title: HSD F1 male derived from HSD F0 male rep04

description:
Drosophila_F1_Male_J04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD


title: CMP_110_34583624

status: Public on Mar 27 2019

type: SRA

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

library_source: transcriptomic

data_processing:
RNA-Seq:Short reads were aligned to the human genome (GRCh37 assembly (hg19)) using Tophat software.
RNA-Seq: The mapping parameter ‘-g 1’ was used to allow one alignment to the reference for a given read
RNA-Seq: The featureCounts software was used to count reads on the basis of the RefSeq gene model. CPM and RPKM expression values were calculated using a script in R
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: CPM and RPKM values from RNA sequencing

molecule: polyA RNA

organism: Homo sapiens

source_name: CMP

extract_protocol:
cDNA was generated according to Smart-seq2 protocol
Illumina sequencing libraries were constructed using the Nextera XT DNA Sample Preparation kit according to manufacturer's protocol.

treatment_protocol: Cells from human bone marrow of healthy adult donors were isolated by FACS

tag: cell type

value: CMP

tag: tissue

value: Bone marrow

tag: disease

value: healthy

tag: phenotype


title: CMP_112_34605585


title: CME569: H3K9me3 ChIP-seq (C)

city: Copenhagen N

first: Daniel

middle: Martin

last: Messerschmidt

state: Zealand

address: 3C Blegdamsvej, Building 18

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

library_source: genomic

data_processing:
Raw reads were aligned to mm9 genome using Bowtie2 (default parameters), before sorting the bam files with samtools sort.
Bigwig files were generated with the bamCoverage fonction of deeptools2.0, using the options --normalizeUsing RPKM --binSize 25 --smoothLength 100.
Peaks were called with Macs2 callpeak (default parameters).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files showing the reads coverage

molecule: genomic DNA

organism: Mus musculus

source_name: E14 Embryonic Stem Cells

growth_protocol: Embryonic stem cells were cultured under standard LIF/FCS conditions.

extract_protocol:
ChIP was performed as previously described {Guccione:2007dy}. Chromatin was fragmented using a BRANSON Digital Sonifier (#S540D) to 250-1000bp fragments, precleared and incubated with antibodies overnight. Antibody/chromatin complexes were incubated for 50% Protein-G Sepharose slurry and washed before elution/decrosslinking in 1% SDS and 0.1 M NaHCO3. DNA was column purified with QIAquick PCR purification Kit, Qiagen.
ChIP DNA concentrations were measured with the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were prepared with the NEBNext Ultra II DNA Library Preparation Kit for Illumina (NEB), following manufacturer’s instructions. PCR conditions were adjusted to starting material concentrations and final elution volumes were reduced. Libraries were quantified by Bioanalyzer (High Sensitivity DNA Kit, Agilent) and PCR (KAPA Library Quantification Kit for Illumina, Roche). ChIP-Seq libraries were pooled and sequenced on the NextSeq500, as a single end (76bp) run

value: mouse embryonic stem cells

tag: antibody

value: alpha-H3K9me3, Abcam, ab8898, 3 ug


title: CME568: FLAG ChIP-seq (C)

value: alpha-FLAG, Sigma, F3165, 5ug


title: C128: 24-week HFD (liver_high fat diet_24 weeks_rep3)

type: RNA

city: Hangzhou

first: Chen

last: Zhiyun

address: No. 9, Street 9, Xiasha economic development zone, Jianggan district

country: China

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

hyb_protocol: The pre-hybridization of MOA v2 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing: The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.

molecule: total RNA

source_name: liver

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: The mice were exposed to continuous light and 12:12 h light/dark cycle, and provided with food and water ad libitum.

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: A total of 24 healthy male SPFC57BL/6 mice aged 6–8 weeks were purchased from Shanghai Sippr-BKLaboratory Animal Co. Ltd. (production license: SCXK (Hu) 2013-0016). All the mice were randomly divided into three groups after one week of adaptive feeding as follows: (i) control group (ND group, 6 mice), which was normally fed with feedstuff (21.5% protein, 12.3% fat, and 66.2% carbohydrate) produced by Jiangsu Synergic Bioengineering Co., Ltd.; (ii) high-fat diet groups (HFD group, 12 mice) were given high-fat diet (comprising 21.6% protein, 36.1% fat, 42.3% carbohydrate; 82.75% basal diet + 10% lard, 2% cholesterol, 0.25% bile salt, and 5% egg yolk powder; feedstuff was produced by Jiangsu Synergic Bioengineering Co., Ltd.)for 16-week (6 mice) and 24-week (6 mice) respectively; (iii) HFD + PTFC group (6 mice) was fed with high-fat diet for six weeks, and intragastric administration of PTFC at 50 mg kg1 d1 was performed for 18 weeks. The normal and the model groups were administered with an equal volume of 0.9% sodium chloride,exposed to continuous light and 12:12 h light/dark cycle, andprovided with food and water ad libitum. Mice in 16-week HFD group were sacriﬁced at the end of week 16. Mice in each group were sacriﬁced at the end of week 24. The mice were fasted on water for 12 h the night before later treatment. Under anesthesia, blood samples were extracted intraocularly, and liver specimens were collected. The right liver lobe was extracted and ﬁxed in 10% neutral formalde-hyde for pathological observation, and the other liver tissues werestored at -70 ℃ for RNA extraction.

tag: gender

value: male

tag: strain

value: liver

tag: development stage

value: 31~33-week age


title: CMP_11_33485595


title: CME566: INPUT (E)

source_name: FLAG-ZFP708-KDEL OE Embryonic Stem Cells (1)


title: D138: PTFC treatment (liver_hight fat dieat 24 weeks and PTFC treatment for 18 weeks_rep1)


title: CD F1 male derived from HSD F0 male rep04

city: New Delhi

first: Manoj

middle: Ramesh

last: Teltumbade

state: Delhi

address: Mathura Road, Near Sukhdev Vihar, bus depo

country: India

institute: Institute of Genomics and Integrative Biology

description:
Drosophila_F1_Male_I04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data was analysed using R/Bioconductor affy and limma packages. Quantile Normalization and RMA background correction was used.

label: biotin

organism: Drosophila melanogaster

source_name: whole fly, 14 days of treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3’ IVT Express Kit).

growth_protocol: 30 adult virgin females (and unmated males) Oregon R flies per vial fed respective diet for 14 days at 25C temperature. Media vials changed after 7 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (RNeasy Microarray Tissue Handbook).

treatment_protocol: At the end of treatment, flies were anesthetized using CO2 and collected in Trizol.

value: whole fly

tag: generation

tag: diet fed

value: CD

tag: diet of ancestral f0 males

value: HSD F0 male

tag: strain/background

value: Oregon R

tag: age

value: 14 days

tag: developmental stage

value: adult

tag: batch


title: HSD F1 male derived from HSD F0 male rep01

description:
Drosophila_F1_Male_J01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CMP_108_34598603


title: CME565: INPUT (B)

source_name: FLAG-ZFP708 OE Embryonic Stem Cells (1)


title: CMP_111_34598605


title: CD F1 male derived from HSD F0 male rep03

description:
Drosophila_F1_Male_I03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CMP_107_34597597


title: B38: 16-week HFD (liver_high fat diet_16 weeks_rep3)

value: 23~25-week age


title: C125: 24-week HFD (liver_high fat diet_24 weeks_rep1)


title: C127: 24-week HFD (liver_high fat diet_24 weeks_rep2)


title: HSD F1 male derived from HSD F0 male rep02

description:
Drosophila_F1_Male_J02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD


title: PAT4694A50

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

institute: Wellcome Trust Centre for Human Genetics

description: Count_table.txt; CPM_table.txt; TPM_table.txt

data_processing:
Real time Analysis (RTA):  HiSeq 4000 - RTA v2.73 and RTAVersion 2.7.7
Base-calling: bcl2fastq v2.17.1.14
Adapter trimming: RNA-seq reads were trimmed for SMARTer and Illumina  adapter sequences using skewer-v0.1.125
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.4 with default parameters to a modified reference genome comprising the dog genome, CanFam3.1, and fasta sequences for ERCC spike-ins
Mark Duplicates: Duplicate reads were marked using MarkDuplicates.jar implemented in Picard tools v1.92
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 81 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) and Transcripts per Million (TPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million and using ENSEMBL annotated read-lengths
Genome_build: CanFam3.1
Supplementary_files_format_and_content: Count_table.txt: raw read counts for all 24674 ENSEMBL annotated genes
Supplementary_files_format_and_content: CPM_table.txt:  Counts per million normalized counts all 24674 ENSEMBL annotated genes
Supplementary_files_format_and_content: TPM_table.txt:  Transcripts per million (gene-length and sequencing depth normalized counts) all 24674 ENSEMBL annotated genes
Supplementary_files_format_and_content: FASTQ_checksum.txt: md5sum of FASTQ files
Supplementary_files_format_and_content: QC_Table.xlsx: Contains two excel sheets with Sheet 1 = sample information with information regarding sequencing depth and mapping QC metrics
Supplementary_files_format_and_content: QC_Table.xlsx: Sheet2= Contains description of column headers of cell metadata in Sheet 1
Supplementary_files_format_and_content: Text

organism: Canis lupus familiaris

source_name: peripheral blood

extract_protocol:
Peripheral blood mononuclear cells were isolated from fresh blood through density gradient centrifugation and stained with an antibody panel consisting of DAPI, CD5, CD21, MHC II, CD11b, CADO48A, and CD14 to identify cells of interest. Cells were sorted on an BD Aria A machine, washed, and resuspended in RNA-Bee prior to RNA extraction using the Direct-zol RNA MicroPrep Kit.
low-input RNA library preparation with Smart-seq2 and Nextera XT DNA Library Prep Kit

value: peripheral blood mononuclear cells

tag: disease state

value: Cancer

value: M-MDSCs

tag: sample type

value: M-MDSC


title: B37: 16-week HFD (liver_high fat diet_16 weeks_rep2)


title: CME505: INPUT (A)

treatment_protocol: no treatment

value: mouse embryonic stem cells


title: CD F1 male derived from HSD F0 male rep02

description:
Drosophila_F1_Male_I02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CMP_106_34599595

tag: cell type

value: CMP

value: Bone marrow

value: healthy


title: HSD F1 female derived from CD F0 male rep04

description:
Drosophila_F1_Female_H04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

tag: tissue

value: CD F0 male

value: female


title: A114: ND (liver_normal diet_24 weeks_rep3)

