title: H3K4me3.TypeB.rep2

value: TypeB


title: D10

status: Public on Feb 12 2020

type: SRA

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

country: USA

institute: Van Andel Research Institute

library_source: genomic

data_processing:
The libraries were sequenced on the HiSeq 2500 platform (Illumina) using custom sequencing primers.
The FASTQ reads were quality trimmed using trimgalore.
The trimmed reads were then aligned using Bismark.
Bismark was used to align reads to the target reference genome and perform methylation calls.
Genome_build: hg19
Supplementary_files_format_and_content: Each txt file contain the following information in order: chromosome #, genomic coordinate, strand, unmethylation count, methylation count, CHH/CHG/CG context of cytosine, exact sequence of the previous context

molecule: genomic DNA

organism: Homo sapiens

source_name: PD_Brain prefrontal cortex neurons (NeuN+)

growth_protocol: Human prefrontal cortex neurons.

extract_protocol:
Neuronal nuclei from prefrontal cotex were isoated by an antibody (NeuN) and flow cytometry approach; DNA were extracted by standard phenol chloroform extraction; Bisulfite padlock probes were designed to humans brain enhancers and promoters (NIH Roadmap Chromm)
We scanned brain-relevant enhancers and promoters genome-wide using the bisulfite padlock probe approach. Padlock probes (n=59,009) were designed using the PP Designer software and synthesized using a programmable microfluidic microarray platform (CustomArray, Inc.). Isolated genomic DNA for each sample was bisulfite-converted and purified using the EZ DNA Methylation-Lightning Kit (Zymo Research). The bisulfite-converted DNA (200 ng) was hybridized to the padlock probes (1.5 ng). Targeted regions were extended using PfuTurbo Cx (Agilent Technologies) and circularization was completed using Ampligase (Epicentre). Non-circularized DNA was digested using an exonuclease cocktail and the remaining circularized DNA was amplified using a common linker sequence in the padlock probe. Libraries were PCR amplified, pooled in equimolar amounts, purified by QIAquick Gel Extraction kit (Qiagen) and quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems).

tag: diagnosis

value: Parkinson's disease (PD)

tag: Sex

value: M

tag: age

tag: pmi

tag: asymmetrygroup

value: Unmatched

tag: brainhemisphere

value: L

tag: duration

tag: tissue/cell type

value: Brain prefrontal cortex neurons(NeuN+)

tag: brain bank

value: U. of Miami Brain Endowment Bank

tag: tissueid

tag: replicate

value: No


title: H3K4me3.Undiff.rep2

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

country: China

institute: Fudan University

data_processing:
Base-calling was performed using CASAVA.
Firstly, All of the Histone modification ChIP-seq data were send to trim-galore to remove adapter contamination and low quality sequences, Phred score of any bases in a reads under 20 and adapter sequence were removed, reads after trimming shorter than 30 were discarded.
Trimmed sequences were then mapped with Bowtie (v2.2.6) using default parameters. Duplicate reads were removed by samtools rmdup -s. Unique and monoclonal mapped reads were extended to 150-bp based on the average sonicated chromatin DNA length.
Spike-in reads were mapped to drosophila genome (dm6) using same parameters.
GenomeCoverageBed (bedtools) was used to transfer bed files to bedGraph files, then spikein reads was used as a normalization factor that equalizes the signal across samples. Normalized bedGraph files were subsequently transferred to bigwig files.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig&bed

organism: Mus musculus

growth_protocol: Spermatogenesis was synchronized and validated as previously described.

extract_protocol:
ChIP assay was carried out as previously described. The sorted homogenous synchronous spermatogenic cells were crosslinked with 1% formaldehyde for 10 mins and then stopped by adding 125 mM Glycine. Chromatin samples were lysed with lysis buffer (20 mM Tris-HCl pH8.0, 500 mM NaCl, 1 mM EDTA, 1% TritonX-100 and 0.1% SDS) and sonicated with Qsonica. Histone modification specific antibody was incubated with chromatin samples overnight at 4 ℃.0.5 ug spike-in antibody (Active motif #61686) and 25 ng spike-in chromatin (Active motif #53083) were used in this ChIP assay according to the manufacture’s guidelines.
DNA samples were analyzed using real time PCR and prepared for deep sequencing according to the manufacture’s guidelines (KAPA Biosystems KK8503 and VAHTS Universal DNA Library Prep Kit for Illumina V3 ND607). Finally, libraries were pooled and sequenced on the Illumina HiSeq 2500 sequencer for 150-bp paired-end sequencing.

treatment_protocol: Briefly, 2-dpp mice were pipette fed 100 μg/g body weight WIN 18,446 (MP), suspended in 1% gum tragacanth, for 7 consecutive days. At Day 8 of WIN 18,446 treatments, these animals were received an i.p. injection of RA (Sigma; 30 μg/g body weight) in dimethyl sulfoxide (DMSO), and were then left to recover for sample collections. The undifferentiated spermatogonia was isolated from Lin28-YFP knockin mice. Testes from 3-week-old Lin28-YFP knockin mice were collected and digested by type I collagenase and 0.25% Trypsin as described previously1. After centrifugation, the pellet was resuspended in DMEM containing 2% BSA at a concentration of 1×106 cells/40 μL, followed by incubating with PE-conjugated anti-CD117 antibody (0.1 μg/106 cells; Molecular probes) for 30 min on ice. The undifferentiated spermatogonia (YFP-positive, PE-negative population) was collected using FACS (BD). The type A1 spermatogonia was isolated from synchronous Stra8-GFPCre mice. Testes were collected and digested. The type A1 spermatogonia (GFP-positive population) was collected using FACS. The type B spermatogonia and different stages of spermatocytes were isolated from synchronous Lin28-YFP and Vasa-tdTomato double positive mice. To isolate the type B spermatogonia, testes were digested and the synchronous advanced spermatogenic cells (tdTomato positive population) were collected using FACS. To isolate different stages of spermatocytes, testes were digested and the cell suspensions were stained with Hoechst 33342. The tdTomato positive 4N population were collected using FACS. The identity of sorted spermatocytes were validated using surface spreading and immunofluorescence.

tag: strain

tag: genotype/variation

value: wild type

tag: cell type

tag: stage during meiotic process

value: Undiff

tag: chip antibody


title: Treatment-naive replicate 7

type: RNA

city: Essen

first: Sied

last: Kebir

address: Hufelandstr. 55

country: Germany

institute: DKFZ-Division Translational Neurooncology at the West German Cancer Center (WTZ)

description:
DE15SHFUKBR100092
Gene expression data

hyb_protocol: Standard Affymetric hybridization protocol

scan_protocol: Standard Affymetric scanning protocol

data_processing:
Probe level summarization was performed via a median polish and data quality checked via the ArrayQualityMetrics package (Kauffmann, Gentleman et al. 2009). Background correction carried out via RMA (Bolstad et al., 2003). The RMA algorithm only uses the sequence information of the PM (positive matches) probes in order to calculate probe affinity values. After background correction data quantile normalization was performed, ensuring that signal distributions across chips were identical. The R-package ‘affy’ (Gautier, Cope et al. 2004) was used to perform all the steps previously described.
Mapping of probesets to genes was based on the Affymetrix “HTA-2_0.na34.hg19.transcript” annotation file, which can be downloaded from the Affymetrix web page.

label: biotin

molecule: total RNA

source_name: Glioblastoma

label_protocol: Biotinylated cRNA were prepared with the standard labelling kit for Affymetrix arrays (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Conditions for cell expansion where applicable

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

treatment_protocol: Radiotherapy and Temozolomide

tag: sample type

value: Tissue glioblastoma sample


title: H3K4me3.A1.rep2

value: homogenous synchronous spermatogenic cells


title: Relapse replicate 6

description:
DE22SHFUKBR100257
Gene expression data


title: D9

source_name: Control_Brain prefrontal cortex neurons (NeuN+)

tag: diagnosis

value: Control

value: F

value: R


title: Remitting_replicate2

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
Reads were processed using the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/)
Individual cells were tagged with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers).
Reads were trimmed at 3' end to remove poly(A) tails with length greater than 5 and at the 5' end for adapters
Reads with barcode base quality less than 10 were filtered out..
Raw reads were aligned to mouse  (GRCm38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 100 genes.

source_name: Remitting_Flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on TdTomato fluorescence. Post-sort, cells were suspended in PBS and 16% Opti-prep.
Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

tag: Sex

value: Female

tag: mouse status

value: EAE remission phase

value: Flow cytometry sorted astrocytes based on TdTomato fluorscence


title: Remitting_replicate1

tag: age


title: H3K4me3.eP.rep1

value: eP


title: Treatment-naive replicate 6

description:
DE34SHFUKBR100138
Gene expression data


title: H3K4me3.Late-Z.rep1

value: Late-Z


title: D8

tag: pmi

tag: asymmetrygroup


title: Treatment-naive replicate 5

description:
DE09SHFUKBR100200
Gene expression data


title: Naïve_replicate3

source_name: Naïve_Flow cytometry sorted astrocytes

value: Naïve mice


title: Naïve_replicate2

value: Male


title: D6

value: Parkinson's disease (PD)

value: M

value: Unmatched

tag: brainhemisphere

value: L

tag: duration

value: Brain prefrontal cortex neurons(NeuN+)


title: Acute_replicate1

source_name: Acute_Flow cytometry sorted astrocytes

value: wild type

value: EAE peak phase


title: D5

value: Control

tag: tissue/cell type

tag: brain bank

value: U. of Miami Brain Endowment Bank

value: Yes


title: Naive_replicate3 [scRNA-seq]

data_processing:
Reads were processed using the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/)
Individual cells were tagged with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers).
Reads were trimmed at 3' end to remove poly(A) tails with length greater than 5 and at the 5' end for adapters
Reads with barcode base quality less than 10 were filtered out..
Raw reads were aligned to mouse  (GRCm38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 500 genes.

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and cell density was quantified. Cells were suspended in PBS and 16% Opti-prep.
Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.

value: male

value: between 74-96 days of age

tag: disease

value: naïve

tag: sample subgroup

value: CNS pellet following Percoll gradient


title: CFA_replicate3 [scRNA-seq]

tag: strain

tag: genotype/variation

value: CFA-only mice


title: D4

value: F

value: R

tag: tissueid

tag: replicate

value: No


title: CFA_replicate2 [scRNA-seq]

tag: cell type


title: Remitting_replicate3 [scRNA-seq]

value: experimental autoimmune encephalomyelitis (EAE)

value: EAE remission phase


title: D3

tag: diagnosis

value: L


title: Relapse replicate 5

description:
DE05SHFUKBR100078
Gene expression data

tag: sample type

value: Tissue glioblastoma sample


title: Remitting_replicate2 [scRNA-seq]

value: wild type

tag: Sex


title: Treatment-naive replicate 3

description:
DE86SHFUKBR100075
Gene expression data


title: Relapse replicate 3

description:
DE51SHFUKBR100123
Gene expression data


title: D2

value: Parkinson's disease (PD)

tag: age

value: Unmatched

value: Brain prefrontal cortex neurons(NeuN+)


title: Naive_replicate2 [scRNA-seq]

value: Naïve mice


title: Remitting_replicate1 [scRNA-seq]

value: male


title: C12

value: Control

tag: pmi

value: U. of Miami Brain Endowment Bank

value: Yes


title: Naive_replicate1 [scRNA-seq]

value: between 74-96 days of age

value: naïve

value: CNS pellet following Percoll gradient


title: Acute_replicate2

value: Female

tag: mouse status

value: EAE peak phase

value: Flow cytometry sorted astrocytes based on TdTomato fluorscence


title: Acute_replicate3 [scRNA-seq]

value: experimental autoimmune encephalomyelitis (EAE)


title: Naïve_replicate1

value: Male


title: C11

value: F

tag: asymmetrygroup

tag: brainhemisphere

value: L

value: No


title: Acute_replicate1 [scRNA-seq]

value: wild type


title: D11

value: Parkinson's disease (PD)

value: M

value: Matched

value: R

tag: duration

tag: tissue/cell type

value: Brain prefrontal cortex neurons(NeuN+)


title: Relapse replicate 4

description:
DE61SHFUKBR100331
Gene expression data

value: Cultured glioblastoma sample


title: 72h-CVB_S14

city: Worcester

first: Pranitha

last: Vangala

address: 55 Lake Avenue North

institute: University of Massachussets Medical School

data_processing:
Illumina bcl2fastq2 v2.20 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: hg19
Supplementary_files_format_and_content: transcript quantification in tpms
Supplementary_files_format_and_content: transcript quantification in counts

source_name: SC-beta cells derived from the embryonic stem cell line HUES8

extract_protocol: Cells were infected with virus at a multiplicity of infection of 10 (or were mock-infected) and collected at 24, 48, and 72 hours for total RNA. RNA-Seq libraries were prepared using SMART-Seq. Pooled libraries were sequenced for 2 x 75 cycles to obtain paired end reads using a NextSeq 500 (Illumina).

