_name: Col-0 24h rep2


title: A12A_Dchs1_1


title: A10A_Dchs1_1


title: pkl-1_24h_rep1

description: Treatment with 4 ºC for 24 h

source_name: pkl-1 24h rep1


title: Col-0_3h_rep2

description: Treatment with 4 ºC for 3 h

source_name: Col-0 3h rep2


title: Col-0_24h_rep1

description: Treatment with 4 ºC for 24 h

source_name: Col-0 24h rep1


title: H7B_Dchs1_3

source_name: iPSC Dchs1

value: 55 days

value: Dchs1 organoid 3


title: H9B_Dchs1_3


title: H8B_Dchs1_3


title: H6B_Dchs1_3


title: H5B_Dchs1_3


title: H4B_Dchs1_3


title: Col-0_3h_rep1

description: Treatment with 4 ºC for 3 h

source_name: Col-0 3h rep1


title: Col-0_0h_rep3

description: Treatment with 4 ºC for 0 h

source_name: Col-0 0h rep3


title: H2B_Dchs1_3


title: H3B_Dchs1_3


title: Col-0_0h_rep 1

description: Treatment with 4 ºC for 0 h

source_name: Col-0 0h rep 1


title: Col-0_0h_rep2

description: Treatment with 4 ºC for 0 h

source_name: Col-0 0h rep2


title: H1B_Dchs1_3


title: H12B_Dchs1_3


title: H11B_Dchs1_3


title: H10B_Dchs1_3


title: Col-0_3h_rep3

description: Treatment with 4 ºC for 3 h

source_name: Col-0 3h rep3


title: G8B_Dchs1_3


title: G9B_Dchs1_3


title: G7B_Dchs1_3


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 7

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

institute: University Medical Center Groningen

data_processing:
Single-end reads were aligned to human reference genome 37 (GRCh37.p13 (GCA_000001405.14), top-level built) using STAR (version 2.5.2).
Genome_build: human reference genome 37 (GRCh37.p13 (GCA_000001405.14)
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample
Supplementary_files_format_and_content: gene.txt: row index

source_name: Ovarian cancer tumor-infiltrating lymphocytes

extract_protocol:
Ovarian tumors from two patients were cut into pieces of <1 mm3 and placed in a T75 culture flask (Nunc™ EasYFlask™ Cell Culture Flasks, cat. no. 156499, ThermoScientific)  with digestion medium, consisting of RPMI (Gibco, Paisley, UK), 10% fetal bovine serum (FBS, Gibco, Paisley, UK), collagenase type IV (1 mg/mL; Gibco, Grand Island, USA), and 12.6 µg/mL   recombinant human DNase (Pulmozyme,Roche, Woerden, the Netherlands) for overnight digestion at room temperature. After digestion, the suspension was strained through a 70 µm filter and washed with PBS. Cells were centrifuged over a Ficoll-Paque gradient (GE Healthcare Bio-Sciences AB, Uppsala, Sweden) and lymphocytes were isolated from between the two layers. After a wash with PBS cells were pelleted. Total cell pellet was suspended in 1ml FBS with 10% dimethylsulfoxide (Merck, Darmstadt, Germany), and stored in liquid nitrogen until further use.   Prior to sequencing, tumor digests were thawed on ice, washed with AIM-V medium (Gibco, Paisley, UK) with 5% pooled human serum (PHS, One Lambda, USA) and centrifuged at 1000 x g. The total cellpellets were resuspended in AIM-V with 5% PHS, and cells were incubated with CD3-BV421, CD4-PerCP-Cy5.5, CD8α-APCeFluor780, CD8β-PEcy7, TCRαβ-APC, CD103-FITC, and CD56-PE antibodies at 4°C for 45 minutes. After gating for CD3+CD4–CD8αβ+TCRαβ+CD56– cells, CD103– and CD103+ single cells were sorted on a Beckman Coulter Astrios cytometer directly into 4 µl lysis buffer (2 µl of 0.2% Triton X-100, Sigma-Aldrich, cat. no. T9284 with 5% recombinant RNase inhibitor (Westburg-Clontech, cat. no. 2313A), 1 µl 10µM barcoded oligo dT primer , and 1 µl 4x10mM dNTP mix)) in 96-well PCR plates. Each well contained a unique indexed Oligo dT primer enabling identification of individual cells after pooled RNA sequencing.   In addition to single cell wells, small bulk populations of 20 cells were sorted per microplate well. Per patient, 40 single CD8+ T cells (20 wells CD103+, 20 wells CD103–) and 20 small bulk 20-cell populations (10 wells CD103+, 10 wells CD103–) were sorted. After sorting, the plate was vortexed and spin down briefly, and incubated at 72°C for 3 minutes. After this step the plate was kept cool.
Custom primers were designed that include a PCR-primer recognition site for pre-PCR, a Unique Molecular Identifier (UMI), a cell barcode (see supplementary Table S4), and a poly T-stretch. Each cell (or pool) is tagged with an oligo dT primer, including the UMI and cell barcode. A template switching pre-PCR is used to generate cDNA. Pools are made of single cells or pools with unique  cell barcodes and 500pg of the pools was  tagmentated and barcoded using a N7xx index and custom P5 hybrid primer (AATGATACGGCGACCACCGAGATCTACACGCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGT*A*C) according the Illumina Nextera XT DNA sample preparation kit protocol(Illumina, cat. no. FC-131-1096). The pools were purified using AMPure beads in a ratio of 0,6:1, to remove primer dimers. Presence and size distribution of the obtained PCR product were checked on a PerkinElmer LabChip GX high-sensitivity DNA chip. A super pool was created by equimolar pooling (1nmol/L) of the Nextera products, and the samples were sequenced on Illumina NextSeq500 2500 using 50 bp paired-end reads, one read for the mRNA transcript, and the other for the cell-barcode. The obtained RNA sequencing data were demultiplexed into individual FASTQ files.

tag: tumor histology

value: High-grade serous

tag: t cell cell surface phenotype

value: CD3+ TCRalphabeta+ CD8alpha+ CD8beta+ CD4- CD56-

tag: cd103 status (1=neg, 2=pos)


