title: 20180404_sample_1


title: 20180329_sample_4

status: Public on Dec 24 2020

type: SRA

city: Solna

first: Leonard

last: Hartmanis

address: Solnavägen 9

department: Cell & Molecular Biology

country: Sweden

institute: Karolinska Institutet

description: m1_patchseq_exon_counts.csv.gz, m1_patchseq_intron_counts.csv.gz

library_source: transcriptomic

data_processing:
Raw sequencing datawas converted to fastq files using Bcl2fastq (version 2.20)
Reads were mapped against the reference genome (mm10) using STAR (version 2.5.4b) as a part of the zUMIs pipeline version 2.5.6b (Parekh 2018)
gene expression levels were quantified using
Genome_build: mm10
Supplementary_files_format_and_content: Expression matrix gene/-sample wise for raw counts. Exonic and intronic counts are supplied.

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Electrophysiological parameters were measured by patch clamping. The cytosols and nuclei of the cells were extracted and transferred to lysis buffer and converted to cDNA for sequencing
Patch-seq (Cadwell 2016)

tag: mrna type

value: L5 PT_1

tag: tissue

value: primary mouse motor cortex

tag: cell type

value: neurons


title: 20180405_sample_2


title: 20180329_sample_5


title: 20180329_sample_3

value: L5 IT_1


title: 20180327_sample_4

value: Pvalb Reln


title: 20180327_sample_1

value: Pvalb Il1rapl2


title: 20180322_sample_7

value: L5 PT_4


title: 20180405_sample_3


title: 20180327_sample_3


title: 20180322_sample_5


title: 20180322_sample_2


title: 20180322_sample_1


title: 20180329_sample_8


title: 20180322_sample_3


title: 20180329_sample_1


title: 20180404_sample_3


title: 20180321_sample_9


title: 20180321_sample_3


title: 20180321_sample_4


title: 20180315_sample_5


title: 20180321_sample_2


title: 20180315_sample_6


title: 20180327_sample_6


title: 20180315_sample_2


title: 20180410_sample_9


title: 20180315_sample_1

value: L5 PT_2


title: 20180327_sample_2

value: Pvalb Gpr149


title: 20180313_sample_8


title: 20180321_sample_8


title: 20180322_sample_6


title: 20180313_sample_3


title: 20180313_sample_7


title: 20180313_sample_1


title: 20180313_sample_2


title: 20180306_sample_1


title: 20180309_sample_7


title: 20180309_sample_6


title: 20180306_sample_5


title: 20180306_sample_2


title: 20180306_sample_3


title: 20180309_sample_4


title: 20180225_sample_5


title: 20180225_sample_7


title: 20180225_sample_3


title: 20180313_sample_9


title: 20180225_sample_1


title: 20180225_sample_2


title: 20180220_sample_1

value: Sst C1ql3_2


title: 20180215_sample_1


title: 20180225_sample_4


title: 20180213_sample_5


title: 20180213_sample_3

value: L5 PT_3


title: 20180208_sample_5

value: L5 IT_2


title: 20180309_sample_8


title: 20180208_sample_4


title: 20180208_sample_3


title: 20180208_sample_1


title: 20180123_sample_7


title: 20180123_sample_6


title: 20180228_sample_3


title: 20180123_sample_3


title: 20180118_sample_6


title: 20180118_sample_10


title: 20180123_sample_1


title: 20180118_sample_7


title: 20180123_sample_5


title: 20180118_sample_4


title: 20180118_sample_1


title: 20180118_sample_2


title: 20180115_sample_7


title: 20180220_sample_2


title: 20180115_sample_5


title: 20180115_sample_9


title: 20180322_sample_4


title: 20180115_sample_8


title: 20180111_sample_5

value: L5 IT_3


title: 20180110_sample_8


title: 20180115_sample_6


title: 20180115_sample_2


title: 20180110_sample_4


title: 20180110_sample_7


title: 20180110_sample_5


title: 20180208_sample_2


title: 20180110_sample_2


title: 20180110_sample_1


title: 20180109_sample_2


title: 20180109_sample_1


title: 20180108_sample_10


title: 20180108_sample_9


title: 20180108_sample_3


title: 20180105_sample_6


title: 20180108_sample_5


title: 20180108_sample_1


title: 20180108_sample_8


title: 20180110_sample_3


title: 20180104_sample_3


title: 20180105_sample_4


title: 20180108_sample_7


title: 20180108_sample_4


title: 20180103_sample_8


title: 20180103_sample_5


title: 20180103_sample_6


title: 20180104_sample_4


title: 20180104_sample_6


title: 20180103_sample_4


title: 20180104_sample_1


title: 20180103_sample_7


title: 20180109_sample_5


title: 20180104_sample_2


title: 20180103_sample_3


title: 20180103_sample_2


title: 20180108_sample_2


title: 20180105_sample_5


title: 20180102_sample_3


title: 20180102_sample_5


title: 20180102_sample_1


title: 20171219_sample_8


title: Pol_II_Ser2P_shWDR43-2_ChIP

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

country: USA

institute: University of Rochester

library_source: genomic

data_processing:
alignment: bowtie2
peak calling: MACS
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph or bed files for the output by MACS

molecule: genomic DNA

source_name: mES cells

growth_protocol: ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Lysates for ChIP-seq were clarified from sonicated cell lysates and protein-DNA complexes were isolated with antibody. chrCLIP-seq protein-RNA complexes were isolated as desribed in chrCLIP-FB-seq protocol.
Libraries were prepared by NEBNEXT ChIP-seq library preparation kit or chrCLIP-FB-seq protocol.

value: mES cells

tag: antibody

value: RNA polymerase II (Ser2P)


title: FB-WDR43_chrCLIP-FB-seq

value: FLAG and streptavidin


title: 20180102_sample_2


title: Pol_II_Ser2P_shCtl-1_ChIP


title: Pol_II_hypoP_shWDR43-2_ChIP

value: RNA polymerase II (8WG16)


title: light damage

type: RNA

city: New York

first: Stefanie

middle: G

last: Wohl

address: 33w 42nd Street

department: Biological and Vision Sciences

institute: SUNY Optometry

description: pooled from 44 adult retinas

hyb_protocol: The miRtagged mature miRNA was then hybridized to a probe pair (reporter probe and capture probe) in the standard nCounter gene expression array workflow.

scan_protocol: 200 ng of total RNA per sample (33 ng/μl, n = 22 mice, pooled sample) was submitted for NanoString analysis.

data_processing: Values from adult Dicer-CKO and wild type MG were normalized against 4 housekeeping genes (β -actin, GAPDH, Rpl19, and B2m), 8 negative controls, and 6 positive controls that were run simultaneously with the samples.

label: barcode

molecule: total RNA

source_name: Rlbp1-CreER:tdTomato mouse

label_protocol: NanoString nCounter® was used for miRNA expression analysis. DNA sequences called miRtags were ligated to the mature miRNAs through complementary oligonucleotides with sequence-specific binding (bridges). All excess tags and ridges were removed, resulting in sequence-specific tagging of mature miRNAs.

extract_protocol: The sorts of 44  light damaged retinas were pooled for the RNA-purification. RNA was extracted and purified with a miRNeasy Micro Kit in accordance with manufacturer’s instructions (Qiagen).

treatment_protocol: Tamoxifen for cre activation: Tamoxifen (Sigma) was administered intraperitoneally at 75 mg/kg in corn oil at 3 consecute days.

value: retina

tag: condition

value: FACS-sorted

tag: age

value: adult

tag: genotype

value: Muller glia light damaged


title: wild type

description: pooled from 40 adult retinas

value: wild type Muller glia (MG)


title: Pol_II_Ser2P_shWDR43-1_ChIP


title: Pol_II_Ser2P_shCtl-2_ChIP


title: WDR43_N-terminus_FLAG-ChIP-seq

value: FLAG, sigma F1804


title: 20171219_sample_3

value: primary mouse motor cortex

value: neurons


title: Pol_II_hypoP_shWDR43-1_ChIP


title: 20171219_sample_6

value: L5 PT_2


title: 20171219_sample_4

value: L5 PT_1


title: WDR43_C-terminus_FLAG-ChIP-seq


title: 20171219_sample_2

value: L5 IT_1


title: 20180103_sample_1


title: cFB-KI-WDR43-FLAG-ChIP-seq


title: Dicer

description: pooled from 26 adult retinas

source_name: Rlbp1-CreER:tdTomato:Dicerf/f mouse

value: Muller glia Dicer-CKO


title: 20180102_sample_4


title: 20171219_sample_1


title: 20171219_sample_7


title: 20171207_sample_7


title: 20171207_sample_2


title: 20171207_sample_1


title: 20171204_sample_6

value: L5 PT_4


title: 20171204_sample_4

value: L5 IT_2


title: WDR43_FL_FLAG-ChIP-seq

value: mES cells


title: 20171204_sample_2


title: 20171207_sample_6


title: 20171204_sample_5


title: P10: Old NSCs

city: Zürich

first: Baptiste

middle: N

last: Jaeger

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zürich

description: Bulk RNA of 100 cells per samples

data_processing:
Reads were adaptor removed and trimmed using cutadapt v2.10 and sickle v1.33 with default parameters.
Reads were mapped against the mouse reference genome GRCm38.p6 using STAR v2.7.6a
The gene count matrice was quantified at the exon level ignoring multimappers using featureCounts from subread v1.6.3.
Samples were quality checked using CountQC. Seurat v3.0 was used to normalize read counts and dimensionality reduce the data
Data analysis was carried out in R version 4.0.3.
Genome_build: mm9
Supplementary_files_format_and_content: metadata and matrix with counts for all cells in txt file

source_name: Old NSCs

growth_protocol: Ex vivo isolation

extract_protocol:
Low input bulk RNAseq (100 cells/sample)
Nextera XT

treatment_protocol: When indicated samples were retrovirally transduced

tag: mouse strain

tag: retrovirally transduced

value: No

tag: age of the mouse at the time of dissection

value: 9 months

value: NSCs isolated from the mouse hippocampi


title: P13: Old NSCs Control IRES-CFP

description: Bulk RNA of 100 cells per samples

source_name: Old NSCs Control IRES-CFP

value: Yes with Control IRES-CFP


title: P15: Old NSCs LMNB1 Over-expression IRES-CFP

description: Bulk RNA of 100 cells per samples

source_name: Old NSCs LMNB1 Over-expression IRES-CFP

value: Yes with Lamin B1-over-expressing-IRES-CFP


title: P12: Old NSCs Control IRES-CFP

description: Bulk RNA of 100 cells per samples


title: P11: Old NSCs Control IRES-CFP

description: Bulk RNA of 100 cells per samples


title: P14: Old NSCs Control IRES-CFP

description: Bulk RNA of 100 cells per samples


title: P18: Old NSCs LMNB1 Over-expression IRES-CFP

description: Bulk RNA of 100 cells per samples


title: P7: Old NSCs

description: Bulk RNA of 100 cells per samples


title: P8: Old NSCs

description: Bulk RNA of 100 cells per samples


title: P9: Old NSCs

description: Bulk RNA of 100 cells per samples


title: P6: Young NSCs

description: Bulk RNA of 100 cells per samples

source_name: Young NSCs

value: 6 weeks


title: 20180327_sample_5

value: Pvalb Gpr149


title: Hs578T, unstimulated control, replicate 1

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: gene expression values are in the q1_FPKM column of Hs578T_RNAsequence.fpkm_tracking

data_processing:
Reference files of the human genome hg19 (NCBI build 37, Feb. 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
RNA-seq reads were aligned and gene expression levels in fragments per kilobase of exon per million fragments mapped (FPKM) were estimated using Tophat/Cufflinks (version 2.0.10 and 2.1.1, respectively) with the default parameter settings (Trapnell et al., 2012).
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM values of genes for each sample, which was generated by Cufflinks.

organism: Homo sapiens

source_name: A human breast cancer cell line, Hs578T

growth_protocol: Hs578T cells were obtained from ATCC. Cells were cultured in Dulbecco's modified Eagle's medium (11965, Gibco) supplemented with 10% fetal bovine serum (SH30910.03; Thermo Fisher Scientific, and 10270-106; Gibco), 50U/mL penicillin, 50μg/mL streptomycin (Penicillin-Streptomycin, 15070-063, Gibco), and 0.01 mg/mL of insulin (12585-014, Gibco). Cells were cultured at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit with the On-Column DNase Digestion Set (QIAGEN).
RNA libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher Scientific) and the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific).

