title: 44L_Abemaciclib_125.0


title: GACGCC: HCC1806_Abemaciclib_1.0

status: Public on Jun 27 2019

type: SRA

city: Boston

first: Kartik

last: Subramanian

address: 200 Longwood Avenue

country: USA

institute: Harvard Medical School

description:
well: M08
barcode: GACGCC
HCC1806_Abemaciclib_1.0

library_source: transcriptomic

data_processing:
barcode and Unique moelcular identifiers (UMIs) were identified for all reads and reads not within one edit distance of a well known barcode were discarded
surviving reads were quasialigned using RapMap.
Reads per well were counted using UMI's, duplicate UMIs were discarded. Mutimapped reads were weighted by  the number of transcirpts they aligned to
Reads counts were collapsed to gene counts by adding all counts for each transcript of a gene.
Genome_build: GRch38
Supplementary_files_format_and_content: .csv file of counts for all gene identifiers that mapped to a mRNA across all 335 samples

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were plated at densitieis ranging from 500 to 2000 cells per well in a 384-well plate and allowed to adhere for 24 hours

extract_protocol:
RNA was extracted using TCL lysis buffer, samples were using universal adapters, barcodes, unique molecular identifiers, and a template switching reverse transcriptase.
Libraries were prepared using Nextera DNA kit (Illumina).
Digitial gene expression (DGE)

treatment_protocol: 24 hours after seeding cells, CDK4/6 inhibitors were added. Cells were lysed in the plates after 6 hours.

tag: cell type

value: HCC1806 breast cancer cell line

tag: cell line

tag: drug treatment

value: Abemaciclib

tag: concentration (um)

tag: time (hours)


title: 43L_Abemaciclib_150.0

data_processing:
Reads were trimmed and clipped for quality control in cutadapt v1.12
Read quality was checked for each sample using FastQC 0.11.5
High-quality reads were then aligned into BAM files through STAR 2.5.3a using the human assembly GRCh37
BAM files were imported into DEXSeq-COUNT 1.14.2 and raw counts TPM and RPKM were calculated.
Genome_build: GRch37
Supplementary_files_format_and_content: .csv file of counts for all gene identifiers that mapped to a mRNA across all samples

organism:
Homo sapiens
Mus musculus

source_name: mouse engrafted with MCF7 cells

growth_protocol: seven-week-old NU/NU nude mice were supplemented with 8 µg/ml 17ß-estradiol by adding it to their drinking water five days prior to tumor engraftment, and replacing it twice per week. Mice were engrafted with 5 x 106 MCF-7 cells 1:1 in growth factor reduced matrigel subcutaneously in each flank, and allowed to grow to ~300 mm3

extract_protocol:
Animals were sacrificed two hours after receiving the last dose. The tumors were excised and cut in half, one half was fixed in 4% formaldehyde at 4˚C and transferred to 0.1% sodium azide after 48 hours, the other flash frozen, and a thin slice from the center of the tumor was placed in RNAlater at 4˚C (Qiagen, Hilden, Germany), after 48 hours the RNAlater was aspirated, and samples were transferred to -80˚C.
Libraries were prepared using a TruSeq Stranded mRNA sample preparation kit

treatment_protocol: The animals were then randomly assigned to treatment groups, and treated daily for four days with ribociclib (150 mg/kg), palbociclib (150 mg/kg), abemaciclib (25, 75, 100, 125, or 150 mg/kg), or vehicle control (0.5% (w/v)

tag: concentration (mg/kg)


title: 43R_Abemaciclib_150.0


title: BM72 ASC

type: RNA

city: Toulouse

first: Nicolas

last: Espagnolle

address: Bâtiment INCERE 4 bis, avenue Hubert Curien

country: France

institute: STROMALab, Université de Toulouse, CNRS  ERL5311, EFS, INP-ENVT, Inserm U1031, UPS, Toulouse, France

description: Gene expression data from human cultivated  adipose tissue derived MSC during 21 days

hyb_protocol: hybridization to human U133 plus 2.0 GeneChip microarrays

scan_protocol: GeneChip scanner 3000 and software AGCC

data_processing: Expression signal values and P-values were obtained for each probe set by use of Transcriptome Analysis Console (TAC) Software.(Affymetrix) .

label: biotin

source_name: Healthy donor adipose tissue

label_protocol: Biotinylated cRNA was amplified by the small sample labelling protocol  (two cycle amplification kit, Affymetrix)

growth_protocol: ASC were cultivated with aMEM (minimum essential medium) + 10% FCS (fetal calf serum) + ciprofloxacin during 21 days,

extract_protocol: Use of Rneasy kit (Qiagen). RNA purity and integrity was checked by use of Bioanalyzer 2100 (Agilent).