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 9


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 4


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 10


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 5


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 3


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 6


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 8


title: G6B_Dchs1_3

tag: Stage

tag: tissue

tag: scrna-seq protocol


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 2


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 10


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 9


title: G3B_Dchs1_3


title: G4B_Dchs1_3


title: 20cell pool CD103+ CD8+ T cell, donor 704, replicate 1


title: G2B_Dchs1_3


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 8


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 7


title: G1B_Dchs1_3


title: G12B_Dchs1_3


title: C10A_Dchs1_1

value: 51 days


title: G11B_Dchs1_3


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 5


title: G10B_Dchs1_3


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 3


title: F9B_Dchs1_3


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 4


title: G5B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 20


title: F8B_Dchs1_3


title: F7B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 18


title: F5B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 19


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 2


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 1


title: F6B_Dchs1_3


title: F3B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 17


title: single CD103+ CD8+ T cell, donor 704, replicate 15


title: F12B_Dchs1_3


title: F10B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 14


title: single CD103+ CD8+ T cell, donor 704, replicate 16


title: single CD103+ CD8+ T cell, donor 704, replicate 13


title: F1B_Dchs1_3


title: E7B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 11


title: 20cell pool CD103+ CD8+ T cell, donor 702, replicate 6


title: single CD103+ CD8+ T cell, donor 704, replicate 12


title: single CD103+ CD8+ T cell, donor 704, replicate 10


title: E6B_Dchs1_3


title: E5B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 8


title: single CD103+ CD8+ T cell, donor 704, replicate 9


title: E4B_Dchs1_3


title: E3B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 5


title: single CD103+ CD8+ T cell, donor 704, replicate 7


title: single CD103+ CD8+ T cell, donor 704, replicate 6


title: E10B_Dchs1_3


title: E12B_Dchs1_3


title: E9B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 4


title: F4B_Dchs1_3


title: E11B_Dchs1_3


title: D7B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 1


title: single CD103+ CD8+ T cell, donor 704, replicate 2


title: D9B_Dchs1_3


title: D8B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 20


title: D5B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 704, replicate 3


title: single CD103+ CD8+ T cell, donor 702, replicate 18


title: D3B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 16


title: D4B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 15


title: D2B_Dchs1_3


title: E1B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 17


title: D12B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 14


title: single CD103+ CD8+ T cell, donor 702, replicate 13


title: single CD103+ CD8+ T cell, donor 702, replicate 12


title: D1B_Dchs1_3


title: D11B_Dchs1_3


title: D10B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 11


title: C9B_Dchs1_3


title: E8B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 19


title: D6B_Dchs1_3


title: C8B_Dchs1_3


title: C7B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 9


title: C6B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 8


title: single CD103+ CD8+ T cell, donor 702, replicate 6


title: C5B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 5


title: single CD103+ CD8+ T cell, donor 702, replicate 4


title: C3B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 3


title: C2B_Dchs1_3


title: C1B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 1


title: C4B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 2


title: C12B_Dchs1_3


title: C11B_Dchs1_3


title: C10B_Dchs1_3


title: single CD103+ CD8+ T cell, donor 702, replicate 10


title: single CD103+ CD8+ T cell, donor 702, replicate 7


title: B9B_Dchs1_3


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 10


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 9


title: B7B_Dchs1_3


title: B8B_Dchs1_3


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 6


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 5


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 4


title: B5B_Dchs1_3


title: B6B_Dchs1_3


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 7


title: B4B_Dchs1_3


title: B3B_Dchs1_3


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 2


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 1


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 3


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 10


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 9


title: B12B_Dchs1_3


title: 20cell pool CD103- CD8+ T cell, donor 704, replicate 8


title: A8B_Dchs1_3


title: B10B_Dchs1_3


title: A9B_Dchs1_3


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 7


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 8


title: A6B_Dchs1_3


title: A5B_Dchs1_3


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 5


title: A4B_Dchs1_3


title: A3B_Dchs1_3


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 2


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 6


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 4


title: A1B_Dchs1_3


title: single CD103- CD8+ T cell, donor 704, replicate 20


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 1


title: single CD103- CD8+ T cell, donor 704, replicate 19


title: single CD103- CD8+ T cell, donor 704, replicate 18


title: A2B_Dchs1_3


title: A11B_Dchs1_3


title: A10B_Dchs1_3


title: H9A_Control_3a

source_name: iPSC Control

value: Control organoid 3


title: A7B_Dchs1_3


title: H8A_Control_3a


title: single CD103- CD8+ T cell, donor 704, replicate 17


title: H7A_Control_3a


title: 20cell pool CD103- CD8+ T cell, donor 702, replicate 3


title: single CD103- CD8+ T cell, donor 704, replicate 13


title: single CD103- CD8+ T cell, donor 704, replicate 14


title: H6A_Control_3a


title: single CD103- CD8+ T cell, donor 704, replicate 15


title: H5A_Control_3a


title: single CD103- CD8+ T cell, donor 704, replicate 12


title: single CD103- CD8+ T cell, donor 704, replicate 11


title: single CD103- CD8+ T cell, donor 704, replicate 10


title: single CD103- CD8+ T cell, donor 704, replicate 16


title: H3A_Control_3a


title: H4A_Control_3a


title: H2A_Control_3a


title: B1B_Dchs1_3


title: single CD103- CD8+ T cell, donor 704, replicate 8


title: single CD103- CD8+ T cell, donor 704, replicate 9


title: single CD103- CD8+ T cell, donor 704, replicate 7