treatment_protocol: Cells were stimuated with TGF-β3, 1 ng/mL (243-B3-010, R&D) for 24 hours.

tag: cell line

value: triple negative breast cancer cell line

tag: tgf-beta stimulation

value: no


title: P16: Old NSCs LMNB1 Over-expression IRES-CFP

description: Bulk RNA of 100 cells per samples


title: Hs578T stimualted with TGF-β, replicate 2

description: gene expression values are in the q4_FPKM column of Hs578T_RNAsequence.fpkm_tracking

value: yes


title: Hs578T stimualted with TGF-β, replicate 1

description: gene expression values are in the q2_FPKM column of Hs578T_RNAsequence.fpkm_tracking


title: P17: Old NSCs LMNB1 Over-expression IRES-CFP

description: Bulk RNA of 100 cells per samples


title: Hs578T, unstimulated control, replicate 2

description: gene expression values are in the q3_FPKM column of Hs578T_RNAsequence.fpkm_tracking


title: P4: Young NSCs

description: Bulk RNA of 100 cells per samples


title: P3: Young NSCs

description: Bulk RNA of 100 cells per samples


title: P2: Young NSCs

description: Bulk RNA of 100 cells per samples


title: Donor-3_CTRL

city: Ithaca

first: Mridusmita

last: Saikia

address: 111 Weill Hall, 237 Tower Road

institute: Cornell University

description:
cDNA obtained using single cell library preparation protocol
Ctrl_combineddata_gene_exon_tagged.dge.txt, Donor-3-DART-seq_gene_exon_tagged.dge.txt

data_processing:
Quality control and filtering steps were performed using Drop-seq tools
Filtered reads were mapped to the human genome using the STAR aligner
Mapped reads were counted and a tab-delimited text files  was created to include data matrix for each cell with gene counts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include data matrix for each cell with gene counts

source_name: Isolated islet sample

growth_protocol: Upon arrival, islets were resuspended in serum media (RPMI-1640 + 10% FBS + 5mM Glucose (or a final glucose concentration of 16.1mM) + 1% Antibiotic-Antimycotic) and allowed to recuperate in the incubator set at 37C and 5.0% CO2. After approximately 36 hours, the islets were transferred into serum free media (RPMI-1640 + 5mM Glucose) for 2 hours. After 2 hours, islets were subjected to respective treatments.

extract_protocol:
Single cells encpsulated with the nano-bead was lysed to release its content. The mRNA hybridizes to the DNA tails of the beads.
After cell lysis, cDNA synthesis was carried out (Maxima Reverse Transcriptase, Thermo Fisher), followed by PCR (2X Kapa Hotstart Ready mix, VWR, 15 cycles). cDNA libraries were tagmented and PCR amplified (Nextera tagmentation kit, Illumina). Finally, libraries were pooled and sequenced (Illumina Nextseq 500, 20x55 bp).

treatment_protocol: islets were subjected to either liraglutide (100nM) or saline treatment for 12 hours (DART-seq) or 24 hours (IHC).

value: pancreatic islet

tag: agent

value: Saline (Ctrl)

tag: Sex

value: male

tag: bmi


title: Donor-3_LIRA

description:
cDNA obtained using single cell library preparation protocol
Lira_combineddata_gene_exon_tagged.dge.txt

value: Liraglutude (Lira)


title: Donor-3 Drop-seq

description:
cDNA obtained using single cell library preparation protocol
Donor-3-Drop-seq_gene_exon_tagged.dge.txt


title: Donor-2_LIRA


title: Donor-2_CTRL

description:
cDNA obtained using single cell library preparation protocol
Ctrl_combineddata_gene_exon_tagged.dge.txt


title: 20180329_sample_2

value: primary mouse motor cortex

value: neurons


title: Donor-1_LIRA


title: KO 30min GP532 rep2

city: Buffalo

first: Andrei

last: Gudkov

address: Elm and Carlton Streets

department: Department of Cell Stress Biology

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Illumina bcl2fastq2/2.20 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mouse reference genome (UCSC mm10/GRCm38) using  STAR RNA-seq aligner v2.6.0 using annotation from the same source with default parameters. Reads were counted per gene using featureCounts as part of Subread package, version 1.6.2 with parameters -Q 10 -t exon -g gene_id.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

growth_protocol: Pathogen-free C57BL/6 male mice were obtained from The Jackson Laboratory and sex and age-matched TLR5-KO (B6(Cg)-Tlr5tm1.2Gewr/J) were obtained from our colony at RPCI. Mice were housed in microisolator cages in a laminar flow unit under ambient light.

extract_protocol:
Livers were collected at 30 min or 24 hrs post-treatment and flash frozen. Total and small RNA was extracted using the miRNeasy mini kit (Qiagen) following the manufacturer’s recommended protocol. DNAse digestion was performed to remove any residual genomic DNA followed by additional washes prior to elution of high-quality RNA in RNase-free water. The purified RNA was quantitatively assessed using a Qubit Broad Range RNA kit (Thermofisher) and its concentration was determined by Ribogreen fluorescent binding. The RNA was further evaluated qualitatively using RNA Nanotape on the 4200 Tapestation (Agilent technologies), where sizing of the RNA was determined, and a qualitative numerical score (RINe) was assigned.
Sequencing libraries were prepared with the RNA HyperPrep Kit with RiboErase (HMR) kit (Roche Sequencing Solutions) from 500 ng total RNA following the manufacturer’s recommended protocol. The resulting pool of DNA libraries was then loaded into the appropriate NovaSeq Reagent cartridge for 100 cycle paired end sequencing and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina, Inc.).

treatment_protocol: At 12 weeks of age, groups of mice (n=3) received a single s.c. injection of GP532 (0.3mg), entolimod (0.3mg), or vehicle (PBST).

tag: strain

value: liver

tag: treatment

tag: time point


title: KO 30min GP532 rep3

tag: tissue


title: KO 30min GP532 rep1


title: KO 30min entolimod rep2

value: entolimod


title: KO 30min entolimod rep1


title: Donor-1_CTRL


title: KO 30min rep3

value: vehicle


title: KO 30min rep2


title: KO 30min rep1


title: Buparlisib 72h, Biological Rep2

city: Nedlands

first: Pilar

last: Blancafort

state: WA

address: 6 Verdun Street

department: Cancer and Cell Biology

country: Australia

institute: Harry Perkins Institute of Medical Research

data_processing:
RNA-seq data underwent pseudo-alignment against the GRCh38 (Ensembl 89) reference genome and quantification using Salmon [Patro, 2017].
Data were imported into R (v 3.5) using the Bioconductor package tximport [Soneson, 2015]  and expression at the gene level (TPM values) was estimated
Genome_build: GRCh38 (Ensembl 89)
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample

growth_protocol: SUM52PE cells were grown in Ham's F12 medium supplemented with 1% antibiotic-antimycotic, 10% FBS, 10mM HEPES buffer, 1ug/mL hydrocortisone and 5ug/mL insulin.

extract_protocol:
Total RNA was extracted from cells using QIAzol Lysis Reagent (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SUM52PE cells were plated in 6-well plates at the density of 400,000 cells/well. The following day cell culture media was replaced with medium containing dactolisib, everolimus or AZD8055 (Selleck Chem, 100nM) or buparlisib (Selleck Chem,1000nM) or vehicle control. After 36 h medium was refreshed and drugs/vehicle control were added again for 36h (total 72h).

tag: cell type

value: buparlisib 72h


title: Buparlisib 72h, Biological Rep1


title: WT 24h GP532 rep3

value: wild type


title: WT 24h GP532 rep2


title: WT 24h GP532 rep1


title: WT 24h entolimod rep2


title: WT 24h entolimod rep3


title: AZD8055 72h, Biological Rep3


title: AZD8055 72h, Biological Rep1


title: Buparlisib 72h, Biological Rep4


title: C2C12 transfected with siRNA-MEG3 oligos, biological rep3

city: shenzhen

first: zishuai

last: wang

address: pengfei road

country: China

institute: CAAS

description:
Gene expression data from C2C12 cells knocking-down lncRNA-MEG3
SiRNA-3

hyb_protocol: For hybridization per probe, denature 1 ml Cot1 DNA (1mg/ml) (Gibco 18440-016) and 250 m l tRNA (as above) at 95° C for 10 min first. For washing: 100 ml of 2X SSC 0.5% SDS RT 20 min. Move each membrane into a new polypuropylen tube and do the last 4 repeated washes as follows: 3 ml each of 2X SSC 0.5% SDS 65° C 30 min(Tanaka et al., 2000).

scan_protocol: RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-2000C, Nanodrop Technologies) .  Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing:
After normalization, significant differentially expressed mRNAs between two groups were identified through Fold change and P-value(|Fold changed|≥2.0 and p≤0.05). Finally, hierarchical clustering was performed to show distinguishable mRNA expression profiling among samples.
Expressed data were normalized using the median normalization.

label: biotin

source_name: C2C12 cells transfected with siRNA-MEG3 oligos

label_protocol: RNA Integrity was determined by gel electrophoresis. Agilent mouse mRNA microarray was used in detecting profiling of the mRNAs expression. Replicated mRNAs were averaged and mRNAs that intensities ≥30 in all samples were chosen for calculating normalization factor.

growth_protocol: C2C12 were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplement with 10% fetal bovine serum and 1% Penicillin-streptomycin (PS, Thermo Scientific) at 37℃ in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted from C2C12 cells and purified with RNeasy minit kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: When C2C12 cells grew to 70% to 80% , 20 um of lnrna-meg3 siRNA was transfected into the cells by lip3000. The method of transfection was in accordance with the instructions.

value: lncRNA-MEG3 knockdown


title: C2C12 transfected with siRNA-MEG3 oligos, biological rep2

description:
Gene expression data from C2C12 cells knocking-down lncRNA-MEG3
SiRNA-2


title: C2C12 transfected with siRNA-NC oligos, biological rep3

description:
Gene expression data from C2C12 cells treated with siRNA-NC as negative control
Con-3

source_name: C2C12 cells transfected with siRNA-NC oligos

value: siRNA-NC

value: control


title: WT 30min GP532 rep3


title: C2C12 transfected with siRNA-NC oligos, biological rep2

description:
Gene expression data from C2C12 cells treated with siRNA-NC as negative control
Con-2


title: WT 30min GP532 rep2


title: C2C12 transfected with siRNA-NC oligos, biological rep1

description:
Gene expression data from C2C12 cells treated with siRNA-NC as negative control
Con-1


title: WT 24h entolimod rep1


title: Everolimus 72h, Biological Rep4

value: everolimus 72h


title: WT 30min entolimod rep1


title: WT 30min entolimod rep2


title: WT 30min entolimod rep3


title: WT 30min rep3


title: C2C12 transfected with siRNA-MEG3 oligos, biological rep1

description:
Gene expression data from C2C12 cells knocking-down lncRNA-MEG3
SiRNA-1


title: shC11ORF16, biological rep01

data_processing:
Image analysis and base-calling was perfromed by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. Sequence data are generated by bcl2fastq 2.17.1.14 pipeline.
Sequence data were aligned to the hg18 genome build using Tophat (v2.0.14)
Expression at the gene level (FPKM values) was estimated and normalized by Cufflinks (v2.2.1), Cuffmerge (v1.0.0) and Cuffnorm (v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

growth_protocol: 10exp5 SUM52 cells were transduced with lentiviral vectors and 72 hours post-transduction cells were treated with 1,25 microgrames/ml of puromycin in triplicate independent experiment for a week.

extract_protocol:
RNA was extracted by QuiagenRNA extraction quit and processed by RNA-Seq
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transduced with

value: shRNA specific for C11orf67


title: shC11ORF16, biological rep02


title: shC11ORF16, biological rep03


title: Everolimus 72h, Biological Rep3


title: Empty vector, biological rep02

value: PKLO empty vector control


title: AZD8055 72h, Biological Rep2


title: WT 30min GP532 rep1


title: Empty vector, biological rep01


title: WT 30min rep1


title: Empty vector, biological rep03


title: Everolimus 72h, Biological Rep2


title: Dactolisib 72h, Biological Rep3

value: dactolisib 72h


title: SC_AS_RG_drug_2-1-TRL

city: San Francisco

first: Hana

last: El-Samad

state: CA

address: 1700 4th Street, Box 2542

department: Biochemistry and Biophysics

institute: University of California San Franicisco

description: Technical Replicate for Library preparation.