value: male

value: liver

value: 30~32-week age


title: A112: ND (liver_normal diet_24 weeks_rep2)


title: A110: ND (liver_normal diet_24 weeks_rep1)

value: 31~33-week age


title: B34: 16-week HFD (liver_high fat diet_16 weeks_rep1)


title: CD F1 male derived from HSD F0 male rep01

description:
Drosophila_F1_Male_I01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

value: CD

value: HSD F0 male

value: Oregon R

value: 14 days

value: adult


title: PAT4694A52

value: peripheral blood mononuclear cells

value: Cancer

value: Monocytes

value: C Mono


title: PAT4694A54


title: CMP_104_34599594

value: CMP

value: Bone marrow

tag: disease

value: healthy


title: PAT4694A43

value: PMN-MDSCs

value: PMN-MDSC


title: CME503: FLAG ChIP-seq (A-1)

value: mouse embryonic stem cells

value: alpha-FLAG, Sigma, F3165, 5ug


title: CMP_103_34600594

tag: phenotype


title: PAT4694A41

value: Neutrophils

value: C PMN


title: CME564: INPUT (C)

tag: antibody


title: HSD F1 female derived from CD F0 male rep03

description:
Drosophila_F1_Female_H03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

value: HSD

value: CD F0 male

tag: gender

value: female


title: PAT4694A2

value: peripheral blood mononuclear cells


title: CMP_102_34590631


title: CME504: FLAG ChIP-seq (A-2)


title: HSD F1 female derived from CD F0 male rep01

description:
Drosophila_F1_Female_H01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: Oregon R

value: 14 days

value: adult


title: CMP_105_34605583

value: CMP


title: CMP_101_34608576

value: Bone marrow


title: PAT4694A1

value: Cancer

value: Monocytes

value: C Mono


title: CMP_100_34601604

value: healthy


title: PAT4694A42


title: HSD F1 female derived from CD F0 male rep02

description:
Drosophila_F1_Female_H02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CD F1 female derived from CD F0 male rep03

description:
Drosophila_F1_Female_G03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: CD


title: PAT4694A40

value: Neutrophils


title: CD F1 female derived from CD F0 male rep04

description:
Drosophila_F1_Female_G04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CMP_10_33498537


title: CMP_099_34588639


title: PAT4694A44

value: PMN-MDSCs

value: PMN-MDSC


title: CD F1 female derived from CD F0 male rep01

description:
Drosophila_F1_Female_G01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly


title: HSD F1 male derived from CD F0 male rep04

description:
Drosophila_F1_Male_F04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD

value: CD F0 male

value: male


title: CD F1 female derived from CD F0 male rep02

description:
Drosophila_F1_Female_G02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: Oregon R

value: female


title: PAT4694A45

value: peripheral blood mononuclear cells


title: CMP_098_34598601

value: CMP


title: PAT4694A48

value: M-MDSCs

value: M-MDSC


title: CMP_09_33483581

value: Bone marrow


title: CMP_08_33480570


title: HSD F1 male derived from CD F0 male rep03

description:
Drosophila_F1_Male_F03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: 14 days

value: adult


title: PAT4694A46

value: Cancer


title: PAT4694A39

value: Neutrophils

value: C PMN


title: CMP_07_33505531

value: healthy


title: GAR4079A49


title: CMP_05_33481569


title: HSD F1 male derived from CD F0 male rep01

description:
Drosophila_F1_Male_F01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly


title: GAR4079A55

value: Monocytes

value: C Mono


title: CMP_06_33483580


title: CD F1 male derived from CD F0 male rep03

description:
Drosophila_F1_Male_E03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: CD

value: CD F0 male

value: male


title: CD F1 male derived from CD F0 male rep04

description:
Drosophila_F1_Male_E04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: Oregon R


title: HSD F1 male derived from CD F0 male rep02

description:
Drosophila_F1_Male_F02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD


title: CMP_03_33478572

value: CMP


title: CD F1 male derived from CD F0 male rep02

description:
Drosophila_F1_Male_E02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: HSD F0 female rep04

description:
Drosophila_F0_Female_D04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: female


title: uterosacral ligament_recurrent pelvic organ prolapse_subject 2

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

country: USA

institute: University of South Dakota

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:recurrent pelvic organ prolapse, POPQ stage:stage III, sample:recurrent POP 2
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

hyb_protocol: 10 micrograms of biotinylated cRNA were mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner.

data_processing: global median normalization, CodeLink Expression Analysis 5.0

source_name: uterosacral ligament_recurrent POP_subject 2

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion from 0.75 micrograms total RNA starting material.

extract_protocol: Uterosacral ligament (USL) tissue samples were obtained at surgery.  The tissue samples were placed in RNAlater (Ambion) in the surgical suite.  For processing, RNAlater was blotted off and the USL sample was minced with scalpels, and soaked in TRI reagent for 1 hour.  The sample was homogenized in TRI reagent (MRC) with a Polytron (Brinkmann).  The samples were centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing upper layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of total RNA was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

tag: Stage

value: postmenopausal

value: uterosacral ligament (USL)

tag: treatment

tag: pathology

value: recurrent pelvic organ prolapse (POP)

tag: popq stage

value: stage III

tag: subject identifier

value: recurrent POP 2


title: GAR4079A54

description: Count_table.txt; CPM_table.txt; TPM_table.txt

value: peripheral blood mononuclear cells

value: Healthy

value: H Mono


title: CMP_02_33505530

value: Bone marrow

value: healthy


title: CMP_01_33479584


title: GAR4079A57

value: Cancer

value: Monocytes

value: C Mono


title: uterosacral ligament_recurrent pelvic organ prolapse_subject 3

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:recurrent pelvic organ prolapse, POPQ stage:stage IV, sample: recurrent POP 3
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_recurrent POP_subject 3

value: stage IV

value: recurrent POP 3


title: uterosacral ligament_recurrent pelvic organ prolapse_subject 4

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:recurrent pelvic organ prolapse, POPQ stage:stage III, sample:recurrent POP 4
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_recurrent POP_subject 4

value: recurrent POP 4


title: GAR4079A56


title: CD F1 male derived from CD F0 male rep01

description:
Drosophila_F1_Male_E01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

tag: generation

tag: diet fed

value: CD

tag: diet of ancestral f0 males

value: CD F0 male

tag: strain/background

value: Oregon R

value: male

value: 14 days

value: adult


title: GAR4079A50

value: peripheral blood mononuclear cells

tag: disease state

value: M-MDSCs

value: M-MDSC


title: HSD F0 female rep02

description:
Drosophila_F0_Female_D02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD

value: female

tag: age

tag: developmental stage

tag: batch


title: Cdx2

city: Ottawa

first: Tanya

middle: Elizabeth

last: Foley

state: ON

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

description:
ChIP'ed genomic DNA
DL_3

data_processing:
Peaks were called using the MACS software, looking for narrow peaks (transcription factors).
General strategy for narrow peaks consists of using the mfold paramter [lower bound=10, uppe boundr=30]
Sequenced reads were trimmed using fastx and aligned to the mm9 reference genome (mouse mm9, NCBI build 37) using BWA.
Annotation was performed using HOMER using RefSeq annotations.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle track formats were generated from aligned reads using FindPeaks.

extract_protocol:
Embryos from timed matings were dissected, crosslinked with 1% formaldehyde, and ChIP performed as previously described (Pilon et al., 2006) with the following modifications: chromatin was sonicated for 1-minute intervals six times using a Branson Sonifier 450 at output 3 with 30% duty cycle, and 10μg of polyclonal rabbit-anti-Cdx2 (Savory et al., 2009b) and pre-immune rabbit-anti-IgG (Sigma) was coupled to 200ul of magnetic protein G Dynabeads (Invitrogen). Samples were purified using the QIAquick PCR Purification Kit (Qiagen) and library preparation and sequencing performed by the Genome Quebec and McGill Innovation Centre using the mm9 reference genome.  ChIP experiments were performed as above using 5μg of antibody against Cdx2 (Savory et al., 2009b), or IgG control (Sigma), coupled to 50μl of protein A/G Sepharose beads (Santa Cruz). DNA purification was followed by PCR using primers directed against sequences flanking putative Cdx response elements (CDREs), identified by TRANSFAC, within genomic intervals associated with enriched Cdx2 occupancy as determined by ChIP-seq. Primers sequences are listed in Table S2.
Purified genomic DNA was sent to Genome Quebec for library construction by standard protocols for sequencing on Illumina platforms.

tag: strain background

value: Mixed

tag: tissue

value: whole embryo

tag: genotype

value: wild type

tag: chip antibody


title: IgG control

description:
ChIP'ed genomic DNA
DL_1

source_name: IgG control

value: anti-IgG


title: uterosacral ligament_primary pelvic organ prolapse_subject 3

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:primary pelvic organ prolapse, POPQ stage:stage III, sample:primary pop 3
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_primary POP_subject 3

tag: Stage

value: postmenopausal

tag: gender

value: uterosacral ligament (USL)

value: primary pelvic organ prolapse (POP)

value: stage III

value: primary pop 3


title: uterosacral ligament_primary pelvic organ prolapse_subject 1

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:primary pelvic organ prolapse, POPQ stage:stage III, sample:primary POP 1
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_primary POP_subject 1

tag: treatment

tag: pathology

value: primary POP 1


title: CD F0 female rep04

description:
Drosophila_F0_Female_C04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

value: CD

value: Oregon R

value: 14 days


title: GAR4079A51

value: peripheral blood mononuclear cells

value: Cancer

tag: cell type

value: M-MDSCs

tag: sample type

value: M-MDSC


title: uterosacral ligament_primary pelvic organ prolapse_subject 2

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:primary pelvic organ prolapse, POPQ stage:stage III, sample:primary POP 2
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_primary POP_subject 2

value: female

tag: popq stage

tag: subject identifier

value: primary POP 2


title: 33377-Mneu

city: Detroit

first: Kay-Uwe

last: Wagner

state: MI

address: 421 East Canfield, EL01TM

department: Department of Oncology

institute: Barbara Ann Karmanos Cancer Institute  Wayne State University School of Medicine

description:
MMTV-neu induced mammary tumor cells
Mneu_Jak1WT_vs_JAK1KO_all.txt

data_processing:
Sequenced reads were trimmed for adapter sequence using cutadapt
Aligned RNA-seq reads to mm10 genome with TopHat 2.1.
Assembled expressed genes and transcripts with Cufflinks 2.2
Computed gene and expression profiles that are computationally less expensive with Cuffquant
Computed normalized tables of expression values with Cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: Mammary tumor cell line

growth_protocol: Cells maintained in 5% FBS DMEMF12 media (to 950ml media we added 2.5ml 10ug/ml Insulin, 40uL of 10ng/ml EGF, 2.0ml of 5ug/ml linoleic acid complex, 1ml of 0.25units/ml fungizone, 50ml of FBS, 5ml of 100 units/ml Pen/Strep, 4.1ml of 100ug/ml hydrocortisone, 4.4ml of 1mg/ml bovine serum albumin, 1ml of 50ug/ml gentamicin, 1.2g sodimu bicarbonate, and 2ml od beta-Mercaptoethanol) under adherent conditions, 37°C and 5%CO2 incubator, Subcultivation ratio: 1:5 to 1:10, medium renewal: 2-3 times per week.