treatment_protocol: no treatment

tag: disease

value: Healthy donor

value: cultivated adipose tissue derived MSC


title: CJP57 ASC

source_name: MM adipose tissue

value: multiple myeloma


title: CTGGCG: PDX1258_Alvocidib_1.0

description:
well: M06
barcode: CTGGCG
PDX1258_Alvocidib_1.0

value: PDX1258 breast cancer PDX

value: Alvocidib


title: GACCGC: PDX1258_Ribociclib_1.0

description:
well: M07
barcode: GACCGC
PDX1258_Ribociclib_1.0

value: Ribociclib


title: 42R_Abemaciclib_100.0


title: CTCCCG: BT549_Ribociclib_1.0

description:
well: M04
barcode: CTCCCG
BT549_Ribociclib_1.0

value: BT549 breast cancer cell line


title: 46L_Abemaciclib_150.0


title: 42L_Abemaciclib_100.0


title: 41R_Palbociclib_150.0

value: Palbociclib


title: CGTCCG: BT549_Abemaciclib_1.0

description:
well: M02
barcode: CGTCCG
BT549_Abemaciclib_1.0


title: CGGGAG: T47D_Alvocidib_0.1

description:
well: L22
barcode: CGGGAG
T47D_Alvocidib_0.1

value: T47D breast cancer cell line


title: 40R_Palbociclib_150.0


title: CGGCAC: T47D_Abemaciclib_0.1

description:
well: L20
barcode: CGGCAC
T47D_Abemaciclib_0.1


title: 39R_Ribociclib_150.0


title: CGGAGC: PDXHCI002_Alvocidib_0.1

description:
well: L19
barcode: CGGAGC
PDXHCI002_Alvocidib_0.1

value: PDXHCI002 breast cancer PDX


title: 39L_Ribociclib_150.0


title: 38L_Ribociclib_150.0


title: CGCTCG: PDXHCI002_Ribociclib_0.3

description:
well: L18
barcode: CGCTCG
PDXHCI002_Ribociclib_0.3


title: CGCGAC: MCF7_Alvocidib_0.1

description:
well: L16
barcode: CGCGAC
MCF7_Alvocidib_0.1

value: MCF7 breast cancer cell line


title: CGCCTC: MCF7_Ribociclib_0.3

description:
well: L15
barcode: CGCCTC
MCF7_Ribociclib_0.3


title: 38R_Ribociclib_150.0


title: 37L_Vehicle

value: Vehicle


title: 37R_Vehicle


title: CTGCGG: PDX1258_Abemaciclib_1.0

description:
well: M05
barcode: CTGCGG
PDX1258_Abemaciclib_1.0


title: CGCCAG: MCF7_Abemaciclib_0.1

description:
well: L14
barcode: CGCCAG
MCF7_Abemaciclib_0.1


title: CGAGCG: Hs578T_Ribociclib_0.3

description:
well: L12
barcode: CGAGCG
Hs578T_Ribociclib_0.3

value: Hs578T breast cancer cell line


title: 35R_Abemaciclib_100.0


title: CGCAGG: Hs578T_Alvocidib_0.1

description:
well: L13
barcode: CGCAGG
Hs578T_Alvocidib_0.1


title: 35L_Abemaciclib_100.0


title: 34R_Abemaciclib_75.0


title: CGTGGG: BT549_Alvocidib_1.0

description:
well: M03
barcode: CGTGGG
BT549_Alvocidib_1.0


title: 40L_Palbociclib_150.0


title: CCTGCG: HCC1806_Alvocidib_0.1

description:
well: L10
barcode: CCTGCG
HCC1806_Alvocidib_0.1


title: CGGCTG: T47D_Ribociclib_0.3

description:
well: L21
barcode: CGGCTG
T47D_Ribociclib_0.3


title: 34L_Abemaciclib_75.0


title: CCGGGT: PDX1258_Alvocidib_0.1

description:
well: L07
barcode: CCGGGT
PDX1258_Alvocidib_0.1


title: 33L_Abemaciclib_25.0


title: CGCGTG: PDXHCI002_Abemaciclib_0.1

description:
well: L17
barcode: CGCGTG
PDXHCI002_Abemaciclib_0.1


title: CCGGTG: HCC1806_Abemaciclib_0.1

description:
well: L08
barcode: CCGGTG
HCC1806_Abemaciclib_0.1


title: 32L_Abemaciclib_25.0


title: CCGCAG: PDX1258_Abemaciclib_0.1

description:
well: L05
barcode: CCGCAG
PDX1258_Abemaciclib_0.1


title: CCCGGA: BT549_Alvocidib_0.1

description:
well: L04
barcode: CCCGGA
BT549_Alvocidib_0.1


title: CCCGAG: BT549_Ribociclib_0.3

description:
well: L03
barcode: CCCGAG
BT549_Ribociclib_0.3


title: 31R_Palbociclib_150.0


title: 36R_Palbociclib_150.0


title: CCGCGA: PDX1258_Ribociclib_0.3

description:
well: L06
barcode: CCGCGA
PDX1258_Ribociclib_0.3


title: 31L_Palbociclib_150.0


title: 30R_Abemaciclib_125.0


title: CCCCCA: BT549_Abemaciclib_0.1

description:
well: L02
barcode: CCCCCA
BT549_Abemaciclib_0.1


title: 36L_Palbociclib_150.0


title: 30L_Abemaciclib_125.0


title: 29L_Abemaciclib_75.0


title: 29R_Abemaciclib_75.0


title: CGACGG: Hs578T_Abemaciclib_0.1

description:
well: L11
barcode: CGACGG
Hs578T_Abemaciclib_0.1


title: 33R_Abemaciclib_25.0


title: CCTCGG: HCC1806_Ribociclib_0.3

description:
well: L09
barcode: CCTCGG
HCC1806_Ribociclib_0.3


title: CGGCGT: T47D_Ribociclib_3.16

description:
well: K22
barcode: CGGCGT
T47D_Ribociclib_3.16


title: CGCTGC: PDXHCI002_Ribociclib_3.16

description:
well: K19
barcode: CGCTGC
PDXHCI002_Ribociclib_3.16


title: CGGACG: T47D_Palbociclib_1.0

description:
well: K20
barcode: CGGACG
T47D_Palbociclib_1.0


title: CGGCCA: T47D_Abemaciclib_0.3

description:
well: K21
barcode: CGGCCA
T47D_Abemaciclib_0.3


title: 28R_Abemaciclib_75.0


title: 26R_Vehicle


title: CGCGGT: PDXHCI002_Abemaciclib_0.3

description:
well: K18
barcode: CGCGGT
PDXHCI002_Abemaciclib_0.3


title: 28L_Abemaciclib_75.0


title: CGCCCT: MCF7_Abemaciclib_0.3

description:
well: K15
barcode: CGCCCT
MCF7_Abemaciclib_0.3


title: CGCCGA: MCF7_Ribociclib_3.16

description:
well: K16
barcode: CGCCGA
MCF7_Ribociclib_3.16


title: 26L_Vehicle


title: CGCACC: MCF7_Palbociclib_1.0

description:
well: K14
barcode: CGCACC
MCF7_Palbociclib_1.0


title: 27R_Ribociclib_150.0


title: CGACCC: Hs578T_Abemaciclib_0.3

description:
well: K12
barcode: CGACCC
Hs578T_Abemaciclib_0.3


title: 25L_Vehicle


title: CCTGGC: Hs578T_Palbociclib_1.0

description:
well: K11
barcode: CCTGGC
Hs578T_Palbociclib_1.0


title: 24L_Vehicle


title: 24R_Vehicle


title: 25R_Vehicle


title: 32R_Abemaciclib_25.0


title: CGCGCA: PDXHCI002_Palbociclib_1.0

description:
well: K17
barcode: CGCGCA
PDXHCI002_Palbociclib_1.0


title: CCGTGC: HCC1806_Ribociclib_3.16

description:
well: K10
barcode: CCGTGC
HCC1806_Ribociclib_3.16


title: 23R_Abemaciclib_125.0


title: CGAGGC: Hs578T_Ribociclib_3.16

description:
well: K13
barcode: CGAGGC
Hs578T_Ribociclib_3.16


title: CCGTCG: HCC1806_Abemaciclib_0.3

description:
well: K09
barcode: CCGTCG
HCC1806_Abemaciclib_0.3


title: 23L_Abemaciclib_125.0


title: 27L_Ribociclib_150.0


title: CCGGCA: HCC1806_Palbociclib_1.0

description:
well: K08
barcode: CCGGCA
HCC1806_Palbociclib_1.0


title: CCGGAC: PDX1258_Ribociclib_3.16

description:
well: K07
barcode: CCGGAC
PDX1258_Ribociclib_3.16


title: 21R_Abemaciclib_100.0


title: 21L_Abemaciclib_100.0


title: CCCTGG: PDX1258_Palbociclib_1.0

description:
well: K05
barcode: CCCTGG
PDX1258_Palbociclib_1.0


title: CCGAGG: PDX1258_Abemaciclib_0.3

description:
well: K06
barcode: CCGAGG
PDX1258_Abemaciclib_0.3


title: 20R_Vehicle


title: 18R_Vehicle


title: CCCCTG: BT549_Ribociclib_3.16

description:
well: K04
barcode: CCCCTG
BT549_Ribociclib_3.16


title: 20L_Vehicle


title: CCCAGC: BT549_Palbociclib_1.0

description:
well: K02
barcode: CCCAGC
BT549_Palbociclib_1.0


title: 18L_Vehicle


title: CCCCGT: BT549_Abemaciclib_0.3

description:
well: K03
barcode: CCCCGT
BT549_Abemaciclib_0.3


title: 17R_Ribociclib_150.0


title: 16R_Abemaciclib_25.0


title: CAGCGC: T47D_Abemaciclib_1.0

description:
well: J21
barcode: CAGCGC
T47D_Abemaciclib_1.0


title: 17L_Ribociclib_150.0


title: 16L_Abemaciclib_25.0


title: AGGGCG: PDXHCI002_Abemaciclib_1.0