tag: time point

tag: agent

value: coxsackievirus B4 (CVB)

value: SC-beta cells


title: 72h-Mock_S3

value: Mock


title: 48h-Mock_S2


title: C9

value: Unmatched

tag: brain bank

value: U. of Miami Brain Endowment Bank


title: Priming_replicate2 [scRNA-seq]

tag: strain

tag: genotype/variation

value: male

value: between 74-96 days of age

tag: disease

value: experimental autoimmune encephalomyelitis (EAE)

tag: sample subgroup

value: EAE priming phase

value: CNS pellet following Percoll gradient


title: Priming_replicate1 [scRNA-seq]

value: wild type

tag: cell type


title: C10

tag: diagnosis

value: Parkinson's disease (PD)

tag: tissueid

tag: replicate

value: No


title: Priming_replicate3 [scRNA-seq]

tag: Sex

tag: age


title: CFA_replicate1 [scRNA-seq]

value: naïve

value: CFA-only mice


title: Treatment-naive replicate 1

description:
DE78SHFUKBR100316
Gene expression data

tag: sample type

value: Tissue glioblastoma sample


title: Input.Spo11KO.Z

value: Spo11 Knockout

value: homogenous synchronous spermatogenic cells

tag: stage during meiotic process


title: 48h-CVB_S12

value: coxsackievirus B4 (CVB)

value: SC-beta cells


title: Treatment-naive replicate 4

description:
DE95SHFUKBR100301
Gene expression data


title: C8

value: Control

value: M

tag: pmi

tag: asymmetrygroup

tag: brainhemisphere

value: R

tag: duration

value: Brain prefrontal cortex neurons(NeuN+)


title: Input.Prdm9KO.Z

value: Prdm9 Knockout


title: Input.Spo11KO.L


title: C7

value: L

tag: tissue/cell type

tag: brain bank

value: U. of Miami Brain Endowment Bank


title: Input.Prdm9KO.L

tag: strain

tag: genotype/variation


title: 24h-Mock_S1

tag: time point

tag: agent

value: Mock


title: 24h-CVB_S10

tag: cell type


title: Input.Dmc1KO.Z

value: Dmc1 Knockout


title: Input.Dmc1KO.L


title: C6

tag: diagnosis

tag: tissueid

value: No


title: Input.Ctrl.Z

value: wild type


title: C5

tag: Sex

tag: replicate


title: Input.Ctrl.L


title: C4

value: Parkinson's disease (PD)

value: F

tag: age

value: Matched


title: Hct15HBC005

data_processing:
Trim Galore was used to trim the 75bp single-end reads prior to genome alignment
STAR index was generated using Ensemble GRCh37.p13 primary assembly genome and the Gencode v19 primary assembly annotation
Read alignment and gene counts were performed using STAR
Gene count matrix was imported into R (v3.4.1) and low expressed genes (counts per million < 1 in more than 30% of samples) were removed prior to trimmed mean of M-values normalization in EdgeR
The limma statistical package19 was used to transform the count matrix to log2-counts per million and fit a robust linear model
Genome_build: hg19
Supplementary_files_format_and_content: Each ReadsPerGene.out.tab file contain the following information in order: gene ID, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA, counts for the 2nd read strand aligned with RNA

source_name: Control_Brain prefrontal cortex

growth_protocol: Fresh-frozen human prefrontal cortex tissue (25-50 mg) was lysed and homogenized in 1 mL TRIzol (Invitrogen) in Precellys Lysing Kit CKMix tubes using a MiniLys homogenizer (Bertin Instruments, two intervals of 10 s on the highest setting with 15 s in between). Homogenate was immediately placed on ice and transferred to DNA LoBind Tubes (Eppendorf)

extract_protocol:
Total RNA was isolated using the standard TRIzol protocol and re-suspended in 85 uL Ultrapure Distilled water (Invitrogen). DNase treatment was performed in solution with the RNase-Free DNase Set (Qiagen) using 5 uL DNase I and 10 uL RDD buffer, followed by a column cleanup using the RNeasy Mini Kit (Qiagen) with two additional washes (75% ethanol) before elution
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems). RNA was sheared to an average of 300 bp. Prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies Inc.) and QuantiFluor® dsDNA System (Promega Corp.). Individually indexed libraries were pooled and 75 bp, single end sequencing was performed on an Illumina NextSeq 500 sequencer using a 75 bp HO sequencing kit (v2) (Illumina Inc.), with all libraries run across 4 flowcells to return a minimum read depth of 40M read pairs per library.  Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

tag: rin

tag: group


title: Input.D

value: homogenous synchronous spermatogenic cells

tag: stage during meiotic process

value: D


title: C3

tag: pmi

tag: asymmetrygroup

value: Unmatched

tag: brainhemisphere


title: Hct15HBA007

value: Control


title: Input.L


title: Input.mZ

value: mZ


title: CO37

value: M

value: R


title: Input.mP

value: mP


title: C2

tag: duration

tag: tissue/cell type

value: Brain prefrontal cortex neurons(NeuN+)

tag: brain bank


title: Input.TypeB

tag: strain

tag: genotype/variation

value: TypeB


title: Input.mPL

tag: cell type

value: mPL


title: CO36

tag: diagnosis


title: C1

value: L

value: U. of Miami Brain Endowment Bank

tag: tissueid

value: Yes


title: Input.Undiff

value: wild type

value: Undiff


title: Input.A1


title: H3K9me2.Spo11KO.Z

value: Spo11 Knockout

tag: chip antibody


title: AN10592

tag: Sex


title: B12

value: Parkinson's disease (PD)

tag: age

tag: replicate


title: HctZZJ006

tag: rin

tag: group


title: AN09933

tag: pmi


title: H3K9me2.Prdm9KO.Z

value: Prdm9 Knockout

value: homogenous synchronous spermatogenic cells

tag: stage during meiotic process


title: H3K9me2.Spo11KO.L


title: B11

tag: asymmetrygroup

value: Matched

tag: brainhemisphere

value: No


title: H3K9me2.Prdm9KO.L


title: AN5209

value: Control

value: M


title: B10

value: F

value: Unmatched

value: R

tag: duration

tag: tissue/cell type


title: H3K9me2.Dmc1KO.Z

tag: strain

value: Dmc1 Knockout


title: AN02888

value: L


title: 5661


title: H3K9me2.Ctrl.L

tag: genotype/variation


title: B9

value: Brain prefrontal cortex neurons(NeuN+)

tag: brain bank

value: U. of Miami Brain Endowment Bank


title: H3K9me2.mP.rep1

value: wild type

tag: cell type

value: mP


title: H3K9me2.D.rep1

value: D


title: H3K9me2.mZ.rep1

value: mZ


title: 5657

tag: diagnosis


title: H3K9me2.L.rep1

tag: chip antibody


title: B7

tag: Sex

tag: tissueid


title: 700

tag: age


title: B6

tag: replicate


title: H3K9me2.TypeB.rep1

value: TypeB


title: 471

source_name: PD_Brain prefrontal cortex

value: Parkinson’s disease (PD)

tag: rin

tag: group


title: H3K9me2.A1.rep1

value: homogenous synchronous spermatogenic cells

tag: stage during meiotic process


title: B5

value: Parkinson's disease (PD)

tag: pmi

tag: asymmetrygroup

value: No


title: H3K9me2.Undiff.rep1

value: Undiff


title: H3K9me3.D.rep1


title: 466

value: M

value: Matched


title: H3K9me3.mP.rep1


title: H3K9me2.Ctrl.Z


title: B4

tag: brainhemisphere

tag: duration


title: 460

value: R


title: H3K9me3.mZ.rep1

tag: strain


title: B8

tag: tissue/cell type


title: H3K9me3.mPL.rep1

tag: genotype/variation

value: mPL


title: H3K9me3.L.rep1

tag: cell type

value: L


title: 458

tag: diagnosis


title: B2

value: Control

value: Brain prefrontal cortex neurons(NeuN+)

tag: brain bank


title: B1

tag: Sex

value: U. of Miami Brain Endowment Bank


title: H3K9me2.mPL.rep1

value: wild type

tag: chip antibody


title: H3K9me3.A1.rep1


title: H3K9me3.Undiff.rep1


title: A11

tag: age

value: Unmatched

tag: tissueid


title: H3K27me3.D.rep1

value: D


title: 398

tag: rin


title: H3K27me3.mP.rep1

value: mP


title: A10

tag: replicate


title: 387

value: Parkinson’s disease (PD)

tag: group


title: H3K27me3.L.rep1

value: homogenous synchronous spermatogenic cells

tag: stage during meiotic process


title: H3K27me3.mZ.rep1

value: mZ


title: H3K27me3.mPL.rep1


title: A9

tag: pmi

tag: asymmetrygroup

value: No


title: 368

value: F


title: H3K9me3.TypeB.rep1

value: TypeB


title: H3K27me3.TypeB.rep1


title: 423

value: Matched


title: 348

value: M

value: R


title: 366

value: L


title: H3K36me3.Spo11KO.Z

value: Spo11 Knockout


title: H3K27me3.Undiff.rep1

value: Undiff


title: A6

value: Control

tag: brainhemisphere

tag: duration

value: Brain prefrontal cortex neurons(NeuN+)

value: U. of Miami Brain Endowment Bank


title: H3K36me3.Spo11KO.L

tag: strain


title: H3K36me3.Prdm9KO.Z

tag: genotype/variation

value: Prdm9 Knockout


title: H3K36me3.Prdm9KO.L

tag: cell type


title: H3K36me3.Dmc1KO.L

value: Dmc1 Knockout


title: 338

tag: diagnosis

value: Parkinson’s disease (PD)


title: A5

tag: tissue/cell type

tag: brain bank

value: Yes


title: 340

tag: Sex


title: A4

value: Parkinson's disease (PD)

tag: age

value: Unmatched


title: 317


title: H3K36me3.Ctrl.L

value: wild type

value: homogenous synchronous spermatogenic cells

tag: chip antibody


title: 286

tag: rin


title: A8

tag: tissueid

tag: replicate

value: No


title: A3

value: M

value: Matched


title: H3K36me3.Ctrl.Z

tag: stage during meiotic process


title: A7

tag: pmi

value: L


title: H3K36me3.D.rep1

value: D


title: H3K36me3.mP.rep1

value: mP


title: A2

tag: asymmetrygroup


title: H3K27me3.A1.rep1


title: H3K36me3.TypeB.rep1

value: TypeB


title: A1

value: Control

tag: brainhemisphere

value: Brain prefrontal cortex neurons(NeuN+)