title: A12B_Dchs1_3


title: single CD103- CD8+ T cell, donor 704, replicate 6


title: H1A_Control_3a


title: H12A_Control_3a


title: H11A_Control_3a


title: H10A_Control_3a


title: single CD103- CD8+ T cell, donor 704, replicate 4


title: single CD103- CD8+ T cell, donor 704, replicate 3


title: G9A_Control_3a


title: G8A_Control_3a


title: single CD103- CD8+ T cell, donor 704, replicate 2


title: single CD103- CD8+ T cell, donor 704, replicate 1


title: G6A_Control_3a


title: G7A_Control_3a


title: single CD103- CD8+ T cell, donor 702, replicate 20


title: single CD103- CD8+ T cell, donor 702, replicate 19


title: G3A_Control_3a


title: G2A_Control_3a


title: G1A_Control_3a


title: G4A_Control_3a


title: single CD103- CD8+ T cell, donor 702, replicate 17


title: single CD103- CD8+ T cell, donor 702, replicate 16


title: single CD103- CD8+ T cell, donor 702, replicate 15


title: G12A_Control_3a


title: G10A_Control_3a


title: F9A_Control_3a


title: G11A_Control_3a


title: single CD103- CD8+ T cell, donor 702, replicate 14


title: F8A_Control_3a


title: single CD103- CD8+ T cell, donor 702, replicate 11


title: single CD103- CD8+ T cell, donor 702, replicate 13


title: single CD103- CD8+ T cell, donor 702, replicate 12


title: single CD103- CD8+ T cell, donor 704, replicate 5


title: single CD103- CD8+ T cell, donor 702, replicate 18


title: F6A_Control_3a


title: G5A_Control_3a


title: single CD103- CD8+ T cell, donor 702, replicate 8


title: single CD103- CD8+ T cell, donor 702, replicate 7


title: F4A_Control_3a


title: F3A_Control_3a


title: single CD103- CD8+ T cell, donor 702, replicate 6


title: single CD103- CD8+ T cell, donor 702, replicate 5


title: single CD103- CD8+ T cell, donor 702, replicate 9


title: single CD103- CD8+ T cell, donor 702, replicate 3


title: F1A_Control_3a


title: F12A_Control_3a


title: single CD103- CD8+ T cell, donor 702, replicate 4


title: E6A_Control_3a


title: E9A_Control_3a


title: single CD103- CD8+ T cell, donor 702, replicate 2


title: F10A_Control_3a


title: E5A_Control_3a


title: single CD103- CD8+ T cell, donor 702, replicate 1


title: P1 H3K27me3-ChIP (C15410195) HeLa

description: processed data file not provided since only used for quality control

source_name: HeLa

value: Epitheloid cervix carcinoma

value: DMEM

value: Diagenode C15410195


title: single CD103- CD8+ T cell, donor 702, replicate 10


title: E4A_Control_3a


title: E8A_Control_3a


title: P1 Input HeLa


title: F5A_Control_3a


title: E3A_Control_3a


title: F7A_Control_3a


title: Utrecht_LimSSc10me3

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI37) using BWA package (mem –t 7 –c 100 –M –R). Multiple reads mapping to the same location and strand were collapsed to single read and only uniquely placed reads were used for peak-calling.
Peaks/regions were called using Cisgenome 2.0 (–e 150 -maxgap 200 –minlen 200). The false peak discovery rate (FDR) was determined by flipping IP and control labels
Regions coordinates from all samples stretched to at least 2000 base pairs and collapsed into a single common list. Overlapping regions were merged based on their outmost coordinates. Only regions supported by at least 3 independent datasets were further analyzed.
Autosomal sequencing reads from each ChIPseq library were overlapped back with the common region list, to set the H3K27ac and H3K4me3 occupancy for every region-sample pair.
Regions with differential H3K27ac and H3K4me3 occupancy between groups were identified using DESeq2 standard settings
Genome_build: hg19
Supplementary_files_format_and_content: cod files containing peak data per sample

source_name: CD14+ monocytes

extract_protocol:
PBMCs were isolated using Ficoll Paque Plus (GE Healthcare) after which CD14+ monocytes were isolated using anti-CD14 microbeads (Miltenyi Biotech, Germany) to reach >95% purity. Freshly isolated monocytes from all subjects were immediately stored for RNA or ChIP analysis.Cells used for ChIPseq or ChIP-PCR were fixed using 1% formaldehyde (Sigma-Aldrich, Saint Louis,MO, USA) for 5 min followed by the addition of 0.125M Tris (pH 7.6) to stop the crosslinking reaction. After 5 min, cells were washed three times with ice-cold PBS and lysed for 10 min in L1 buffer (50 mM Tris, pH 8.0; 2 mM EDTA; 0.1% Nonidet P-40; and 10% glycerol) supplemented with protease inhibitors (5 μg/ml leupeptin, 5 μg/ml pepstatin, and 1 mM PMSF) and phosphatase inhibitors (1 mM Na3VO4, 20 μM PAO, and 50 mM NaF). Nuclei were pelleted at 1000xg in a cold microfuge and resuspended in L2 buffer (50 mM Tris, pH 8.0; 5 mM EDTA; and 1% SDS plus inhibitors). Chromatin was then sheared by sonication (180 seconds at 1000 cycles,  17.9 of duty factor and 450 of peak power on a Covaris S220 (Woburn, MA, USA), centrifuged to pellet debris and finally 10 times diluted in dilution buffer (50 mM Tris, pH 8.0; 0.5% Nonidet P-40; 0.2 M NaCl; and 5 mM EDTA). Nuclear extracts from 1 million monocytes were immunoprecipitated with 5 μg anti-H3K4me3 (07-473, Merck Millipore, Billerica, MA, USA), anti H3K27ac (AB4729, Abcam, Cambridge, UK)
DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research), end-repair, a-tailing, and ligation of sequence adaptors was done using Truseq nano DNA sample preparation kit (Illumina). Samples were PCR amplified, checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and barcoded libraries were sequenced 75bp single-end on Illumina NextSeq500 sequencer.

value: peripheral blood

tag: origin

value: lcSSc patient

tag: chip antibody

value: H3K4me3 (07-473, Merck Millipore)


title: Utrecht_LimSSc11me3


title: Utrecht_LimSSc9me3


title: E1A_Control_3a


title: E12A_Control_3a


title: Utrecht_LimSSc6me3


title: Utrecht_LimSSc4me3


title: E7A_Control_3a


title: P1 H3K4me3-ChIP HeLa

value: Millipore 04-745


title: E11A_Control_3a


title: Utrecht_LimSSc3me3


title: miRNA Old-liver-2

city: Ya'an

first: Jianning

last: Chen

state: Sichuan

address: 46, Xinkang Road

institute: Sichuan Agricultural University

description:
domestic pig
miRNA_tpm.txt

data_processing:
Illumina HiSeq 4000 was used to sequence the lncRNA libraries and 150 bp paired-end reads were obtained, and Illumina MiSeq platform was used to sequence the small RNA library preparations, and 50 bp single-end reads were produced.
Clean reads were obtained from raw data after removing the adapter, ploy-N and low quality reads. Clean reads were aligned to the Ensemble (Susscrofa 10.2) using TopHat2 (v2.0.14) with default parameters.
Mapped reads of each sample were assembled by using the StringTie (v1.2.3) software.
Coding Potential Calculator (CPC) (0.9) and Pfam Scan (v1.5) were used to examine the transcript coding potential.
LncRNA, mRNA, and circRNA, expression levels of transcripts per million (TPMs) were obtained using Salmon (v0.6.0)
Software mirdeep2 (v2.0.0.5) was used to identify the potential miRNA and to predict novel miRNA.
miRNA expression levels of transcripts per million (TPMs) were obtained using Salmon (v0.6.0)
Genome_build: Suscrofa.10.2 from Ensemble
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