description:
well: J18
barcode: AGGGCG
PDXHCI002_Abemaciclib_1.0


title: CACGCG: T47D_Abemaciclib_3.16

description:
well: J20
barcode: CACGCG
T47D_Abemaciclib_3.16


title: 15L_Abemaciclib_150.0


title: 14R_Ribociclib_150.0


title: 14L_Ribociclib_150.0


title: CACCGG: PDXHCI002_DMSO_0.0

description:
well: J19
barcode: CACCGG
PDXHCI002_DMSO_0.0

value: DMSO


title: AGGCGG: PDXHCI002_Abemaciclib_3.16

description:
well: J17
barcode: AGGCGG
PDXHCI002_Abemaciclib_3.16


title: AGCCGC: MCF7_Abemaciclib_1.0

description:
well: J15
barcode: AGCCGC
MCF7_Abemaciclib_1.0


title: 13R_Ribociclib_150.0


title: ACGGCC: MCF7_Abemaciclib_3.16

description:
well: J14
barcode: ACGGCC
MCF7_Abemaciclib_3.16


title: AGCGCC: MCF7_DMSO_0.0

description:
well: J16
barcode: AGCGCC
MCF7_DMSO_0.0


title: 13L_Ribociclib_150.0


title: ACGCGC: Hs578T_DMSO_0.0

description:
well: J13
barcode: ACGCGC
Hs578T_DMSO_0.0


title: ACCCGG: Hs578T_Abemaciclib_3.16

description:
well: J11
barcode: ACCCGG
Hs578T_Abemaciclib_3.16


title: CAGGCC: T47D_DMSO_0.0

description:
well: J22
barcode: CAGGCC
T47D_DMSO_0.0


title: ACCGCG: Hs578T_Abemaciclib_1.0

description:
well: J12
barcode: ACCGCG
Hs578T_Abemaciclib_1.0


title: CTCTCC: HCC1806_Abemaciclib_1.0

description:
well: J09
barcode: CTCTCC
HCC1806_Abemaciclib_1.0


title: GGACCA: HCC1806_DMSO_0.0

description:
well: J10
barcode: GGACCA
HCC1806_DMSO_0.0


title: TTGTCC: PDX1258_DMSO_0.0

description:
well: J07
barcode: TTGTCC
PDX1258_DMSO_0.0


title: TTTGGC: HCC1806_Abemaciclib_3.16

description:
well: J08
barcode: TTTGGC
HCC1806_Abemaciclib_3.16


title: AB3746 (MARS ssRNAseq)

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: To comply with the institutional review board, the raw files for human samples have been uploaded to the European Genome-phenome Archive (EGA) at the European Bioinformatics Institute (EBI).

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: biopsy

growth_protocol: Biopsies from visceral adipose tissue from the omental depot (OAT) were obtained from five obese individuals and one lean donor with participant informed consent obtained after the nature and possible consequences of the studies were explained under protocols approved by the Institutional Review Boards of the Perelman School of Medicine at the University of Pennsylvania, the Children’s Hospital of Philadelphia, or the Tel Aviv Sourasky Medical Center.

extract_protocol:
The obese donors underwent bariatric surgery, the lean donor underwent cholecystectomy. OAT samples were placed in 1 mL of DMEM, and finely minced under sterile conditions before digestion in 50 mL of DMEM with 3 mg/1 mL collagenase IV (Gibco). Samples were incubated at 37°C in a rotating oven for 20-60 min. Adipocyte and stromal vascular fractions (SVF) were separated by centrifugation, and red blood cells (RBCs) were removed from the SVF by histopaque gradient (Sigma).
Single-cell RNA-sequencing libraries were prepared using the MARS-seq pipeline, and sequenced on the MiSeq 500 or HiSeq 2500 Sequencing System (Illumina).

tag: tissue

value: omental adipose tissue

tag: organ

value: OAT

value: total immune cells

tag: selection marker

tag: infection

tag: gender

value: female

tag: bmi

tag: replicate id

value: OAT_CD45_obese _4 _9

tag: age (years)


title: AB3747 (MARS ssRNAseq)

value: OAT_CD45_obese _5 _10


title: AB3749 (MARS ssRNAseq)

value: OAT_CD45_obese _5 _12


title: 15R_Abemaciclib_150.0

value: Abemaciclib


title: DAH170 (10x ssRNAseq)

data_processing:
10x genomics pipeline
Genome_build: hg38
Supplementary_files_format_and_content: compressed, tab-delimited text files for barcodes, features and single cell gene expression matrix

growth_protocol: Biopsies from visceral adipose tissue from the omental depot (OAT) were obtained from an obese individual with participant informed consent obtained after the nature and possible consequences of the studies were explained under protocols approved by the Institutional Review Boards of the Perelman School of Medicine at the University of Pennsylvania, the Children’s Hospital of Philadelphia, or the Tel Aviv Sourasky Medical Center.

extract_protocol:
The obese donor underwent bariatric surgery. OAT samples were placed in 1 mL of DMEM, and finely minced under sterile conditions before digestion in 50 mL of DMEM with 3 mg/1 mL collagenase IV (Gibco). Samples were incubated at 37°C in a rotating oven for 20-60 min. Adipocyte and stromal vascular fractions (SVF) were separated by centrifugation, and red blood cells (RBCs) were removed from the SVF by histopaque gradient (Sigma).
Single-cell RNA-sequencing libraries were prepared using the Chromium platform (10x genomics), and sequenced on the HiSeq 2500 Sequencing System (Illumina).

value: EAT

value: whole adipose tissue


title: DAH170_55 (10x ssRNAseq)


title: AB3743 (MARS ssRNAseq)

value: OAT_CD45_obese _4 _6


title: AB3748 (MARS ssRNAseq)

value: OAT_CD45_obese _5 _11


title: TCGAAG: PDX1258_Abemaciclib_1.0

description:
well: J06
barcode: TCGAAG
PDX1258_Abemaciclib_1.0

value: PDX1258 breast cancer PDX


title: AB3745 (MARS ssRNAseq)

value: OAT_CD45_obese _4 _8


title: AB3744 (MARS ssRNAseq)

value: OAT_CD45_obese _4 _7


title: GTCAAG: BT549_Abemaciclib_1.0

description:
well: J03
barcode: GTCAAG
BT549_Abemaciclib_1.0

value: BT549 breast cancer cell line


title: GTGACT: BT549_DMSO_0.0

description:
well: J04
barcode: GTGACT
BT549_DMSO_0.0

value: DMSO


title: TCCAAC: PDX1258_Abemaciclib_3.16

description:
well: J05
barcode: TCCAAC
PDX1258_Abemaciclib_3.16


title: AB3742 (MARS ssRNAseq)

value: omental adipose tissue

value: male

value: OAT_CD45_obese _3 _5


title: AB3741 (MARS ssRNAseq)

value: OAT

value: total immune cells

value: OAT_CD45_obese _3 _3


title: AB3740 (MARS ssRNAseq)

value: OAT_CD45_obese _3 _2


title: GGCAAT: BT549_Abemaciclib_3.16

description:
well: J02
barcode: GGCAAT
BT549_Abemaciclib_3.16

value: Abemaciclib


title: AB3739 (MARS ssRNAseq)

value: OAT_CD45_obese _3 _1


title: CAGCCG: T47D_Alvocidib_1.0

description:
well: I22
barcode: CAGCCG
T47D_Alvocidib_1.0

value: T47D breast cancer cell line

value: Alvocidib


title: CACGGC: T47D_DMSO_0.0

description:
well: I21
barcode: CACGGC
T47D_DMSO_0.0


title: AB3687 (MARS ssRNAseq)

value: OAT_CD45_obese _3 _4


title: CACCCC: T47D_Ribociclib_1.0

description:
well: I20
barcode: CACCCC
T47D_Ribociclib_1.0

value: Ribociclib


title: AGGGGC: PDXHCI002_Alvocidib_1.0

description:
well: I19
barcode: AGGGGC
PDXHCI002_Alvocidib_1.0

value: PDXHCI002 breast cancer PDX


title: AB3593 (MARS ssRNAseq)

value: OAT_CD45_CTL _1 _5


title: AB3591 (MARS ssRNAseq)

value: OAT_CD45_CTL _1 _2


title: AGGCCC: PDXHCI002_DMSO_0.0

description:
well: I18
barcode: AGGCCC
PDXHCI002_DMSO_0.0

value: DMSO


title: AB3592 (MARS ssRNAseq)

value: omental adipose tissue

value: OAT_CD45_CTL _1 _3


title: AB3590 (MARS ssRNAseq)