title: H3K36me3.mZ.rep1

value: mZ


title: 268

value: R

tag: group


title: 239

value: Parkinson’s disease (PD)


title: H3K36me3.Dmc1KO.Z

tag: strain

value: Dmc1 Knockout


title: H3K36me3.mPL.rep1

tag: genotype/variation

value: mPL


title: H3K36me3.L.rep1

tag: cell type


title: Relapse replicate 2

description:
DE88SHFUKBR100330
Gene expression data

tag: sample type

value: Cultured glioblastoma sample


title: 226

tag: diagnosis

value: Unmatched


title: H3K36me3.A1.rep1

value: wild type

value: homogenous synchronous spermatogenic cells


title: LP: larp1dko_torin_RNA_rep2

city: New Haven

first: Carson

middle: C

last: Thoreen

state: CT

address: 333 Cedar St. SHM B 145

department: Cellular and Molecular Physiology

institute: Yale School of Medicine

description: RNA from sgLARP1+sgLARP1B HEK-293T cells treated with 250 nM Torin 1 for 2h

data_processing:
Basecalls performed using CASAVA 1.8.
Sequenced reads were trimmed for adaptor sequence using fastx toolkit with command line fastx_clipper -Q33 -c -a [adapter sequence]. For WT and sgLARP1 samples adapter sequence was CTGTAGGCACCATCAAT, and for sgLARP1/1B samples adapter sequence was AGATCGGAAGAGCAC. For the double knock out ribo-seq samples, all samples were originally in a single fastq file and reads contained unique molecular identifiers (UMI). Reads from this file were adapter trimmed and then split according to sample-specific barcodes in the reads, generating the fastq files here deposited and incorporating the 5 nt UMIs at the end of the read name. For the double knock out RNA-seq samples, the first nt of each read was removed with fastx_trimmer -f 2.
Reads were then filtered for human rRNA sequences using bowtie2 (version 2.2.9.0) with default parameters.
Unmapped reads were aligned to the hg19 human genome using tophat2 (v2.1.1) using default parameters and ucsc hg19 GTF file. For the double knock out ribo-seq data, all UMI-duplicate alignments were removed
Aligned footprint and RNA reads mapping to CDS regions were quantified using HTSeq-count (htseq-count -f bam -t CDS, htseq-count -f bam -t CDS -s reverse for sgLARP1+sgLARP1B RNA sample), using a ucsc hg19 GTF file containing gene ids. The resulting counts were compared per genotype separately, using DESeq (design = ~ sampletype + condition + sampletype:condition).
Genome_build: hg19
Supplementary_files_format_and_content: htseq-count, txt

source_name: HEK-293T, sgLARP1+sgLARP1B

growth_protocol: Cells were grown in DMEM + 10%FBS.

extract_protocol:
Cells were lysed on plate in 15 mM Hepes pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton-X100. Clarified lysates were split in two to make libraries for ribosome profiling and RNA-seq.
For ribosome profiling lysates were RNase I treated and centrifuged through a sucrose cushion. RNA was extracted from the resulting ribosome pellet by proteinase K treatment and acid phenol extraction. rRNA was removed with the Ribo-Zero Gold kit. 28-34 nt footprints were then isolated on polyacrylamide gel, dephosphorylated followed by 5' adapter ligation (in case of the double knock out samples, this adapter contained a unique molecular identifier and an additional barcode) and reverse transcription. The resulting cDNA was circularized and PCR amplified, incorporating Illumina sequences. For RNA-seq on WT cells RNA was extracted from the lysate by proteinase K digestion followed by phenol acid extraction and fragmented by alkaline hydrolysis. 40-80 nt fragments were purified and libraries were further prepared similar to the RPF libraries. For sgLARP1 and sgLARP1/1B cells, RNA-seq libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep kit along with the NEBNext rRNA Depletion kit. RPF libraries for LARP1/1B DKO cells were sequenced twice to improve coverage. These samples are identified with "reseq" in the sample name.

treatment_protocol: Cells were treatred with 250 nM Torin 1 or an equivalent volume of vehicle (DMSO) for 2 h.

tag: cell line

tag: treatment

value: Torin 1


title: H3K36me3.Undiff.rep1

value: Undiff


title: LP: larp1dko_torin_RNA_rep1


title: H3K27ac.Spo11KO.Z


title: 216

tag: age

tag: Sex

value: M

value: L


title: H3K27ac.Spo11KO.L

tag: chip antibody


title: LP: larp1dko_dmso_RNA_rep2

description: RNA from sgLARP1+sgLARP1B HEK-293T cells treated with DMSO for 2h

value: DMSO


title: H3K27ac.Prdm9KO.L


title: 194

tag: rin


title: H3K27ac.Dmc1KO.Z


title: 106

value: Matched


title: LP: larp1dko_dmso_RNA_rep1


title: LP: larp1dko_torin_RPF_rep2

description: RPF from sgLARP1+sgLARP1B HEK-293T cells treated with 250 nM Torin 1 for 2h

data_processing:
Library strategy: Ribosome profiling
Basecalls performed using CASAVA 1.8.
Sequenced reads were trimmed for adaptor sequence using fastx toolkit with command line fastx_clipper -Q33 -c -a [adapter sequence]. For WT and sgLARP1 samples adapter sequence was CTGTAGGCACCATCAAT, and for sgLARP1/1B samples adapter sequence was AGATCGGAAGAGCAC. For the double knock out ribo-seq samples, all samples were originally in a single fastq file and reads contained unique molecular identifiers (UMI). Reads from this file were adapter trimmed and then split according to sample-specific barcodes in the reads, generating the fastq files here deposited and incorporating the 5 nt UMIs at the end of the read name. For the double knock out RNA-seq samples, the first nt of each read was removed with fastx_trimmer -f 2.
Reads were then filtered for human rRNA sequences using bowtie2 (version 2.2.9.0) with default parameters.
Unmapped reads were aligned to the hg19 human genome using tophat2 (v2.1.1) using default parameters and ucsc hg19 GTF file. For the double knock out ribo-seq data, all UMI-duplicate alignments were removed
Aligned footprint and RNA reads mapping to CDS regions were quantified using HTSeq-count (htseq-count -f bam -t CDS, htseq-count -f bam -t CDS -s reverse for sgLARP1+sgLARP1B RNA sample), using a ucsc hg19 GTF file containing gene ids. The resulting counts were compared per genotype separately, using DESeq (design = ~ sampletype + condition + sampletype:condition).
Genome_build: hg19
Supplementary_files_format_and_content: htseq-count, txt


title: H3K27ac.Dmc1KO.L


title: H3K27ac.Ctrl.L


title: H3K27ac.Ctrl.Z


title: 81


title: H3K27ac.D.rep1

value: D


title: LP: larp1dko_torin_RPF_rep1


title: H3K27ac.mP.rep1

value: mP


title: LP: larp1dko_dmso_RPF_rep2

description: RPF from sgLARP1+sgLARP1B HEK-293T cells treated with DMSO for 2h


title: 51


title: H3K27ac.mZ.rep1

value: mZ


title: LP: larp1dko_dmso_RPF_rep1


title: H3K27ac.L.rep1


title: H3K27ac.mPL.rep1


title: H3K27ac.A1.rep1


title: 93C: larp1sko_torin_RNA_rep2

description: RNA from sgLARP1 HEK-293T cells treated with 250 nM Torin 1 for 2h

source_name: HEK-293T, sgLARP1


title: Acute_replicate2 [scRNA-seq]

value: male

value: between 74-96 days of age

tag: disease

value: experimental autoimmune encephalomyelitis (EAE)

tag: sample subgroup

value: EAE peak phase

value: CNS pellet following Percoll gradient


title: H3K27ac.Prdm9KO.Z

tag: stage during meiotic process


title: H3K27ac.Undiff.rep1


title: TGA4_8

city: Dallas

first: Tao

last: Wang

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center

data_processing:
Alignment(TopHat)
Differential expression analysis(edgeR)
Genome_build: mm9
Supplementary_files_format_and_content: Normalized rpkm by preprocessCore

source_name: liver

extract_protocol:
FFPE RNA Isolation Kit(Invitrogen)
NuGen RNA-Seq lbraries were made from the purified RNA and indexed libraries were multiplexed in a single flow cell lane and underweet 75 bp single-end sequencing on a NextSeq 500 using the High Output Kit v2.

tag: genotype

value: transgenic

tag: tissue

value: liver


title: 41

value: Parkinson’s disease (PD)

tag: pmi

value: R

tag: group

value: Unmatched


title: 93C: larp1sko_torin_RNA_rep1

tag: genotype/variation

value: Torin 1


title: H3K4me3.Prdm9KO.Z

tag: strain

value: Prdm9 Knockout

tag: cell type

value: homogenous synchronous spermatogenic cells


title: H3K4me3.Spo11KO.Z

value: Spo11 Knockout


title: TGA4_4


title: TGA4_2


title: 93C: larp1sko_dmso_RNA_rep2

description: RNA from sgLARP1 HEK-293T cells treated with DMSO for 2h

value: DMSO


title: H3K4me3.Spo11KO.L


title: 79

tag: diagnosis

value: F

value: L

value: Matched


title: TGA3_8


title: TGA3_4


title: H3K4me3.Dmc1KO.L

value: Dmc1 Knockout


title: H3K4me3.Prdm9KO.L


title: H3K4me3.Dmc1KO.Z


title: H3K4me3.Ctrl.L

value: wild type


title: H3K4me3.Ctrl.Z


title: 93C: larp1sko_torin_RPF_rep2

description: RPF from sgLARP1 HEK-293T cells treated with 250 nM Torin 1 for 2h

tag: cell line


title: H3K27ac.TypeB.rep1

value: TypeB


title: 93C: larp1sko_dmso_RNA_rep1

tag: treatment


title: 93C: larp1sko_torin_RPF_rep1


title: H3K4me3.D.rep1

value: D


title: Treatment-naive replicate 2

description:
DE43SHFUKBR100073
Gene expression data

tag: sample type

value: Tissue glioblastoma sample


title: TGA3_2

value: transgenic

value: liver


title: H3K4me3.mP.rep1

value: mP


title: TGA2_8


title: 93C: larp1sko_dmso_RPF_rep2

description: RPF from sgLARP1 HEK-293T cells treated with DMSO for 2h


title: H3K4me3.mZ.rep1

value: mZ


title: H3K4me3.mPL.rep1

value: mPL


title: H3K4me3.L.rep1


title: TGA2_4


title: TGA2_2


title: H3K4me3.TypeB.rep1


title: H3K4me3.A1.rep1


title: 93C: larp1sko_dmso_RPF_rep1


title: 35YW: hek293_torin_RNA_rep2

description: RNA from WT HEK-293T cells treated with 250 nM Torin 1 for 2h

value: wild-type

value: Torin 1


title: H3K4me3.Undiff.rep1

value: homogenous synchronous spermatogenic cells

value: Undiff


title: 35YW: hek293_torin_RNA_rep1


title: 35YW: hek293_dmso_RNA_rep2

description: RNA from WT HEK-293T cells treated with DMSO for 2h

value: DMSO


title: 35YW: hek293_dmso_RNA_rep1


title: TGA1_2


title: WT4_8


title: 35YW: hek293_torin_RPF_rep1

description: RPF from WT HEK-293T cells treated with 250 nM Torin 1 for 2h


title: WT4_4


title: 35YW: hek293_dmso_RPF_rep2

description: RPF from WT HEK-293T cells treated with DMSO for 2h


title: WT4_2


title: 35YW: hek293_dmso_RPF_rep1


title: TGA1_8


title: TGA1_4


title: 35YW: hek293_torin_RPF_rep2


title: WT2_8


title: WT3_2


title: 22_02_2013_G08_S4.CEL SSc

city: Cologne

first: Pia

last: Moinzadeh

address: Kerpener Str 62

institute: University of Cologne

description: Gene expression data of SSc patients compared to healthy controls

hyb_protocol: RNA was hybridized and scanned to the Human Genome U219 96-array plate using the GeneTitanR instrument (Thermo Fischer Scientific).