data_processing:
Sequencing data was trimmed, aligned, and checked for quality using the Bluebee genomics analysis pipeline.  S. cerevisiae samples were run using the “FWD S. cerevisiae (R64) Lexogen QuantSeq 2.2.3” protocol, and K. lactis samples were run using the “FWD K. lactis (ASM241v1) Lexogen Quantseq2.2.3” protocol
Counts were generated from the resultant fastq files using custom GTFs that included 3'UTR annotations and the CDS of each gene.  For S. cerevisiae 3'UTRs were identified using information from Nagalakshmi et al. 2008, and for K. lactis the 3'UTR was estimated to be 400bp downstream of the stop codon for the purpose of assigning counts to genes.   Counts were then generated from the .bam files using htseq in intersection-nonempty mode.   See https://github.com/heineike02/UTR_annotation for details on the custom GTF files.
Gene count data was processed to yield estimates for raw expression (rlog values) for all experiments as well as Log Fold Change and adjusted pValue estimates for differential expression between conditions using the DESeq2 package in R (Love, Huber, and Anders 2014).  After filtering samples that failed quality control, our RNA-seq dataset contained 59 S. cerevisiae samples and 35 K. lactis samples which were sequenced in the same run.  These samples included the WT +/- drug and AS +/- drug experiments as well as experiments with Msn2/4 deletion and Rph1/Gis1 deletion mutants.  In each species, we kept only genes that had 2 or more counts in at least 3 samples for that species.  The rlog was calculated using the rlog function with blind=FALSE, and an experimental design which combined the presence of the AS mutation, transcription factor deletion status and presence of drug into a single factor.  Mean rlog data for each condition was calculated by averaging rlog values across replicates.  To calculate distributions of rlog values for all genes in S. cerevisiae, 443 orfs classified as dubious in the saccharomyces_cerevisiae_R64-2-2_20170117 GFF were filtered out.     Log Fold Change and adjusted p-values for differential expression between samples was calculated from deseq using a False Discovery Rate of 1% for the relevant contrast (PKA-AS strains +/- drug at 50 min, or ΔMsn2/4 or ΔKL.Msn2 PKA-AS strains +/- drug at 50 min).  Custom scripts for further RNA sequencing analysis and enrichment are located at https://github.com/heineike02/yeast_esr_expression_analysis
Genome_build: S. cerevisiae: R64, K. lactis: ASM241v1 stored in Bluebee genomics protocols 26 Oct 2018.
Supplementary_files_format_and_content: read_count .txt files are tab separated and contain gene names and counts for each gene.  Matrices containing count data for each species are also included (20181017_countdata_postQC_KL.csv and 20181017_countdata_postQC_SC.csv).
Supplementary_files_format_and_content: Tables containing LFC and pvalues for AS strains contrasting 1-NM-PP1 vs control treatment as generated by DESEQ2 are also included for each species either with no transcription factor mutation (20200603_deseq_KL_AS_WT_nmpp1.csv and 20200603_deseq_SC_AS_WT_nmpp1.csv) or with the Msn2/4 deletion (20201003_deseq_KL_AS_M24_nmpp1.csv and 20201003_deseq_SC_AS_M24_nmpp1.csv).
Supplementary_files_format_and_content: Tables containing mean rlog values as generated by DESEQ2 for all conditions are included (20200603_rlog_mean_KL.csv and 20200603_rlog_mean_SC.csv)

organism: Saccharomyces cerevisiae

source_name: exponential growth in YPD

growth_protocol: Cells were grown overnight at 30°C in YPD to saturation, and then diluted to obtain a 30ml of cells with an OD600 of 0.5 in 4-6 hours assuming a lag time of 90 min and a doubling time of 90 min for S. cerevisiae and 110min for K. lactis.

extract_protocol:
Cultures were split into two 5ml aliquots prior to spinning down at 3850RPM (331rcf) on an Eppendorf 5810R benchtop centerfuge for 3min.  After spinning down, supernatants were poured out and remaining supernatant was aspirated off with a P1000 pipette.   Cells were then flash frozen in liquid nitrogen and stored at  -80°C.  RNA extraction was performed using the hot acid-phenol extraction protocol of (Solís et al. 2016) with the following changes.  Initial cell volume was 5ml instead of 1.5ml and thus the initial spin for collecting the cells was done for 3min at 3850RPM (331rcf) instead of 30s at 13000RPM (15871rcf).  Acid-phenol:chloroform:isoamyl alcohol (IAA) (125:24:1), pH 4.5 (AM9722) was used instead of pure Acid-Phenol because the chloroform aids in the separation of nucleic acid from proteins and lipids, and the IAA prevents foaming.  The spin following heat incubation was performed at room temperature instead of at 4°C.  A second 400µl chloroform wash was included prior to removing the aqueous phase from the phase lock tubes.  22µl of 3M NaOAc, pH5.2 was added instead of 30µl to precipitate the DNA.  Ethanol Precipitation was done overnight instead of for 30 min.
3’ Sequencing Libraries were prepared using the Lexogen QuantSeq 3’mRNA-Seq Library Prep kit FWD using dual indices for each sample.  Select libraries were checked for quality on the Bioanalyzer using a High Sensitivity DNA chip.  Library concentrations were calculated using a Qbit 2.0 Fluorometer (Invitrogen), and 2.65 ng per sample were pooled and sequenced on an Illumina Hiseq 4000 sequencer to an average depth of between 245,000 and 5.6 million reads per sample (median 2.53 million).

treatment_protocol: The culture was divided into two 12ml treatment and control cultures and 3.6µl of 10mM 1-NM-PP1 (for a final concentration of 3µM) or DMSO was added respectively.  Each culture was incubated while shaking at 250RPM and 30°C for 50 min prior to collection.

value: TRUE

value: 3uM 1-NM-PP1


title: Wild Type, biological rep03


title: SC_AS_WT_cont_2017

description: Biological replicate collected in 2017

value: DMSO


title: Wild Type, biological rep02


title: SC_AS_RGM24_drug_4-1


title: Dactolisib 72h, Biological Rep4


title: FB-WDR43-FLAG-input

value: mES cells

tag: antibody

value: input


title: SC_AS_RG_drug_4-1


title: Dactolisib 72h, Biological Rep1


title: Vehicle Control 72h, Biological Rep4

value: vehicle control 72h


title: Wild Type, biological rep01


title: WT 30min rep2

value: liver

value: male

tag: age


title: SC_AS_RGM24_cont_4-1


title: SC_AS_RG_cont_4-1


title: SC_AS_RG_cont_2-1-TRL


title: SC_AS_RG_drug_2-2-TRR

description: Technical Replicate for RNA extraction. Dropped from analysis because of low counts and poor mapping.


title: SC_AS_M24_cont_4-1


title: Vehicle Control 72h, Biological Rep3


title: FB-WDR43-FLAG-ChIP-seq

value: FLAG, sigma F1804


title: SC_WT_RGM24_drug_3-1

value: FALSE


title: HFD 3

city: St Louis

first: Natalia

middle: Sara

last: Harasymowicz

state: MO

address: Clayton Ave

department: Orthopaedic Surgert

institute: Washington University in St Louis

description: CD45CD11b myeloid cells from HFD3

data_processing:
Paired-end sequencing reads were processed by Cell Ranger (10x Genomics software, version 2.0.0). Reads were aligned to the mm9 for genome annotation, demultiplexing, barcode filtering, and gene quantification. Cell Ranger also removes any barcode that has less than 10% of the 99th percentile of total unique molecular identifiers (UMI) counts per barcode as these barcodes are considered to be associated with empty droplets. After this quality control, gene barcode matrices for each sample were generated by counting the number of UMIs for a given gene (as row) in individual cell (as column). For each sample, ~2,200-2,500 cells were captured.
To assess the difference in composition of cell populations, we performed global unsupervised clustering analysis scRNA-seq datasets. First, gene barcode matrices were input into Seurat R package (version 2.4). We then removed the low-quality cells with less than 200 or more than 7,000 detected genes, or if their mitochondrial gene content was more than 5%. Note that the cutoff criteria were adjusted in few cases due to the sequencing depth and the variations in mitochondrial gene content from datasets. Genes that were detected in less than 3 cells were filtered out. After filtering out low-quality cells or cell doublets, the gene expression was then natural log transformed and normalized for scaling the sequencing depth to 10,000 molecules per cell. Next, to reduce the variance introduced by unwanted sources, we regressed out variation in gene expression driven by cell cycle stages and mitochondrial gene expression with vars.to.regress argument in function ScaleData in Seurat. We then used FindVariableGenes function in Seurat to identify highly variable genes across cells for downstream analysis. Dimensionality reduction on the data was then performed by computing the significant principal components on highly variable genes. We then performed unsupervised clustering by using FindClusters function in Seurat with the resolution argument set to 0.6 and clusters were then visualized in tSNE plot.
Genome_build: mm9
Supplementary_files_format_and_content: gene list (_genes.tsv) and cell barcodes (_barcodes.tsv) as well as gene/barcode matrices (_matrix.mtx) are provided for each sample

source_name: visceral adipose tissue

extract_protocol:
For scRNA-seq, flow cytometry analysis, and flow cytometry sorting, mouse Epi/VAT were minced and digested in 4-6 mg/ml collagenase I, (Sigma-Aldrich), 4-6 mg/ml collagenase II (Roche), and 1% BSA (Sigma-Aldrich) in Hanks Balanced Salt Solution (Sigma-Aldrich) at 37°C for 45 min with agitation (180 rpm), then strained through a 70-μm strainer in PBS with 0.1% BSA. The cell suspension was centrifuged at 300xg for 5 min, the supernatant removed, and the cell pellet resuspended in PBS with 0.1% BSA. Red blood cell lysis was performed (BioLegend), followed by wash and centrifugation (300g, 5 min), resuspension in PBS, and straining through a 40μm filter. For scRNA-seq experiment, the SVF suspension was blocked in the anti-mouse CD16/32 antibody (BioLegend) for 30 min at 4°C followed by antibody incubation with CD11b-Alexa Fluor 488 and CD45-APC (BioLegend) for 30 at 4°C. Cells were then washed twice with PBS and sorted using fluorescence-activated cell sorting (FACS) (SY3200 Synergy, Sony Biotechnology).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: sorted CD45CD11b cells

tag: diet

value: HFD


title: SC_WT_M24_drug_3-1


title: SC_AS_RG_cont_2-2-TRR

description: Technical Replicate for RNA extraction.


title: Vehicle Control 72h, Biological Rep2


title: SC_AS_M24_drug_4-1


title: Lung, H5_S10

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
Fastqs generated, trimmed, aligned with STAR followed by DeSeq2, EdgeR and Cuffdiff for DEG
Genome_build: mm10
Supplementary_files_format_and_content: abundance.fpkm.txt, abundance.htseq.txt

source_name: Lung

extract_protocol:
Library construction was performed according to Illumina TruSeq Starnded Total RNA sample preparation protocol
Coding and non-coding RNA-seq

value: humanized NOG-EXL

tag: infection

value: Pneumocystis murina

tag: time

value: 6 weeks post-infection

value: lung


title: SC_WT_RG_drug_3-1


title: HFD 2

description: CD45CD11b myeloid cells from HFD2


title: SC_WT_WT_drug_3-1


title: HFD 1

description: CD45CD11b myeloid cells from HFD1


title: Lung, H4_S9


title: SC_WT_M24_cont_3-1


title: Lung, H3_S8


title: SC_WT_RGM24_cont_3-1


title: Control 3

description: CD45CD11b myeloid cells from Control 3

value: control


title: Control 2

description: CD45CD11b myeloid cells from Control 2


title: SC_WT_RG_cont_3-1


title: CN6

city: Davis

first: Barbara

last: Blanco-Ulate

address: 1 Shields Ave.