organism: Sus scrofa

source_name: Liver tissue

extract_protocol:
TRIzol Reagent (Invitrogen, CA, USA) was used to extract the total RNA, and subsequently treated with DNase and purified by using an RNeasy Mini Kit (Qiagen, CA, U.S.A.)
RNA samples were prepared by using about 5 µg RNA per sample. LncRNA sequencing libraries were generated by using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® ((New England Biolabs Ipswich, Massachusetts, USA) according the manufacturer’s provided information and library qualities were analyzed by the Agilent Bioanalyzer 2100 system. Small RNA library was prepared by using a total of 5 μg of RNA per sample as an input material. In order to generate sequencing libraries, NEBNext® Multiplex Small RNA sequencing Library Prep Set for Illumina® ((New England Biolabs Ipswich, Massachusetts, USA) was used by following the manufacturer’s provided information and to attribute sequences to each sample index codes were added. An Agilent Bioanalyzer 2100 system was used to test the library quality

tag: development stage

value: Old

value: Liver

tag: age

value: 8 years after birth


title: miRNA Young-liver-1

description:
domestic pig
miRNA_tpm.txt

value: Yong

value: 180 days after birth


title: E10A_Control_3a

extract_protocol:
Single cells from dissociated organoids were sorted into 96 well plates using FACS and cDNA was obtained using SmartSeq2 protocol (Picelli et al., Nature Protocols, 2014). Neurons from 2d culture were encapsulated into droplets and cDNA was generated using 10X Genomics single cell 3' v2 kit.
Libraries for SmartSeq2 data were generated using the NexteraXT kit. Libraries from 2d cultured neurons were generated using the 10X Genomics 3' Single Cell v2 kit.

value: 55 days


title: Utrecht_LimSSc1me3


title: Utrecht_HC13me3

value: healthy donor


title: D8A_Control_3a


title: Utrecht_LimSSc2me3


title: D7A_Control_3a


title: Yjr_KO_H3K4me3-2

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

country: Germany

institute: BIOTEChnology Center TU Dresden

data_processing:
bcl2fastq 1.8.4
ChIP-seq reads were mapped to sacCer3 S. cerevisiae genome assembly using BWA and parallel version of pBWA (0.5.9-r32-MPIpatch2).
Uniquely mapped reads were filtered (-q 1) and PCR duplicates (reads with same start and mapped to same strand) were removed using Samtools (rmdup).
Read lengths were computationally extended to 150-bp strand specifically and stored in Bam format.
Genome_build: sacCer3 S. cerevisiae
Supplementary_files_format_and_content: The Bam files were subject to coverage calculation using the bamCoverage utility of deepTools for a sliding window of 40 bp, normalized using RPKM parameters, and stored in BigWig format.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown over night in rich medium. Reinoculated the overnight grown cluture in frech medium and grown untill mid log phase of culture (OD of 0.8-1.0).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library was prepared following " NEBnext Ultra DNA Libprep Kit" protocol

tag: strain

tag: genotype/variation

value: H3K4me3 (Abcam, ab8580)


title: Utrecht_HC12me3


title: WT_H3K4me3-2

value: WT


title: Yjr_KO_H3K4me3-3


title: D6A_Control_3a

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers for SmartSeq2 data (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.). Cellranger (v 2.1.0) was used for basecalling for 10X data.
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.). For 10X data, demultiplexing was performed using Cellranger (v 2.1.0).
or SmartSeq2 data, reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.9. For 10X data, alignment to GRCh38 was performed using Cellranger (v 2.1.0).
For SmartSeq2 data, Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1. For 10X data, gene count matrix was computed using Cellranger (v 2.1.0)
For 10X data, barcode is found in R1 from bp 1-16 and UMI is found in bp 17-26.
Genome_build: GRCh38.77
Supplementary_files_format_and_content: For SmartSeq2 data, data frame including sample name, gene ID, and FPKM values for each single cell. For 10X data, log transformed and normalized gene expression values as computed by Seurat (v 2.3.0) with gene IDs and cell barcode information for Dchs1 and Ctrl cells used in further analysis.

value: Control organoid 3


title: Sdc1_pMut_and_Yjr_KO_H3K4me3-2

value: Sdc1_pMut and Yjr_KO


title: Sdc1_pMut_and_Yjr_KO_H3K4me3-1


title: Yjr_KO_H3K4me3-1


title: Utrecht_LimSSc5me3


title: Utrecht_HC10me3


title: D5A_Control_3a


title: Sdc1_pMut_and_Yjr_KO_H3K4me2-1

value: H3K4me2 (Diagenode, pAB-035-050)


title: Yjr_KO_H3K4me2-2


title: miRNA Young-liver-2

description:
domestic pig
miRNA_tpm.txt


title: miRNA Old-liver-1

description:
domestic pig
miRNA_tpm.txt


title: Utrecht_HC8me3


title: Yjr_KO_H3K4me2-1


title: D9A_Control_3a


title: WT_H3K4me2-1


title: WT_H3K4me2-2


title: D4A_Control_3a


title: D3A_Control_3a


title: Sdc1_pMut_and_Yjr_KO_H3K4me1-2

value: H3K4me1 (Diagenode, pAB-037-050)


title: WT_H3K4me3-1


title: Sdc1_pMut_and_Yjr_KO_H3K4me1-1


title: D2A_Control_3a


title: E2A_Control_3a


title: Utrecht_HC5me3

value: peripheral blood


title: D1A_Control_3a


title: Yjr_KO_H3K4me1-1


title: D12A_Control_3a


title: Set1_KO_H3K4me3

value: Mutant Set1_KO


title: WT_H3K4me1-1


title: Utrecht_HC2me3

value: H3K4me3 (07-473, Merck Millipore)


title: Yjr_KO_H3K4me1-2


title: Sdc1_pMut_and_Yjr_KO_H3K4me2-2


title: Utrecht_HC1me3


title: Utrecht_DiffSSc11me3

value: dcSSc patient


title: Sdc1_KO_H3K4me3-A

value: Mutant Sdc1_KO


title: D10A_Control_3a


title: Utrecht_DiffSSc10me3


title: WT_H3K4me3-A


title: Dpy30_KO_H3K4me3-A

value: Mutant SDpy30_KO


title: Set1_KO_H3K4me2


title: Sdc1_pMut_H3K4me2-B

value: Mutant Sdc1_pMut


title: C9A_Control_3a


title: C8A_Control_3a


title: WT_H3K4me1-2


title: Utrecht_HC4me3


title: Dpy30_KO_H3K4me2-B

value: Mutant Dpy30_KO


title: Sdc1_pMut_H3K4me2-A


title: Utrecht_HC7me3


title: C6A_Control_3a


title: D11A_Control_3a


title: C5A_Control_3a


title: C7A_Control_3a


title: WT_H3K4me2-B


title: Sdc1_KO_H3K4me2-A


title: Utrecht_DiffSSc2me3


title: WT_H3K4me2-A


title: Utrecht_DiffSSc9me3


title: Utrecht_DiffSSc4me3


title: Sdc1_KO_H3K4me2-B


title: Set1_KO_H3K4me1


title: Utrecht_DiffSSc1me3


title: Sdc1_pMut_H3K4me1-A


title: C4A_Control_3a


title: Sdc1_pMut_H3K4me1-B


title: Utrecht_LimSSc11Ac

value: lcSSc patient

value: H3K27ac (AB4729, Abcam)