data_processing: All statistical analyses were carried out using the R system for statistical computing, version 3.2.3, whereas support vector machines (SVM) were trained and evaluated using the R package 'e1071', version 1.6-8.  We used Ingenuity pathway analysis (IPA) to collect more information about signaling pathways, networks and gene functions

source_name: whole blood

label_protocol: Gene expression analysis was performed using the Thermo Fischer Scientific Human Genome U219 96-array plate. To process the RNA samples, we used the Beckman Biomek FX TPE System (Beckman Coulter Inc., Indianapolis) by the manufacturer HT-IVT express 2.0.6 standard protocol from Thermo Fischer Scientific.

extract_protocol: Total RNA was extracted using a PAXGene Blood RNA kit (PreAnalytiX GmbH) according to the manufacturer’s instructions.

value: blood

tag: disease state

value: SSc


title: 20_02_2013_D10_S5.CEL SSc

scan_protocol: RNA was hybridized and scanned to the Human Genome U219 96-array plate using the GeneTitanR instrument (Thermo Fischer Scientific).


title: WT3_4


title: 22_02_2013_G10_S43.CEL SSc


title: 22_02_2013_E02_S36.CEL healthy control

description: healthy control

value: healthy control


title: WT3_8

value: wild type


title: 22_02_2013_G02_S41.CEL healthy control

description: healthy control


title: 20_02_2013_H12_S29.CEL healthy control

description: healthy control


title: WT2_4


title: 22_02_2013_G03_S8.CEL SSc


title: 22_02_2013_H07_S6.CEL SSc


title: 22_02_2013_C06_S9.CEL SSc


title: 20_02_2013_H09_S38.CEL healthy control

description: healthy control


title: 22_02_2013_F09_S31.CEL healthy control

description: healthy control


title: 22_02_2013_B12_S40.CEL healthy control

description: healthy control


title: WT2_2


title: 22_02_2013_H10_S7.CEL SSc


title: 20_02_2013_H10_S30.CEL healthy control

description: healthy control


title: 22_02_2013_F11_S37.CEL healthy control

description: healthy control


title: 22_02_2013_D04_S32.CEL healthy control

description: healthy control


title: 22_02_2013_B05_S27.CEL SSc


title: 22_02_2013_A08_S33.CEL healthy control

description: healthy control


title: 20_02_2013_A05_S42.CEL SSc


title: 22_02_2013_A05_S3.CEL SSc


title: WT1_8


title: 22_02_2013_E06_S26.CEL SSc


title: 20_02_2013_E05_S28.CEL healthy control

description: healthy control


title: 22_02_2013_C03_S22.CEL SSc


title: WT1_4


title: 22_02_2013_A01_S23.CEL SSc


title: 22_02_2013_B07_S25.CEL SSc


title: EAE_rep3 [F11]

data_processing:
DGE libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
Reads were first demulitplex using Picard (v.2.17.11) IlluminaBaseCallsToSam.
Reads were aligned using GRCh38 mouse genome with STAR (v2.4.2a) with default parameters
Duplicate reads are marked with Picard UmiAwareMarkDuplicatesWithMateCigar to identify duplicate reads based on UMI sequence and alignment start site.
Gene are then quantified using RSEM v1.2.21 with paired-end option and accessed for quality using RNA-SeQC.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format with gene ID, symbol, and RPKM

source_name: EAE mouse

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the 3' DGE protocol as described (Soumillon et al., bioRxiv 2014)

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse. ICV injection of 100 ng IL-1b and 50 ng TNFa. Cells were isolated 24 hours post-injection of IL1b/TNFa

tag: Sex

value: Male

tag: age

value: experimental autoimmune encephalomyelitis (EAE)

value: Flow cytometry sorted astrocytes


title: EAE_rep2 [E11]


title: WT1_2


title: naïve_IL1b_tnfa_rep3 [C11]

source_name: IL1b/TNFa-ICV injected mouse

value: IL1b/TNFa-ICV injected


title: EAE_rep1 [D11]


title: naïve_IL1b_tnfa_rep2 [B11]


title: naïve_IL1b_tnfa_rep1 [A11]


title: 22_02_2013_F01_S18.CEL SSc


title: 20_02_2013_H11_S19.CEL SSc


title: 20_02_2013_C12_S20.CEL SSc


title: 22_02_2013_C12_S17.CEL SSc


title: G7_Scrmbl_rep3

data_processing:
DGE libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
Reads were first demulitplex using Picard (v.2.17.11) IlluminaBaseCallsToSam; with well indices CCGGCA (F4), CGCACC (F7), CGGACG (F10), CGTCCG (G1), GACGCC (G4), and GCCCAG (G7).
Reads were aligned using GRCh38 mouse genome with STAR (v2.4.2a) with default parameters
Duplicate reads are marked with Picard UmiAwareMarkDuplicatesWithMateCigar to identify duplicate reads based on UMI sequence and alignment start site.
Gene are then quantified using RSEM v1.2.21 with paired-end option and accessed for quality using RNA-SeQC.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format with gene ID, symbol, and RPKM

source_name: Flow cytometry sorted astrocytes

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: astrocytes

value: sgScrmbl-targeted


title: 22_02_2013_B08_S2.CEL SSc


title: G4_Scrmbl_rep2


title: 20_02_2013_D04_OV9.CEL SSc


title: 22_02_2013_B11_S21.CEL SSc


title: 22_02_2013_E09_S13.CEL SSc


title: G1_Scrmbl_rep1


title: 20_02_2013_H07_S15.CEL SSc


title: 20_02_2013_C09_S12.CEL SSc


title: 22_02_2013_D03_S10.CEL SSc


title: 22_02_2013_C02_S16.CEL SSc


title: Relapse replicate 1

description:
DE18SHFUKBR100329
Gene expression data

value: Cultured glioblastoma sample


title: 20_02_2013_B08_OV87.CEL healthy control

description: healthy control


title: F10_Mafg_rep3

value: sgMafg-targeted


title: 20_02_2013_F12_OV83.CEL healthy control

description: healthy control


title: F7_Mafg_rep2


title: F4_Mafg_rep1


title: 22_02_2013_C01_Ov84.CEL healthy control

description: healthy control


title: R5_Remitting_Cranialnerves_rep3

data_processing:
The right reads were trimmed using fastx (v0.0.13) fastx_trimmer.
Sequencing reads was aligned against the mm10 genome using STAR with default parameters and --quantMode geneCounts to count unique reads mapped
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited gene counts generated from STAR geneCounts

extract_protocol:
Protocol largely derived from Sanz et al. 2009, PNAS. Each CNS region was microdissected and homogenized in supplemented homogenization buffer (HB-S). Debris was pelleted, and supernatant was immunoprecipitated with an anti-HA antibody (Sigma, #H9658, 1:150) overnight. Following washes, RNA was purifiied using a Qiagen RNeasy purification kit (Qiagen, #74106). mRNA was then isolated using mRNA DIRECT kit (Thermo Fisher, #61012).
Libraries were prepared using a similar protocol as MARS-seq (Jaitin et al. Science 2014).