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of tomato and the pathogen of interest with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum SL4.0
Supplementary_files_format_and_content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

organism: Solanum lycopersicum

source_name: fruit pericarp

extract_protocol:
At day of harvest, fruit pericarp and epidermal tissue of the blossom end halves of fruit were collected and immediately frozen in liquid nitrogen. Frozen tissue was lysed using a Retsch® Mixer Mill MM 400. A total of 1 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v.2 (Illumina, CA) from isolated RNA. Each library was barcoded and analyzed with the High Sensitivity DNA Analysis Kit for the Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Libraries were sequenced as single-end 50-bp reads on an Illumina HiSeq 4000 platform by the DNA Technologies Core at the UC Davis Genome Center.

tag: genotype

value: Cnr/nor

tag: ripening stage

value: RR


title: MSUMSU_3

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

data_processing:
adapter trimming using cutadapt v1.18
alignment to GRCm38 genome using STAR v2.6.1c
determination of raw counts using subread (v1.6.1) featureCounts
differential expression analysis using DESeq2 v1.24.0
Genome_build: Ensembl GRCm38.96
Supplementary_files_format_and_content: tab-separated text containing rlog-normalized count data

source_name: collagenase-digested mouse paw

growth_protocol: Mice were housed in cages that were maintained in a room with temperature 22 ± 1°C and relative humidity 50–60% on a 12h light/dark cycle. Water and food were provided ad libitum.

extract_protocol:
RNA was extracted using RNAeasy kit (Qiagen) + DNAse1 kit for removal of genomic DNA, all according to the manufacturer's instructions
Barcoded RNA sequencing libraries were prepared from total RNA using TruSeq Stranded mRNA Sample Preparation Kit, according to the manufacturer’s instructions (Illlumina).

treatment_protocol: Left paw was injected with MSU crystals at day 0 and then again at day 9

value: MSU primed

value: BALB/c

value: WT

value: synovial fibroblasts


title: SC_AS_RGM24_drug_3-1

value: TRUE

value: 3uM 1-NM-PP1


title: Lung, H1_S7


title: CN5


title: SC_WT_WT_cont_3-1

value: DMSO


title: MSUMSU_2


title: NC6


title: Control 1

description: CD45CD11b myeloid cells from Control 1


title: CN4


title: KL_AS_RG_drug_2-2

organism: Kluyveromyces lactis


title: SC_AS_M24_drug_3-1


title: KL_AS_RGM24_drug_2-2


title: MSUMSU_1


title: NC2

value: MG


title: SC_AS_WT_drug_3-2


title: KL_AS_M24_drug_2-2


title: nMSU_3

value: non-primed


title: KL_AS_WT_drug_2-2


title: SC_AS_RG_drug_3-2


title: CN3


title: KL_WT_WT_drug_2-2

value: FALSE


title: nMSU_2


title: CN2


title: SC_AS_RGM24_cont_3-1


title: nMSU_1


title: light damaged MG

description: reactive MG after light damage

hyb_protocol: Following fragmentation, cRNA were hybridized on Human Gene 1.0 ST array, washed and stained as per manufacturer guidelines.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The microarray data was normalized and analyzed with Affymetrix Power Tools software and TM4 Multi-Experiment Viewer software and and AltAnalyze software.

source_name: light damage

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix). Cy3 cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: FACS-purified Muller glia cells from adult retinas

extract_protocol: Total RNA was extracted (RNeasy kit, Qiagen)  then checked for integrity and run as per manufacturer’s guidelines on the Mouse Gene 1.0 ST microarray (Affymetrix). cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: For light damage, adult mice were exposed to bright white light (10,000 lux) for 8 hours.

tag: protocol

value: light damage

value: retina, Muller glia


title: SC_AS_RG_cont_3-1


title: Insular Cortex IP Rep 3

first: Jeffrey

middle: M

last: Friedman

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
RNA sequencing raw data was uploaded and analyzed using BaseSpace apps (RNA-seq Alignment (Star aligner) and RNA-seq Differential Expression (DEseq2); Illumina) using an alignment to annotated mRNAs in the mouse genome (UCSC, Mus musculus assembly mm10).
RNA reads were aligned with BaseSpace STAR aligner
Differential expression of novel and reference transcripts with DEseq2 in Baseplace RNA-seq Differential Expression
Genome_build: mm10
Supplementary_files_format_and_content: gene expression counts for each individual sample

source_name: Insular Cortex

extract_protocol:
Fourteen days after injection mice were sacrificed by cervical dislocation and the insular cortex was rapidly dissected in ice-cold Buffer B (1xHBSS, 4 mM NaHCO3, 2.5 mM HEPES [pH 7.4], 35 mM Glucose) with 100 mg/ml cycloheximide (Sigma). The dissected pieces were pooled in 3 groups of 5-6 brains each and transferred to a glass homogenizer (Kimble Kontes 20), and homogenized in 1.5 ml ice-cold Buffer C (10 mM HEPES [pH 7.4], 150 mM KCl, 5 mM MgCl2) with 0.5 mM DTT (Sigma), 80 U/ml RNasin Plus (Promega), 40U/ml Superase-In (Life Technologies), 100 mg/ml cycloheximide, protease inhibitor cocktail (Roche) and 100 ng/ml GFP-Trap Protein (ChromoTek). Tissue samples were homogenized three times at 250 rpm and ten times at 750 rpm on a variable-speed homogenizer (Glas-Col) at 4°C. Homogenates were transferred to microcentrifuge tubes and clarified at 2,000xg for 10 min at 4°C. 140 μl each of 10% IGEPAL CA-630 (NP-40; Sigma) and 1,2-diheptanoyl-sn-glycero-3-phospho-choline (DHPC at 100 mg/0.69 ml; Avanti Polar Lipids) was added to the supernatant. The solutions were mixed and centrifuged again at 17,000xg for 15 min at 4°C. The resulting supernatants were transferred to new tubes and 50 μl of each cleared lysate was mixed with 50 μl Lysis Buffer (0.7 μl β-mercaptoethanol/100 μl Lysis Buffer; Agilent Absolutely RNA Nanoprep Kit) and stored at -80° for later preparation as input RNA. The remaining lysates (approximately 1.5 ml) were used for immunoprecipitation. The beads incubating with GFP antibodies were washed twice in Buffer A with 0.5 mM DTT, 80 U/ml RNasin Plus and 100 mg/ml cycloheximide before the cleared brain lysates were added. The immunoprecipitation was allowed to run at 4°C for 40 min. Beads were washed four times with Buffer D (10 mM HEPES [pH 7.4], 350 mM KCl, 5 mM MgCl2, 1% NP40) with 0.5 mM DTT, 80 U/ml RNasin Plus and 100 mg/ml cycloheximide. Before removing the last wash solution the beads were moved to a new tube. After the final wash, RNA was eluted by adding 100 μl Lysis Buffer and purified using the Absolutely RNA Nanoprep Kit (Agilent).
cDNA was amplified using SMARTer Ultralow Input RNA for Illumina Sequencing Kit and sequenced on an Illumina HiSeq2500 platform.

treatment_protocol: Syn-NBL10 mice were injected with CAV-GFP into the CeA.

value: Brain


title: SC_AS_WT_cont_3-1


title: KL_AS_RG_cont_2-2


title: KL_AS_M24_cont_2-2


title: CN1


title: KL_AS_RGM24_cont_2-2


title: SC_AS_WT_drug_2017


title: KL_AS_WT_cont_2-2


title: Insular Cortex IP Rep 2


title: Insular Cortex IP Rep 1


title: Insular Cortex Input Rep 3


title: KL_WT_WT_cont_2-2


title: SC_AS_RGM24_drug_2-1


title: Insular Cortex Input Rep 2


title: Insular Cortex Input Rep 1


title: KL_AS_RGM24_drug_3-1


title: SC_AS_RG_drug_2-1


title: KL_AS_RG_drug_3-1


title: KL_AS_M24_drug_3-1


title: SC_AS_M24_drug_2-1


title: SC_AS_M24_cont_3-1


title: SC_AS_WT_drug_2-1


title: KL_WT_WT_drug_3-1


title: ATAC_mTOR_KO_2

city: Cincinnati

first: Yi

last: Zheng

state: OH

address: 3333 Burnet Ave MLC7013

department: Experimental Hematology and Cancer Biology

institute: CINCINNATI CHILDRENS HOSP MED CTR

description: ATAC-seq

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated by MACS1.4

source_name: mTOR KO HSC cells

extract_protocol:
50,000 sorted HSC cells from poly(I:C)-treated WT control, mTOR KO and mTOR KO;c-Myc Het mice were lysed in a cold lysis buffer. Transposase reaction were performed for 30 min at 37 °C immediately after the nuclei preparation. The samples were purified using a Qiagen MinElute kit.
The ATAC-seq libraries were amplified using NEBnext PCR master mix followed by purified using Qiagen MinElute PCR Purification Kit (Qiagen, 28004), and then run on the Illumina sequencer HiSeq 2500.

tag: group

value: KO Mutant

value: Adult


title: SC_AS_RGM24_cont_2-1


title: SC_AS_M24_cont_2-1


title: ATAC_mTOR_KO_Myc_Het_2

description: ATAC-seq

source_name: mTOR KO;c-Myc Het HSC cells

value: mTOR KO;c-Myc Het


title: ATAC_mTOR_WT_2

description: ATAC-seq

source_name: mTOR WT HSC cells

value: Control


title: KL_AS_RGM24_cont_3-1


title: KL_AS_M24_cont_3-1


title: SC_AS_RG_cont_2-1


title: KO2

city: Birmingham

first: Matthew

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

department: Pediatrics

institute: University of Alabama at Birmingham

description: processed data file: normalized_counts_nv.txt

data_processing:
The following pipeline, built with the Snakemake (v5.2.2) workflow system was used: QC was performed with FastQC and low-quality bases were removed with Trim Galore (v. 0.4.5).
Reads were quasi-mapped and quantified with Salmon (v0.12.0, flag `--gencode` was enabled for index generation. Flags `-l ISR`, `--gcBias`, and `--validateMappings` were enabled for quasi-mapping mode).
The mm10 Gencode release 21 was utilized for quasi-mapping. Gene-level summarization was performed with tximport (v1.10.0) and differential expression was conducted with DESeq2 (v1.22.1) in R (v3.5.3).
A cutoff of adjusted p-value < 0.05 (Benjamini-Hochberg False Discovery Rate method) and absolute log2 fold change >=1 were used to determine differentially expressed genes (DEGs).
Upregulated and downregulated DEGs were separately submitted to the NIH Database for Annotation, Visualization and Integrated Discovery (DAVID, v6.8) for Gene Ontology and pathway analysis using p-value <0.05 as the cutoff.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: normalized_counts_nv.txt: Tab-delimited text file which contains the normalized gene-level counts for each biological sample.

source_name: TA skeletal muscle

extract_protocol:
Total RNA was extracted following mechanical homogenization using the GenElute Total RNA Purification Kit (MilliporeSigma; Cat# RNB100-50RXN) following the manufacturer’s guidelines.
Libraries were prepared using the Sure Select Stranded RNA-seq Kit (Agilent G6961B) following manufacturer’s protocol. The sequencing was performed on the Illumina HiSeq2500 with paired-end mode by the UAB Heflin Center for Genomic Sciences core facility. The ribominus method was utilized for ribosomal depletion (RiboMinus kit, LifeTech, CAT#A15026).

tag: genotype/variation

value: Dock3 KO

value: TA skeletal muscle


title: KL_AS_RG_cont_3-1


title: KL_AS_WT_drug_2017-1-2

description: Biological replicate collected in 2017


title: C57_4

value: WT


title: SC_WT_M24_drug_2-1


title: SC_WT_RG_drug_2-1


title: KL_AS_WT_cont_2017-1-2

description: Biological replicate collected in 2017


title: KO1


title: KL_AS_WT_drug_3-1


title: ATAC_mTOR_KO_Myc_Het

description: ATAC-seq


title: KL_AS_M24_drug_4-2


title: SC_AS_WT_cont_2-1


title: SC_WT_RGM24_drug_2-1


title: C57_1


title: KL_AS_WT_cont_3-1


title: undamaged control MG

description: undamaged MG

source_name: undamaged control

value: undamaged control


title: KO3


title: KL_AS_M24_cont_4-2

value: TRUE


title: ATAC_mTOR_WT_AZD

description: ATAC-seq

growth_protocol: HSC cells from poly(I:C)-treated mTOR WT control mice were sorted by FACS and then cultured in StemSpan SFEM (STEMCELL, 09600 ) medium.