value: male

value: OAT_CD45_CTL _1 _1


title: AGCGGG: PDXHCI002_Ribociclib_1.0

description:
well: I17
barcode: AGCGGG
PDXHCI002_Ribociclib_1.0


title: AGCCCG: MCF7_Alvocidib_1.0

description:
well: I16
barcode: AGCCCG
MCF7_Alvocidib_1.0

value: MCF7 breast cancer cell line


title: ACGGGG: MCF7_DMSO_0.0

description:
well: I15
barcode: ACGGGG
MCF7_DMSO_0.0


title: ACCGGC: Hs578T_Alvocidib_1.0

description:
well: I13
barcode: ACCGGC
Hs578T_Alvocidib_1.0

value: Hs578T breast cancer cell line


title: ACCCCC: Hs578T_DMSO_0.0

description:
well: I12
barcode: ACCCCC
Hs578T_DMSO_0.0


title: ACGCCG: MCF7_Ribociclib_1.0

description:
well: I14
barcode: ACGCCG
MCF7_Ribociclib_1.0


title: GTACCG: Hs578T_Ribociclib_1.0

description:
well: I11
barcode: GTACCG
Hs578T_Ribociclib_1.0


title: AB3584 (MARS ssRNAseq)

value: OAT

value: total immune cells

value: OAT_CD45_obese _1 _3


title: AB3583 (MARS ssRNAseq)

value: OAT_CD45_obese _1 _2


title: AB3588 (MARS ssRNAseq)

value: female

value: OAT_CD45_obese _2 _9


title: AB3586 (MARS ssRNAseq)

value: OAT_CD45_obese _2 _7


title: AB3587 (MARS ssRNAseq)

value: OAT_CD45_obese _2 _8


title: CCTTCC: HCC1806_Alvocidib_1.0

description:
well: I10
barcode: CCTTCC
HCC1806_Alvocidib_1.0

value: HCC1806 breast cancer cell line

value: Alvocidib


title: TCTGCA: PDX1258_Alvocidib_1.0

description:
well: I07
barcode: TCTGCA
PDX1258_Alvocidib_1.0

value: PDX1258 breast cancer PDX


title: TAGTGG: PDX1258_DMSO_0.0

description:
well: I06
barcode: TAGTGG
PDX1258_DMSO_0.0

value: DMSO


title: TTCCTC: HCC1806_Ribociclib_1.0

description:
well: I08
barcode: TTCCTC
HCC1806_Ribociclib_1.0

value: Ribociclib


title: Az2_d22

city: Reykjavik

first: Zuzana

last: Budkova

address: Vatnsmyrarvegi 14

department: BioMedical Center, School of Health Sciences

country: Iceland

institute: University of Iceland

data_processing:
Kallisto v0.43
Sleuth
Genome_build: Ensembl 83
Supplementary_files_format_and_content: Kallist h5 or tsv abundance measurements

source_name: VA10, a bronchial epithelial cell line

growth_protocol: Cells cultured in Transwell filter inserts with DMEM/F12 supplemented with 2%UltroserG

extract_protocol:
RNA extracted with standard Trizol protocol.
Libraries were prepared according to Illumina's instructions for HiSeq 2500

treatment_protocol: Medium replaced 3x/week with addition of AZM or ethanol control.

value: bronchial epithelial cell line

tag: passages

tag: time point (days)


title: CCAACC: HCC1806_DMSO_0.0

description:
well: I09
barcode: CCAACC
HCC1806_DMSO_0.0

tag: cell type


title: GTTCGA: PDX1258_Ribociclib_1.0

description:
well: I05
barcode: GTTCGA
PDX1258_Ribociclib_1.0

tag: cell line


title: Az3_d22


title: Az2_d10


title: Az1_d22


title: AB3589 (MARS ssRNAseq)

description: To comply with the institutional review board, the raw files for human samples have been uploaded to the European Genome-phenome Archive (EGA) at the European Bioinformatics Institute (EBI).

value: omental adipose tissue

value: OAT_CD45_obese _2 _10


title: GTACAC: BT549_Alvocidib_1.0

description:
well: I04
barcode: GTACAC
BT549_Alvocidib_1.0

value: BT549 breast cancer cell line

tag: drug treatment


title: AB3585 (MARS ssRNAseq)

value: OAT

value: male

value: OAT_CD45_obese _1 _4


title: GGGATT: BT549_DMSO_0.0

description:
well: I03
barcode: GGGATT
BT549_DMSO_0.0

tag: concentration (um)


title: Az1_d10


title: GCTTAC: BT549_Ribociclib_1.0

description:
well: I02
barcode: GCTTAC
BT549_Ribociclib_1.0

tag: time (hours)


title: Az3_d10


title: Az2_d4


title: CGACTT: T47D_Palbociclib_0.1

description:
well: H21
barcode: CGACTT
T47D_Palbociclib_0.1

value: T47D breast cancer cell line

value: Palbociclib


title: Az1_d4


title: Ctrl1_d22


title: CAAGCT: PDXHCI002_Palbociclib_0.1

description:
well: H18
barcode: CAAGCT
PDXHCI002_Palbociclib_0.1

value: PDXHCI002 breast cancer PDX


title: Ctrl3_d10


title: CATGGT: T47D_Alvocidib_0.1

description:
well: H20
barcode: CATGGT
T47D_Alvocidib_0.1


title: ATCGAG: PDXHCI002_Alvocidib_0.1

description:
well: H17
barcode: ATCGAG
PDXHCI002_Alvocidib_0.1


title: Ctrl1_d10


title: Ctrl2_d10


title: Ctrl3_d4


title: TTGGAT: MCF7_Palbociclib_0.1

description:
well: H15
barcode: TTGGAT
MCF7_Palbociclib_0.1

value: MCF7 breast cancer cell line


title: Ctrl2_d4


title: ACCGTA: MCF7_Abemaciclib_0.1

description:
well: H16
barcode: ACCGTA
MCF7_Abemaciclib_0.1

value: Abemaciclib


title: Ctrl1_d4


title: TTTTCT: MCF7_Alvocidib_0.1

description:
well: H14
barcode: TTTTCT
MCF7_Alvocidib_0.1


title: TTTTAG: Hs578T_Abemaciclib_0.1

description:
well: H13
barcode: TTTTAG
Hs578T_Abemaciclib_0.1

value: Hs578T breast cancer cell line


title: TTTCAA: Hs578T_Palbociclib_0.1

description:
well: H12
barcode: TTTCAA
Hs578T_Palbociclib_0.1


title: Az3_d4


title: TTTATG: Hs578T_Alvocidib_0.1

description:
well: H11
barcode: TTTATG
Hs578T_Alvocidib_0.1

value: Alvocidib


title: 7_diff155_49_C8

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence using Trimmomatic v0.33 with arguments -threads 10 input.1.fastq.gz input.2.fastq.gz output.1.trimmed.fastq.gz output.1U.trimmed.fastq.gz output.2.trimmed.fastq.gz output.2U.trimmed.fastq.gz ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:30
Trimmed and high quality reads were aligned using STAR v2.4.2a on index created using hg19 genome assembly and Ensembl 74 annotation. Software parameters are as follows STAR --runThreadN 10 --runMode alignReads --genomeDir hg19 --genomeLoad LoadAndKeep --readFilesCommand zcat --outFilterIntronMoti fs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 80000000000 --outFileNamePrefix output.STAR. --readFilesIn output.1.trimmed.fastq.gz output.2.trimmed.fastq.gz
Normalized bigwig tracks were generated using Bedtools genomeCoverageBed program with parameters genomeCoverageBed -ibam input.bam -split -bg -g hg19.fa.fai -scale no_mapped_reads > output.bg and then bedgraph files were converted to bigwig files using UCSC tools bedGraphToBigWig utility
SubRead v1.5.0 package was use to assign read pairs to genes and generate count tables. The following parameters were used: featureCounts -T 10 -p -s 1 –primary -t exon -g gene_id -a annotation.gtf -o counts.tsv input.bam
Sequenced reads were quasi-mapped and gene expression was quantified using sailfish v0.10.0 using Gencode v19 annotation as index. The following parameters were used: sailfish quant -i gencode.v19.index -o outdir -p 12 -1 input.1.fastq.gz -2 input.2.fastq.gz –enforceLibCompat -g gencode.v19.index.genes –numBootstraps 20 –biasCorrect -l IU
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: LUHMES-derived neurons

growth_protocol: LUHMES cells were cultured and differentiated according to published protocol (Shah et al., 2016).