value: Female

tag: disease

value: Remitting

tag: region

value: Cranial nerves

tag: molecule subtype

value: immunoprecipitated mRNA via HA-tagged Rpl22 ribosomal subunit


title: R4_Remitting_Cerebellum_rep3

value: Cerebellum


title: 22_02_2013_D12_Ov86.CEL healthy control

description: healthy control

value: blood


title: 22_02_2013_H03_Ov82.CEL healthy control

description: healthy control


title: 22_02_2013_D10_Ov81.CEL healthy control

description: healthy control


title: 22_02_2013_B09_Ov85.CEL healthy control

description: healthy control


title: 22_02_2013_B02_Ov77.CEL healthy control

description: healthy control


title: 20_02_2013_G12_OV8.CEL SSc

value: SSc


title: 20_02_2013_C07_OV79.CEL healthy control

description: healthy control

value: healthy control


title: 20_02_2013_G02_OV76.CEL healthy control

description: healthy control


title: R2_Remitting_SC_rep3

value: Spinal Cord


title: 22_02_2013_D02_Ov75.CEL healthy control

description: healthy control


title: Q5_Remitting_Cranialnerves_rep2


title: 20_02_2013_A07_OV74.CEL healthy control

description: healthy control


title: 20_02_2013_A03_OV69.CEL SSc


title: Q4_Remitting_Cerebellum_rep2


title: 20_02_2013_D01_OV70.CEL SSc


title: 20_02_2013_F07_OV73.CEL SSc


title: Q3_Remitting_Parenchyma_rep2

value: Parenchyma


title: 20_02_2013_B03_OV64.CEL SSc


title: 22_02_2013_D08_Ov80.CEL healthy control

description: healthy control


title: Q2_Remitting_SC_rep2


title: Q1_Remitting_Cortex_rep2

value: Cortex


title: 20_02_2013_B10_OV72.CEL SSc


title: 20_02_2013_B04_OV63.CEL SSc


title: P4_Remitting_Cerebellum_rep1


title: 20_02_2013_E04_OV60.CEL SSc


title: 20_02_2013_G03_OV6.CEL SSc


title: 22_02_2013_D06_Ov62.CEL SSc


title: 20_02_2013_F02_OV61.CEL SSc


title: 20_02_2013_H04_OV59.CEL SSc


title: 20_02_2013_E01_OV58.CEL healthy control

description: healthy control


title: P3_Remitting_Parenchyma_rep1


title: P2_Remitting_SC_rep1


title: 20_02_2013_B05_OV57.CEL SSc


title: 20_02_2013_E09_OV55.CEL SSc


title: P1_Remitting_Cortex_rep1


title: 20_02_2013_G06_OV53.CEL SSc


title: P5_Remitting_Cranialnerves_rep1


title: 20_02_2013_E03_OV5.CEL healthy control

description: healthy control


title: 20_02_2013_F01_OV50.CEL SSc


title: O5_Naive_Cranialnerves_rep3

value: Naive


title: O3_Naive_Parenchyma_rep3


title: O4_Naive_Cerebellum_rep3


title: 22_02_2013_B10_OV46.CEL SSc


title: 20_02_2013_H05_OV48.CEL SSc


title: 20_02_2013_C05_OV47.CEL SSc


title: O1_Naive_Cortex_rep3


title: 20_02_2013_E07_OV44.CEL SSc


title: N5_Naive_Cranialnerves_rep2


title: 20_02_2013_E06_OV49.CEL SSc


title: 22_02_2013_F06_OV7.CEL SSc


title: 20_02_2013_E02_OV67.CEL SSc


title: 20_02_2013_D02_OV51.CEL SSc


title: N4_Naive_Cerebellum_rep2


title: 20_02_2013_G09_OV42.CEL SSc


title: 20_02_2013_G10_OV38.CEL SSc


title: 20_02_2013_C02_OV41.CEL SSc


title: 20_02_2013_B11_OV39.CEL SSc


title: 20_02_2013_F03_OV36.CEL SSc


title: O2_Naive_SC_rep3


title: N3_Naive_Parenchyma_rep2


title: 20_02_2013_D03_OV35.CEL SSc


title: 22_02_2013_C09_OV43.CEL SSc


title: 22_02_2013_F10_OV34.CEL SSc


title: 22_02_2013_F07_OV40.CEL SSc


title: 20_02_2013_E08_OV37.CEL SSc


title: 20_02_2013_G01_OV31.CEL SSc


title: 20_02_2013_C01_OV32.CEL SSc


title: 20_02_2013_B02_OV27.CEL SSc


title: 22_02_2013_C04_OV29.CEL SSc


title: 22_02_2013_F02_OV26.CEL SSc


title: 20_02_2013_F04_OV45.CEL SSc


title: 20_02_2013_H08_OV30.CEL SSc


title: 20_02_2013_A02_OV25.CEL SSc


title: N2_Naive_SC_rep2


title: N1_Naive_Cortex_rep2


title: M5_Naive_Cranialnerves_rep1


title: M4_Naive_Cerebellum_rep1


title: M3_Naive_Parenchyma_rep1


title: M2_Naive_SC_rep1


title: 20_02_2013_G05_OV23.CEL SSc


title: M1_Naive_Cortex_rep1


title: 20_02_2013_C03_OV24.CEL SSc


title: L1_Acute_Cortex_rep3

value: Acute


title: 20_02_2013_H02_OV22.CEL SSc


title: 20_02_2013_A10_OV19.CEL SSc


title: 22_02_2013_E01_OV2.CEL SSc


title: L5_Acute_Cranialnerves_rep3


title: 20_02_2013_C04_OV20.CEL SSc


title: 20_02_2013_A11_OV21.CEL SSc


title: K5_Acute_Cranialnerves_rep2


title: 20_02_2013_A09_OV17.CEL SSc


title: 20_02_2013_E11_OV11.CEL SSc


title: K4_Acute_Cerebellum_rep2


title: 20_02_2013_F06_OV14.CEL SSc


title: 20_02_2013_E12_F4.CEL SSc


title: 20_02_2013_G11_OV1.CEL SSc


title: L4_Acute_Cerebellum_rep3


title: 20_02_2013_F11_F27.CEL SSc


title: 20_02_2013_B01_OV12.CEL SSc


title: 20_02_2013_H01_OV18.CEL SSc


title: 20_02_2013_B12_OV13.CEL healthy control

description: healthy control


title: 20_02_2013_D09_OV78.CEL healthy control

description: healthy control


title: K3_Acute_Parenchyma_rep2


title: 22_02_2013_B03_F8.CEL SSc


title: 20_02_2013_D12_F5.CEL SSc


title: 22_02_2013_H02_OV10.CEL SSc


title: K2_Acute_SC_rep2


title: 20_02_2013_H03_OV15.CEL SSc


title: 22_02_2013_D09_F37.CEL SSc


title: 22_02_2013_A10_F23.CEL SSc


title: 20_02_2013_A08_F24.CEL SSc


title: 22_02_2013_G06_F38.CEL SSc


title: 22_02_2013_E04_F19.CEL SSc


title: J5_Acute_Cranialnerves_rep1


title: 20_02_2013_G07_F15.CEL SSc


title: J3_Acute_Parenchyma_rep1


title: J4_Acute_Cerebellum_rep1


title: 20_02_2013_F08_F2.CEL SSc


title: 20_02_2013_C11_F14.CEL SSc


title: J2_Acute_SC_rep1


title: J1_Acute_Cortex_rep1


title: DGM-00342_d7_am

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include the RefSeq unique ID with gene ID and location, gene ID  and the FPKM values for all samples

source_name: DGM-00342_d7, alveolar macrophage

extract_protocol:
Total RNA was extracted with TRIzol with subsequent RNA clean-up using the RNeasy  RNA purification kit to remove residual DNA
The TruSeq RNA v2 Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500.

tag: individual

tag: smoking status

tag: time

value: alveolar macrophage


title: Nrf_KD_rep3

data_processing:
Reads were aligned against the GRCm38 mouse genome using STAR (v.2.5.3) with parameters --twopassMode Basic --alignIntronMax 1000000 --sjdbOverhang 37 --alignMatesGapMax 1000000
Reads were marked for duplicates using Picard (v.2.7.1)
Reads were removed for duplicates, mapping quality below 30, unmapped reads, mate unmapped, and multi-mapped.
Reads were counted using FeatureCounts from Subread (1.5.0) in pair-end mode
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing Gene IDs and number of reads mapping to that gene

source_name: Nrf_KD_flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)

tag: strain background

value: male

value: Flow cytometry sorted astrocytes


title: Nrf_KD_rep2

tag: genotype/variation


title: 22_02_2013_E08_F11.CEL SSc

tag: tissue


title: 22_02_2013_A09_F12.CEL SSc


title: 20_02_2013_A12_F1.CEL SSc


title: 22_02_2013_A03_E7.CEL SSc


title: 20_02_2013_E10_E35.CEL SSc


title: DGM-11213_d7_am

source_name: DGM-11213_d7, alveolar macrophage


title: 20_02_2013_G04_E5.CEL SSc


title: DGM-12942_d7_am

source_name: DGM-12942_d7, alveolar macrophage


title: 20_02_2013_A04_E37.CEL SSc


title: 20_02_2013_B07_E36.CEL SSc


title: Scrmbl_rep3

source_name: Scrmbl_flow cytometry sorted astrocytes

value: sgScrmbl-targeted

tag: cell type


title: DGM-00244_d7_am

source_name: DGM-00244_d7, alveolar macrophage

value: Ecig+nicotine


title: 20_02_2013_F05_E32.CEL SSc


title: 20_02_2013_C08_E33.CEL SSc


title: 20_02_2013_C10_E26.CEL SSc


title: 20_02_2013_D06_E25.CEL SSc


title: 20_02_2013_A06_E24.CEL SSc


title: 22_02_2013_D01_E31.CEL SSc


title: 20_02_2013_F10_E21.CEL SSc


title: 22_02_2013_C10_E2.CEL SSc


title: Scrmbl_rep2


title: DGM-01774_d7_am

source_name: DGM-01774_d7, alveolar macrophage


title: Nrf_KD_rep1


title: WT_rep3

source_name: WT_flow cytometry sorted astrocytes

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 200 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: littermate control willd type


title: Scrmbl_rep1


title: 20_02_2013_D08_E1.CEL SSc


title: WT_rep2


title: DGM-12971_d7_am

source_name: DGM-12971_d7, alveolar macrophage


title: 20_02_2013_B09_E19.CEL SSc


title: DGM-13029_d7_am

source_name: DGM-13029_d7, alveolar macrophage


title: DGM-12941_d7_am

source_name: DGM-12941_d7, alveolar macrophage


title: WT_rep1


title: Csf2_KO_rep2

source_name: Csf2_KO_flow cytometry sorted astrocytes

value: CSF2RB Aldh1l1-CreERT2-Csf2rb(f/f)


title: Csf2_KO_rep3


title: DGM-00342_d1_am

source_name: DGM-00342_d1, alveolar macrophage

value: nonsmoker


title: 22_02_2013_H08_D97.CEL healthy control

description: healthy control

source_name: whole blood


title: DGM-11213_d1_am

source_name: DGM-11213_d1, alveolar macrophage


title: DGM-13050_d7_am

source_name: DGM-13050_d7, alveolar macrophage


title: Csf2_KO_rep1


title: 22_02_2013_H11_D99.CEL healthy control

description: healthy control


title: 20_02_2013_H06_D92.CEL healthy control

description: healthy control


title: DGM-12942_d1_am

source_name: DGM-12942_d1, alveolar macrophage


title: EAE-3 [S4]

data_processing:
Reads were trimmed using Cutadapt (v1.14) to remove adapters and low quality reads.
Trimmed reads were then aligned to GRCm38 genome using Bismark (v0.20.1) and Bowtie2 (v0.20.1) with default settings.
Duplicated reads were removed using paired end mode
Methylation counts and percentages were extracted using bismark_methylation_extractor
Percentage methylation were visualized using IGV (v2.3.59)
Genome_build: GRCm38
Supplementary_files_format_and_content: bedgraph file with percent methylation at each CpG position

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, cells were pelleted, washed, and genomic DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit kit (Qiagen, #69504).
Bisulfite converted DNA libraries were generated by using the Zymo Pico-Methyl DNA kit (Zymo Research, #D5455) according to the manufacturer's protocol.

treatment_protocol: Induction of EAE in mice intracranially transduced with pLenti-U6-sgMafg-Gfap-Cas9-2A-EGFP-WPRE or pLenti-U6-sgScrmbl-Gfap-Cas9-2A-EGFP-WPRE or non-transduced naive mice. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

tag: strain

value: wild type

tag: sample group

value: undergoing EAE transduced with non-targeting lentiviruses


title: 22_02_2013_C07_D91.CEL healthy control

description: healthy control

value: blood


title: 22_02_2013_C08_D96.CEL healthy control

description: healthy control

value: healthy control


title: 20_02_2013_F09_E14.CEL SSc

value: SSc


title: 20_02_2013_C06_D74.CEL SSc


title: 22_02_2013_F08_D90.CEL healthy control

description: healthy control


title: EAE-2 [S3]


title: DGM-13039_d7_am

source_name: DGM-13039_d7, alveolar macrophage


title: 20_02_2013_D11_D68.CEL SSc


title: DGM-01774_d1_am

source_name: DGM-01774_d1, alveolar macrophage


title: WT-3 [S2]

value: naïve


title: 22_02_2013_G09_D86.CEL healthy control

description: healthy control


title: 22_02_2013_E10_D87.CEL healthy control

description: healthy control


title: 22_02_2013_E12_D88.CEL healthy control

description: healthy control


title: 20_02_2013_D07_D75.CEL SSc


title: 22_02_2013_G07_D93.CEL healthy control

description: healthy control


title: 22_02_2013_D07_D7.CEL SSc


title: WT-1 [S1]


title: 22_02_2013_G04_D66.CEL SSc


title: 22_02_2013_F04_D67.CEL SSc


title: DGM-13050_d1_am

source_name: DGM-13050_d1, alveolar macrophage


title: DGM-13039_d1_am

source_name: DGM-13039_d1, alveolar macrophage


title: 22_02_2013_G01_D65.CEL SSc


title: 22_02_2013_E03_D63.CEL SSc


title: 22_02_2013_D11_D98.CEL healthy control

description: healthy control


title: 22_02_2013_H12_D61.CEL SSc


title: DGM-12971_d1_am

source_name: DGM-12971_d1, alveolar macrophage


title: DGM-13029_d1_am

source_name: DGM-13029_d1, alveolar macrophage


title: 22_02_2013_B04_D57.CEL SSc


title: 22_02_2013_A12_D89.CEL healthy control

description: healthy control


title: DGM-00342_d7_sm

source_name: DGM-00342_d7, small airway epithelium brushing

value: small airway epithelium brushing


title: DGM-12941_d1_am

source_name: DGM-12941_d1, alveolar macrophage


title: DGM-11213_d7_sm

source_name: DGM-11213_d7, small airway epithelium brushing


title: DGM-12942_d7_sm

source_name: DGM-12942_d7, small airway epithelium brushing


title: 22_02_2013_G11_D55.CEL SSc


title: 20_02_2013_G08_D6.CEL SSc


title: 22_02_2013_H06_D56.CEL SSc


title: 22_02_2013_H05_D35.CEL SSc


title: 22_02_2013_H09_D52.CEL SSc


title: DGM-00244_d7_sm

source_name: DGM-00244_d7, small airway epithelium brushing


title: 22_02_2013_H04_D42.CEL SSc


title: 22_02_2013_H01_E17.CEL SSc


title: knock out MCD female 1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data of liver of knock out MCD female

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: liver of knock out MCD female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: non-alcoholic fatty liver disease Mice were housed in pathogen-free, ~22°C environment with light/dark cycle of 12:12. Mice were fed a regular chow ad libitum until 8 weeks of age.