extract_protocol:
Total RNA was extracted from JAK1 deficient mammary tumor cell lines and wildtype controls expressing JAK1 using the RNeasy Mini Kit (Qiagen).
The Super-Script II kit from Invitrogen with oligo-dT primers was used to perform the first-strand synthesis according to the manufacture’s protocol. Quality control was performed using a BioAnalyzer 2100,and RNA samples were processed using the TruSeq RNA Sample kit.

treatment_protocol: Treatment with Puromycin (5ug/10ml media) of cell lines with number 45555, 47298, and 45566B.

tag: strain

value: FVB/N

tag: genetic status

value: Jak1 Wildtype

tag: type

value: Tumor-derived cell line


title: 46295-D6

value: Jak1 Knockout


title: uterosacral ligament_control_subject 3

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:endometrial hyperplasia without atypia, POPQ stage:stage I, sample:control 3
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_control_subject 3

value: postmenopausal

value: uterosacral ligament (USL)

value: endometrial hyperplasia without atypia

value: stage I

value: control 3


title: uterosacral ligament_primary pelvic organ prolapse_subject 4

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:primary pelvic organ prolapse, POPQ stage:stage III, sample:primary POP 4
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_primary POP_subject 4

value: primary pelvic organ prolapse (POP)

value: stage III

value: primary POP 4


title: GAR4079A53

value: peripheral blood mononuclear cells

tag: disease state

value: Healthy

value: Monocytes

value: H Mono


title: CD F0 female rep02

description:
Drosophila_F0_Female_C02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

tag: generation

tag: diet fed

value: CD

tag: diet of ancestral f0 males

tag: strain/background

value: Oregon R

value: female

tag: age

value: 14 days

tag: developmental stage

value: adult

tag: batch


title: 33373-Mneu

value: FVB/N

value: Jak1 Wildtype

value: Tumor-derived cell line


title: CD F0 female rep03

description:
Drosophila_F0_Female_C03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

tag: tissue

tag: gender


title: uterosacral ligament_recurrent pelvic organ prolapse_subject 1

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:recurrent pelvic organ prolapse, POPQ stage:stage III, sample:recurrent POP 1
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_recurrent POP_subject 1

tag: Stage

value: postmenopausal

value: uterosacral ligament (USL)

tag: treatment

tag: pathology

value: recurrent pelvic organ prolapse (POP)

value: recurrent POP 1


title: uterosacral ligament_control_subject 4

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:endometrial hyperplasia with atypia, POPQ stage:stage I, sample:control 4
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_control_subject 4

value: endometrial hyperplasia with atypia

tag: popq stage

value: stage I

tag: subject identifier

value: control 4


title: GAR4079A52

value: peripheral blood mononuclear cells

value: Healthy

tag: cell type

value: Monocytes

tag: sample type

value: H Mono


title: CD F0 female rep01

description:
Drosophila_F0_Female_C01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

value: CD

value: Oregon R

value: female


title: uterosacral ligament_control_subject 1

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:endometrial hyperplasia without atypia, POPQ stage:stage I, sample:control 1
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_control_subject 1

value: endometrial hyperplasia without atypia

value: control 1


title: HSD F0 male rep04

description:
Drosophila_F0_Male_B04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: HSD

value: male

value: 14 days

value: adult


title: HSD F0 female rep03

description:
Drosophila_F0_Female_D03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: 45566B-Cre-Puro

tag: strain

value: FVB/N

tag: genetic status

value: Jak1 Knockout

tag: type

value: Tumor-derived cell line


title: uterosacral ligament_control_subject 2

description:
species: human subject, stage:postmenopausal, gender:female, tissue:uterosacral ligament biopsy, treatment:none, pathology:endometrial cancer, POPQ stage:stage I, sample:control 2
Approval for the use of human subjects was obtained from the Institutional Review Board and patients provided written informed consent.

source_name: uterosacral ligament_control_subject 2

value: postmenopausal

value: uterosacral ligament (USL)

value: endometrial cancer

value: stage I

value: control 2


title: GAR4079A37

description: Count_table.txt; CPM_table.txt; TPM_table.txt

value: peripheral blood mononuclear cells

tag: disease state

value: Healthy

value: Neutrophils

value: H PMN


title: 45566B-Wt-Puro

value: Jak1 Wildtype


title: 47298-Cre-Puro

description:
MMTV-neu induced mammary tumor cells
isogenic_fpkm.txt


title: GAR4079A35


title: GAR4079A36


title: GAR4079A34


title: 47298-Wt-Puro


title: 45555-Wt-Puro


title: GAR4079A33


title: NCF-02

city: Dublin

first: Sebastian

last: Vencken

address: Catherine McAuley Centre, Nelson Street

department: Clinical Research Centre

country: Ireland

institute: University College Dublin

description:
NA
SAMPLE 12

data_processing:
Amplification curves were recorded with the Quantstudio 12K Flex software and Cts obtained. Using ExpressionStudio Version 1.1 dCts were calculated by normalising to U6 snoRNA and fold-changes between the CF and Non-CF groups were calculated.
Matrix normalised sheet reports signals normalised against U6 snoRNA. Fold Change sheet reports CF/Non-CF expression

label: FAM

source_name: Bronchial epithelium

label_protocol: BEC RNA samples were used for high-throughput miRNA expression analysis. RNA concentrations were measured using the Qubit 3.0 fluorimeter (ThermoFisher Scientific, USA) and the Qubit RNA HS Assay kit (ThermoFisher Scientific, USA).  754 miRNAs were reverse transcribed and pre-amplified as per manufacturer’s protocol using the Megaplex™ Primer Pools, Human Pools Set v3.0 (ThermoFisher Scientific, USA) combined with the TaqMan MicroRNA Reverse Transcription Kit (ThermoFisher Scientific, USA) and the TaqMan PreAmp Master Mix (ThermoFisher Scientific, USA) respectively. High throughput quantitative real-time PCR (qPCR) was performed with the TaqMan OpenArray Human MicroRNA Panels (ThermoFisher Scientific, USA) as per manufacturer’s protocol on the QuantStudio 12K Flex system (ThermoFisher Scientific, USA).

extract_protocol: Isolation of total RNA, including miRNAs, from the purified BECs was performed with the miRNeasy Micro kit (Qiagen, Switzerland). Samples were eluted in 14 µl RNase-free water.

treatment_protocol: Bronchial brushing samples were taken from CF patients during routine disease-specific clinical bronchoscopy, while brushings from non-CF patients were taken during bronchoscopy for diagnostic purposes. The bronchial brushes containing sample were immediately transferred to ice-cold Collection medium (EMEM (Gibco, USA) completed with 10 U/ml penicillin-streptomycin, 2.5 µg/ml Amphotercin B, 5 µg/ml gentamycin (Gibco, USA) and 80 µg/ml tobramycin (Calbiotech, UK)). Samples were processed on the same day. While kept on ice, tissue and mucus were visibly dislodged from the brushes into the medium. With brushes held suspended in their respective tubes, the tubes were centrifuged at 240 g for 10 minutes at 4°C. Supernatant was subsequently removed and the pellets were resuspended in 3 ml ice-cold completed Bronchial Epithelial Growth Medium (BEGM; Lonza, Switzerland). Tissue was pelleted by centrifugation at 240 g for 5 minutes at 4°C and after removing the supernatant, the pellet was resuspended in 200 µl BEGM. Blood cells were depleted by combining the EasySep Human CD45 and Human Glycophorin A immunomagnetic depletion kits (#18259 and #18352; Stemcell Technologies, Canada). To the suspension, 6 µl CD45 antibody and 15 µl GlyA antibody from these kits were added and thoroughly mixed by pipetting. The suspension was incubated on ice for 15 minutes after which 27 µl of magnetic particles were added and mixed. The mixture was incubated on the bench for 10 minutes after which it was made up to 2.5 ml with BEGM at room temperature. Magnetic particles were purified with the EasySep magnet for 10 minutes and the supernatant was decanted to a new tube. This was centrifuged at 240 g for 5 minutes at 4°C and the supernatant was removed. To the remaining pellet, 700 µl QIAzol Lysis Reagent (Qiagen, Germany) and after vortexing the lysate was stored at -80°C.

value: Paediatric primary bronchial epithelial cells

tag: group id

value: Non-CF

tag: health status

value: Recurrent respiratory tract infection

tag: genotype

value: Male

tag: age (y)


title: HSD F0 male rep02

description:
Drosophila_F0_Male_B02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

source_name: whole fly, 14 days of treatment

tag: tissue

value: whole fly

tag: generation

tag: diet fed

value: HSD

tag: diet of ancestral f0 males

tag: strain/background

value: Oregon R

value: male

tag: age

value: 14 days

tag: developmental stage

value: adult

tag: batch


title: GAR4079A39

source_name: peripheral blood

value: Cancer

tag: cell type

tag: sample type

value: C PMN


title: PCF-06

description:
ΔF508/ΔF508
SAMPLE 11

value: CF

value: Cystic fibrosis

tag: gender


title: HSD F0 male rep03

description:
Drosophila_F0_Male_B03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: CD F0 male rep04

description:
Drosophila_F0_Male_A04
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: CD


title: PCF-24b

description:
ΔF508/ΔF508
SAMPLE 10


title: GAR4079A38

value: peripheral blood mononuclear cells

value: Neutrophils


title: HSD F0 male rep01

description:
Drosophila_F0_Male_B01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.