extract_protocol:
Total RNA was isolated from all generated cell lines at day 9 of differentiation using either an RNeasy Mini kit or an AllPrep DNA/RNA Mini kit (Qiagen). Genomic DNA contamination was removed with a DNA-free kit (Ambion) and remaining DNA-free RNA was tested for purity using PCR for GAPDH genomic locus. Total RNA was tested on 2100 Bioanalyzer (Agilent Technologies) to ensure a RIN quality higher than 9 and quantified using Nanodrop.
Equal amounts of total RNA (1 µg to 2.5 µg) were taken forward for library preparation and ERCC RNA Spike-in control mixes (Ambion) were added according to manufacturer guide. Ribosomal RNA was depleted using the Ribo-Zero Gold rRNA Removal module (Epicentre, Illumina) and isolated mRNA was tested for purity on 2100 Bioanalyzer (Agilent Technologies). mRNA was quantified with Qubit and equal amounts used for cDNA synthesis and 3’ terminal tagging using ScriptSeq v2 RNA-seq library preparation kit (Epicentre, Illumina). The library was PCR amplified to add adaptors and barcodes.
ScriptSeq v2 RNA-seq library preparation kit

treatment_protocol: Cells were modified using CRISPR system for KO and infected with lentiviruses carrying MeCP2 for OE.

value: LUHMES-derived neurons

tag: cell line name

value: OE R306C

tag: differentiation

tag: developmental stage

tag: mecp2 expression level


title: TTTAAC: HCC1806_Abemaciclib_0.1

description:
well: H10
barcode: TTTAAC
HCC1806_Abemaciclib_0.1

value: HCC1806 breast cancer cell line


title: CGATTG: T47D_Abemaciclib_0.1

description:
well: H22
barcode: CGATTG
T47D_Abemaciclib_0.1


title: 11_diff156_49_C8

tag: tissue


title: 12_diff156_50_B8

value: OE R111G


title: 3_diff154_49_C8


title: 8_diff155_50_B8


title: CATCAG: PDXHCI002_Abemaciclib_0.1

description:
well: H19
barcode: CATCAG
PDXHCI002_Abemaciclib_0.1


title: TTGTTA: HCC1806_Palbociclib_0.1

description:
well: H09
barcode: TTGTTA
HCC1806_Palbociclib_0.1


title: Ctrl2_d22

value: bronchial epithelial cell line


title: TTCTAA: HCC1806_Alvocidib_0.1

description:
well: H08
barcode: TTCTAA
HCC1806_Alvocidib_0.1


title: TTCATA: PDX1258_Abemaciclib_0.1

description:
well: H07
barcode: TTCATA
PDX1258_Abemaciclib_0.1

value: PDX1258 breast cancer PDX


title: 4_diff154_50_B8


title: 10_diff156_33_C10

value: OE 11x


title: TTATGT: PDX1258_Palbociclib_0.1

description:
well: H06
barcode: TTATGT
PDX1258_Palbociclib_0.1


title: TTAGAA: BT549_Abemaciclib_0.1

description:
well: H04
barcode: TTAGAA
BT549_Abemaciclib_0.1

value: BT549 breast cancer cell line


title: TTATCA: PDX1258_Alvocidib_0.1

description:
well: H05
barcode: TTATCA
PDX1258_Alvocidib_0.1


title: 6_diff155_33_C10


title: TTACTA: BT549_Palbociclib_0.1

description:
well: H03
barcode: TTACTA
BT549_Palbociclib_0.1


title: TTAAGA: BT549_Alvocidib_0.1

description:
well: H02
barcode: TTAAGA
BT549_Alvocidib_0.1


title: 9_diff156_32_A8

value: OEC


title: CCGATT: T47D_Palbociclib_1.0

description:
well: G22
barcode: CCGATT
T47D_Palbociclib_1.0


title: 1_diff154_32_A8


title: h_MeCP2_OE_Syn_E5_105

value: OE 4x


title: CAGTCA: T47D_Ribociclib_0.1

description:
well: G20
barcode: CAGTCA
T47D_Ribociclib_0.1

value: T47D breast cancer cell line

value: Ribociclib


title: h_MeCP2_OE_Syn_E5_104


title: 5_diff155_32_A8


title: CCACAT: T47D_Palbociclib_3.16

description:
well: G21
barcode: CCACAT
T47D_Palbociclib_3.16

value: Palbociclib


title: AGGGAT: PDXHCI002_Palbociclib_3.16

description:
well: G18
barcode: AGGGAT
PDXHCI002_Palbociclib_3.16

value: PDXHCI002 breast cancer PDX


title: h_MeCP2_OE_Syn_E5_103


title: CACCAA: PDXHCI002_Palbociclib_1.0

description:
well: G19
barcode: CACCAA
PDXHCI002_Palbociclib_1.0


title: h_MeCP2_OE_Syn_E5_102


title: h_MeCP2_OE_Syn_E4_105


title: AGACCT: PDXHCI002_Ribociclib_0.1

description:
well: G17
barcode: AGACCT
PDXHCI002_Ribociclib_0.1


title: TCTTTC: MCF7_Palbociclib_1.0

description:
well: G16
barcode: TCTTTC
MCF7_Palbociclib_1.0

value: MCF7 breast cancer cell line


title: CT-17

city: nanjing

first: siyu

last: chen

address: #639 longmian avenue

country: China

institute: China Pharmaceutical University

description: RNA expression in the liver of mice subjected to 6-week constant darkness and collected at CT-17

data_processing:
Quality of RNA libraries was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA).
Library sequencing was performed on HiSeq 3000 sequencing platform (Illumina Company, USA).
All sequenced reads were trimmed for adaptor sequence, were masked for low-complexity or low-quality sequence, and then were mapped to reference genome GRCm38 (mm10) using Tophat (Version 2.0.13), allowing only unique alignments (read-mismatches = 2, read-gap-length = 2).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene ID and expression level in reads count for each sample

organism: Mus musculus

growth_protocol: Male C57BL/6J mice were maintained in a 12 h light:dark cycle and in a temperature- and humidity-controlled environment.

extract_protocol:
Liver samples were pooled, and total RNA was extracted with Trizol reagent (Invitrogen).
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq3000 by a 2X150 bp run.

treatment_protocol: For fasting/re-feeding experiments, male C57BL/6J mice were either fed ad libitum, or subjected to 16-h fasting (from ZT9 to ZT1 the next day) or 16-h fasting followed by 20-h re-feeding. For constant darkness experiments, male C57BL/6J mice were maintained under LD for 1 week and subsequently subjected to DD for 6 weeks.