title: Dpy30_KO_H3K4me1-B


title: Dpy30_KO_H3K4me1-A


title: Utrecht_DiffSSc5me3


title: Utrecht_LimSSc10Ac


title: C2A_Control_3a

value: 55 days


title: Sdc1_KO_H3K4me1-B


title: Sdc1_KO_H3K4me1-A


title: Utrecht_LimSSc9Ac


title: WT_H3K4me1-B


title: C1A_Control_3a


title: WT_H3K4me1-A


title: C12A_Control_3a


title: Utrecht_LimSSc6Ac


title: C11A_Control_3a


title: Jhd2_KO_C2_RNA [Yjr_KO_1]

description:
Yjr_KO_1
L10345_Track-29510

data_processing:
bcl2fastq 2.17.1.14
RNA-seq data were processed using Tuxedo suite and custom scripts for further downstream analysis (Trapnell et al. 2012).
Tuxedo suite consists of TopHat (aligns the reads and map them to the genome) (Trapnell et al. 2009), Cufflinks (uses the read alignment map to assemble reads into transcripts) (Trapnell et al. 2010)
Genome_build: sacCer3 S. cerevisiae
Supplementary_files_format_and_content: genes.read_group_tracking.csv.gz; tab separated files listing the genes in rows and several values as columns (fraw frags, FKPM); column replicate list the used sample where 0 corresponds to the first replicate and 1 to the 2nd (per condition)

source_name: Jhd2 deletion

growth_protocol: Cells were grown in YPD (rich medium) untill mid log phase (5*107 cells were collected per sample)

extract_protocol:
Total RNA was isolated using YeaStar RNA Kit (Zymo research, R1002). To eliminate residual DNA total RNA was treated with DNase I (RNase_free DNase, Qiagen) before purification using RNeasy Kit (Qiagen). The quality of RNA was determined using Bioanalyzer (Agilent) to verify an RNA integrity number (RIN) for each sample in the range 7-8.1. The NEBNext rRNA Depletion kit was used to remove ribosomal RNA from total RNA sample.
Library was prepared following " NEBnext Ultra Directional RNA version 1 Libprep Kit" protocol

value: Jhd2 deletion


title: Sdc1_mut + Jhd2_KO_C2_RNA [Sdc1_YjrKO_1]

description:
Sdc1_YjrKO_1
L10347_Track-29512

source_name: Sdc1 point mutant + Jhd2 deletion

value: Sdc1 point mutant + Jhd2 deletion


title: Jhd2_KO_C1_RNA [Yjr_KO_0]

description:
Yjr_KO_0
L10344_Track-29509


title: Utrecht_LimSSc5Ac


title: Sdc1_mut + Jhd2_KO_C1_RNA [Sdc1_YjrKO_0]

description:
Sdc1_YjrKO_0
L10346_Track-29511


title: Utrecht_LimSSc4Ac


title: Sdc1_mut_C2_RNA [Sdc1_mut_1]

description:
Sdc1_mut_1
L10343_Track-29508

source_name: Sdc1 point mutant

value: Sdc1 point mutant


title: Sdc1_mut_C1_RNA [Sdc1_mut_0]

description:
Sdc1_mut_0
L10342_Track-29507


title: C3A_Control_3a

value: Control organoid 3


title: Utrecht_LimSSc3Ac


title: Dpy30_KO_C2_RNA [Dpy30_KO_1]

description:
Dpy30_KO_1
L10341_Track-29506

source_name: Sdc1_DPY30 motif deletion

value: Sdc1_DPY30 motif deletion


title: Dpy30_KO_C1_RNA [Dpy30_KO_0]

description:
Dpy30_KO_0
L10340_Track-29505


title: C10A_Control_3a


title: B9A_Control_3a


title: Sdc1_KO_C2_RNA [Sdc1_KO_1]

description:
Sdc1_KO_1
L10339_Track-29504

source_name: Sdc1 deletion

value: Sdc1 deletion


title: B8A_Control_3a


title: Sdc1_KO_C1_RNA [Sdc1_KO_0]

description:
Sdc1_KO_0
L10338_Track-29503


title: WT_C2_RNA [AR42_1]

description:
AR42_1
L10337_Track-29502

source_name: WT (Wild Type)

value: WT (Wild Type)


title: Utrecht_LimSSc1Ac

value: peripheral blood


title: B7A_Control_3a


title: Utrecht_HC13Ac

value: healthy donor


title: B6A_Control_3a


title: Utrecht_HC12Ac


title: B5A_Control_3a


title: B4A_Control_3a


title: Utrecht_HC8Ac


title: rna_WT_CS_a

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

institute: Monash University

description: mRNA_wild-type replicate 1_15 deg

data_processing:
Library strategy: TCP-seq
Read quality-trimming and adapter-trim/selection; as outlined in Step 147 of  doi:10.1038/nprot.2016.189 with the following alteration to the cutadapt call: cutadapt --discard-untrimmed -a CTGTAGGCACCATCAATAGATCGGAAGA -e 0.0 -O 12 tr_$bn
Read quality-trimming and adapter-trim from 5' end; as outlined in Step 148 of doi:10.1038/nprot.2016.189
Stepwise subtractive mapping; as outlined in Step 149 of doi:10.1038/nprot.2016.189
Mapping to transcript + 1kb flanking using STAR;  as outlined in Step 150 of doi:10.1038/nprot.2016.189
Classify alignments by position within transcript (5'UTR, ORF, etc.). For total-RNA fractions also add a re-classification after altering the 5'UTR:ORF boundary using the length-percentile normalizing algorithm and the sample's SSU-footprinting data.
Filter out 21 manually identified 'spike' artefacts from alignments, listed in file all_artefacts.txt
Filter out all alignments < 14 nt long
Count alignments falling within each position class per transcript
Genome_build: SacCer3
Supplementary_files_format_and_content: Bed format

molecule: cytoplasmic RNA

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD600 of ~  0.7 in SC medium (maintaining selection for plasmids as needed) and subjected to temperature shifts as indicated