title: GAR4079A47

value: PMN-MDSCs

value: PMN-MDSC


title: GAR4079A46


title: 45555-Cre-Puro

tag: strain

value: FVB/N

tag: genetic status

value: Jak1 Knockout

tag: type

value: Tumor-derived cell line


title: T_3h_3

city: Dalian

first: Xiufang

last: Dong

state: Liaoning

address: No.1st Qinggongyuan, Ganjingzi district

institute: Dalian Polytechnic University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: GCF_000371365.1_Musca_domestica-2.0.2_genomic.fna
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Apostichopus japonicus

source_name: Body wall

extract_protocol:
Total RNA was extracted from nine samples (three biological replicates each of CON, T_1h and T_3h) using miRNeasy mini kit (Qiagen, Duesseldorf, Germany) following the manufacturer's instructions.
Approximately 10 μg of total RNA was used for transcriptome cDNA library construction using mRNA Seq sample preparation kit (Illumina, San Diego, USA).Then we performed the paired-end sequencing on an Illumina Hiseq 4000 (LC Sciences, USA) following the manufacturer’s recommended protocol and generated a total of million paired-end reads of 150 bp length.

tag: body weight

value: Body wall


title: Parental Rep 1

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Rd Rm 2404

institute: Case Western Reserve University

description: RNA extracted from D2.OR derivatives grown in 3D culture for 7 days

data_processing:
Generated sequencing reads were assessed for quality using FastQC
The reads were trimmed for adapter sequences and low-quality nucleotides at the ends of the reads using Trim Galore
Reads that passed quality control were  aligned to the mouse genome (Mus musculus, GRCm38/mm10) using TopHat
The TopHat output was analyzed for differential expression using the Cufflinks suite of tools
Genome_build: mm8
Supplementary_files_format_and_content: .xlsx file including raw frags, internal and external scaled frags, and FKPM values for each gene from each sample and replicate

source_name: D2.OR organoids propagated in 3D-cultures for 7 days

growth_protocol: D2.OR derivatives were grown in 3D-organotypic cultures for 7 days.

extract_protocol:
Cells were non-enzymatically extracted from 3D culture using Cultrex 3D-Culture Cell Harvesting Kit (Trevigen) according to manufacturer's protocol. RNA was harvested using Trizol reagent. 1 ug of total cellular RNA was used for preparation of sequencing libraries using the TruSeq Stranded Total RNA library prep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown in DMEM supplemented with 10% FBS, 5% Cultrex, and 1% Pen/Strep. Media was replaced every other day.

tag: genotype

value: parental

value: Pre-malignant hyperplastic alveolar cells

tag: cell line


title: NCF-06

description:
NA
SAMPLE 7

value: Paediatric primary bronchial epithelial cells

tag: group id

value: Non-CF

tag: health status

value: Recurrent respiratory tract infection

value: Male

tag: age (y)


title: BORG Rep 1

value: BORG-expressing


title: Parental Rep 2


title: PCF-04

description:
ΔF508/ΔF508
SAMPLE 6

value: CF

value: Cystic fibrosis


title: T_1h_2

tag: tissue


title: GAR4079A44

value: peripheral blood mononuclear cells

tag: disease state

value: Cancer


title: NCF-05

description:
NA
SAMPLE 9

value: Recurrent wheeze, tracheomalacia


title: T_3h_2


title: BORG Rep 2


title: PCF-27

description:
ΔF508/ΔF508
SAMPLE 8


title: T_1h_3


title: T_3h_1


title: HSD F0 female rep01

description:
Drosophila_F0_Female_D01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

tag: generation

tag: diet fed

value: HSD

tag: diet of ancestral f0 males

tag: strain/background

value: Oregon R

value: female

tag: age

value: 14 days

value: adult


title: NCF-01

description:
NA
SAMPLE 4

tag: cell type

value: Asthma, malacia

tag: gender


title: CD F0 male rep01

description:
Drosophila_F0_Male_A01
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: CD

value: male

tag: developmental stage

tag: batch


title: NCF-03

description:
NA
SAMPLE 5

value: Paediatric primary bronchial epithelial cells

value: Non-CF

value: Tracheomalacia


title: GAR4079A45

value: PMN-MDSCs

tag: sample type

value: PMN-MDSC


title: GAR4079A43

value: peripheral blood mononuclear cells

value: Neutrophils

value: C PMN


title: siPTPN3_T_01

city: Hang Zhou

first: BO

last: YUAN

address: Zijingang Campus

institute: Zhejiang University

data_processing:
Sequencing reads were trimmed to 50 bp and mapped to the human genome (hg19) using Tophat v2.1.1.
Mapped reads (~95% of total reads) were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Bedgraph

growth_protocol: HaCaT cells were cultured in MEM-EBSS medium  supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using Trizol reagent.  VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (NR601-01) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with TGF-beta (2 ng/ml) for 8 hours

value: HaCaT

value: Human immortalized keratinocytes

tag: genotype/variation

value: PTPN3 KD

tag: treatment

value: TGF-beta (2 ng/ml) for 8 h


title: PCF-11

description:
ΔF508/ΔF508
SAMPLE 2

tag: group id

value: CF

value: Cystic fibrosis

tag: genotype

value: Male


title: CON_3

tag: body weight

value: Body wall


title: NCF-04

description:
NA
SAMPLE 3

tag: health status

value: Recurrent wheeze

tag: age (y)


title: GAR4079A40

tag: tissue

tag: disease state

value: Cancer


title: GAR4079A42


title: siPTPN3_01

tag: cell line

value: none (control)


title: T_1h_1


title: CD F0 male rep02

description:
Drosophila_F0_Male_A02
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

value: whole fly

tag: generation

tag: diet fed

value: CD

tag: diet of ancestral f0 males

tag: strain/background

value: Oregon R

value: male

value: 14 days

value: adult


title: PCF-28

description:
ΔF508/ΔF508
SAMPLE 1

tag: cell type

value: Paediatric primary bronchial epithelial cells

tag: gender


title: siControl_01

value: HaCaT

value: Human immortalized keratinocytes

value: Parental


title: GAR4079A48

value: peripheral blood mononuclear cells

value: PMN-MDSCs

tag: sample type

value: PMN-MDSC


title: CON_2

value: Body wall


title: GAR4079A41

value: Neutrophils

value: C PMN


title: CD F0 male rep03

description:
Drosophila_F0_Male_A03
Gene expression data using Affymetrix Drosophila Genome 2.0 array.

tag: age

tag: developmental stage

tag: batch


title: KO2 [mouse P30]

status: Public on Mar 26 2019

city: Tel Aviv

first: Boaz

last: Barak

address: 122 Sharett Bldg

country: Israel

institute: Tel Aviv University

description:
160229Fen_D16-1893
processed data file: Supplementary_Table_1_Mouse_P30_cortex_bulk_RNAseq_and_pathways_analysis.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Firecrest is the module used for image analysis.
Bustard is the module used for base calling.
Generation of Recursive Analyses Linked by Dependency (GERALD) is the module used for sequence alignment, data visualization, filtering, and alignment. The following two alignment programs work within the GERALD module: Efficient Large-Scale Alignment of Nucleotide Databases (ELAND), aligns for up to two errors from a reference for the first 32 bases, and PhageAlign.
RSEM (version 1.2.15) was used to estimate gene expression levels based on mm9 UCSC known gene annotations. The count table was imported into DESeq (version 1.10.1) for differential gene expression testing.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Supplementary_Table_1_Mouse_P30_cortex_bulk_RNAseq_and_pathways_analysis.xlsx: Excel file includes FPKM values for each sample.

source_name: Whole cortex, P30

extract_protocol:
Mice were decapitated after an isofluorane overdose and the whole cortex was dissected and snap-frozen on dry ice. Total RNA was extracted using the RNeasy Mini kit (QIAGEN) following the standard user manual.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: Gtf2i (f/f)NexCre(+/-)

value: Whole cortex

value: Postnatal day 30


title: KO1 [mouse P30]

description:
160229Fen_D16-1892
processed data file: Supplementary_Table_1_Mouse_P30_cortex_bulk_RNAseq_and_pathways_analysis.xlsx


title: KO3 [mouse P30]

description:
160229Fen_D16-1894
processed data file: Supplementary_Table_1_Mouse_P30_cortex_bulk_RNAseq_and_pathways_analysis.xlsx


title: GAR4079A58

value: Cancer

value: Monocytes

value: C Mono


title: siControl_T_01

tag: treatment

value: TGF-beta (2 ng/ml) for 8 h


title: KO2 [mouse P1]

description:
D16-3909
processed data file: Supplementary_Table_1_Mouse_P1_cortex_bulk_RNAseq_and_pathways_analysis.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Firecrest is the module used for image analysis.
Bustard is the module used for base calling.
Generation of Recursive Analyses Linked by Dependency (GERALD) is the module used for sequence alignment, data visualization, filtering, and alignment. The following two alignment programs work within the GERALD module: Efficient Large-Scale Alignment of Nucleotide Databases (ELAND), aligns for up to two errors from a reference for the first 32 bases, and PhageAlign.
RSEM (version 1.2.15) was used to estimate gene expression levels based on mm9 UCSC known gene annotations. The count table was imported into DESeq (version 1.10.1) for differential gene expression testing.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Supplementary_Table_1_Mouse_P1_cortex_bulk_RNAseq_and_pathways_analysis.xlsx: Excel file includes FPKM values for each sample.

source_name: Whole cortex, P1

value: Postnatal day 1


title: Control1 [mouse P1]

description:
D16-3905
processed data file: Supplementary_Table_1_Mouse_P1_cortex_bulk_RNAseq_and_pathways_analysis.xlsx

value: Gtf2i (f/f)NexCre(-/-)


title: Control2 [mouse P30]

description:
160229Fen_D16-1890
processed data file: Supplementary_Table_1_Mouse_P30_cortex_bulk_RNAseq_and_pathways_analysis.xlsx


title: Control1 [mouse P30]

description:
160229Fen_D16-1889
processed data file: Supplementary_Table_1_Mouse_P30_cortex_bulk_RNAseq_and_pathways_analysis.xlsx


title: KO1 [mouse P1]

description:
D16-3908
processed data file: Supplementary_Table_1_Mouse_P1_cortex_bulk_RNAseq_and_pathways_analysis.xlsx


title: KO3 [mouse P1]

description:
D16-3910
processed data file: Supplementary_Table_1_Mouse_P1_cortex_bulk_RNAseq_and_pathways_analysis.xlsx


title: Control2 [mouse P1]

description:
D16-3906
processed data file: Supplementary_Table_1_Mouse_P1_cortex_bulk_RNAseq_and_pathways_analysis.xlsx


title: Ascites of patient 1-1281

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Fragmented and biotin labeled cDNA was hybridized to Affymetrix Human Gene 1.0 ST arrays for 18 hours at 45C with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0007 fluidics protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalization using R package Affy 1.42.3
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Cells from ovarian cancer patient's ascites fluid

label_protocol: Samples were enzymatically fragmented and biotinylated using the NuGEN Applause WT-Amp ST System and Encore Biotin Module.