value: Liver

tag: strain

tag: Sex

value: male


title: 2_diff154_33_C10

value: LUHMES-derived neurons


title: CT-9

description: RNA expression in the liver of mice subjected to 6-week constant darkness and collected at CT-9


title: TTTTGA: MCF7_Palbociclib_3.16

description:
well: G15
barcode: TTTTGA
MCF7_Palbociclib_3.16


title: CT-5

description: RNA expression in the liver of mice subjected to 6-week constant darkness and collected at CT-5


title: h_MeCP2_OE_Syn_E4_102


title: fasted-refed

description: RNA expression in the liver of mice subjected to 16-h fasting followed by 20-h re-feeding


title: TTTGTA: MCF7_Ribociclib_0.1

description:
well: G14
barcode: TTTGTA
MCF7_Ribociclib_0.1


title: h_MeCP2_OE_Syn_E4_104


title: CT-1

description: RNA expression in the liver of mice subjected to 6-week constant darkness and collected at circadian time (CT)-1


title: TTTACA: Hs578T_Ribociclib_0.1

description:
well: G11
barcode: TTTACA
Hs578T_Ribociclib_0.1

value: Hs578T breast cancer cell line


title: TTGATT: HCC1806_Palbociclib_1.0

description:
well: G10
barcode: TTGATT
HCC1806_Palbociclib_1.0

value: HCC1806 breast cancer cell line


title: RRBS Chr4-cl WT (2i + Vit. C)

city: Bethesda

first: Gernot

last: Wolf

state: Maryland

address: 6 Center Drive

department: NICHD

institute: NIH

library_source: genomic

data_processing:
Reads were processed using Trim Galore (--illumina --paired –rrbs) to trim bad quality bases and adaptors. Additionally, the first 5 nt of R2 and the last 3 nt of R1 and R2 were trimmed.
Reads were then mapped to the reference genome (mm9) using Bismark (Krueger and Andrews, 2011) to extract methylation calling results
Genome_build: mm9
Supplementary_files_format_and_content: Interval files with coordinates of CpG sites and methylation status

molecule: genomic DNA

source_name: ES cells

growth_protocol: ES cells were grown in either standard ES cell media containing 20% FCS and LIF or for one week in 2i media containing vitamin C as described previously (Blaschke et al., 2013)

extract_protocol:
Genomic DNA was purified from WT and Chr4-cl KO ES cells using the Quick-gDNA purification kit (Zymo Research).
Libraries were constructed with the NEXTflex™ Bisulfite-Seq Kit (Bioo Scientific) using MspI digestion to fragment DNA.

value: ES cells

tag: genotype/variation

value: Chr4-cl WT

tag: growth condition

value: 2i + Vitamin C


title: h_MeCP2_OE_CMV_E6_104

value: OE 11x


title: CT-21

description: RNA expression in the liver of mice subjected to 6-week constant darkness and collected at CT-21


title: Chr13.2-cl KO B6 ES cells #80

data_processing:
Reads were aligned to the mouse reference genome using Tophat (--I 200000 --g 1)
Mapped reads were converted to bigwig files with DeepTools (--normalizeUsing RPKM --ignoreDuplicates).
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files

source_name: Embryonic stem cells

growth_protocol: ES cells were grown in DMEM supplemented with 20% FCS and LIF or in 2i media as indicated in the sample information.

extract_protocol:
Total RNA from ES cells was purified and depleted from genomic DNA using the RNeasy Plus minikit (Qiagen). Tissues were lysed using TRIzol reagent and RNA was purified after Isopropanol precipitation with RNeasy columns (Qiagen)
RNA libraries were prepared for sequencing using the TruSeq RNA Sample Prep Kit v2 (Illumina) or the SureSelect mRNA sequencing kit (Agilent) and polyA enrichment.

value: Embryonic stem cells

value: Chr13.2-cl KO/KO

tag: media

value: 20% FCS


title: Chr13.2-cl WT B6 ES cells #18

value: Chr13.2-cl WT


title: h_MeCP2_OE_CMV_E6_102


title: h_MeCP2_OE_CMV_E6_105


title: ad-libitum

description: RNA expression in the liver of mice fed ad libitum

source_name: fed ad libitum


title: TTTCTT: Hs578T_Palbociclib_1.0

description:
well: G13
barcode: TTTCTT
Hs578T_Palbociclib_1.0


title: TTTAGT: Hs578T_Palbociclib_3.16

description:
well: G12
barcode: TTTAGT
Hs578T_Palbociclib_3.16


title: Chr13.2-cl WT B6 ES cells #69


title: RRBS Chr4-cl KO (serum)

value: Chr4-cl KO

value: serum


title: Chr13.1-cl KO B6 ES cells #65

value: Chr13.1-cl KO/KO


title: Chr13.1-cl KO B6 ES cells #14


title: Chr13.1-cl WT B6 ES cells #10

value: Chr13.1-cl WT


title: h_MeCP2_OE_CMV_C10_105


title: TTGAAA: HCC1806_Palbociclib_3.16

description:
well: G09
barcode: TTGAAA
HCC1806_Palbociclib_3.16

value: Palbociclib


title: CT-13

description: RNA expression in the liver of mice subjected to 6-week constant darkness and collected at CT-13

value: Liver

value: male


title: TTCAAT: HCC1806_Ribociclib_0.1

description:
well: G08
barcode: TTCAAT
HCC1806_Ribociclib_0.1

value: Ribociclib


title: Chr10-cl KO B6 ES cells #76

value: Chr10-cl KO/KO


title: h_MeCP2_OE_CMV_C10_103

value: LUHMES-derived neurons


title: Chr10-cl KO B6 ES cells #34


title: fasted

description: RNA expression in the liver of mice subjected to 16-h fasting (from ZT9 to ZT1 the next day)