extract_protocol: Total RNA was isolated from whole liver tissue using InviTrap Spin Universal RNA Mini Kit, according to the manufacturer’s instructions.

treatment_protocol: Prior start of the experiment (after 8 weeks), both HepCAV1ko and HepCAV1wt mice were randomly divided into two groups with either feeding the MCD diet (N=12) or control diet containing methionine and choline (N=12) for 4 weeks.

tag: genotype

value: caveolin-1 KO

tag: diet

value: MCD

tag: gender

value: female


title: 22_02_2013_B06_D37.CEL SSc

tag: disease state


title: knock out MCD female 2


title: 22_02_2013_F05_D30.CEL SSc


title: DGM-01774_d7_sm

source_name: DGM-01774_d7, small airway epithelium brushing


title: 22_02_2013_G05_D31.CEL SSc

source_name: whole blood


title: 20_02_2013_D05_D45.CEL SSc


title: 22_02_2013_A06_D36.CEL SSc


title: knock out control female 3

description: Gene expression data of liver of knock out control female

source_name: liver of knock out control female

value: con


title: knock out MCD male 1

description: Gene expression data of liver of knock out MCD male

source_name: liver of knock out MCD male

value: male


title: 22_02_2013_C05_D26.CEL SSc


title: 22_02_2013_D05_D28.CEL SSc


title: 22_02_2013_E05_D29.CEL SSc


title: knock out MCD male 2


title: 22_02_2013_A04_D22.CEL SSc


title: DGM-13050_d7_sm

source_name: DGM-13050_d7, small airway epithelium brushing


title: DGM-13039_d7_sm

source_name: DGM-13039_d7, small airway epithelium brushing


title: DGM-12971_d7_sm

source_name: DGM-12971_d7, small airway epithelium brushing


title: DGM-13029_d7_sm

source_name: DGM-13029_d7, small airway epithelium brushing


title: 20_02_2013_B06_D23.CEL SSc


title: DGM-12941_d7_sm

source_name: DGM-12941_d7, small airway epithelium brushing


title: DGM-00342_d1_sm

source_name: DGM-00342_d1, small airway epithelium brushing


title: Colon Innate Lymphoid cells

city: Nantes

first: Ahmed

last: Abidi

state: Loire Atlantique

address: CHU Nantes - Hôtel Dieu 30 Bd Jean Monnet

country: France

institute: INSERM

description: FACS-sorted Lin- CD127+ colon cells

data_processing:
FASTQ were generated from Illumina NextSeq 500
FASTQ files were demultiplexed using CellRanger count v3.0.1 (10X Genomics) and aligned on the Rnor_6.0 rat reference genome
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: filtered and unfiltered outputs from CellRanger count containing a dense matrix of counts in mtx format, a list of cell barcodes in tsv format and a list of detected genes in tsv format

organism: Rattus norvegicus

source_name: Colon

extract_protocol:
Fat and endothelial cells were removed from the tissue. Colon was digested and ILCs were sorted by flow cytometry as Lin- CD127+  cells
scRNA-seq libraries were produced with the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10X Genomics). Libraries were then sequenced on a rapid run flowcell (75bp) with an Illumina NextSeq 500

value: Sprague-Dawley (SPD)

value: Colon Innate Lymphoid cells

tag: cell population

value: FACS-sorted Lin- CD127+ colon cells


title: 22_02_2013_A11_D17.CEL SSc


title: BV2 in DMEM

city: Tsukuba

first: Fuminori

last: Tsuruta

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from BV-2 cells cultured in DMEM

hyb_protocol: DNA samples were hybridized at 45°C for 17 hours on Mouse Gene 1.0 ST arrays and the samples were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console software and Affymetrix Transcriptome Analysis Console software.

label: Biotin Allonamide Triphosphate

source_name: mouse microglia

label_protocol: Biotinylated fragmented DNA were prepared according to the GeneChip WT Terminal Labeling and Hybridization kit protocol (Affymetrix) from 5.5 ug total DNA

growth_protocol: BV-2 cells were incubated with wither DMEM or DMEM/F12 at 5% CO2 and 37°C for over 1 day.

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

tag: cell

tag: treatment

value: cultured in DMEM


title: knock out control female 2


title: 22_02_2013_F03_D106.CEL SSc


title: 22_02_2013_A02_D20.CEL SSc


title: knock out control male 3

description: Gene expression data of liver of knock out control male

source_name: liver of knock out control male


title: 22_02_2013_C11_D18.CEL SSc


title: knock out control female 1


title: wild type MCD female 3

description: Gene expression data of liver of wild type MCD female

source_name: liver of wild type MCD female

value: WT


title: wild type MCD female 1


title: 22_02_2013_A07_D1.CEL SSc


title: 22_02_2013_E11_D104.CEL SSc


title: 22_02_2013_G12_D21.CEL SSc


title: 22_02_2013_E07_D102.CEL SSc


title: DGM-12942_d1_sm

source_name: DGM-12942_d1, small airway epithelium brushing

value: nonsmoker


title: BV2 in DMEM/F12

description: Gene expression data from BV-2 cells cultured in DMEM/F12

value: cultured in DMEM/F12


title: DGM-11213_d1_sm

source_name: DGM-11213_d1, small airway epithelium brushing


title: knock out control male 2


title: 22_02_2013_F12_D11.CEL SSc

value: blood


title: wild type MCD male 3

description: Gene expression data of liver of wild type MCD male

source_name: liver of wild type MCD male


title: knock out control male 1


title: DGM-00244_d1_sm

source_name: DGM-00244_d1, small airway epithelium brushing


title: wild type MCD female 2


title: DGM-01774_d1_sm

source_name: DGM-01774_d1, small airway epithelium brushing


title: DGM-13050_d1_sm

source_name: DGM-13050_d1, small airway epithelium brushing


title: wild type MCD male 2


title: wild type MCD male 1


title: DGM-13039_d1_sm

source_name: DGM-13039_d1, small airway epithelium brushing


title: wild type control female 3

description: Gene expression data of liver of wild type control female

source_name: liver of wild type control female


title: DGM-12971_d1_sm

source_name: DGM-12971_d1, small airway epithelium brushing


title: MS patient 4-9

data_processing:
Reads were processed using the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/)
Individual cells were tagged with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers).
Reads were trimmed at 3' end to remove poly(A) tails with length greater than 5 and at the 5' end for adapters
Reads with barcode base quality less than 10 were filtered out..
Raw reads were aligned to human (GRCh38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 200 genes.

source_name: CNS Percoll pellet

extract_protocol:
A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and cell density was quantified. Cells were suspended in PBS and 16% Opti-prep.
Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.

treatment_protocol: Following rapid autopsy, samples were immediately incubated in Hibernate (Life Technologies, #A1247601) for 8-18 hours prior to processing.

tag: subject status

value: Multiple sclerosis (MS) patient

tag: subject group

value: secondary progressive MS (SPMS)


title: wild type control female 2


title: MS patient 4-7


title: DGM-13029_d1_sm

source_name: DGM-13029_d1, small airway epithelium brushing

tag: individual

tag: smoking status


title: DGM-12941_d1_sm

source_name: DGM-12941_d1, small airway epithelium brushing

tag: time


title: FTC133_CHI3L1_siRNA

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

description: FTC-133 cells transfected with CHI3L1 siRNA

data_processing:
Quality control: FastQC, MultiQC, ReSeqTools
Quality trimming: Trimmomatic
BlastQC: DIAMOND
Read mapping: HISAT2 (GRCh38)
Alignment QC: RSeQC, Qualimap
Read summarization: featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: normalizedReadCounts.csv

source_name: Thyroid cancer cells

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Thyroid cancer cells

value: CHI3L1 knockdown


title: wild type control female 1


title: MS patient 4-6


title: Es-04-Liver

city: Singapore

first: Linfa

address: 8 college road

department: Programme in Emerging Infectious Diseases

country: Singapore

institute: Duke-NUS Medical School

data_processing:
After trimming and cleaning for quality assurance (including distribution of reads)
reads were de novo assembled with Bowtie2/Tophat then blasted  to the E. spelaea reference genome (NCBI genome database:GCA_003508835.1 ) with Bowtie and RSEM abundance estimation was performed
FPKM was calculated using TopHat/Cufflinks v2.2.1 usingthe annotated :Espe1 as a guide for reference mapping and genome size .
HTseq and edgeR were used for subsequent counting and DEG analysis
Genome_build: Espe.v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (FPKM from cufflinks includes cufflinks id, locus tag, gene symbol, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status)

organism: Eonycteris spelaea

source_name: Es liver

growth_protocol: Wild Eonycteris spelaea bats - damaged and injured (physically) but otherwise healthy according to vets. Mostly torn wings that can't repair (barbed wire fence etc)

extract_protocol:
Tissue prepared fresh into RNA later - soaked overnight then replaced and snap frozen. Homogenised with ceramic beads in a homogenizer - extract qith Qiagen microor qiagen micro plus kit.
Total RNA was checked using the RNA 6000 LabChip Kit on the Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNAseq libraries were prepared using Illumina Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit following the manufacturer’s instructions (Illumina, San Diego, California, USA). Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted and applied to an Illumina flow cell using the Illumina cBOT system. Sequencing was performed on an Illumina HiSeq 3000 sequencer at the Duke-NUS Genome Biology Facility with the paired-end 150-bp read option.

treatment_protocol: No treatment

value: healthy

tag: tissue

value: liver

value: control


title: Es-04-Lung

source_name: Es lung

value: lung


title: PA-33-F Lung

data_processing:
After trimming and cleaning for quality assurance (including distribution of reads)
reads were mapped  to the P.alecto reference genome (NCBI genome database:ASM32557v1 scaffold3,  v1.01 ) with Bowtie and RSEM abundance estimation was performed
FPKM was calculated using TopHat/Cufflinks v2.2.1 using :ASM32557v1 as a guide for reference mapping and genome size .
HTseq and edgeR were used for subsequent counting and DEG analysis
Genome_build: ASM32557v1 , 101
Supplementary_files_format_and_content: tab-delimited text files include FPKMs or counts for each Sample

organism: Pteropus alecto

source_name: Lung, whole tissue

growth_protocol: Wild pteropus alecto bats - damaged and injured (physically) but otherwise healthy according to vets. Mostly torn wings that can't repair (barbed wire fence etc)

extract_protocol:
Tissue prepared fresh into RNA later - soaked overnight then replaced and snap frozen. Homogenized with ceramic beads in a homogenizer - extract with Qiagen micro plus kit.
Total RNA was checked using the RNA 6000 LabChip Kit on the Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNAseq libraries were prepared using Illumina Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit following the manufacturer’s instructions (Illumina, San Diego, California, USA). Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted and applied to an Illumina flow cell using the Illumina cBOT system. Sequencing was performed on an Illumina HiSeq 3000 sequencer at the Duke-NUS Genome Biology Facility with the paired-end 150-bp read option.