extract_protocol: Total RNA was extracted by Qiagen miRNEasy Mini kit according to the manufacturer's instructions.

value: ascites

tag: patient id

tag: corresponding primary tumor geo accession id


title: Control3 [mouse P1]

description:
D16-3907
processed data file: Supplementary_Table_1_Mouse_P1_cortex_bulk_RNAseq_and_pathways_analysis.xlsx

tag: tissue


title: Ascites of patient 1-1287


title: Epithelial ovarian cancer 1-1272

source_name: Frozen archival epithelial ovarian cancer tumors samples

value: epithelial ovarian cancer


title: Ascites of patient 1-1272


title: Ascites of patient 1-0996


title: Ascites of patient 1-0683


title: Ascites of patient 1-0817


title: Ascites of patient 1-1250


title: Control3 [mouse P30]

description:
160229Fen_D16-1891
processed data file: Supplementary_Table_1_Mouse_P30_cortex_bulk_RNAseq_and_pathways_analysis.xlsx


title: CON_1

tag: body weight


title: Affected female 4

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were produced using standard Illumina HiSeq equipment and software.
Reads were aligned to the mouse genome by Rsubread version 1.10.2.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene. The supplementary file GenewiseCounts.txt.gz contains the read counts for all samples combined into one file.

source_name: neural tissue

extract_protocol:
The brains to just posterior of the otic vesicle were dissected from E9.5 embryos and RNA was isolated using the RNeasy micro kit (Qiagen 74004; Germany).
RNA libraries were prepared for an Illumina HiSeq 2000 sequencer using standard Illumina TruSeq protocols.

tag: background strain

tag: genotype

tag: Sex

value: female


title: Affected female 1


title: Affected female 2


title: Control male 4

value: male


title: Control female 2


title: Control female 1


title: Control male 3


title: Control female 3


title: Control male 2


title: Control male 1


title: Mouse embryonic stem cells DKO51

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

data_processing:
Illumina Casava1.8.1 software used for basecalling
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph-format containing the genomic methylation ratios of the respective sample

source_name: Mouse embryonic stem cells

extract_protocol:
Genomic DNA was prepared following the published procedure by Mohn and colleagues (Mohn, Weber, Schübeler, & Roloff, Methods Mol Biol, 2009;507:55-64).
5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

tag: strain background

value: mixed C57BL/6 x 129

value: Mouse embryonic stem cells

value: double knock out DKO deficient for TET1 and TET2 enzymes


title: ATAC_JUN_kd2

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

data_processing:
Quality control of ATAC-seq data was performed using Fastqc v0.11.5, and then low-quality bases and adaptor contamination were trimmed by cutadapt 1.15 with default configuration
ATAC-seq reads were aligned to the hg19 genome assembly using BOWTIE2  version 2.2.6 with the --local configuration
Duplicate reads were marked by Picard Markduplicates 2.18.0
Duplicate reads and unmapped reads were removed by samtools view -f 2 -F 1804 (1.7)
BAM files were loaded into MCAS2.1.1 for peaks calling with --broad parameters and input as control.
Genome_build: hg19
Supplementary_files_format_and_content: BED6+4. 1st: chromosome, 2nd: start position of peak, 3rd: end position of peak, 4th: peak name, 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start

source_name: coronary artery smooth muscle cells

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) derived from normal human donor hearts were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications (all tested negative for mycoplasma contamination) at passage 2 and were maintained in growth-supplemented smooth muscle basal media (Lonza # CC-3182) according to the manufacturer’s instructions. All experiments were performed on HCASMCs between passages 4 and 7.

extract_protocol:
Approximately 5e4 fresh cells were collected and nuclei-enriched fractions were extracted with cold resuspension buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin). Nuclei pellets were collected by centrifugation and resuspended with transposition reaction buffer containing Tn5 transposases (Illumina Nextera). Transposition reactions were incubated at 37 °C for 30 min, followed by DNA purification using the DNA Clean-up and Concentration kit (Zymo D4013).
Libraries were amplified using Nextera barcodes and High-Fidelity polymerase (NEB M0541S) and purified using Agencourt Ampure XP beads (Beckman Coulter A63880) double-side selection (0.5X:0.9X).

treatment_protocol: TCF21 cDNA and shRNA virus were used as described before (Nurnberg, et al, Plos Genetic 2015). JUN cDNA virus was purchased from OriGene (TL320397).

value: coronary artery smooth muscle cells

tag: lines

tag: passage

value: JUN knockdown


title: ATAC_JUN_kd1

tag: cell type


title: H3K27ac_TCF21_Ctrl

data_processing:
Quality control of ChIP-seq data was performed using Fastqc v0.11.5, and then low-quality bases and adaptor contamination were trimmed by cutadapt 1.15 with default configuration
ChIP-seq reads were aligned to the hg19 genome assembly using BWA mem version 0.7.17-r1188 with the default configuration
Duplicate reads were marked by Picard MarkDuplicates 2.18.0
Duplicate reads and unmapped reads were removed by samtools view -f 2 -F 1804 (1.7)
BAM files were loaded into MCAS2.1.1 for peaks calling with --broad parameters and input as control.
Genome_build: hg19
Supplementary_files_format_and_content: BED6+4. 1st: chromosome, 2nd: start position of peak, 3rd: end position of peak, 4th: peak name, 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
Libraries were prepared with KAPA Hyper Prep kit (KK8502) per standrad instruction.

treatment_protocol: siRNA transfection was performed using Lipofectamine RNAiMAX (Life Technologies). JUN (s7659)  silencer select siRNAs were purchased from Thermo Fisher Scientific. For lentivirus transduction study, TCF21 cDNA and shRNA virus were used as described before (Nurnberg, et al, Plos Genetic 2015). JUN cDNA virus was purchased from OriGene (TL320397).

tag: antibody

value: control


title: Input_JUN

value: input control


title: DNA_S6_hifibre1

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

data_processing:
Base calling: Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.19.1.403 pipeline was used to generate the sequence data.
Data filtering: FastX Toolkit was used to trim low quality bases from the 5’ end of reads using a minimum phred threshold of 10 and minimum length of 18
Read alignment: BWA aln version 0.7.10 with default settings
Abundance measurement: FeatureCounts version 1.5.1 was used to count uniquely mapped reads (mapQ>10) at promoters, defined as +/- 3kbp from the transcription start site.
Differential methylation analysis was performed with edgeR version 3.16.5
Genome_build: GRCm38 with gene annotations from Ensembl version 77
Supplementary_files_format_and_content: Count matrices in tabular format

source_name: spleen

growth_protocol: C57Bl/6  mice were individually housed (due to mice being coprophagic, which could result in microbiome contamination) in the same room and had access to food and water ad libitum during the course of the study.

extract_protocol:
Genomic DNA was isolated using the Qiagen Dneasy Blood and Tissue Kit. Genomic DNA was fragmented by sonication in the (Diagenode Bioruptor).  1 μg of fragmented DNA underwent methyl-CpG enrichment using the MethylMiner Methylated DNA Enrichment kit (Thermo Fisher Scientific).
Methyl-CpG DNA fractions underwent sequencing library preparation with NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs). Library concentration was assayed using MultiNA bioanalyser (Japan). Barcoded libraries were pooled to equimolar ratios.

treatment_protocol: Mice were fed a control diet lacking resistant starches or a diet rich in resistant starches (high resistant starch SF11-025; Specialty Feeds). Both diets had a similar amount of protein, lipids, vitamins, sodium, potassium and sodium to potassium ratio. Acetate supplementation was given as 100 mM magnesium acetate (all Merck Millipore) in drinking water refreshed twice per week. Mice received the different diets from 3 weeks prior to minipump surgery to the end of the study.

tag: strain

tag: diet

value: high fibre


title: H3K27ac_JUN_KD


title: H3K27ac_JUN_Ctrl


title: ATAC_JUN_Ctrl

value: JUN control


title: ATAC_TCF21_kd

value: TCF21 knockdown


title: H3K27ac_TCF21_KD


title: DNA_S8_hifibre3


title: DNA_S7_hifibre2


title: ATAC_TCF21_OE

value: TCF21 overexpression


title: DNA_S4_ctrl4


title: DNA_H8_hifibre3

source_name: left ventricle


title: DNA_S16_hifibre4


title: DNA_S12_acetate2

value: acetate suppl.


title: DNA_S17_acetate3


title: DNA_S11_acetate1


title: Mouse embryonic stem cells wt4

value: wild type


title: DNA_S2_ctrl2


title: Input_TCF21


title: DNA_S3_ctrl3


title: DNA_H7_hifibre2


title: ATAC_TCF21_Ctrl

value: TCF21 control


title: DNA_H4_ctrl4


title: DNA_H2_ctrl2


title: DNA_H1_ctrl1


title: DNA_H17_acetate3


title: DNA_H11_acetate1


title: DNA_H16_hifibre4


title: DNA_H12_acetate2


title: DNA_H6_hifibre1


title: DNA_S1_ctrl1


title: LPS_35

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: LPS 100ng/ml

data_processing:
Reads were aligned to the miRBase mouse reference using the BWA read aligner
quantitation (FPKM)
Genome_build: miRBase
Supplementary_files_format_and_content: FPKM values

extract_protocol:
Total RNA (mRNA + miRNAs) was extracted using the NucleoSpin miRNA extraction kit (Macherey-Nagel; Düren, Germany) according to the manufacturer’s recommendation.
Sequencing libraries were prepared  using an Illumina HiSeq 2500 sequencer (Illumina, San Diego, CA) .