title: Chr13.2-cl KO B6 ES cells #90


title: h_MeCP2_OE_CMV_E6_103


title: TTATAC: PDX1258_Palbociclib_3.16

description:
well: G06
barcode: TTATAC
PDX1258_Palbociclib_3.16

value: PDX1258 breast cancer PDX


title: Chr4-cl KO B6 ES cells #1

value: Chr4-cl KO/KO


title: TTAGTT: PDX1258_Ribociclib_0.1

description:
well: G05
barcode: TTAGTT
PDX1258_Ribociclib_0.1


title: h_MeCP2_OEC_CMV_A8_105

value: OEC


title: h_MeCP2_OE_CMV_C10_102

value: OE 11x


title: TTACAT: BT549_Palbociclib_1.0

description:
well: G04
barcode: TTACAT
BT549_Palbociclib_1.0

value: BT549 breast cancer cell line


title: Chr4-cl KO B6 ES cells #8

value: Embryonic stem cells

value: 20% FCS


title: h_MeCP2_OE_CMV_C10_104


title: Chr4-cl WT B6 ES cells #16

value: Chr4-cl WT


title: h_MeCP2_OEC_CMV_A8_103


title: Chr4-cl KO B6/129 ES cells #6


title: Chr4-cl KO B6/129 ES cells #41


title: TTATTG: PDX1258_Palbociclib_1.0

description:
well: G07
barcode: TTATTG
PDX1258_Palbociclib_1.0


title: h_MeCP2_OEC_CMV_A8_104


title: Chr10-cl WT B6 ES cells #46

value: Chr10-cl WT


title: Chr4-cl WT B6/129 ES cells #49


title: Chr4-cl WT B6/129 ES cells #26


title: TTAAAG: BT549_Ribociclib_0.1

description:
well: G02
barcode: TTAAAG
BT549_Ribociclib_0.1


title: Chr4-cl WT B6 ES cells #14


title: h_MeCP2_KO_H4_105


title: Chr13.1-cl WT B6 ES cells #7


title: TGATAA: T47D_Palbociclib_3.16

description:
well: F22
barcode: TGATAA
T47D_Palbociclib_3.16

value: T47D breast cancer cell line


title: TTAATC: BT549_Palbociclib_3.16

description:
well: G03
barcode: TTAATC
BT549_Palbociclib_3.16


title: h_MeCP2_OE_Syn_E4_103

value: OE 4x


title: TGAATA: T47D_Ribociclib_1.0

description:
well: F21
barcode: TGAATA
T47D_Ribociclib_1.0


title: h_MeCP2_KO_H4_103


title: h_MeCP2_KO_H4_104


title: TCTATA: T47D_Abemaciclib_0.1

description:
well: F20
barcode: TCTATA
T47D_Abemaciclib_0.1

value: Abemaciclib


title: Chr10-cl WT B6 ES cells #25


title: TCTAAT: PDXHCI002_Palbociclib_3.16

description:
well: F19
barcode: TCTAAT
PDXHCI002_Palbociclib_3.16

value: PDXHCI002 breast cancer PDX

value: Palbociclib


title: h_MeCP2_KO_D10_105


title: TCAATT: PDXHCI002_Ribociclib_1.0

description:
well: F18
barcode: TCAATT
PDXHCI002_Ribociclib_1.0

value: Ribociclib


title: TCAAAA: PDXHCI002_Abemaciclib_0.1

description:
well: F17
barcode: TCAAAA
PDXHCI002_Abemaciclib_0.1


title: h_MeCP2_KO_D10_104


title: h_MeCP2_KO_D10_103


title: h_MeCP2_KO_D10_102


title: TATTCA: MCF7_Palbociclib_3.16

description:
well: F16
barcode: TATTCA
MCF7_Palbociclib_3.16

value: MCF7 breast cancer cell line


title: h_MeCP2_KO_H4_102

value: LUHMES-derived neurons


title: TATCTA: MCF7_Abemaciclib_0.1

description:
well: F14
barcode: TATCTA
MCF7_Abemaciclib_0.1


title: h_MeCP2_OEC_CMV_A8_102


title: TATTAC: MCF7_Ribociclib_1.0

description:
well: F15
barcode: TATTAC
MCF7_Ribociclib_1.0


title: TATCAT: Hs578T_Palbociclib_3.16

description:
well: F13
barcode: TATCAT
Hs578T_Palbociclib_3.16

value: Hs578T breast cancer cell line


title: h_MeCP2_ctr_E10_103

value: WT


title: h_MeCP2_ctr_E10_105


title: h_MeCP2_ctr_E10_102


title: TATACT: Hs578T_Ribociclib_1.0

description:
well: F12
barcode: TATACT
Hs578T_Ribociclib_1.0


title: TAGATA: HCC1806_Palbociclib_3.16

description:
well: F10
barcode: TAGATA
HCC1806_Palbociclib_3.16

value: HCC1806 breast cancer cell line


title: h_Mecp2_KO_H4_76


title: h_Mecp2_KO_H4_74


title: TATAAG: Hs578T_Abemaciclib_0.1

description:
well: F11
barcode: TATAAG
Hs578T_Abemaciclib_0.1


title: TACAAA: PDX1258_Palbociclib_3.16

description:
well: F07
barcode: TACAAA
PDX1258_Palbociclib_3.16

value: PDX1258 breast cancer PDX


title: h_Mecp2_KO_D10_76


title: h_Mecp2_KO_D10_74


title: TAATCT: PDX1258_Ribociclib_1.0

description:
well: F06
barcode: TAATCT
PDX1258_Ribociclib_1.0


title: h_Mecp2_KO_H4_70


title: TACATT: HCC1806_Abemaciclib_0.1

description:
well: F08
barcode: TACATT
HCC1806_Abemaciclib_0.1


title: TAACTT: BT549_Palbociclib_3.16

description:
well: F04
barcode: TAACTT
BT549_Palbociclib_3.16

value: BT549 breast cancer cell line


title: h_Mecp2_KO_D10_72


title: h_Mecp2_KO_D10_70


title: TAACAA: BT549_Ribociclib_1.0

description:
well: F03
barcode: TAACAA
BT549_Ribociclib_1.0


title: h_Mecp2_ctr_E10_76


title: h_MeCP2_ctr_E10_104


title: h_Mecp2_ctr_E10_74


title: TAAACA: BT549_Abemaciclib_0.1

description:
well: F02
barcode: TAAACA
BT549_Abemaciclib_0.1


title: TGAAAT: T47D_Abemaciclib_0.3

description:
well: E22
barcode: TGAAAT
T47D_Abemaciclib_0.3


title: TCTTAA: T47D_DMSO_0.0

description:
well: E21
barcode: TCTTAA
T47D_DMSO_0.0

value: DMSO


title: h_Mecp2_ctr_E10_72


title: TCATTA: T47D_Abemaciclib_3.16

description:
well: E20
barcode: TCATTA
T47D_Abemaciclib_3.16


title: h_Mecp2_ctr_E10_70


title: TCATAT: PDXHCI002_Abemaciclib_0.3

description:
well: E19
barcode: TCATAT
PDXHCI002_Abemaciclib_0.3


title: h_KD_scrambled_control_2_43

value: SC


title: Input Chr4-cl WT B6/129 ES cells #26.

data_processing:
Reads were mapped using Bowtie or Bowtie2, as indicated in the sample information.
Mapped reads were converted to bigwig files with DeepTools (--normalizeUsing RPGC --ignoreDuplicates).
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig coverage files

source_name: B6/129 ES cells

growth_protocol: ES cells were grown on feeder MEFs in standard ES cell media containing 20% FCS and LIF or in 2i media as indicated in the sample information.

extract_protocol:
Native chromatin was purified and immunoprecipitated as described previously (Karimi et al., 2011). Cross-linked ChIP was performed as described previously (references are given in the sample information).
Illumina Truseq (Chr2-cl WT and KO ES cells) or DNA SMART kit (Takara) (all other samples)

value: Chr4-cl WT

value: ES cells

tag: culture media

value: 20% FCS

tag: chip antibody

value: n/a (Input)

tag: ChIP

value: ChIP (O'Geen et al.)

tag: mapping

value: Bowtie (-5 3 --best)


title: TAGAAT: HCC1806_Ribociclib_1.0

description:
well: F09
barcode: TAGAAT
HCC1806_Ribociclib_1.0

tag: cell type

tag: cell line

tag: drug treatment


title: h_Mecp2_KO_H4_72

tag: cell line name


title: Input Chr4-cl KO B6/129 ES cells #6.

value: Chr4-cl KO


title: TATTTG: PDXHCI002_DMSO_0.0

description:
well: E18
barcode: TATTTG
PDXHCI002_DMSO_0.0

value: PDXHCI002 breast cancer PDX

tag: concentration (um)

tag: time (hours)


title: h_KD_scrambled_control_2_42

tag: differentiation

tag: developmental stage

tag: mecp2 expression level


title: Input Chr4-cl KO B6/129 ES cells #41

tag: strain

value: Native ChIP


title: Input Chr4-cl KO B6 testis (2 weeks)

source_name: B6 testis

tag: genotype/variation

value: testis

value: ChIP (Khil et al. 2012)


title: h_KD_scrambled_control_2_41

tag: tissue

value: LUHMES-derived neurons


title: TATTGT: PDXHCI002_Abemaciclib_3.16

description:
well: E17
barcode: TATTGT
PDXHCI002_Abemaciclib_3.16

value: Abemaciclib


title: h_KD_scrambled_control_2_40


title: TAATAG: PDX1258_Abemaciclib_0.1

description:
well: F05
barcode: TAATAG
PDX1258_Abemaciclib_0.1

value: PDX1258 breast cancer PDX


title: Input Chr4-cl KO B6/129 ES cells #6


title: Input Chr4-cl WT B6/129 ES cells #49


title: h_Mecp2_overexpressed_2_43

value: OE 3x


title: H3K27ac Chr4-cl KO B6  testis (2 weeks)


title: TATGTT: MCF7_Abemaciclib_0.3

description:
well: E16
barcode: TATGTT
MCF7_Abemaciclib_0.3

value: MCF7 breast cancer cell line


title: TATGAA: MCF7_DMSO_0.0

description:
well: E15
barcode: TATGAA
MCF7_DMSO_0.0

value: DMSO


title: H3K4me3 Chr4-cl KO B6  testis (2 weeks)


title: TATATC: MCF7_Abemaciclib_3.16

description:
well: E14
barcode: TATATC
MCF7_Abemaciclib_3.16


title: h_Mecp2_overexpressed_2_42


title: TATAGA: Hs578T_Abemaciclib_0.3

description:
well: E13
barcode: TATAGA
Hs578T_Abemaciclib_0.3

value: Hs578T breast cancer cell line


title: Input Chr4-cl WT B6 testis (2 weeks)