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in a freezer mill.  SSU RNaseI footprints and total RNA fractions were extracted from each yeast culture essentially as described in Archer SK et al (2016),Nature 535, 570-574.
Sequencing libraries were generated (size selection, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) as described in Ingolia NT et al 2009.  Science 324(5924):218-223

treatment_protocol: All cultures were cross linked using freshly depolymerized 30% w/v paraformaldehyde for 20min on ice.

value: 15 deg

tag: fraction

value: a

value: wild-type DED1 (NSY4)


title: Utrecht_HC7Ac


title: rna_WT_TS_a

description: mRNA_wild-type replicate 1_37 deg

value: 37 deg

value: wild-type DED1 (NSY10)


title: rna_TIF1_b

description: mRNA_37 replicate 2_37 deg

value: b

value: wild-type TIF1 (NSY20)


title: rna_ded1tsdbp1_a

description: mRNA_ded1-ts dbp1Δ replicate 1_37 deg

value: ded1-ts dbp1delta (NSY15)


title: rna_ded1tsdbp1_b

description: mRNA_ded1-ts dbp1Δ replicate 2_37 deg


title: rna_WT_CS_b

description: mRNA_wild-type replicate 2_15 deg


title: B3A_Control_3a

first: Sabina

last: Kanton

address: 318 Campus Drive

institute: Stanford University

value: 55 days


title: rna_WT_TS_b

description: mRNA_wild-type replicate 2_37 deg


title: rna_ded1ts_a

description: mRNA_ded1-ts replicate 1_37 deg

value: ded1-ts (NSY11)


title: rna_TIF1_a

description: mRNA_TIF1 replicate 1_37 deg


title: Sdc1_pMut_H3K4me3-A

value: Mutant Sdc1_pMut

value: H3K4me3 (Abcam, ab8580)


title: rna_ded1cs_b

description: mRNA_ded1-cs replicate 2_15 deg

value: ded1-cs (NSY5)


title: B12A_Control_3a

value: Control organoid 3


title: Utrecht_HC5Ac

value: H3K27ac (AB4729, Abcam)


title: rna_ded1ts_b

description: mRNA_ded1-ts replicate 2_37 deg


title: Utrecht_HC4Ac

value: peripheral blood


title: rna_ded1cs_a

description: mRNA_ded1-cs replicate 1_15 deg


title: WT_C1_RNA [AR42_0]

description:
AR42_0
L10414_Track-29513

value: WT (Wild Type)


title: Utrecht_LimSSc2Ac

value: lcSSc patient


title: rna_dbp1_a

description: mRNA_dbp1Δ replicate 1_37 deg

value: a

value: dbp1delta (NSY14)


title: Utrecht_HC10Ac

value: healthy donor


title: Utrecht_HC2Ac


title: rna_dbp1_b

description: mRNA_dbp1Δ replicate 2_37 deg

value: 37 deg


title: A9A_Control_3a


title: B1A_Control_3a


title: Ft_WT_TS_a

description: ribo_wild-type replicate 1_37 deg

value: wild-type DED1 (NSY10)


title: Utrecht_DiffSSc11Ac

value: dcSSc patient


title: Ft_WT_CS_b

description: ribo_wild-type replicate 2_15 deg

value: 15 deg

value: b

value: wild-type DED1 (NSY4)


title: Utrecht_DiffSSc10Ac


title: Ft_TIF1_b

description: ribo_TIF1 replicate 2_37 deg

value: wild-type TIF1 (NSY20)


title: A7A_Control_3a

value: 55 days


title: Ft_TIF1_a

description: ribo_TIF1 replicate 1_37 deg


title: A8A_Control_3a


title: A5A_Control_3a


title: Ft_ded1tsdbp1_b

description: ribo_ded1-ts dbp1Δ replicate 2_37 deg

value: ded1-ts dbp1delta (NSY15)


title: Ft_ded1ts_b

description: ribo_ded1-ts replicate 2_37 deg

value: ded1-ts (NSY11)


title: Utrecht_DiffSSc9Ac

value: H3K27ac (AB4729, Abcam)


title: Ft_WT_CS_a

description: ribo_wild-type replicate 1_15 deg


title: Utrecht_DiffSSc7Ac

value: peripheral blood


title: B10A_Control_3a

value: Control organoid 3


title: Ft_ded1cs_b

description: ribo_ded1-cs replicate 2_15 deg

value: ded1-cs (NSY5)


title: A3A_Control_3a


title: Ft_ded1tsdbp1_a

description: ribo_ded1-ts dbp1Δ replicate 1_37 deg

value: a


title: Ft_ded1cs_a

description: ribo_ded1-cs replicate 1_15 deg


title: A2A_Control_3a


title: Utrecht_HC1Ac


title: Ft_WT_TS_b

description: ribo_wild-type replicate 2_37 deg


title: Ft_dbp1_b

description: ribo_dbp1Δ replicate 2_37 deg

value: dbp1delta (NSY14)


title: Utrecht_DiffSSc5Ac


title: Ft_dbp1_a

description: ribo_dbp1Δ replicate 1_37 deg


title: Utrecht_DiffSSc4Ac


title: A1A_Control_3a


title: spt6-F249K_2

city: Salt Lake City

first: Tim

last: Formosa

state: UT

address: 15 N Medical Dr East RM 4100

department: Biochemistry

institute: University of Utah School of Medicine

description:
spt6-F249K_log2_f.bw
spt6-F249K_log2_r.bw

data_processing:
Reads were aligned to the genome index using Novocraft Novoalign version 2.8.3. The index was built containing genomic sequence plus known splice junctions as was built using the USeq application MakeTranscriptome, version 8.8.8 (http://useq.sourceforge.net). Up to 10 multiple mappings were allowed.
Raw alignments were processed to convert splice alignments to genomic alignments using USeq SamTranscriptomeParser, version 9.1.3. One alignment was kept per read.
Stranded, spliced, read-depth normalized coverage was generated with bam2wig (BioToolBox, version 1.60, https://github.com/tjparnell/biotoolbox). The three replicates were depth-normalized to Reads Per Million (RPM) prior to taking a mean coverage.
Coverage files were converted to log2 scale by adding 1 to the RPM value and taking the log2 value using manipulate_wig (BioToolBox, version 1.60). Wig files were converted to bigWig.
Genome_build: SacCer3
Supplementary_files_format_and_content: BigWig files representing stranded, spliced, read-depth normalized mean coverage of three replicates.