value: LPS


title: THC_LPS_39

description: THC + LPS


title: THC_37

description: THC 10uM

value: THC


title: THC_LPS_33

description: THC + LPS


title: Ctrl_34

description: Ctrl

value: Ctrl


title: CBD_LPS_38

description: CBD + LPS


title: DNA_S18_acetate4

value: male


title: Ctrl_28

description: Ctrl


title: LPS_29

description: LPS 100ng/ml


title: CBD_LPS_32

description: CBD + LPS


title: CBD_30

description: CBD 10uM

value: CBD


title: THC_LPS_27

description: THC + LPS


title: CBD_LPS_26

description: CBD + LPS


title: CBD_24

description: CBD 10uM


title: Affected female 3

value: female


title: THC_25

description: THC 10uM


title: DNA_H3_ctrl3


title: LPS_23

description: LPS 100ng/ml


title: CBD_36

description: CBD 10uM


title: CD4spleenTRM.2

city: Minneapolis

first: Milcah

last: Scott

state: MN

address: 2101 6th Street Se

department: Department of Microbiology and Immunology

institute: University of Minnesota

data_processing:
Cutadapt was used to remove the first three nucleotides of the sequencing read which were derive from the Clontech template-switching oligo. Initial quality control analysis of RNA sequencing (FASTQ) data for each sample was performed using the FastQC software (version 0.11.5).
Trimmomatic (version 0.33) was used to trim FASTQ data.
UCSC version mm10 (GRCm38, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)) was used as the mouse reference genome. HISAT2 (version 2.0.2-beta) was used to map single-end reads.
Insertion size metrics were calculated for each sample using Picard software (version 1.126) (http://picard.sourceforge.net.).  Mapping statistics are summarized in Table S4. Samtools (version 1.3_BCFTools_HTSLib) was used to sort and index the bam files.
Gene abundance estimates were generated using the Rsubread featureCounts program.
Genome_build: UCSC version mm10 (GRCm38, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)).
Supplementary_files_format_and_content: Gene abundance estimates  generated with the Rsubread featureCounts program are provided in a tab-deliminited file.

growth_protocol: P14 TCR transgenic CD8 T cells, specific for the H-2Db-restricted LCMV gp33-41 epitope, were transferred to adult naïve female C57BL/6J  mice, which were then infected with LCMV Armstrong one day later.   54 days post LCMV-Armstrong mice were sacrificed.

extract_protocol:
Sorted cells were homogenized using QIAshredder columns (QIAGEN) and RNA was extracted using an RNeasy micro kit (QIAGEN) per the manufacturer’s instructions.
Sequencing libraries were prepared using the Clontech SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit.

treatment_protocol: CD4+ CD45.1+ SMARTA TCM (CD62L+ CD69-), TEM (CD62L- CD69-) and SLO TRM (CD62L- CD69+) populations were sorted from spleen of LCMV immune chimeras using a BD FACSAria II. Isolation of TRM cells from the female reproductive tract (FRT) and small intestine epithelial and lamina propria compartment was done by enzymatic digestion. The resulting single-cell suspensions from the three different tissues were used as a source for sorting CD69+C62L- TRM cells.

value: CD4+ CD45.1+ SMARTA Spleen (SLO) TRM (CD62L- CD69+)


title: CD4spleenTRM.3


title: CD4spleenTRM.1

value: CD4+ CD45.1+ SMARTA SLO TRM (CD62L- CD69+)


title: CD4spleenTEM.3

value: CD4+ CD45.1+ SMARTA TEM (CD62L- CD69-)


title: CD4spleenTEM.2


title: THC_31

description: THC 10uM


title: CD4spleenTCM.6

value: CD4+ CD45.1+ SMARTA TCM (CD62L+ CD69-)


title: Ctrl_22

description: Ctrl


title: CD4LP69posTRM.2

value: CD4+ CD45.1+ SMARTA samll intestine lamina propria (LP) Tissue Resident Memory Cells (CD62L- CD69+) (TRM)


title: CD4spleenTCM.5


title: CD4LP69posTRM.1


title: CD4spleenTCM.3


title: CD4FRT69posTRM.3

value: CD4+ CD45.1+ SMARTA the female reproductive tract (FRT) Tissue Resident Memory Cells (CD62L- CD69+) (TRM)


title: CD4FRT69posTRM.1


title: CD4IEL69posTRM.1

value: CD4+ CD45.1+ SMARTA the small intestine epithelial (IEL) Tissue Resident Memory Cells (CD62L- CD69+) (TRM)


title: SAM24343379 Omentum BAP1 KO

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from mouse mesothelial cells

extract_protocol:
Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen) and 0.5
ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The
libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million
single end 50 bp reads.

value: mesothelial cells

tag: primary tissue

value: Omentum

value: BAP1 KO


title: SAM24343378 Omentum BAP1 KO

tag: genotype/variation


title: CD4FRT69posTRM.2


title: SAM24343380 Omentum BAP1 KO


title: SAM24343376 Omentum WT

value: WT


title: CD4IEL69posTRM.2


title: BAP1 KO

data_processing:
Illumina v1.8 software used for basecalling
Single-cell RNA-seq data were processed with an in-house analysis pipeline.  Reads were demultiplexed based on perfect matches to known 10x cell barcode  sequences. These sequences were downloaded from the 10x genomics website  (Chromium Single Cell 3' v2 kit).
A gene-barcode matrix was generated for each sample using  the Cell Ranger pipeline v2.1 from 10X Genomics. We used the following filtering criteria: 1)  Include genes with detected expression in at least 2 cells; 2) Include cells where at least 20 genes  are detected; 3) Discard cells where the count of unique molecular identifier is either less than  2000 or greater than 9000. We used Seurat v2.0 (29) for dimensionality reduction, clustering, and  visualization with default recommended parameters.
For each sample the R1 file provides the barcode representing the cell and the R2 file provides the insert sequence
Genome_build: mm10

source_name: Epidermal cells

extract_protocol:
Epidermal cells from neonates of the same genotype were pooled (Rosa26-CreERT2, n=11; Bap1fl/fl Rosa26-CreERT2, n=9) and cultured in medium M254 (Thermo Fisher Scientific) containing 1× human melanocyte growth supplement (HMGS, Thermo Fisher Scientific) with 100 nM 4-OHT for 4 days.  After 3 more days of culture without 4-OHT, cell suspensions were prepared with Accutase (Sigma) and approximately 6,000 viable cells processed for single-cell RNA-seq with the Chromium Single Cell 3’ Library and Gel bead kit v2 (10x Genomics).
cDNAs and libraries were prepared according to manufacturer instructions (10× Genomics)

value: Epidermal cells

tag: background

tag: age

value: bap1 knockout


title: SAM24338426 Skin BAP1 KO

source_name: RNA from primary mouse melanocytes

value: primary mouse melanocytes

value: Skin


title: SAM24343374 Omentum WT


title: SAM24343381 Omentum BAP1 KO


title: SAM24338428 Skin BAP1 KO


title: BAP1 WT

value: bap1 wildtype


title: SAM24343377 Omentum WT


title: SAM24338423 Skin WT


title: CD4spleenTEM.1


title: SAM24338424 Skin WT


title: SAM24338425 Skin WT


title: SAM24338427 Skin BAP1 KO


title: CD4LP69posTRM.3


title: Trpv1 replicate 4

city: Bethesda

first: Hans Juergen

last: Solinski

state: MD

address: 9000 Rockville Pike Bldg. 35, Rm. 3F143

institute: NIH/NIDCR

description: RawCountFile.txt

data_processing:
Illumina RTA version 1.18.66.3 software used for basecalling.
Data was demultiplexed with bcl2fastq version 2.17, trimmed to remove low quality read ends as well as potential adapter readthrough with trimmomatic version 0.33 ("SEEDMISMATCHES": 2, "PALINDROMECLIPTHRESHOLD": 40, "SIMPLECLIPTHRESHOLD": 15, "WINDOWSIZE": 4, "WINDOWQUALITY": 15, "LEADINGQUALITY": 3, "TRAILINGQUALITY": 3, "CROPLENGTH": 0, "HEADCROPLENGTH": 0, "MINLEN": 36, "TARGETLENGTH": 50, "STRICTNESS": 0) and mapped to the mouse genome GRCm38 using star version 2.4.2a in the two-pass mode ("FILTERINTRONMOTIFS": "RemoveNoncanonicalUnannotated", "SAMSTRANDFIELD": "None", "FILTERTYPE": "BySJout", "FILTERMULTIMAPNMAX": 10, "ALIGNSJOVERHANGMIN": 5, "ALIGNSJDBOVERHANGMIN": 3, "FILTERMISMATCHNMAX": 10, "FILTERMISMATCHNOVERLMAX": 0.3, "ALIGNINTRONMIN": 21, "ALIGNINTRONMAX": 0, "ALIGNMATESGAPMAX": 0, "WIGTYPE": "None", "WIGSTRAND": "Stranded").
featureCounts utility (Liao et al., Bioinformatics, 2014) was used to create raw per-gene read counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: A tab-delimited matrix table in .txt-format with raw per-gene read counts for Sst- and Trpv1-libraries (each in quadruplicates) is given.

source_name: DRG

growth_protocol: Mice were housed in small social groups (4-5 animals) in individually ventilated cages under 12-hour light/dark cycling and fed ad libitum.

extract_protocol:
With 3-5 weeks of age, DRG neurons were acutely dissociated from mice of both genders as described previously (Li et al., Proc Natl Acad Sci U S A, 2017). Briefly, DRG were harvested and incubated in 5 mg/mL Collagenase/Dispase (10269638001, Millipore-Sigma) for 30 minutes. Cells were mechanically dissociated and between 150-250 eGFP- or tdTomato-positive cells per mouse were hand-picked. Each picking session included one sample per genotype to potentially identify experimentally induced biases. A total of 4 independent samples per genotype were generated. Total RNA was extracted with a PicoPure™ RNA isolation kit (ThermoFisher Scientific, Waltham, MA) using the manufacturer’s instructions. cDNA was produced and amplified using the Ovation® RNA-seq system V2 (NuGEN, San Carlos, CA) according the manufacturer’s protocol.
Sequencing libraries were generated using the Nextera XT method (Illumina, San Diego, CA).

treatment_protocol: Sst-IRES-Cre and Trpv1-IRES-Cre pups at P2 were intraperitoneally injected with AAV9-CAG-FLEX-eGFP-WPRE or AAV9-CAG-FLEX-tdTomato-WPRE (10 μL, 1x1013 vg/mL).