extract_protocol:
50,000 cultured mTOR WT HSC cells treated with DMSO, AZD2014 or Rapamycin were lysed in a cold lysis buffer. Transposase reaction were performed for 30 min at 37 °C immediately after the nuclei preparation. The samples were purified using a Qiagen MinElute kit.
The ATAC-seq libraries were amplified using NEBnext PCR master mix followed by purified using Qiagen MinElute PCR Purification Kit (Qiagen, 28004), and then run on the Illumina sequencer HiSeq 2500

treatment_protocol: HSC cells were treated with DMSO, or 200nM AZD2014 or 1 µM rapamycin and then followed by ATAC-seq assay.

value: cultured mTOR WT HSC cells


title: SC_WT_M24_cont_2-1

value: DMSO


title: SC_WT_RG_cont_2-1


title: KL_AS_RG_drug_4-2

value: 3uM 1-NM-PP1


title: ATAC_mTOR_WT_Rapamycin

description: ATAC-seq


title: SC_WT_RGM24_cont_2-1


title: ATAC_mTOR_WT_DMSO

description: ATAC-seq


title: KL_AS_RG_cont_4-2


title: SC_WT_WT_drug_2-1


title: SC_WT_WT_cont_2-1


title: C57_3


title: SC_AS_RG_drug_1-1


title: SC_AS_RGM24_drug_1-1


title: KL_AS_RGM24_drug_1-1


title: KL_AS_RG_drug_1-1


title: SC_AS_M24_drug_1-1


title: KL_AS_WT_drug_1-1


title: mTOR_WT_MYC_ChIP-seq

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Peak calling was performed using MACS1.4 with a default p value cut off.
bed files were generated by MACS1.4
Genome_build: mm10

extract_protocol:
HSC cells from poly(I:C)-treated WT control and mTOR KO mice were purified by FACS sorting and fixed with 1% formaldehyde for 10 min at room temperature. Nuclei were isolated and sonicated in sonication buffer (100mM NaCl, 50mM Tris (pH 8), 5mM EDTA pH 8, and 0.5% SDS). Sonicated chromatin was used for immunoprecipitation by incubation with anti-H3K27ac, anti-H3K4me3, anti-Myc antibody overnight at 4°C.
The ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and then run on the Illumina sequencer HiSeq 2500.


title: KL_AS_M24_drug_1-1


title: mTOR_KO_MYC_ChIP-seq


title: SC_AS_WT_drug_1-1


title: H3K4me3_mTOR_KO


title: SC_AS_RGM24_cont_1-1


title: KL_AS_RGM24_cont_1-1


title: KL_WT_WT_drug_1-1


title: H3K4me3_mTOR_WT


title: SC_AS_M24_cont_1-1


title: SC_AS_RG_cont_1-1


title: H3K27Ac_mTOR_KO


title: H3K27Ac_mTOR_WT


title: KL_AS_RG_cont_1-1


title: KL_AS_M24_cont_1-1


title: SC_WT_RGM24_drug_1-1


title: KL_WT_WT_cont_1-1


title: KL_AS_WT_cont_1-1


title: SC_AS_WT_cont_1-1


title: SC_WT_RG_drug_1-1


title: SC_WT_WT_drug_1-1


title: SC_WT_M24_drug_1-1


title: SC_WT_RGM24_cont_1-1


title: normal esophageal epithelial cell 3

city: Jiaxiang

last: LEI

state: Zhejiang

address: NO. 118 of Jia hang Road,Jiaxing

institute: Jiaxing Unviersity

description: normal esophageal tissues of Kazakh esophageal cancer patients

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for4x180k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: esophageal epithelial

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the mirVana RNA Isolation Kit following the manufacturer's recommendations.RNA was pured using QIAGEN RNeasy® Mini Kit. RNA wasquantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: control

value: normal esophageal

tag: disease

value: Kazakh esophageal cancer


title: normal esophageal epithelial cell 2


title: SC_WT_M24_cont_1-1

value: FALSE


title: highly expression DNMT1 cell 3

value: highly expression DNMT1


title: highly expression DNMT1 cell 2


title: normal esophageal epithelial cell 1


title: SAT_PBS

status: Public on Dec 23 2020

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

data_processing:
processed with 10X standardard cellranger (3.1.0) pipeline reference (cellranger-mm10-3.0.0) using STAR aligner (version 2.6)
Genome_build: cellranger-mm10-3.0.0
Supplementary_files_format_and_content: standard output of cellranger with gzipped barcode, features (gene), and Unique Molecular Identifier (UMI)

source_name: SAT

extract_protocol:
Cells were prepared according to 10x Genomics® Single Cell Protocols Cell Preparation Guide, followed by MACS Dead Cell Removal Kit 130-090-101 and RBC removal
single-cell transcritpome caputred by 10X 3' Reagent Kiits (v3)
After running on 10X Chromium Single Cell Controller, gel beads-in-emulsion (GEMs) were generated. The barcoded and full-length cDNAs were produced after incubation of the GEMs and amplified via PCR.
Library was qualified by Agilent Bioanalyzer 2100 and quantified by real-time PCR on QuantStudio3. Sequenced was done with Illumina NextSeq 550 System using High Output Kit v2.5 (50,000 reads per cell).

value: VFB

value: subcutaneous  adipose tissue

value: Stromal/vascular


title: amniotic fluid fetal cells 47

type: genomic

city: Fuzhou

first: Hailong

last: Huang

state: Fujian

address: No.18 Daoshan Road, Gulou District

institute: Fujian Maternity and Child Health Hospital

description: Hybridized to CytoScan 750K

hyb_protocol: DNA was processed as follows. Restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer`s instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 750K

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console (AGCC version 4.0.0.1567). Data processing and analysis (CEL file generation, smoothing and segmentation) were used Chromosome Analysis Suite (version 3.3).
Copy number variation status (CNV)

label: Biotin

source_name: amniotic fluid fetal cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA of fetal cells in amniotic fluid or cord blood sampling was extracted with using the QIAamp DNA extraction kit (Qiagen, Dusseldorf, Germany)

value: amniotic fluid fetal cells

tag: diagnosis

value: 17p12 microdeletion syndrome


title: SAT_D-CAN

tag: treatment

value: D-CAN (ASC-targeting peptide)


title: amniotic fluid fetal cells 40

description: Hybridized to CytoScan 750K

value: microduplication of 15q13.3


title: Tumor_D-CAN

source_name: tumor

value: subcutaneous MycCap tumor

value: Cancer and Stromal/vascular


title: amniotic fluid fetal cells60

description: Hybridized to CytoScan 750K

value: microduplication of 16p13.11


title: Tumor_PBS

value: Control


title: Sham ODE

city: Omaha

first: Rohit

last: Gaurav

state: NE

address: 985910 Nebraska Medical Center

department: Internal Medicine-Allergy

institute: University of Nebraska Medical Center

data_processing:
Cellranger 3.0.0 was used for basecalling, demultiplexing and initial analyses to create the single cell matrix.
In spedific, cellranger mkfastq and cellranger count were used for this purpose with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample

extract_protocol:
Lungs were removed from mice and digested with Collagenase I + Dnase I + Heparin, single cells were isolated from suspension with 10x chromium controller, reverse transcription and cDNA amplification was performed, sequencing was done at average depth of 50,000 reads per cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4 treatment groups (mice): Sham (saline injection, saline inhalation), collagen‐induced arthritis (CIA; CIA injection, saline inhalation), ODE (saline injection, ODE inhalation), and CIA + ODE (CIA injection, ODE inhalation). CIA was induced with two subcutaneous tail injections (100 μg) of chick type II collagen (2 mg/ml) emulsified in Freund's complete adjuvant (FCA) on day 1 and in Freund's incomplete adjuvant (IFA) on day 21. Sham injections and saline inhalation were conducted with sterile PBS. 50 µl of intranasal saline or 12.5% ODE daily for 5 weeks (weekends excluded) was used to induce airway inflammatory disease.

tag: strain

value: Lung

value: 6-8 Week

value: Saline+ODE


title: amniotic fluid fetal cells 66

description: Hybridized to CytoScan 750K

value: Heterozygosity is absent on chromosome 18


title: highly expression DNMT1 cell 1

tag: tissue

value: normal esophageal

value: Kazakh esophageal cancer


title: Sham Saline

value: Saline+Saline


title: cord blood sampling 68

description: Hybridized to CytoScan 750K

source_name: cord blood sampling

value: cord blood sampling

value: microdeletion of 16p11.2


title: amniotic fluid fetal cells 43

description: Hybridized to CytoScan 750K

tag: cell type

value: amniotic fluid fetal cells

value: microduplication of 1q21.1


title: KO1_Progenitors

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

institute: Yale University

data_processing:
Base calling performed using CASAVA 1.8
Quality control on fastq files was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Demultiplexing, genome alignment and gene counting was performed using 10x Genomics Cell Ranger software.
Downstream data analysis and visualization was performed in R using the Seurat R toolkit for single cell genomics.
Imputation of technical zeroes using ALRA algorithm (Linderman, G.C et. Al. BioRxiv, 2018)
Genome_build: mm10
Supplementary_files_format_and_content: Data matrices from Cellranger output

source_name: Bone marrow derived haematopoietic progenitors (Lineage negative, cKit positive) from C57/BL6 Daedalus (Linc7) knockout mice

growth_protocol: Mice deficient in the Daedalus locus were generated by injection of Cas9 RNA and chimeric guideRNAs flanking the locus (SuppTable1) into C57/B6N embryos as previously reported. The offspring of one of these mice were interbred to create a line of Daedalus deficient mice. All mice were housed and maintained under pathogen-free conditions in Yale University animal facilities. Female sex-matched  littermates from heterozygous crossings between 4 and 12 weeks old were used for this experiment.

extract_protocol:
Cells were sorted into PBS + 0.01% BSA (ThermoFisher UltraPure BSA Cat#:AM2616), washed twice and counted using a hemocytometer, counts were checked using a Countess II Automated Cell Counter (ThermoFisher).
10x Single Cell Library Preparation; Single cell libraries were generated using 10x Genomics Chromium Controller instrument and associated kits. RNA was sequenced on a HiSeq2500/4000 with 75bp pair-ended reads.

treatment_protocol: Purified populations of haematopoietic progenitors were sorted from WT and KO littermate mice as described in the methods section. The progenitor populations sorted were gated on lineage negative cells (Lineage cocktail: B220, CD4, CD8, CD11b, CD11c, CD19, Gr1, NK1.1, TCRgd, Ter119). The population was enriched for haematopoietic progenitors by sorting for the pan-haematopoietic progenitor marker c-Kit. No other markers were used in an effort to obtain an unbiased cross section of early haematopoietic development in these mice.

tag: strain background

value: Daedalus knockout

tag: tissue/cell type

value: Sorted from mice in the steady state, with no immunological challenge or disease.


title: amniotic fluid fetal cells 69

description: Hybridized to CytoScan 750K

value: 22q11.21 microdeletion syndrome


title: CIA injection Saline

tag: age

value: CIA+Saline


title: amniotic fluid fetal cells 3

description: Hybridized to CytoScan 750K

value: microduplication of 15q13.3


title: CIA injection ODE

value: CIA+ODE


title: SC_WT_RG_cont_1-1

source_name: exponential growth in YPD

value: FALSE

value: DMSO


title: KO2_Progenitors

value: Bone marrow derived haematopoietic progenitors


title: WT3_Progenitors

source_name: Bone marrow derived haematopoietic progenitors (Lineage negative, cKit positive) from C57/BL6 Daedalus (Linc7) wildtype mice

value: Daedalus wildtype


title: amniotic fluid fetal cells 35

description: Hybridized to CytoScan 750K

value: microduplication of 16p13.13p13.12


title: Lac vs.reference stationary phase_3

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

institute: Technische Universtität Braunschweig

hyb_protocol: 300 ng of Cy3-labeled RNA and 300 ng of Cy5-labeled RNA were mixed and fragmented, and hybridized to the microarray at 65 °C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned with the help of the Agilent C Scanner (Agilent Technologies, USA) using the software Agilent Scan Controll 8.4.1

data_processing: For feature extraction the software Feature Extraction 10.7.3.1 (Agilent Technologies, USA) was used, data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).

organism: Clostridioides difficile 630

source_name: Clostridioides difficile 630∆erm at stationary phase grown in casamino acids medium supplemented with 0.5 g/L L-lactate

label_protocol: RNA samples were labelled with Cy3 (later growth phases) and Cy5 (exponential growth phase) using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: The C. difficile 630∆erm strain (DSM28645) (Hussain, HA, 2005) obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ, Braunschweig, Germany) was grown anaerobically at 37 °C in a defined medium containing 10 g/L casamino acids (Cartman and Minton, 2010; Neumann-Schaal et al. 2015) and supplemented with 2 g/L glucose or 0.5 g/L L-lactate.