value: Lung

tag: Sex

value: F


title: PA-30-M Lung

value: M


title: MS patient 4-5


title: MS patient 4-4


title: wild type control male 3

description: Gene expression data of liver of wild type control male

source_name: liver of wild type control male

value: con

value: male


title: Es-02-Spleen

source_name: Es spleen

value: spleen


title: wild type control male 1

value: WT


title: FTC133_Control_siRNA

description: FTC-133 cells transfected with control siRNA

tag: cell type


title: PA-24-M Lung


title: knock out MCD female 3

source_name: liver of knock out MCD female

value: caveolin-1 KO

value: MCD

value: female


title: MS patient 4-3

value: Multiple sclerosis (MS) patient

value: secondary progressive MS (SPMS)


title: PA-27-F Lung


title: wild type control male 2


title: MS patient 4-8


title: MS patient 4-2


title: MS patient 4-1


title: PA-18 Liver

source_name: Liver, whole tissue

value: Liver


title: RH (96-well), extracellular

city: Stanford

first: Yuan

last: Xue

state: CA

address: 318 Campus Drive

institute: Stanford University

data_processing:
Fastqs are aligned to Toxoplasma gondii GT1 references (for RH parasites) or ME49 references (for Pru and ME49 parasites), ToxoDB version 36 (2/13/2018), concatenated with ERCC RNA spike-in using STAR aligner (version 2.6.0c)
Gene counts are quantified using htseq-count (version 0.10.0). A modified version of htseq-count was used to count reads that multiply maps to more than one region with equal alignment score by counting 1/N, where N is the number of regions it maps. We used GT1 (for RH parasites) or ME49 (for Pru and ME49 parasites) gff3 annotation files, ToxoDB version 36 (2/13/2018), concatenated with ERCC RNA spike-in.
We filtered samples by read depth, gene counts, percentage of reads that map to ribosomal genes and ERCC. Preprocessing parameters and scripts are available on https://github.com/xuesoso/singleToxoplasmaSeq
Toxoplasma gondii GT1 (ToxoDB version 36, 2/13/2018)
Genome_build: Toxoplasma gondii ME49 (ToxoDB version 36, 2/13/2018)
Supplementary_files_format_and_content: h5ad (hdf5). Contains gene expression matrix, meta-annotation for each sample, meta-annotation for each gene.

molecule: polyA RNA

organism: Toxoplasma gondii

source_name: 10T 1/2 tissue culture

growth_protocol: Toxoplasma was propagated in 10T ½ embryonic fibroblast cells prior to syringe release and extraction.

extract_protocol:
Syringe lysis of the fibroblast host cells and release of the parasites. Extracellular parasites are stained with live/dead stain (e.g. PI) and sorted onto Smart-seq2 lysis buffer plate with SONY SH-800 FACS sorter.
Smart-seq2 followed by Illumina Nextera XT library construction kit.

treatment_protocol: Some of the ME49 and Pru parasites were treated with alkaline (pH 8.2) for 3, 5, or 7 days prior to extraction.

tag: strain

value: RH

tag: culture type

value: RH (96-well), extracellular


title: ES-02 Liver

value: healthy

value: liver

value: control


title: MS patient 3-5


title: PA-15 Liver


title: RH (384-well), extracellular

value: RH (384-well), extracellular


title: PA-12 Liver


title: Es-02-Lung

value: lung


title: Pru, day 7 after alkaline induction, extracellular

value: Pru

tag: time point


title: U2OS_siRTEL1_APH_RNaseH

city: Copenhagen

first: Ivan

last: Vogel

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

data_processing:
Library strategy: DRIP-seq
Alignment performed with BWA software
Peaks were called using software from Macheret and Halazonetis (Nature 2018) from reads mapped with quality score at least 60.
Genome_build: hg19
Supplementary_files_format_and_content: BED format created with custom scripts from the output of the peak calling algorithm

source_name: Osteosarcoma cells

extract_protocol: Samples were prepared by DRIP protocol, purified and then sequenced following BGI ChIP-Sequencing

value: U2OS Osteosarcoma cell line

value: bone


title: Control5

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 1.3).
Cellranger mkfastq demultiplexed libraries based on sample indices and generated FASTQ files
Cellranger count performed alignment against hg38 human genome using STAR , filtering, and feature counting for unique molecular identifier (UMI)
Genome_build: hg38
Supplementary_files_format_and_content: csv format with rows as genes and columns as cells

extract_protocol:
For samples 1-3: Tissue was mechanically dissociated, treated with 0.25% trypsin and 25ug/mL Dnase for 30 min at 37C, and then passed through a 140um nylon mesh. The resulting cells were then separated on 30% percoll gradient to remove myelin and erythrocytes. For samples 4-5: A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and cell density was quantified. Cells were suspended in PBS and 16% Opti-prep.
For samples 1-3: Libraries were created according to the 10X Genomics protocol (Zheng et al. Nature Communications 2017). For samples 4-5: Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.

tag: disease

value: Healthy control tissue; glioblastoma patient


title: MS patient 3-4


title: PA-21-F Lung

tag: disease state

value: Lung

value: F


title: Es-04-Spleen

value: spleen


title: Pru, day 5 after alkaline induction, extracellular


title: U2OS_siRTEL1_APH


title: Control4


title: PA-18 Spleen

source_name: Spleen, whole tissue


title: Pru, day 3 after alkaline induction, extracellular


title: PA-15 Spleen


title: MS patient 3-3

description:
Sample 4-19
2_HG37GDMXX.2.TACGCTGC

data_processing:
Reads were processed using the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/)
Individual cells were tagged with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers).
Reads were trimmed at 3' end to remove poly(A) tails with length greater than 5 and trimmed at the 5' end for adapters
Reads with barcode base quality less than 10 were filtered out
Raw reads were aligned to human (GRCh38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 200 genes.

value: Multiple sclerosis (MS) patient


title: U2OS_siRTEL1_RNaseH


title: Pru, day 0 after alkaline induction, extracellular


title: MS patient 3-2

description:
Sample 4-16
2_HG37GDMXX.2.GGAGCTAC

value: secondary progressive MS (SPMS)


title: PA-12 Spleen


title: ME49, day 3 after alkaline induction, extracellular


title: U2OS_siCTRL_RNaseH


title: PA-09 Spleen


title: ME49, day 0 after alkaline induction, extracellular


title: MS patient 3-1

description:
Sample 4-18
2_HG37GDMXX.2.CGGAGCCT


title: U2OS_siCTRL


title: PA-09 Liver

value: Liver


title: U2OS_siRTEL1


title: MET4

status: Public on Feb 11 2020

city: Salt

first: Jessica

last: Latorre

address: C/ Dr Castany s/n

country: Spain

institute: IDIBGI

description: Test 3

data_processing:
The normalization was performed using the raw Ct value-average of raw Cts for all miRNAs with reliable results
Target miRNA signals normalized to the average; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_miRNA mean)]
The web-based software package gives the raw threshold cycle data.
Fold Change data file reports test/control (i.e., palmitate/BSA) ratios.
Normalized data file includes normalized signal (against the average of all miRNAs detected).
Fold Change worksheet reports test/control (i.e., palmitate/BSA) ratios.

label: TaqMan

source_name: Metformin

label_protocol: PCR assays were performed using the TaqMan™ Array Human MicroRNA A+B Cards Set v3.0 (ThermoFisher Scientific, Waltham, Massachusetts, USA). Catalog # 4444913.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit and retrotranscribed using Megaplex™ RT Primers and TaqMan™ MicroRNA Reverse Transcription Kit   RT Primers, TaqMan™   MicroRNA Reverse Transcription Kit

value: Primary human hepatocytes

tag: activation agent

value: METFORMIN

value: 24h treatment


title: CMET1

description: Control 3

source_name: Control Metformin

value: PBS


title: PA3

description: Test 1

source_name: Palmitate

value: PALMITATE


title: CC1

description: Test 2

source_name: Compound C

value: COMPOUND C


title: MET1

description: Test 3


title: CPA2

description: Control 1

source_name: Control palmitate

value: BSA


title: MET3

description: Test 3


title: CC4

description: Test 2


title: CCC3

description: Control 2

source_name: Control Compound C

value: DMSO


title: CPA3

description: Control 1


title: PA4

description: Test 1


title: CC3

description: Test 2


title: CCC4

description: Control 2


title: CMET2

description: Control 3


title: PA2

description: Test 1


title: knock out MCD male 3

source_name: liver of knock out MCD male

tag: genotype

value: caveolin-1 KO

tag: diet

value: MCD

tag: gender

value: male


title: 46_icsi_veh_e12placenta

first: Jennifer

last: Chan

state: New York

address: 1470 Madison Ave, Hess 9-201

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: NormalizedICSIPlacentaTranscripts.csv

data_processing:
Fastq files containing an average of 50 million reads were processed for pseudoalignment and abundance quantification using Kallisto (version 0.43.1).
The transcriptome was aligned to the EnsemblDB Mus musculus package (version 79).
Count data were filtered for at least 6 cpm per gene across all groups, normalized, and dispersions were estimated per condition with a maximum sharing mode using DESeq.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Comma separated values file containing normalized abundance measures.
Genome_build: GRCm38.p6
Genome_build: GRCh38

source_name: Placenta

extract_protocol:
Pregnant ICR surrogate dams were deeply anesthesized with isoflurane on E12.5, and each uterine horn was removed where conceptuses were harvested. Fetal brains, placentas and tails were flash frozen in liquid nitrogen and stored at -80°C until processing.
Libraries for RNA sequencing were made using a TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to manufacturer’s protocol.

tag: developmental age

value: embryonic day 12.5

value: C57BL/6:129 F2 hybrids

tag: treatment

value: Vehicle EV ICSI


title: 14_icsi_cort_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv

value: Corticosterone EV ICSI


title: 48_icsi_veh_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: 24_icsi_cort_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: 58_icsi_cort_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: 31_icsi_cort_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: 55_icsi_cort_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: 6_icsi_veh_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: 44_icsi_veh_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: 60_icsi_cort_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: 60_icsi_cort_e12brain

description: NormalizedICSIBrainTranscripts.csv

source_name: Brain


title: 58_icsi_cort_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: 48_icsi_veh_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: 51_icsi_veh_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: 46_icsi_veh_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: 44_icsi_veh_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: 24_icsi_cort_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: 55_icsi_cort_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: 14_icsi_cort_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: 67_icsi_veh_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: L_Med_day4

data_processing:
Fastq files containing an average of 10 million reads per sample were trimmed for adaptor sequence, aligned using mapper.pl, and quantified using quantifier.pl with miRDeep2 (version 2.0.0.8).
For miRNA-sequencing of mus musculus sperm and DC2 EVs, fastq files containing an average of 10 million reads per sample were trimmed for adaptor sequence, aligned using mapper.pl, and quantified using quantifier.pl with miRDeep2 (version 2.0.0.8).
Data were filtered for greater than 2 counts in at least 3 samples across all groups, then normalized, and dispersions were estimated per-condition using empirical values with DESeq.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Comma separated values file containing normalized abundance measures.
Genome_build: GRCm38.p6
Genome_build: GRCh38

source_name: DC2 Extracellular vesicle

extract_protocol:
EVs were isolated from conditioned media using differential ultracentrifugation. Briefly, cellular debris was removed from the media by centrifugation at 200g for 10 min, 2000 g for 10 min, and 10,000 g for 30 min. EVs were pelleted by ultracentrifugation at 100,000 g for 1 hour using the Optima L-90K Ultracentrifuge and SW 32 Ti swinging bucket rotor (Beckman Coulter). The EV pellet was resuspended in TriZol reagent and frozen at -80°C until further analysis. EVs were not pooled for any experiments in these studies.
Small RNA libraries were constructed using the NEBNext Small RNA Library Prep Set for Illumina (NEB) according to manufacturer’s protocol

value: Immortalized cell line

value: 4 days

value: Corticosterone (500ng/mL)


title: 51_icsi_veh_e12placenta

description: NormalizedICSIPlacentaTranscripts.csv


title: I_Med_day4


title: K_Med_day4


title: I_Low_day4

value: Corticosterone (50ng/mL)


title: J_Low_day4


title: K_Veh_day4

value: Vehicle


title: J_Veh_day4


title: K_Med_day7

value: 7 days


title: I_Med_day7


title: I_Veh_day4


title: J_Med_day7


title: 67_icsi_veh_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: L_Low_day7