value: dorsal root ganglion


title: SAM24343375 Omentum WT


title: Trpv1 replicate 3

description: RawCountFile.txt


title: SAM24332671 Embryo cKO_D4_4OHT

value: BAP1 knockout

value: protected BAP1 mESc

value: Embryo


title: SAM24332684 Embryo C91A_D4_4OHT

value: knock-in BAP1 C91A mutant


title: Trpv1 replicate 1

description: RawCountFile.txt


title: Trpv1 replicate 2

description: RawCountFile.txt


title: SAM24332689 Embryo dKO_D4_4OHT

value: RNF2-BAP1 double knockout


title: SAM24332681 Embryo C91A_D4

value: BAP1 C91A control


title: Sst replicate 3

description: RawCountFile.txt


title: SAM24332660 Embryo WT_D4

value: BAP1 wt


title: Sst replicate 4

description: RawCountFile.txt


title: Sst replicate 1

description: RawCountFile.txt


title: Sst replicate 2

description: RawCountFile.txt


title: SAM24332659 Embryo WT_D4


title: SAM24332668 Embryo cKO_D4

value: BAP1 knockout control


title: SAM24332690 Embryo dKO_D4_4OHT


title: SAM24332679 Embryo C91A_D4


title: T26_Th1

city: Hershey

first: Yasin

last: Uzun

state: PA

address: 700 HMC Crescent Rd

department: Department of Pediatrics

institute: Pennsylvania State University College of Medicine

data_processing:
Basecalls performed using Illumina Casava version 1.8
RNA-Seq reads were mapped to human genome (hg9) using Tophat. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses.
Transcripts were assembled using Cufflinks using mapped fragments outputted by Tophat. Ensembl (GRCh37) was used as the source of annotated genes and transcript isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: text files of FPKM matrix were generated for each cell at transcript (isoform) and gene level

source_name: Effector memory TH1 cells

extract_protocol:
TH1 and TREG cells were sorted into TRIzol-LS and total mRNA was isolated using RNeasy Micro Kit (Qiagen). Total RNA was treated with DNase (Ambion) to remove genomic DNA.
Libraries were prpared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to manufacturer's instructions. Bioanalyzer, KAPA qPCR were done before pooling libraries for sequencing on Illumina HiSeq2500 in paired-end mode with the read length of 75 nt.

tag: disease state

tag: individual

value: Peripheral Blood

value: Effector memory TH1 cells


title: CLF_PEDS0005_T2a (metastatic cell line_adherent)

city: Boston

first: Andrew

middle: Lee

last: Hong

state: MA

address: 450 Brookline Avenue, DA1514

department: Pediatric Oncology

institute: Dana-Farber / Boston Children's / Broad Institute

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: GenePattern ExpressionFileCreator v13, Robust Multi-array Average (RMA) algorithm with R2.15.3 and RMA background correction on all CEL files. Then we performed Hierarchical clustering using settings of one minus pearson correlation & linkage complete. Clustering performed at https://software.broadinstitute.org/morpheus/

source_name: cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: Cells grown in respective media until cells reached 80% confluence. Cells harvested by washing cells in PBS, scraping cells off the plate, 0.5G spin at 4C for 5 minutes, aspirate PBS and then snap freezing samples.

extract_protocol: Rneasy Plus Mini Kit

treatment_protocol: No treatment

tag: cell line

value: metastatic RMC cancer cell line (Adherent)

tag: cell source

value: pleural effusion


title: CLF_PEDS0005_T1 (primary cell line)

value: primary RMC kidney cancer cell line

value: kidney


title: SAM24332667 Embryo cKO_D4


title: SAM24332669 Embryo cKO_D4


title: T25_Th1

tag: tissue


title: SAM24332683 Embryo C91A_D4_4OHT


title: SAM24332670 Embryo cKO_D4_4OHT


title: SAM24332688 Embryo dKO_D4_4OHT


title: T24_Th1


title: T23_Treg

source_name: Effector memory TREG cells

value: Effector memory TREG cells


title: T26_Treg


title: SAM24332658 Embryo WT_D4


title: CLF_PEDS0005_T2b (metastatic cell line_suspension)

value: metastatic RMC cancer cell line (Suspension)


title: SAM24332682 Embryo C91A_D4_4OHT


title: T21_Treg


title: T22_Treg


title: T23_Th1


title: SAM24332680 Embryo C91A_D4


title: SAM24332672 Embryo cKO_D4_4OHT


title: CLF_PEDS9001_T (primary cell line)

value: primary RMC cancer cell line


title: T22_Th1


title: C14_Treg

value: control


title: C15_Treg


title: T21_Th1


title: NOX2-KO, LSC, Rep 2

city: Aurora

first: Shanshan

last: Pei

state: CO

institute: University of Colorado

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32
MAPPING - SHRiMP_2_2_3
Genome_build: GRCm38.p4 + Gencode-M6 Annotation
Supplementary_files_format_and_content: A txt file containing fpkm values of all samples

source_name: LSC from NUP98/HOXA9 + BCR/ABL leukemic mice

growth_protocol: freshly flow sorted

extract_protocol:
QIAGEN RNeasy Plus
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used for next generation sequencing library construction per manufacturer’s protocols.
mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3’-adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size.

value: Flow-sorted mouse leukemic LSC

tag: rep

value: Rep 2


title: C15_Th1


title: T25_Treg


title: C13_Treg


title: NOX2-KO, LSC, Rep 1

value: Rep 1


title: C14_Th1


title: WT, LSC, Rep 2

value: wild type


title: C13_Th1


title: T24_Treg


title: C12_Treg


title: WT, LSC, Rep 1


title: C12_Th1


title: Gplus3

city: Modena

first: Martina

last: Dori

address: Via G. Campi 287

department: Department of Life Sciences

country: Italy

institute: Center for Genome Research

data_processing:
Base calling was performed with bcl2fastq 1.8.4
Sequenced reads were trimmed for adapter sequence, then mapped to mm9 using gsnap (2014-10-09) with the support of Ensembl 67 for splice site detection and the following parameters (-d mm9 --gunzip --use-sarray=1 -B 4 -t 6 -N 1 -s Ensembl-67.ss.iit --merge-distant-samechr -n 5 -A sam -w 500000)
Unmapped reads were used to predict circular RNA using find_circ from Memczack et. al 2013; all predicted circRNAs in all cell populations were collected together and uniq ones kept to generate a reference file
circRNAs from the reference were diveded according to genomic location (ENSEMBL gene v67) in genic (if start-end base coincided with start-end of an exon) and other that included genic with start-end base falling within exon or introns, antisense and intergenic. The former were diveded into intron and exons, the latter considered a single exon. For each exon intron the RPKM value was calculated and based on sequencing of 10 candidate circRNA, RPKM threshold was chosen.
Exon-intron that fulfilled RPKM filetring were merged back together to determine the exact sequence and exon-intron structure of all expressed circRNA. The list of expressed intron/exon was then used to generate a read count table (expressed.count.table.txt) using featureCounts (Subread package v 1.6.0) with the following option: -O -s2 -Q1
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited file with the raw count for each sample, output of featureCounts. For each circRNA, the predicted start-end coordinates are provided

source_name: Newborn neurons

extract_protocol:
Brain of E14.5 embryos were dissected to remove meningies, ganglionic eminences and olofactory bulb. The isolated lateral cortex was then dissociated using the Neural Tissue Dissociation Kit with papain (Miltenyi Biotech, cat. no. 130-092-628) according to the manufacturer’s protocol and cell suspension was then sorted with a BD FACS Aria III using the reporter endogenous fluoresence. Sorted cells were kept on ice and total RNA was then extracted using the Quick RNA Mini Prep (Zymo Research, cat. no. R1054). Prior to library construction, total RNA was treated with RNaseR (Epicentre, cat. no. RNR07250)
Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, cat. no. E7760) without mRNA enrichment

value: brain lateral cortex

value: Embryonic day (E) 14.5

value: Newborn neurons


title: C11_Treg

value: Peripheral Blood


title: C11_Th1

value: Effector memory TH1 cells


title: T26_Treg_Input

data_processing:
Basecalls performed using Illumina Casava version 1.8
ChIP-Seq reads were mapped to human genome (hg9) using Bowtie2. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses.
[.wig] Aligned reads were quantified in 200bp windows along the genome
[.bed] Every subject has one input control for each cell (Th1 and Treg).
All the peaks were called using input control as the background.
Peaks were called using MACS 1.4 in default settings with FDR cutoff 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: variableStep Wiggle format text file

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using ThruPLEX® DNA-seq Kit (Rubicon Genomics) according to the protocol from the vendor. Qubit, bioanalyzer and KAPA qPCR were done before pooling for sequencing on HiSeq 2500 platform.

tag: chip antibody


title: T26_Th1_H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: T26_Th1_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: T26_Th1_Input


title: T25_Th1_H3K4me1


title: T25_Th1_Input


title: T24_Treg_Input


title: T25_Treg_H3K4me1


title: T25_Th1_H3K27ac


title: T25_Treg_H3K27ac


title: WS3 [human]

description:
WS3
processed data file: Supplementary_Table_2_Human_frontal_cortex_RNAseq_and_pathways_analysis.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Firecrest is the module used for image analysis.
Bustard is the module used for base calling.
Generation of Recursive Analyses Linked by Dependency (GERALD) is the module used for sequence alignment, data visualization, filtering, and alignment. The following two alignment programs work within the GERALD module: Efficient Large-Scale Alignment of Nucleotide Databases (ELAND), aligns for up to two errors from a reference for the first 32 bases, and PhageAlign.
RSEM (version 1.2.15) was used to estimate gene expression levels based on hg19 UCSC known gene annotations. The count table was imported into DESeq (version 1.10.1) for differential gene expression testing.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Supplementary_Table_2_Human_frontal_cortex_RNAseq_and_pathways_analysis.xlsx: Excel file includes FPKM values for each sample.

source_name: WS frontal cortex

extract_protocol:
Tissue was received from NeuroBioBank. Total RNA was extracted using the RNeasy Mini kit (QIAGEN) following the standard user manual.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease status

value: Williams syndrome

value: Frontal cortex


title: T26_Treg_H3K4me1

value: Effector memory TREG cells


title: T26_Treg_H3K27ac


title: RminusGminus1

source_name: Neural proliferative progenitor cells

value: Neural proliferative progenitor cells


title: Gplus2


title: RminusGminus3


title: RminusGminus2


title: Gplus1


title: RplusGminus3

source_name: Neural differentiative progenitor cells

value: Neural differentiative progenitor cells


title: RplusGminus1


title: T24_Treg_H3K4me1


title: WS2 [human]

description:
WS2
processed data file: Supplementary_Table_2_Human_frontal_cortex_RNAseq_and_pathways_analysis.xlsx


title: RplusGminus2


title: T25_Treg_Input


title: T24_Treg_H3K27ac


title: T24_Th1_Input


title: WS1 [human]

description:
WS1
processed data file: Supplementary_Table_2_Human_frontal_cortex_RNAseq_and_pathways_analysis.xlsx


title: Control3 [human]

description:
C3
processed data file: Supplementary_Table_2_Human_frontal_cortex_RNAseq_and_pathways_analysis.xlsx

source_name: Control frontal cortex

value: Control


title: Control1 [human]

description:
C1
processed data file: Supplementary_Table_2_Human_frontal_cortex_RNAseq_and_pathways_analysis.xlsx


title: Otel-SV40-R3-sgBLM

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

country: France

institute: Institut Curie

description: Gene expression data from BLM-depleted cells

hyb_protocol: Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip Human gene 2.0 array (Affymetrix) at 45 °C for 16–20 h. After hybridization, nonspecifically bound material was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: Raw data were treated, normalized and summarized using oligo R package.