extract_protocol: Bacterial RNA was extracted using the Qiagen RNeasy Kit Mini (Qiagen, Hilden, Germany) according to manufacturer’s instructions with minor modifications. Briefly, pellets from a 45 mL culture were resolved in 200 µl TE buffer and 15 mg/ml lysozyme, incubated for 30 min at room temperature and vigorously mixed every 2 min for 10 sec for enzymatically disruption of cells. Approximately 700 µL of RLT buffer and one spatula of glass beads were added and mixed vigorously for 3 min for mechanical disruption of cells. Samples were centrifuged (3 min, 10.000 rpm) and supernatant was mixed with 470 µL of 100% ethanol. Afterwards, RNA purification was carried out using the Qiagen RNeasy Kit protocol. DNA contaminating the RNA samples was removed using RNase-free DNase I twice (Qiagen, Hilden, Germany). The RNA was further assessed by analysis on the Bionanalyzer 2100 (Agilent, Santa Clara, CA) and RNA 6000 Nano Reagents (Agilent, Santa Clara, CA). According to the amount of RNA extracted and its quality (RINs>8), the best samples per time point were used for transcriptomic analysis.

treatment_protocol: Samples were taken in the exponential growth (at 1/2 ODmax) and at the beginning of the stationary phase (ODmax).

tag: supplementation

value: 0.5 g/L L-lactate

source_name: Clostridioides difficile 630∆erm at stationary phase grown in casamino acids medium (reference)


title: amniotic fluid fetal cells 42

description: Hybridized to CytoScan 750K

value: microduplication of 20q13.2


title: WT1_Progenitors


title: amniotic fluid fetal cells 32

description: Hybridized to CytoScan 750K

value: microdeletion of 16p12.2


title: Glc vs.reference stationary phase_4

source_name: Clostridioides difficile 630∆erm at stationary phase grown in casamino acids medium supplemented with 2 g/L glucose

value: 2 g/L glucose


title: SC_WT_WT_cont_1-1

extract_protocol:
Cultures were split into two 5ml aliquots prior to spinning down at 3850RPM (331rcf) on an Eppendorf 5810R benchtop centerfuge for 3min.  After spinning down, supernatants were poured out and remaining supernatant was aspirated off with a P1000 pipette.   Cells were then flash frozen in liquid nitrogen and stored at  -80°C.  RNA extraction was performed using the hot acid-phenol extraction protocol of (Solís et al. 2016) with the following changes.  Initial cell volume was 5ml instead of 1.5ml and thus the initial spin for collecting the cells was done for 3min at 3850RPM (331rcf) instead of 30s at 13000RPM (15871rcf).  Acid-phenol:chloroform:isoamyl alcohol (IAA) (125:24:1), pH 4.5 (AM9722) was used instead of pure Acid-Phenol because the chloroform aids in the separation of nucleic acid from proteins and lipids, and the IAA prevents foaming.  The spin following heat incubation was performed at room temperature instead of at 4°C.  A second 400µl chloroform wash was included prior to removing the aqueous phase from the phase lock tubes.  22µl of 3M NaOAc, pH5.2 was added instead of 30µl to precipitate the DNA.  Ethanol Precipitation was done overnight instead of for 30 min.
3’ Sequencing Libraries were prepared using the Lexogen QuantSeq 3’mRNA-Seq Library Prep kit FWD using dual indices for each sample.  Select libraries were checked for quality on the Bioanalyzer using a High Sensitivity DNA chip.  Library concentrations were calculated using a Qbit 2.0 Fluorometer (Invitrogen), and 2.65 ng per sample were pooled and sequenced on an Illumina Hiseq 4000 sequencer to an average depth of between 245,000 and 5.6 million reads per sample (median 2.53 million).


title: Glc vs.reference stationary phase_3


title: Lac vs.reference stationary phase_2


title: Glc vs.reference stationary phase_1


title: Lac vs.reference exponential phase_2

source_name: Clostridioides difficile 630∆erm at exponential phase grown in casamino acids medium supplemented with 0.5 g/L L-lactate

source_name: Clostridioides difficile 630∆erm at exponential phase grown in casamino acids medium (reference)


title: Lac vs.reference exponential phase_4


title: Lac vs.reference stationary phase_4


title: amniotic fluid fetal cells 19

description: Hybridized to CytoScan 750K

value: amniotic fluid fetal cells


title: Lac vs.reference stationary phase_1


title: amniotic fluid fetal cells 17

description: Hybridized to CytoScan 750K

value: microduplication of 17q13.42


title: Anterior Escort Cells scRNA-seq

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

department: Computational Biology

institute: Stowers Institute for Medical Research

description: 10x Genomics

data_processing:
Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline (version 2.1.1). Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using cavefish genome astMex1, ensembl 87 gene model. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters.
Genome_build: dm6
Supplementary_files_format_and_content: cellranger output raw count matrix in hdf5 format

organism: Drosophila melanogaster

source_name: AnteriorEscortCells

growth_protocol: Drosophila cultured at 25 degree for 5 days, ovaries were dissected and diassociated with type II collagenase, and mature eggs were fltered and discarded.

extract_protocol: Single Cell 3' Reagent kits v2 User Guide Rev D (10X Genomics)

value: Ovary

value: Escort Cells


title: Lac vs.reference exponential phase_3


title: HAP1_Tile21_R3DB6_P2_L1

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

data_processing:
Library strategy: amplicon
Paired reads were overlapped and error-corrected with PEAR v0.9.6; only perfectly matching pairs were used. For each tile, all possible single-codon mutation sequences were enumerated, and the count of reads exactly matching each mutant sequence was tabulated.
Genome_build: N/A
Supplementary_files_format_and_content: MSH2_HAP1_raw_count.tsv is in tab-separated text file format, and contains counts of single-mutant (or wildtype) tile-seq reads. Each row corresponds to a single variant (var_nt and var_AA columns indicate the codon and amino-acid substitutions, respectively); rows marked “TileXX_nt_wt” contain counts of wildtype reads for that tile (#XX).  Each column is a single sample (condition x timepoint x replicate); “WT_plasmid” column contains counts from tile-seq of wild-type MSH2 plasmid DNA.

source_name: HAP1 MSH2ko cell line

growth_protocol: Human HAP1 cells (Horizon Discovery) were cultured in IMDM supplemented with 10% fetal bovine serum, 100 U/ml penicillin and 100 g/ml streptomycin. During routine passaging, cells were washed with PBS pH 7.4 and dissociated with TrypLE Express.

extract_protocol:
Genomic DNA was isolated from 1-3x107 cells using the Quick-DNA Midiprep Plus kit (Zymo Research.
For each sample, 16 replicate PCR reactions were assembled, each with 0.5 µg of gDNA as template (template copy number of 2.4x106 genome equivalents). Integrated inserts (~3.7 kbp), including MSH2 cDNA and associated barcode, were PCR amplified with PrimeSTAR GXL (Takara). Each set of 16 replicate amplicons was pooled and purified with SPRI beads. Tile-specific primers were used to further amplify the mutagenized tile using 10 ng full-length amplicon (≥ 2.6x109 copies) as template. Dual-indexed illumina adapters were then added by a subsequent round of PCR.

treatment_protocol: Each mutant tile cell population was spiked with barcoded knock-in control cells (MSH2 WT: to 10% of the population, A636P: to 0.5%), then split and expanded in triplicate 10 cm dishes in media supplemented with 1 µg mL-1 doxycycline to induce MSH2 expression. From each baseline passage (“P0”) culture, 107 cells were collected for gDNA extraction, and cells were split into 6-TG treated and mock-treated cultures, with media containing 1 µg mL-1 puromycin, 1 µg mL-1 doxycycline, 5 µg mL-1 blasticidin (to enforce MSH2 expression), with and without 1 uM 6-TG, respectively. Cells were grown to confluence for two rounds, at each round harvesting ≥107 cells for gDNA extraction and seeding with 3x106 cells to avoid population bottlenecks.

tag: selection (d=dox, db=dox+blast, db6=dox+blast+6tg)

tag: replicate


title: HAP1_Tile21_R2DB6_P2_L1


title: Middle Escort Cells scRNA-seq

description: 10x Genomics

source_name: MiddleEscortCells


title: Glc vs.reference exponential phase_3

source_name: Clostridioides difficile 630∆erm at exponential phase grown in casamino acids medium supplemented with 2 g/L glucose