title: K_Low_day7


title: J_Low_day7


title: I_Low_day7


title: K_Med_day11

value: 11 days


title: 6_icsi_veh_e12brain

description: NormalizedICSIBrainTranscripts.csv


title: J_Med_day11


title: K_Veh_day7


title: L_Veh_day7


title: J_Veh_day7


title: K_Low_day11


title: I_Veh_day7


title: DGM-00244_d1_am

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include the RefSeq unique ID with gene ID and location, gene ID  and the FPKM values for all samples

source_name: DGM-00244_d1, alveolar macrophage

tag: individual

tag: smoking status

value: nonsmoker

value: alveolar macrophage


title: J_Low_day11


title: K_Low_day4


title: J_Med_day4


title: L_Med_day7


title: L_Low_day4


title: I_Med_day11


title: L_Low_day11


title: J_Veh_day11


title: I_Low_day11


title: L_Veh_day11


title: K_Veh_day11


title: X7989_Stress20

description: NormalizedMouseSpermMirs.csv

source_name: Sperm

extract_protocol:
The caudal epididymis was minced in 1% bovine serum albumin in 3 mL warmed PBS and allowed to sit at room temperature for 30 minutes. The 1% BSA including sperm and epididymal tissue were transferred to a conical tube and incubated in a water bath at 37°C for 30 minutes. The top 2 mL of supernatant was transferred to a new conical tube and incubated at 37°C for 10 minutes. The top 1.5mL of this supernatant was transferred to a new tube and centrifuged for 5 minutes at 4000 rpm at 4°C. The supernatant was removed and the pellet containing mature sperm was flash frozen and stored at -80°C until processing. Sperm samples were not pooled for any experiments in these studies.
Small RNA libraries were constructed using the NEBNext Small RNA Library Prep Set for Illumina (NEB) according to manufacturer’s protocol

value: Adult

value: C57BL/6:129 F1 hybrids

value: 20 weeks

value: Chronic variable stress


title: I_Veh_day11


title: X8012_Stress20

description: NormalizedMouseSpermMirs.csv


title: X8011_Stress20

description: NormalizedMouseSpermMirs.csv


title: 31_icsi_cort_e12brain

description: NormalizedICSIBrainTranscripts.csv

value: embryonic day 12.5


title: X7988_Stress20

description: NormalizedMouseSpermMirs.csv


title: X7977_Stress20

description: NormalizedMouseSpermMirs.csv


title: X7970_Stress20

description: NormalizedMouseSpermMirs.csv


title: X7987_Control20

description: NormalizedMouseSpermMirs.csv

value: Control


title: X7969_Stress20

description: NormalizedMouseSpermMirs.csv


title: X7975_Control20

description: NormalizedMouseSpermMirs.csv


title: X7976_Control20

description: NormalizedMouseSpermMirs.csv


title: X7967_Control20

description: NormalizedMouseSpermMirs.csv


title: X7982_Control20

description: NormalizedMouseSpermMirs.csv


title: X7981_Control20

description: NormalizedMouseSpermMirs.csv


title: X8113_Stress9

description: NormalizedMouseSpermMirs.csv

value: 9 weeks


title: X8112_Stress9

description: NormalizedMouseSpermMirs.csv


title: X7948_Stress9

description: NormalizedMouseSpermMirs.csv


title: X7953_Stress9

description: NormalizedMouseSpermMirs.csv


title: X8116_Control9

description: NormalizedMouseSpermMirs.csv


title: X8019_Control9

description: NormalizedMouseSpermMirs.csv


title: X7955_Control9

description: NormalizedMouseSpermMirs.csv


title: X7954_Control9

description: NormalizedMouseSpermMirs.csv


title: X7945_Control9

description: NormalizedMouseSpermMirs.csv


title: X7946_Control9

description: NormalizedMouseSpermMirs.csv


title: X7944_Control9

description: NormalizedMouseSpermMirs.csv


title: X7957_Stress9

description: NormalizedMouseSpermMirs.csv


title: CCR6+ ILC3 from Maf.flox mice rep 3

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: Maf.flox mice

growth_protocol: ILC3s were FACS-sorted from the small intestine. NKp46+ CCR6- and NKp46- CCR6+ ILC3s were defined as viable CD45+ Lin- CD127+ KLRG1- NK1.1- NKp46+/- CCR6+/- cells. Lineage includes  anti-CD5, anti-CD8a, anti-CD3, anti-Gr-1, anti-TCRgd, anti-FceRIa, anti-CD19 and anti-CD11c.

extract_protocol:
Total RNA was purified with miRNeasy Micro Kit (Qiagen) from FACS sorted ILC3s isolated from small intestine. RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
For poly-A dependent cDNA synthesis and a first amplification step the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) was used. After quality control (High sensitivity DNA Kit, Agilent) and concentration measurement (Qubit dsDNA HS Assay Kit, Invitrogen), 150 pg of the purified cDNA was used for tagmentation and library completion with the Nextera XT library preparation kit (Illumina). In the following, 2x75 nucleotides paired-end sequencing was performed on a NextSeq 500 using a mid-output flow cell.

tag: donor

value: replicate 3

value: NKp46- CCR6+ ILC3

value: Small intestine


title: NKp46+ ILC3 from Maf.flox mice rep 1

value: replicate 1

value: NKp46+ CCR6- ILC3

tag: tissue


title: NKp46+ ILC3 from Maf.flox mice rep 2

value: replicate 2


title: NKp46+ ILC3 from Maf.flox mice rep 3


title: X7952_Stress9

description: NormalizedMouseSpermMirs.csv


title: X7986_Control20

description: NormalizedMouseSpermMirs.csv


title: X7968_Control20

description: NormalizedMouseSpermMirs.csv


title: NKp46+ ILC3 from Rorc.Cre Maf.flox mice rep 3

source_name: Rorc.Cre Maf.flox mice


title: CCR6+ ILC3 from Maf.flox mice rep 1


title: CCR6+ ILC3 from Rorc.Cre Maf.flox mice rep 2


title: NKp46+ ILC3 from Rorc.Cre Maf.flox mice rep 2


title: CCR6+ ILC3 from Rorc.Cre Maf.flox mice rep 3


title: CCR6+ ILC3 from Maf.flox mice rep 2


title: CCR6+ ILC3 from Rorc.Cre Maf.flox mice rep 1


title: ATAC-seq_DP_NOD_Rep2B_Rep1T

city: Philadelphia

first: Naomi

last: Goldman

state: PA

address: 324 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania

data_processing:
ATAC-seq libraries were pair-end sequenced by Illumina NextSeq 500. Bowtie2 was used for alignment. In NOD mice, aligned reads were shifted to BL6 coordinates with MMARGE (PMID: 29893919) utilizing the NOD VCF files (version 5) from the Mouse Genomes Project (PMID: 21921910). Reads aligned to the mitochondrial genome or chrY as well as reads mapping to multiple genomic loci were discarded from downstream analyses. Additionally, Picard was used to mark and remove duplicates. Furthermore, for each ATAC-seq library the insert size was calculated by Picard.
Genome_build: GRCm38
Supplementary_files_format_and_content: Bigwig files were generated by bedtools genomecov and wigToBigWig normalizing tracks to tags-per-million

source_name: CD4+ CD8+ thymocytes

extract_protocol:
ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., 2013). Fifty thousand cells were pelleted at 550 x g and washed with 1 mL 1x PBS, followed by treatment with 50 μL lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After pelleting nuclei, the pellets were resuspended in 50 μL transposition reaction with 2.5 μL Tn5 transposase (FC-121-1030; Illumina). The reaction was incubated in a 37°C water bath for 45 minutes. Tagmented DNA was purified using a MinElute Reaction Cleanup Kit (Qiagen) and amplified with varying cycles, depending on the side reaction results. Libraries were purified using a QIAQuick PCR Purification Kit (Qiagen).
Libraries were paired-end sequenced (38bp+38bp) on a NextSeq 550 (Illumina). Libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent).

treatment_protocol: Thymi of mice were dissociated through a 70µM mesh filter (Falcon) in RPMI 1640 (Corning) with 1% FBS (Sigma-Aldrich), and single cell suspensions were stained with 7AAD (Biolegend) for live cell distinction, as well as PE CD4 (RM404) and APC CD8a (53-6.7) for double-positive CD4+ CD8+ T cell isolation. Sorting was performed on FACS Aria II (BD Biosciences), with forward scatter–height by forward scatter–width and side scatter–height by side scatter–width parameters being used to exclude doublets. Purity was verified after sorting.

value: Thymus

value: NOD/ShiLtJ


title: ATAC-seq_DP_NOD_Rep2B_Rep3T


title: ATAC-seq_DP_F1_36_Rep2B_Rep3T

value: (NOD/ShiLtJ X C57BL/6) F1 mice


title: ATAC-seq_DP_F1_36_Rep2B_Rep2T


title: ATAC-seq_DP_F1_34_Rep1B_Rep3T


title: ATAC-seq_DP_BL6_Rep2B_Rep1T


title: ATAC-seq_DP_BL6_Rep2B_Rep2T


title: ATAC-seq_DP_F1_34_Rep1B_Rep1T


title: ATAC-seq_DP_NOD_Rep1B_2T


title: ATAC-seq_DP_NOD_Rep2B_Rep2T


title: ATAC-seq_DP_F1_36_Rep2B_Rep1T


title: ATAC-seq_DP_BL6_Rep1B_2T


title: ATAC-seq_DP_BL6_Rep1B_1T


title: ATAC-seq_DP_BL6_Rep2B_Rep3T


title: ATAC-seq_DP_NOD_Rep1B_1T


title: ATAC-seq_DP_NOD_Rep1B_4T


title: PS16.18.06

description: NormalizedHumanSpermMirs.csv

data_processing:
Reads were trimmed at the 3’ end to remove any trailing adaptor sequence using the Trimmomatic tool.
After read trimming, reads shorter than 15 bp were discarded before downstream analyses.
Trimmed reads were then aligned to the human reference genome build GRCh38 using the Bowtie short read aligner, allowing for 2 mismatches and a seed length of 15. The expression of each known miRNA from miRbase v22 were computed using HTSeq python.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma separated values file containing log2 normalized abundance measures
Genome_build: GRCm38.p6
Genome_build: GRCh38

extract_protocol:
Cryopreserved sperm samples were thawed, suspended in PureSperm Buffer (Nidacon), then mature sperm were enriched by centrifugation (300 g, 15 min) through a 50% PureSperm density gradient (Nidacon). Sperm were then lysed in TRIzol-LS (Thermo Fisher) reagent, supplemented with 0.2 M β-mercaptoethanol and 100 mg of nuclease-free stainless-steel beads, by homogenization on a Disruptor Genie (Scientific Industries) at 3000 rpm for 5 min. RNA, enriched for small RNA, was isolated using Qiagen’s miRNeasy Mini kit according to manufacturer’s instructions.
Libraries were constructed using the TruSeq small RNA Library Prep Kit (Illumina) with 10 ng of small RNA according to the manufacturer’s protocol. Post-PCR cleanup and size selection for products > 100 bp was performed using AMPure XP bead purification. Library size distribution and quantification was performed using on a TapeStation 4200 (Agilent) using their High Sensitivity D1000 screentape. Individually barcoded libraries were pooled to achieve ~10 million reads per sample and sequenced on an Illumina NextSeq 550 (36-bp single-end).

tag: subject

tag: collection

tag: stress category

value: Recovering-stress


title: PS16.18.04

description: NormalizedHumanSpermMirs.csv


title: NKp46+ ILC3 from Rorc.Cre Maf.flox mice rep 1

tag: cell type

tag: strain


title: PS16.18.02

description: NormalizedHumanSpermMirs.csv


title: PS16.18.03

description: NormalizedHumanSpermMirs.csv


title: PS16.14.06

description: NormalizedHumanSpermMirs.csv

value: Stable-stress


title: PS16.14.05

description: NormalizedHumanSpermMirs.csv