source_name: SV40-transformed human skin fibroblasts

label_protocol: Using 100ng of total RNA, double-stranded cDNA was synthesized with random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing many copies of antisense cRNA. In the second cycle of cDNA synthesis, random hexamers are used to prime reverse transcription of the cRNA from the first cycle to produce single-stranded DNA in the sense orientation. cDNA was synthesized using the GeneChip WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix). The sense cDNA was then fragmented by uracil DNA glycosylase and apurinic/apyrimidic endonuclease-1 and biotin-labeled with terminal deoxynucleotidyl transferase using the GeneChip WT Terminal labeling kit (Affymetrix).

growth_protocol: Skin human SV40-fibroblasts were transduced by lentivirus to depleted BLM or not by CRISPR-Cas9. Cells were selected with puromycine.

extract_protocol: 48h after seeding, total RNA was extracted with Nucleospin kit and eluted in 40µl (Nanodrop quantification).

treatment_protocol: BLM-depleted or non-depleted cells were seed and allow to grow for 48h.

tag: genotype

value: KO


title: Otel-SV40-R3-EV

description: Gene expression data from non-depleted cells

value: WT


title: Otel-SV40-R2-sgBLM


title: Otel-SV40-R1-EV


title: Control2 [human]

description:
C2
processed data file: Supplementary_Table_2_Human_frontal_cortex_RNAseq_and_pathways_analysis.xlsx


title: Otel-SV40-R1-sgBLM


title: FS_IM_IL4c_14

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

data_processing:
Raw fastq data were assess for quality using FASTQC
Raw read pairs were aligned to the reference transciptome (Ensembl transcripts, release 87) using bowtie2 version 2.2.7 with parameters --very-sensitive -p 30 --no-discordant -x Mouse_REL87 –no-unal
Alignments were stored in sorted, indexed BAM files generated using samtools v1.3
Counts per transcript were extracted from the BAM files using samtools idxstats
All downstream analyses were conducted in R using Bioconductor packages.
Genome_build: Ensembl Mus musculus transcripts, release 87
Supplementary_files_format_and_content: Plain text files containing raw counts

source_name: Interstitial MO

growth_protocol: Samples generated from cells isolated from murine tissues.

extract_protocol:
Single cell suspensions were generated from the relevant murine tissues and macrophage samples were purified via FACS sorting. Each sample was lysed with RLT buffer (Qiagen) and RNA isolated with RNeasy microkits (Qiagen) according to the manufacturers instructions. Sample RNA integrity was confirmed using TapeStation (Agilent), with all samples showing RNA integrity numbers of ~8.8-10. RNA quality was assessed by Fragment Analyzer (Advanced Analytical Technologies), and 20 ng total RNA was used for each library.
RNA samples were processed with an Illumina TruSeq RNA Access Library prep kit, following the manufacturers instructions. Libraries were quantified with Qubit HS (ThermoFisher) and Fragment Analyzer (Advanced Analytical Technologies).
Indexed libraries were pooled and sequenced on an Illumina NextSeq 500 using paired-end chemistry with 75 bp read length.

treatment_protocol: Samples were from mice treated with Dulbeccos PBS (control) or IL-4 complex (IL-4c:  IL-4/anti IL-4mAb). Recombinant murine IL-4 was combined with rat IgG1 anti-IL-4 mAb 11B11 (BioXcell) at a 1:5 molecular weight ratio52. Mice were injected i.p. with 5 μg of IL-4 (complexed to 11B11) or Dulbeccos PBS on d0 and d2. Tissues were collected for cell isolation on d4 post initial injection.

tag: treatment

tag: macrophage

value: IM


title: T24_Th1_H3K27ac

tag: cell type


title: FS_IM_IL4c_15


title: T23_Treg_H3K27ac


title: T23_Treg_H3K4me1


title: T23_Treg_Input


title: T24_Th1_H3K4me1


title: T22_Treg_Input


title: T23_Th1_Input


title: T23_Th1_H3K4me1


title: FS_AM_IL4c_08

source_name: Alveolar MO

value: AM


title: FS_IM_PBS_13

value: PBS


title: FS_AM_IL4c_09


title: T22_Treg_H3K4me1


title: FS_AM_PBS_06


title: T23_Th1_H3K27ac


title: FS_AM_IL4c_07


title: T22_Th1_Input


title: T22_Treg_H3K27ac2


title: FS_AM_PBS_05


title: FS_IM_PBS_12


title: FS_PEC_IL4c_04

source_name: PEC

value: PEC


title: T22_Th1_H3K4me1


title: T22_Th1_H3K27ac


title: FS_PEC_PBS_02


title: FS_PEC_IL4c_03


title: T21_Treg_Input


title: FS_PEC_PBS_01


title: T21_Treg_H3K4me1


title: T21_Treg_H3K27ac


title: E6 YFP CD24-

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread 1.29.6.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation. Read counts were separately obtained for each exon. Supplementary files provide both gene-level and exon-level counts.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: lineage-negative tumor cells

extract_protocol:
RNA was isolated from freshly sorted cells with the miRNeasy Micro Kit (50) (Qiagen Catalog #217084).
mRNA reverse transcription cDNA libraries were prepared using either the TruSeq RNA Sample preparation kit (Illumina) or the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) following the manufacturer’s instructions.

tag: strain

tag: tumor

tag: fluorescent marker

value: YFP

value: Live lineage-negative tumor cells

tag: cell population

tag: sequencing date

tag: sample id

tag: library prepation protocol

value: TruSeq


title: E6 YFP CD24+


title: C15_Treg_H3K4me1

tag: disease state

value: control

tag: individual

value: Peripheral Blood

value: H3K4me1 (Abcam, ab8895)


title: C15_Treg_Input

tag: tissue


title: T21_Th1_H3K4me1

value: Effector memory TH1 cells


title: T21_Th1_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: T21_Th1_Input


title: E6 RFP CD24-

value: RFP


title: ATAC-seq_Bcat_PosteriorPituitary_GFPpos_R2

city: Baltimore

middle: F

last: Sabbagh

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
ATAC-seq data were aligned using Bowtie2 (Version 2.3.2 t -X 2000 --no-mixed --no-discordant) and then duplicate reads were removed (picard MarkDuplicates). Peaks were called using MACS2 (Version 2.1.1.20160309 callpeak --nomodel --keep-dup all --shift −100 --extsize 200 --call-summits) (Zhang et al., 2008). Peaks were then filtered for fold-change >2 and -log(qvalue) >2. deepTools was used to visualize ATAC-seq peaks on the browser (bamCoverage -bs 1 --normalizeUsing RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak and .bw

source_name: beta-catenin stabilized GFP-positive sorted cells from posterior pituitary

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
For ATAC-seq, ~50,000 GFP-positive FACS-sorted cells were resuspended in ice-cold lysis buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 0.1% Igepal CA-630) and immediately centrifuged at 500 x g for 10 minutes at 4° Celsius to prepare nuclei.  The resulting nuclear pellet was resuspended in a 50 ul reaction volume in Tn5 transposase and transposase reaction buffer (FC-121-1030, Illumina Inc., San Diego, CA) and the tagmentation reaction was continued for 30 minutes at 37° Celsius.
Tagmented DNA was purified using QIAGEN MinElute GelExtraction kit (28604, Qiagen). ATAC-seq libraries were PCR amplified for 11 cycles. Agencourt AMPure XP beads (A63880, Beckman Coulter) were used to purify ATAC-seq libraries, which were then paired-end sequenced for 36 cycles on a NextSeq500.

value: Tie2-GFP; Pdgfb-CreER; BcatEx3fl

tag: age

value: Adult

tag: Sex

value: Male

value: Posterior Pituitary

value: Vascular endothelial cells


title: E5 RFP CD24-


title: E5 RFP CD24+


title: ATAC-seq_WT_PosteriorPituitary_GFPpos_R2

source_name: Wild-Type GFP-positive sorted cells from posterior pituitary


title: C15_Th1_H3K4me1

tag: chip antibody


title: C15_Th1_Input


title: ATAC-seq_WT_PosteriorPituitary_GFPpos_R1

tag: genotype


title: ATAC-seq_Bcat_AnteriorPituitary_GFPpos_R2

source_name: beta-catenin stabilized GFP-positive sorted cells from anterior pituitary

value: Anterior Pituitary


title: ATAC-seq_Bcat_PosteriorPituitary_GFPpos_R1


title: C15_Th1_H3K27ac

source_name: Effector memory TH1 cells


title: C15_Treg_H3K27ac

value: Effector memory TREG cells


title: C14_Th1_Input


title: E6 RFP CD24+


title: C14_Treg_H3K27ac


title: C14_Treg_Input


title: ATAC-seq_Bcat_AnteriorPituitary_GFPpos_R1


title: ATAC-seq_WT_AnteriorPituitary_GFPpos_R1

source_name: Wild-Type GFP-positive sorted cells from anterior pituitary


title: C14_Treg_H3K4me1

source_name: Effector memory TREG cells


title: ATAC-seq_WT_AnteriorPituitary_GFPpos_R2


title: ATAC-seq_Bcat_Cerebellum_GFPpos_R2

source_name: beta-catenin stabilized GFP-positive sorted cells from cerebellum

value: Cerebellum


title: C14_Th1_H3K4me1


title: ATAC-seq_WT_Cerebellum_GFPpos_R2

source_name: Wild-Type GFP-positive sorted cells from cerebellum


title: C13_Treg_H3K4me1


title: ATAC-seq_Bcat_Cerebellum_GFPpos_R1


title: C14_Th1_H3K27ac


title: C13_Th1_Input


title: C13_Th1_H3K4me1


title: ATAC-seq_WT_Cerebellum_GFPpos_R1


title: C13_Treg_Input