source_name: Whole yeast cells

growth_protocol: Cultures were grown to logarithmic phase in rich medium at 30° C and harvested by centrigugation.

extract_protocol:
RNA was extracted from cell pellets using an acid phenol procedure followed by pelleting in CsCl2, resuspension, ethanol precipitation, and purification by Qiagen Rneasy mini kit.
Sequencing libraries were constructed using NEBNext® Multiplex Oligos (Index Primers Set 1 and Set 2) and NEBNext® ChIP-seq Library Prep Reagent Set for Illumina, and subjected to 50 bp single-end sequencing in an Illumina Hiseq2500 sequencer.

tag: culture conditions

value: Rich medium, 30°, log phase

tag: genotype


title: spt6-F249K_1


title: spt16-11_3

description:
spt16-11_log2_f.bw
spt16-11_log2_r.bw


title: A12A_Control_3a


title: Ft_ded1ts_a

description: ribo_ded1-ts replicate 1_37 deg

value: 37 deg


title: A11A_Control_3a


title: A4A_Control_3a


title: spt16-11_2

description:
spt16-11_log2_f.bw
spt16-11_log2_r.bw


title: Utrecht_DiffSSc1Ac


title: Utrecht_DiffSSc2Ac


title: spt16-11_1

description:
spt16-11_log2_f.bw
spt16-11_log2_r.bw


title: spt16-G132D_3

description:
spt16-G132D_log2_f.bw
spt16-G132D_log2_r.bw


title: spt16-G132D_2


title: A10A_Control_3a


title: Fipco3_NSC_2

city: Jerusalem

first: Nissim

last: Benvenisty

state: Outside the United States or Canada

address: Edmond J. Safra Campus, Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Reads were mapped to the human reference genome (GRCh38/hg38) using Tophat2
Normalized FPKM values for each sample were obtained using Cufflinks (Trapnell et al., 2010)
Expression threshold was defined as 0.3, elevating genes with a lower expression to this level.
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample;

source_name: iPSC-derived NPCs

growth_protocol: FXS-iPSCs were differentiated using a previously reported neural differentiation protocol with slight modifications (Kim et al., 2010). Briefly, iPSC colonies were cultured as embryoid bodies for 4 days on low attachment plates in human embryonic stem-cell media without FGF2, supplemented with 5µM dorsomorphin (Tocris Bioscience) and 5µM SB431542 (Cayman Chemicals). EBs were then plated for neural expansion on 0.2% gelatin-coated plates and cultured for 6 additional days in DMEM-F12 medium (Sigma) supplemented with 1×N2 (Invitrogen), 2mM L-glutamine and 20ng/ml FGF2 (Invitrogen).

extract_protocol:
RNA was isolated using NucleoSpin RNA Plus kit (Macherey-Nageland). For RNA sequencing analysis, poly(A) pull-down was used to enrich mRNAs from total RNA samples (200 ng–1 µg per sample, RIN > 9)
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Cells were then treated with 5-azadC for 6 days. Cell media was replaced daily, supplemented with fresh 5-azadC.

tag: group

value: Edited FXS-NPCs

tag: cell type

value: iPSC-derived neural progenitor cells


title: spt16-G132D_1


title: Fipco3_NSC_1


title: ISL1new

city: beijing

first: guo

last: ting

address: 52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital & Institute, Beijing

data_processing:
Basecalls performed using CASAVA version 1.8
aligned to the GRCh38 genome assembly using Hisat2（version:2.0.4）
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample ...

source_name: SGC7901 cells

extract_protocol:
Total RNA was harvested using Qiagen Kit.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The SGC7901 cells were transfected by ISL1 Lentivirus and blank lentivirus as control.

tag: passages

value: gastic cancer cell line

tag: cell line

tag: shRNA

value: ISL1 expression lentivirus


title: pob3-Q308K H3-K56Q_3

description:
H3K56Q_pob3-Q308K_log2_f.bw
H3K56Q_pob3-Q308K_log2_r.bw


title: FXS_NSC_AZA_2

value: 5-aza-2-deoxycytidine treated FXS-NPCs


title: H3-K56R_3

description:
H3K56R_log2_f.bw
H3K56R_log2_r.bw


title: pob3-Q308K H3-K56Q_2


title: FXS-NSC-AZA5


title: pob3-Q308K H3-K56Q_1


title: Con

value: gastric cancer cell line

value: blank lentivirus


title: H3-K56R_2

description:
H3K56R_log2_f.bw
H3K56R_log2_r.bw


title: H3-K56Q_3

description:
H3K56Q_log2_f.bw
H3K56Q_log2_r.bw


title: H3-K56R_1

description:
H3K56R_log2_f.bw
H3K56R_log2_r.bw


title: ISL1-new

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using BWA.
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
Peaks were called using MACS
Genome_build: hg19
Supplementary_files_format_and_content: bed format peak call output using macs

extract_protocol:
Cell lysates were clarified from sonicated nuclei and ISL1-DNA complexes were isolated with ISL1 antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The SGC7901 cells were transfected byISL1 Lentivirus.

value: gastric cancer cell


title: H3-K56Q_2

description:
H3K56Q_log2_f.bw
H3K56Q_log2_r.bw


title: FXS_NSC_CTRL_2

value: FXS-NPCs


title: ISL1-old


title: pob3-Q308K_2

description:
pob3-Q308K_log2_f.bw
pob3-Q308K_log2_r.bw


title: FXS-NSC-Control


title: H3-K56Q_1

description:
H3K56Q_log2_f.bw
H3K56Q_log2_r.bw


title: pob3-Q308K_3


title: spt6-F249K_3


title: pob3-Q308K_1


title: input-old


title: WT_3

description:
WT_log2_f.bw
WT_log2_r.bw

value: WT


title: input-new


title: Fetal liver HSPC,infected with MLLT3-OE vector sample4

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

description:
M4
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
diffOE4w_6s_paired_edgeR.txt
MLLT3_OE_4w_HSPC_4

data_processing:
Alignment: TopHat v2.0.14. parameters --no-coverage-search --library-type fr-firststrand -o
Coverage file: Genomecov, Bedtools, parameters -bg -split –ibam
Tags: Maketagdirectory
RPKM: analyzeRepeats.pl. parameters -rna hg19 -noadj or -rpkm -strand - -count exons -condenseGenes
DGE: getDiffExpression.pl
Genome_build: hg19
Supplementary_files_format_and_content: txt containing RPKM and DGE

source_name: human FL CD34+CD38-/lowCD90+GFP+

growth_protocol: Fetal Liver is mechanically disrupted. CD34+ cells cells are magnetically separated. The indicated phenotype are facs sorted.