title: cord blood sampling 28

description: Hybridized to CytoScan 750K

value: cord blood sampling

value: microduplication of 2q36.1q36.2


title: Glc vs.reference exponential phase_2


title: Posterior Escort Cells scRNA-seq

description: 10x Genomics

source_name: PosteriorEscortCells


title: amniotic fluid fetal cells 31

description: Hybridized to CytoScan 750K

value: microdeletion of 15q13.2q13.3


title: HAP1_Tile21_R1DB6_P2_L1


title: amniotic fluid fetal cells 15

description: Hybridized to CytoScan 750K

value: microduplication of Xq28


title: HAP1_Tile21_R2DB_P2_L1

value: DB


title: HAP1_Tile21_R2_P0_L1

value: D


title: Lac vs.reference exponential phase_1


title: HAP1_Tile21_R3_P0_L1


title: HAP1_Tile21_R3DB_P2_L1


title: Glc vs.reference exponential phase_1


title: HAP1_Tile21_R1_P0_L1


title: HAP1_Tile21_R1DB_P2_L1


title: HAP1_Tile20_R3DB6_P2_L2


title: cord blood sampling 4

description: Hybridized to CytoScan 750K

value: microduplication of 15q13.3


title: cord blood sampling 38

description: Hybridized to CytoScan 750K

value: microduplication of 16p13.11


title: cord blood sampling 3

description: Hybridized to CytoScan 750K

value: Heterozygosity is absent on chromosome 4


title: HAP1_Tile20_R2DB6_P2_L2


title: amniotic fluid fetal cells 16

description: Hybridized to CytoScan 750K

value: microduplication of 2p16.1


title: HAP1_Tile20_R1DB6_P2_L2


title: HAP1_Tile20_R3DB_P2_L2


title: HAP1_Tile20_R3_P0_L2


title: HAP1_Tile20_R2_P0_L2


title: HAP1_Tile20_R1_P0_L2


title: HAP1_Tile19_R2DB6_P2_L1


title: HAP1_Tile19_R3DB6_P2_L1


title: Glc vs.reference exponential phase_4


title: amniotic fluid fetal cells 7

description: Hybridized to CytoScan 750K

value: 22q11.2 microduplication syndrome


title: HAP1_Tile19_R1DB6_P2_L1


title: HAP1_Tile20_R2DB_P2_L2


title: HAP1_Tile19_R2DB_P2_L1


title: HAP1_Tile20_R1DB_P2_L2


title: HAP1_Tile19_R3_P0_L1


title: HAP1_Tile19_R3DB_P2_L1


title: HAP1_Tile18_R3DB6_P2_L1


title: HAP1_Tile19_R1_P0_L1


title: HAP1_Tile18_R2DB6_P2_L1


title: amniotic fluid fetal cells 20

description: Hybridized to CytoScan 750K

value: microduplication of 10q21.1


title: HAP1_Tile19_R2_P0_L1


title: HAP1_Tile18_R1DB6_P2_L1


title: HAP1_Tile19_R1DB_P2_L1


title: amniotic fluid fetal cells 14

description: Hybridized to CytoScan 750K

value: microdeletion of Xp22.31


title: HAP1_Tile18_R2DB_P2_L1


title: HAP1_Tile17_R2DB6_P2_L2


title: HAP1_Tile18_R3_P0_L1


title: HAP1_Tile17_R2_D_L1


title: HAP1_Tile18_R3DB_P2_L1


title: HAP1_Tile18_R1DB_P2_L1


title: HAP1_Tile18_R1_P0_L1


title: Glc vs.reference stationary phase_2

value: 2 g/L glucose


title: HAP1_Tile17_R2DB_P1_L1


title: HAP1_Tile17_R3DB_P2_L1


title: HAP1_Tile17_R3DB6_P2_L1


title: HAP1_Tile17_R3DB6_P1_L1


title: HAP1_Tile17_R2DB_P2_L1


title: HAP1_Tile17_R1DB6_P1_L1


title: HAP1_Tile17_R2_P0_L1


title: HAP1_Tile17_R3_P0_L1


title: HAP1_Tile17_R1DB_P2_L1


title: HAP1_Tile16_R1DB6_P2_L2


title: HAP1_Tile16_R1_P0_L2


title: HAP1_Tile16_R3DB6_P2_L1


title: HAP1_Tile16_R3DB6_P1_L1


title: HAP1_Tile16_R2DB6_P2_L1


title: HAP1_Tile16_R1DB_P2_L1


title: HAP1_Tile16_R1DB6_P1_L1


title: HAP1_Tile16_R2DB_P2_L1


title: HAP1_Tile17_R1DB6_P2_L1


title: HAP1_Tile16_R3_P0_L1


title: HAP1_Tile18_R2_P0_L1


title: HAP1_Tile15_R1DB_P2_L1


title: HAP1_Tile15_R2DB6_P2_L1


title: HAP1_Tile15_R1DB6_P2_L1


title: HAP1_Tile15_R3DB_P2_L1


title: HAP1_Tile15_R3DB6_P1_L1


title: HAP1_Tile15_R2DB6_P1_L1


title: HAP1_Tile15_R1DB6_P1_L1


title: HAP1_Tile14_R2DB_P2_L1


title: HAP1_Tile15_R2_P0_L1


title: HAP1_Tile14_R3DB_P2_L1


title: HAP1_Tile15_R3DB6_P2_L1


title: HAP1_Tile14_R1DB_P2_L1


title: HAP1_Tile16_R2DB6_P1_L1


title: HAP1_Tile14_R2DB6_P2_L1


title: HAP1_Tile14_R1DB6_P2_L1


title: HAP1_Tile15_R1_P0_L1


title: HAP1_Tile16_R3DB_P2_L1


title: HAP1_Tile14_R2DB6_P1_L1


title: HAP1_Tile14_R3DB6_P1_L1


title: HAP1_Tile14_R3DB6_P2_L1


title: HAP1_Tile14_R1DB6_P1_L1


title: HAP1_Tile14_R2_P0_L1


title: HAP1_Tile13_R3DB6_P2_L1


title: HAP1_Tile15_R2DB_P2_L1


title: HAP1_Tile14_R1_P0_L1


title: HAP1_Tile14_R3_P0_L1


title: HAP1_Tile13_R2DB6_P2_L1


title: HAP1_Tile15_R3_P0_L1


title: HAP1_Tile13_R3DB_P2_L1


title: HAP1_Tile13_R1DB_P2_L1


title: HAP1_Tile13_R2DB_P2_L1


title: HAP1_Tile13_R1DB6_P2_L1


title: HAP1_Tile12_R3DB6_P2_L1


title: HAP1_Tile12_R1DB_P2_L1


title: HAP1_Tile12_R2DB_P2_L1


title: HAP1_Tile12_R1DB6_P2_L1


title: HAP1_Tile12_R3DB_P2_L1


title: HAP1_Tile12_R2DB6_P2_L1


title: HAP1_Tile12_R2_P0_L1


title: HAP1_Tile12_R3_P0_L1


title: HAP1_Tile11_R3DB_P2_L1


title: HAP1_Tile11_R1DB6_P2_L1


title: HAP1_Tile11_R2DB_P2_L1


title: HAP1_Tile11_R3DB6_P2_L1


title: HAP1_Tile10_R2DB6_P2_L1


title: HAP1_Tile10_R3DB6_P2_L1


title: HAP1_Tile13_R3_P0_L1


title: HAP1_Tile13_R1_P0_L1


title: HAP1_Tile13_R2_P0_L1


title: HAP1_Tile11_R2_P0_L1


title: HAP1_Tile11_R3_P0_L1


title: HAP1_Tile10_R3DB_P2_L1


title: HAP1_Tile10_R1DB6_P2_L1


title: HAP1_Tile10_R2DB_P2_L1


title: HAP1_Tile10_R1DB_P2_L1


title: HAP1_Tile11_R2DB6_P2_L1


title: HAP1_Tile10_R2_P0_L1


title: HAP1_Tile10_R1_P0_L1


title: HAP1_Tile10_R3_P0_L1


title: HAP1_Tile12_R1_P0_L1


title: HAP1_Tile11_R1_P0_L1


title: HAP1_Tile9_R1DB_P2_L1


title: HAP1_Tile9_R1DB6_P2_L1


title: HAP1_Tile9_R2DB_P2_L1


title: HAP1_Tile9_R3DB6_P2_L1


title: HAP1_Tile8_R3DB6_P2_L1


title: HAP1_Tile9_R2DB6_P2_L1


title: HAP1_Tile9_R3_P0_L1


title: HAP1_Tile16_R2_P0_L1


title: HAP1_Tile8_R2DB_P2_L1


title: HAP1_Tile8_R2DB6_P2_L1


title: HAP1_Tile11_R1DB_P2_L1


title: HAP1_Tile7_R3DB6_P2_L1


title: HAP1_Tile8_R2_P0_L1


title: HAP1_Tile8_R1DB_P2_L1


title: HAP1_Tile7_R2DB_P2_L1


title: HAP1_Tile8_R1_P0_L1


title: HAP1_Tile8_R3_P0_L1


title: HAP1_Tile9_R3DB_P2_L1


title: HAP1_Tile7_R1DB_P2_L1


title: HAP1_Tile7_R3_P0_L1


title: HAP1_Tile9_R1_P0_L1


title: HAP1_Tile7_R3DB_P2_L1


title: HAP1_Tile7_R2_P0_L1


title: HAP1_Tile8_R3DB_P2_L1


title: HAP1_Tile8_R1DB6_P2_L1


title: HAP1_Tile6_R2DB_P2_L1


title: HAP1_Tile6_R1DB6_P2_L1


title: HAP1_Tile6_R2_P0_L1


title: HAP1_Tile7_R1_P0_L1


title: HAP1_Tile6_R3DB6_P2_L1


title: HAP1_Tile6_R1DB_P2_L2


title: HAP1_Tile6_R3DB_P2_L1


title: HAP1_Tile7_R2DB6_P2_L1


title: HAP1_Tile6_R3_P0_L1


title: HAP1_Tile6_R2DB6_P2_L1


title: HAP1_Tile6_R1_P0_L1


title: HAP1_Tile7_R1DB6_P2_L1


title: HAP1_Tile5_R3DB6_P2_L1


title: HAP1_Tile5_R3DB_P2_L1


title: HAP1_Tile5_R1DB6_P2_L1


title: HAP1_Tile5_R2DB_P2_L1


title: HAP1_Tile5_R1DB_P2_L1


title: HAP1_Tile5_R3_P0_L1


title: HAP1_Tile4_R1DB_P2_L2


title: HAP1_Tile5_R2_P0_L1


title: HAP1_Tile5_R1_P0_L1


title: HAP1_Tile4_R2DB_P2_L1


title: HAP1_Tile4_R3DB_P2_L1


title: HAP1_Tile4_R2DB6_P2_L1


title: HAP1_Tile4_R3DB6_P2_L1


title: HAP1_Tile4_R3_P0_L1


title: HAP1_Tile4_R2_P0_L1


title: HAP1_Tile4_R1_P0_L1


title: HAP1_Tile3_R1_P0_L2


title: HAP1_Tile3_R3_P0_L2


title: HAP1_Tile3_R1DB_P2_L2


title: HAP1_Tile3_R2_P0_L2


title: HAP1_Tile3_R1DB6_P2_L1


title: HAP1_Tile3_R2DB_P2_L1


title: HAP1_Tile2_R1_P0_L2


title: HAP1_Tile2_R1DB_P2_L2


title: HAP1_Tile3_R3DB6_P2_L1


title: HAP1_Tile3_R3DB_P2_L1


title: HAP1_Tile2_R3DB6_P2_L1


title: HAP1_Tile2_R2DB_P2_L1


title: HAP1_Tile2_R1DB6_P2_L1


title: HAP1_Tile2_R3DB_P2_L1


title: HAP1_Tile2_R2DB6_P2_L1


title: HAP1_Tile4_R1DB6_P2_L2


title: HAP1_Tile1_R2_P0_L1


title: HAP1_Tile1_R3DB6_P2_L1


title: HAP1_Tile1_R3_P0_L1


title: HAP1_Tile2_R3_P0_L1


title: HAP1_Tile2_R2_P0_L1


title: HAP1_Tile3_R2DB6_P2_L1


title: HAP1_Tile1_R2DB6_P2_L1


title: HAP1_Tile1_R2DB_P2_L1


title: HAP1_Tile1_R1DB_P2_L2


title: HAP1_Tile1_R1_P0_L1


title: Donor_3_MSC_ChIPseq [primary human TH1 cells]

city: WEST LAFAYETTE

first: Majid

last: Kazemian

state: IN

address: 201 S. University Street

department: Biochemistry and Computer Science

institute: Purdue University

data_processing:
The expression values obtained by RSEM v1.3.1 using the following parameters (rsem-calculate-expression --no-bam-output --bowtie-n 1 --bowtie-m 100 --seed-length 28 --paired-end). Rsem index was created based on hg19.
Differentially expressed genes between any two conditions were obtained using edgeR. The raw read counts were obtained from the "expected counts" column in rsem results. The criteria for selecting differentially expressed genes are Fold Change >1.5 FDR<=0.05, and RPKM>4 in at least one of the two compared conditions.
Alignment for ChIP-seq data were generated by Bowtie1 with following parameters (bowtie --chunkmbs 1000 -S -m 1).
Peak calling for ChIP-seq data was done using macs2 2.1.2 using parameters (macs2 callpeak -f BAMPE --nomodel)
Bigwig files were generated using bamCoverage 3.2.0 with parameters (bamCoverage --normalizeUsing BPM --minMappingQuality 30 --ignoreDuplicates --extendReads 250 --blackListFileName hg19.blacklist.bed)
Genome_build: hg19
Supplementary_files_format_and_content: normalized abundance measurements (text file) include RPKM values for each sample
Supplementary_files_format_and_content: bigwig files (.bw)

source_name: primary human TH1 cells

growth_protocol: resting primary human CD4 T cells differentiated into Th1 cells were expanded in the presence of IL2 for 10 days.

extract_protocol:
For STAT3 ChIP-seq, formaldehyde-fixed human Th1 cells were sonicated using sonicator (Vibra Cell, SONICS) and resulting chromatin fragments equivalent to 10 million cells were isolated by centrifugation and STAT3 bound chromatin complexes were isolated with the anti-STAT3 antibody. For RNA-seq experiments, Total RNA isolated from human Th1 cells that were either not stimulated or stimulated with different IL-6 variants for 6 hours.
ChIP-Seq libraries were prepared using the KAPA LTP library preparation kit (Roche Sequencing) and the NextFlex DNA barcode adoptors (Bioo Scientific, PerkinElmer) for multiplexing and libraries were then sequenced on Illumina Hi-Seq 4000 platform (GeneWiz). For RNAseq, 500 ng of total RNA was used for library preparation with the KAPA mRNA HyperPrep Kit (KK8580, Roche sequencing solutions, Roche) and barcoded NEXTFLEX adapters (NOVA-514103, Perkin Elmer) for NGS Multiplexing. After final amplification of adaptor ligated PCR products were size separated using AMPure XP Bead-based Size Selection (A63880; Beckman Coulter) and eluted in 12 ul.  After quantification by Qbit 3 fluorometer (Invitrogen), 24 barcoded samples are combined into a single pulled library and sequenced at  on an Illumina HiSeq4000 platform by Genewiz Europe.

treatment_protocol: after 24 hours starvation in the absence of IL2, cells were stimulated with the different HyIL6 for 1 hour (ChIP-seq experiments) or 6 hours (RNA-seq experiments) in the presence or absence of the inhibitor (MSC2530818, CDK8 inhibitor)

tag: chip antibody

value: Human TH1 cells


title: Donor_3_HyIL6_MSC_ChIPseq [primary human TH1 cells]


title: Donor_3_Input_ChIPseq [primary human TH1 cells]

value: Input


title: Donor_3_Control_ChIPseq [primary human TH1 cells]

value: Control


title: Donor_2_HyIL6_ChIPseq [primary human TH1 cells]


title: Donor_2_Control_ChIPseq [primary human TH1 cells]


title: Donor_1_HyIL6_MSC_ChIPseq [primary human TH1 cells]


title: oe12_2907

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

data_processing:
The transcriptome reads were cleaned from adapters and low quality bases using the cutadapt program.
The genes were quantified using RSEM (with bowtie2 as an aligner and defaults otherwise)
Differentially expressed (DE) genes were identified by applying DESeq2 program.
Genome_build: Oeuropaea_451_v1.0 (https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Oeuropaea)
Supplementary_files_format_and_content: Processed data files include all genes raw reads (matrix_genes); normalized counts, batch corrected for trees using the limma package (limma_corrected_counts) and DESeq2 statistical analysis file.

organism: Olea europaea

source_name: dried tree

growth_protocol: Trees were irrigated with 1.2 litters/day

extract_protocol:
Branches were frozen and grounded in liquid nitrogene. RNA was extracted using CTAB.
RNA libraries were prepared for sequencing using an in-house developed protocol, compatible with Illumina standard protocols. Briefly poly-A transcripts were purified and fragmented. Reverse transcription and  adapter binding were performed.

treatment_protocol: Dried trees were watered in the first 2 weeks with 1 liter/week and then with no irrigations for the next 2 weeks

tag: tree

tag: day

value: branch


title: Donor_2_HyIL6_MSC_ChIPseq [primary human TH1 cells]


title: oe12_2305


title: oe12_0606


title: HAP1_Tile1_R3DB_P2_L1


title: Donor_1_MSC_ChIPseq [primary human TH1 cells]


title: HAP1_Tile5_R2DB6_P2_L1


title: HAP1_Tile1_R1DB6_P2_L1


title: Donor_1_HyIL6_ChIPseq [primary human TH1 cells]


title: oe12_0705


title: oe11_2907

source_name: watered tree


title: Donor_1_Control_ChIPseq [primary human TH1 cells]


title: Donor_1_Input_ChIPseq [primary human TH1 cells]


title: HAP1_Tile9_R2_P0_L1


title: oe11_0606


title: oe11_2305


title: Donor_3_HyIL6_MSC_RNAseq [primary human TH1 cells]


title: oe11_0705


title: Donor_3_HyIL6_ChIPseq [primary human TH1 cells]


title: Donor_3_MSC_RNAseq [primary human TH1 cells]


title: Donor_3_HyIL6_RNAseq [primary human TH1 cells]


title: Donor_2_HyIL6_MSC_RNAseq [primary human TH1 cells]


title: oe8_0705


title: oe8_0606


title: Donor_2_MSC_RNAseq [primary human TH1 cells]


title: oe9_0606


title: Donor_1_HyIL6_MSC_RNAseq [primary human TH1 cells]


title: oe9_0705


title: Donor_1_MSC_RNAseq [primary human TH1 cells]


title: Donor_2_HyIL6_RNAseq [primary human TH1 cells]


title: Donor_3_Unstimulated_RNA-seq [primary human TH1 cells]


title: oe8_2907


title: oe9_2305


title: oe4_0705


title: oe4_0606


title: Donor_1_Unstimulated_RNA-seq [primary human TH1 cells]


title: oe4_2907


title: Total lung RNA isolated from IL-31RA KO mice treated with bleomycin [Dan14]

first: Anil

last: Jegga

address: 240 Albert Sabin Way

department: Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description:
Dan14
GpD IL31RA KO-Bleo

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Lungs

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: IL-31RA KO

tag: agent

value: bleomycin


title: oe4_2305


title: oe3_0606


title: Total lung RNA isolated from IL-31RA KO mice treated with bleomycin [Dan15]

description:
Dan15
GpD IL31RA KO-Bleo


title: Total lung RNA isolated from IL-31RA KO mice treated with bleomycin [Dan16]

description:
Dan16
GpD IL31RA KO-Bleo


title: oe3_2907


title: oe3_2305


title: oe9_2907


title: oe8_2305


title: Donor_1_HyIL6_RNAseq [primary human TH1 cells]


title: oe3_0705


title: Total lung RNA isolated from IL-31RA KO mice treated with saline [Dan11]

description:
Dan11
GpC IL31RA KO-Sal

value: saline


title: Donor_2_Unstimulated_RNA-seq [primary human TH1 cells]


title: Total lung RNA isolated from IL-31RA KO mice treated with saline [Dan10]

description:
Dan10
GpC IL31RA KO-Sal


title: Total lung RNA isolated from wildtype C57BL/6 mice treated with bleomycin [Dan8]

description:
Dan8
GpB WT-Bleo

value: wildtype


title: Total lung RNA isolated from IL-31RA KO mice treated with bleomycin [Dan13]

description:
Dan13
GpD IL31RA KO-Bleo


title: Total lung RNA isolated from IL-31RA KO mice treated with saline [Dan9]

description:
Dan9
GpC IL31RA KO-Sal


title: Total lung RNA isolated from wildtype C57BL/6 mice treated with saline [Dan4]

description:
Dan4
GpA WT-Sal


title: Total lung RNA isolated from wildtype C57BL/6 mice treated with bleomycin [Dan6]

description:
Dan6
GpB WT-Bleo


title: Total lung RNA isolated from wildtype C57BL/6 mice treated with bleomycin [Dan7]

description:
Dan7
GpB WT-Bleo


title: KO_LMPP

data_processing:
Base calling performed using CASAVA 1.8
Quality control on fastq files was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read trimming and adapter removal using FastX toolkit
Alignment to mouse genome GRCm38/mm10 performed using Bowtie2 (Trapnell et. Al. Genome Biology, 2013)
Post alignment processing, QC and sorting using SAMtools, Picard and BEDtools
Peak calling using MACS2, conversion from BEDgraph to bigwig files for visualization, data visualization and checking using IGV browser.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files - an indexed binary format for graphical display of called peaks

source_name: Bone marrow derived haematopoietic progenitors (LMPPs: cKit+, Sca1+, Flt3hi) from C57/BL6 Daedalus (Linc7) knockout mice

growth_protocol: Mice deficient in the Daedalus locus were generated by injection of Cas9 RNA and chimeric guideRNAs flanking the locus (SuppTable1) into C57/B6N embryos as previously reported. The offspring of one of these mice were interbred to create a line of Daedalus deficient mice. All mice were housed and maintained under pathogen-free conditions in Yale University animal facilities. Female and male sex-matched  littermates from heterozygous crossings between 4 and 12 weeks old were used for this experiment.

extract_protocol:
Purified populations of haematopoietic progenitors were spun down in FACS medium, washed and RNA was extracted. Cells were washed once and resuspended in PBS, centrifuged again and resuspended in 50ul of lysis buffer at 4°C. The cells were centrifuged at 500g for 10 mins at 4°C, the supernatant was removed and the sample was resuspended in 5ul of Nextera transposition reaction mix and incubated at 37°C for 30 minutes.
Library amplification was performed using Nextera PCR primers and NEBNext High-Fidelity 2x PCR Master Mix, thermocycling was performed at 72°C for 5 minutes for initial primer extension, followed by at 98°C for 30 seconds and then 5 cycles of 10 seconds at 98°C, 30 seconds at 63°C and 1 minute at 72°C. The appropriate number of additional cycles was determined via qPCR using an aliquot of the PCR mix and iTaq Universal SYBR Green Supermix (BioRad). Additional amplification via PCR was performed for a number of cycles calculated from the qPCR amplification plot. Library concentration and quality was assessed using a Bioanalyzer, and sequencing performed on an Illumina HiSeq 2500.

treatment_protocol: Purified populations of haematopoietic progenitors were sorted from WT and KO littermate mice as described in the methods section. The progenitor populations sorted were gated on lineage negative cells (Lineage cocktail: B220, CD4, CD8, CD11b, CD11c, CD19, Gr1, NK1.1, TCRgd, Ter119). Three subpopulations were separated based on expression of three markers - cKit, Sca1 and Flt3/CD135, these populations are as follows Haematopoietic stem cells (HSCs: cKit+, Sca1+, Flt3-ve); multipotent progenitors (MPPs: cKit+, Sca1+ Flt3lo); lymphoid-primed multipotent progenitors (MPPs: cKit+, Sca1+ Flt3hi).

tag: genotype/variation

value: Daedalus knockout

value: Bone marrow derived haematopoietic progenitors.

value: Sorted from mice in the steady state, with no immunological challenge or disease.

tag: molecule subtype

value: ATAC Assay DNA (Nextera-amplified transposition fragments)


title: Total lung RNA isolated from wildtype C57BL/6 mice treated with bleomycin [Dan5]

description:
Dan5
GpB WT-Bleo


title: Total lung RNA isolated from wildtype C57BL/6 mice treated with saline [Dan3]

description:
Dan3
GpA WT-Sal


title: KO_HSC

source_name: Bone marrow derived haematopoietic progenitors (HSCs: cKit+, Sca1+, Flt3-ve) from C57/BL6 Daedalus (Linc7) knockout mice

tag: treatment


title: WT_LMPP

source_name: Bone marrow derived haematopoietic progenitors (LMPPs: cKit+, Sca1+, Flt3hi) from C57/BL6 Daedalus (Linc7) wildtype mice

tag: strain

value: Daedalus wildtype


title: Total lung RNA isolated from wildtype C57BL/6 mice treated with saline [Dan2]

description:
Dan2
GpA WT-Sal


title: Total lung RNA isolated from IL-31RA KO mice treated with saline [Dan12]

description:
Dan12
GpC IL31RA KO-Sal


title: WT_HSC

source_name: Bone marrow derived haematopoietic progenitors (HSCs: cKit+, Sca1+, Flt3-ve) from C57/BL6 Daedalus (Linc7) wildtype mice


title: Total lung RNA isolated from wildtype C57BL/6 mice treated with saline [Dan1]

description:
Dan1
GpA WT-Sal


title: Daedalus_KO2_HSC

description:
Sorted from mice in the steady state, with no immunological challenge or disease.
In order to better assess the transcriptomic changes resulting from ablation of the Daedalus locus we performed an RNA-seq analysis on progenitors from Daedalus KO and WT mice.
Daedalus_RNASeq_Gene_Expression.txt

data_processing:
Base calling performed using CASAVA 1.8
Quality control on fastq files was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Alignment and junction mapping to mouse genome GRCm38/mm10 performed using Tophat2 and Bowtie2 (Trapnell et. Al. Genome Biology, 2013)
Transcript quantitation, normalization and differential expression testing performed using Cufflinks ((Trapnell et. al. 2012 Nature Protocols)
Data analysis and visualization performed in R, using packages cummeRbund (http://compbio.mit.edu/cummeRbund/) and pheatmap (https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of normalized FPKM between samples

source_name: Bone marrow derived haematopoietic progenitors (HSCs: cKit+, Sca1+, Flt3-ve) from Daedalus (Linc7) knockout mice

growth_protocol: Mice deficient in the Daedalus locus were generated by injection of Cas9 RNA and chimeric guideRNAs flanking the locus (SuppTable1) into C57/B6N embryos as previously reported. The offspring of one of these mice were interbred to create a line of Daedalus deficient mice. All mice were housed and maintained under pathogen-free conditions in Yale University animal facilities. Female and male littermates from heterozygous crossings between 4 and 12 weeks old were used for this experiment.

extract_protocol:
Purified populations of haematopoietic progenitors were spun down in FACS medium, washed and RNA was extracted. Purified RNA was obtained using QIAGEN RNeasy Micro kit or Zymo-research Direct-zol RNA Microprep kit.
mRNA for RNAseq analysis was purified using PolyA+ selection and processed by the Yale Center for Genome Analysis using standard methodology using Illumina TruSeq mRNA-Seq Sample Prep Kits, library quality and concentration assayed using a Bioanalyzer, RNA was sequenced on a HiSeq2500 with 75bp pair-ended reads.

tag: cell type/tissue

value: knockout


title: Daedalus_KO1_LMPP

source_name: Bone marrow derived haematopoietic progenitors (LMPPs: cKit+, Sca1+, Flt3hi) from Daedalus (Linc7) knockout mice


title: Daedalus_KO1_MPP

source_name: Bone marrow derived haematopoietic progenitors (MPPs: cKit+, Sca1+, Flt3lo) from Daedalus (Linc7) knockout mice


title: Daedalus_KO2_MPP


title: Daedalus_WT2_LMPP

source_name: Bone marrow derived haematopoietic progenitors (LMPPs: cKit+, Sca1+, Flt3hi) from Daedalus (Linc7) wildtype mice

value: wild type


title: Daedalus_WT1_LMPP