extract_protocol:
Cells are FACS sorted in RLT and RNA is extracted using RNeasy Mini kit (Qiagen)
KAPA RNA HyperPrep Kit with RiboErase (HMR)

treatment_protocol: Cells are infected with CTR or MLLT3-OE virus and cultured on OP9M2 stroma

value: FL-HSPC

value: MLLT3 overexpression

tag: time


title: WT_1

description:
WT_log2_f.bw
WT_log2_r.bw


title: Fetal liver HSPC,infected with MLLT3-OE vector sample3

description:
M3
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
diffOE4w_6s_paired_edgeR.txt
MLLT3_OE_4w_HSPC_3


title: 0.5% DMSO, 1 hr, rep 3

city: Berkeley

first: Jamie

middle: HD

last: Cate

address: 748 Stanley Hall

institute: University of California Berkeley

description:
JCNL005J_S10_L005
processed data file:
846_vs_Veh_Deseq_poststall.csv
503_vs_Veh_Deseq_poststall.csv

data_processing:
library strategy: Ribo-seq
Illumina Casava1.7 software used for basecalling.
De-multiplexed reads were stripped of 3′ adapters with the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and aligned to the human ribosomal RNA sequences using Bowtie to remove ribosomal RNA-mapped reads.
Read not aligning to rRNA sequences were aligned to  UCSC/Gencodev24 known coding Canonical Transcripts of the Grch38 human reference genome using Bowtie.
Reads that mapped to more than 1 position of the reference transcriptome were filtered out.
Reads were mapped along the transcripts, an mRNA P site-offset was determined depending on the size of the fragment as 14 nt for fragment of 26 nucleotides or less, 15 nt for fragments of 27 to 29 nucleotides, and 16 nt for fragments of 30 nucleotides or more. Codon maps were then generated for the CDS of each transcript using custom Python scripts
DMax value was calculated for each transcript as the maximum difference between cumulative normalized reads in PF-06378503 or PF-06744846 treated and untreated (DMSO control) samples
For each sample, a Z-score transformation of the DMax values was calculated using the scale function in R and the DMax positions with a Z-score greater than or equal to 2 were considered putative stalled transcripts.
A differential expression analysis was then performed in R using DEseq for transcripts that had more than 30 counts mapping to CDS reads located 3’ of the DMax position, or 10 codons after the start codon for transcripts lacking a clear DMax value. Reads 10 codons before the end of the transcript were also omitted. Transcripts showing a log2 fold change and FDR adjusted p-value < 0.05 were considered significant.
Genome_build: Dec. 2013 Grch38(hg38)
Supplementary_files_format_and_content: .csv files containing the DEseq analysis

source_name: Huh7_0.5% DMSOfor 1 hr

growth_protocol: Overnight cultures of 7x10^5 Huh7 cells in 10 cm dishes

extract_protocol:
Rinsed with phosphate-buffered saline (PBS) containing cycloheximide (100 µg/mL) and triturated in lysis buffer (20 mM Tris-Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide, 1% Triton X-100 and 25 U/mL DNAse I, Promega). The lysates were aliquoted, flash frozen and stored at -80 °C until used for ribosome footprint library preparation.
Ribosomes and libraries were prepared as described in Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012;7: 1534–1550.

treatment_protocol: Treated with 1.5 µM PF-06744846, 1.5 µM PF-06378503, or 0.5% DMSO control for 1 hr, in biological triplicate

tag: treatment

value: 0.5% DMSOfor 1 hr

tag: molecule subtype

value: mRNA, ribosome protected fragments


title: pob3-Q308K H3-K56Q3

data_processing:
Reads were aligned to the yeast genome version SacCer3 using Novocraft novoalign version 2.8, with adapter trimming, no multi-mapping, and filtered for a minimum mapping quality of 13.
Duplicate alignments were randomly sub-sampled to a level of 40% relative to non-duplicate reads using bam_partial_dedup, version 1.7, https://github.com/tjparnell/HCI-Scripts/tree/master/BamFile.
Fragment coverage was generated using bam2wig version 1.52 (https://github.com/tjparnell/biotoolbox) with an extension of 150 bp, skipping chrMito, depth normalized to Reads Per Million, and converted to bigWig format.
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig files representing the nucleosome fragment coverage, normalized to Reads Per Million.

growth_protocol: Cultures were grown to logarithmic phase in rich medium at 30° C and harvested by centrifugation.

extract_protocol:
Cells were subjected to cross-linking with formaldehyde (1%) for 20 min at room temperature. Glycine (final 0.2 M) was added to quench crosslinking and cells were washed with 1X Tris-buffered saline. Cell walls were removed with 500 U lyticase, 37° 20 minutes, or until >90% of cells are spheroplasted and collected by centrifugation.
Cells were lysed in MNase digestion buffer and 10 U MNase, then incubated at 37° for 15 minutes, and the reaction stopped, diluted, and crosslinks reversed by incubating 5 hours at 65°. DNA was precipitated with ethanol, then treated with RNase A, followed by Proteinase K digestion and purification on Qiagen Qiaquick columns.
Sequencing libraries were constructed using NEBNext® Multiplex Oligos (Index Primers Set 1 and Set 2) and NEBNext® ChIP-seq Library Prep Reagent Set for Illumina. Ligated samples were purified by electrophoresis through 1.5% agarose, excising the 270 bp mononocleosome band (150 bp + 120 bp adaptors), purified on a Qiagen gel extraction kit. Samples were then subjected to 50 bp single-end sequencing in an Illumina Hiseq2500 sequencer.


title: 0.5% DMSO, 1 hr, rep 2

description:
JCNL001B_S2_L001
processed data file:
846_vs_Veh_Deseq_poststall.csv
503_vs_Veh_Deseq_poststall.csv


title: pob3-Q308K H3-K56Q2


title: pob3-Q308K H3-K56Q1


title: 0.5% DMSO, 1 hr, rep 1

description:
JCNL009R_S2_L001
processed data file:
846_vs_Veh_Deseq_poststall.csv
503_vs_Veh_Deseq_poststall.csv


title: H3-K56Q2


title: 1.5 µM PF-06378503, 1 hr, rep 3

description:
JCNL008P_S16_L008
processed data file:
503_vs_Veh_Deseq_poststall.csv