value: Chr4-cl WT


title: H3K4me1 Chr4-cl WT B6 testis (2 weeks)


title: h_Mecp2_overexpressed_2_40


title: TAGTTT: Hs578T_DMSO_0.0

description:
well: E12
barcode: TAGTTT
Hs578T_DMSO_0.0


title: H3K4me1 Chr4-cl KO B6/129 ES cells #6

value: ES cells

value: 20% FCS

value: ChIP (O'Geen et al. 2010)


title: H3K4me3 Chr4-cl KO B6/129 ES cells #6

value: Bowtie (-5 3 --best)


title: h_control_non-infected_2_43

value: WT


title: H3K27ac Chr4-cl WT B6/129 ES cells #26


title: h_control_non-infected_2_42


title: H3K4me3 Chr4-cl WT B6/129 ES cells #26


title: H3K4me1 Chr4-cl WT B6/129 ES cells #26


title: Input Chr4-cl WT B6/129 ES cells #26

value: n/a (Input)


title: h_control_non-infected_2_41


title: KAP1 Chr4-cl KO B6/129 ES cells #6 [KAP1-GFP]

value: Chr4-cl KO


title: TACTTA: HCC1806_Abemaciclib_0.3

description:
well: E10
barcode: TACTTA
HCC1806_Abemaciclib_0.3

value: HCC1806 breast cancer cell line


title: TACTAT: HCC1806_DMSO_0.0

description:
well: E09
barcode: TACTAT
HCC1806_DMSO_0.0


title: H3K4me1 Chr4-cl KO B6  testis (2 weeks)

value: testis

value: ChIP (Khil et al. 2012)


title: h_Mecp2_overexpressed_2_41

value: LUHMES-derived neurons


title: h_control_non-infected_2_40


title: TAATTC: HCC1806_Abemaciclib_3.16

description:
well: E08
barcode: TAATTC
HCC1806_Abemaciclib_3.16

value: Abemaciclib


title: H3K4me3 Chr4-cl WT B6 testis (2 weeks)


title: H3K9me3 Chr4-cl KO B6/129 ES cells #41

value: H3K9me3 (Active Motif #39161)

value: Native ChIP


title: H3K27ac Chr4-cl WT B6 testis (2 weeks)


title: KAP1 Chr4-cl WT B6/129 ES cells #26 [KAP1-GFP]


title: h_Mecp2_KD3_2_43


title: H3K27ac Chr4-cl KO B6/129 ES cells #6


title: TAATGA: PDX1258_Abemaciclib_0.3

description:
well: E07
barcode: TAATGA
PDX1258_Abemaciclib_0.3

value: PDX1258 breast cancer PDX


title: H3K9me3 Chr4-cl KO B6/129 ES cells #6


title: H3K9me3 Chr4-cl WT B6/129 ES cells #49


title: H3K9me3 Chr4-cl WT B6/129 ES cells #26


title: h_Mecp2_KD3_2_42


title: TAGTAA: Hs578T_Abemaciclib_3.16

description:
well: E11
barcode: TAGTAA
Hs578T_Abemaciclib_3.16

value: Hs578T breast cancer cell line


title: h_Mecp2_KD3_2_41


title: TAAGTA: PDX1258_DMSO_0.0

description:
well: E06
barcode: TAAGTA
PDX1258_DMSO_0.0

value: DMSO


title: TAAGAT: PDX1258_Abemaciclib_3.16

description:
well: E05
barcode: TAAGAT
PDX1258_Abemaciclib_3.16


title: h_Mecp2_KD3_2_40


title: TAAATG: BT549_Abemaciclib_0.3

description:
well: E04
barcode: TAAATG
BT549_Abemaciclib_0.3

value: BT549 breast cancer cell line


title: h_Mecp2_KD2_2_43


title: GTTTTA: BT549_Abemaciclib_3.16

description:
well: E02
barcode: GTTTTA
BT549_Abemaciclib_3.16


title: h_Mecp2_KD2_2_40


title: h_Mecp2_KD2_2_42


title: replicate2 ChIP IP WT

data_processing:
Pre-process reads with Trimmomatic version 0.32 ILLUMINACLIP:nextera.fa:2:40:15 MINLEN:25
Align to genome with bwa v0.7.5a-r405
Filter for unique primary alignments with Samtools 1.3.1
Remove duplicate reads with Picard v1.107
Remove mitochondrial reads and blacklisted regions with bedtools 2.27
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files of aligned reads

extract_protocol:
LUHMES-derived neurons at day 9 of differentiation with four levels of MeCP2: KO, WT, OE 4x and OE 11x (see Table S1) were crosslinked with 1% of Formaldehyde (Sigma) in the medium for 10 min at RT and quenched with 2.5 M Glycine (Sigma) for 2 min at RT. Cells were washed with PBS, scraped from the plate and centrifuged. Crosslinked nuclei were isolated using hypotonic buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3mM MgCl2, 0.1% [v/v] Igepal CA-630) and counted using a haemocytometer. Chromatin from ~4x106 nuclei was sonicated for 20 cycles (30 sec ON and 30 sec OFF) on the high power setting using a Bioruptor (Diagenode). Crosslinked and sonicated chromatin was mixed with 60 ng of sonicated Drosophila chromatin (Active Motif) as a spike-in and the mix was incubated overnight at 4 ºC with antibodies against MeCP2 (D4F3, Cell Signalling) plus spike-in antibody (Active Motif). After overnight incubation, magnetic Protein G coated beads (Thermo Scientific) were added and incubated further 4 hours at 4 ºC. Beads were washed and chromatin was reverse-crosslinked overnight at 65 ºC. DNA was then purified using Agencourt AMPure XP (Beckman Coulter) beads.
For ChIP-seq library preparation, IPs for each condition were pooled together to achieve 5 ng total DNA as a starting material. For example, 3-4 IPs were pooled together for the KO sample and 2 IPs were pooled for the WT sample. Libraries were prepared using NEBNext Ultra II DNA library Prep kit (NEB) for both IPs and corresponding inputs.
NEBNext Ultra II kit (NEB)

tag: div

value: day 9

tag: passage

value: LUHMES

tag: genotype

value: anti- MeCP2


title: GATTAA: T47D_Palbociclib_0.1

description:
well: D21
barcode: GATTAA
T47D_Palbociclib_0.1

value: T47D breast cancer cell line

value: Palbociclib


title: GTAAAT: T47D_Alvocidib_1.0

description:
well: D22
barcode: GTAAAT
T47D_Alvocidib_1.0

value: Alvocidib


title: TAAAGT: BT549_DMSO_0.0

description:
well: E03
barcode: TAAAGT
BT549_DMSO_0.0


title: GAATTA: T47D_Ribociclib_3.16

description:
well: D20
barcode: GAATTA
T47D_Ribociclib_3.16

value: Ribociclib


title: replicate2 ChIP IP KO

value: MeCP2 KO

tag: chip antibody


title: GAATAT: PDXHCI002_Alvocidib_1.0

description:
well: D19
barcode: GAATAT
PDXHCI002_Alvocidib_1.0

value: PDXHCI002 breast cancer PDX


title: HepaRG liver cells, no treatment, 24h, replicate 2

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: Cells from the human cell line HepaRG, after differentiation, enriched for hepatocyte-like cells

hyb_protocol: Affymetrix human gene 1.0ST arrays (Affymetrix, Santa Clara, CA, USA) were hybridized with 2.3μg of fragmented target, at 45°C for 16 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The RMA algorithm was applied to the data, using Affymetrix Expression Console software.

source_name: Differentiated, hepatocyte-like HepaRG cells in culture, 24h after starting experiment

label_protocol: For each sample, 100ng of total RNA were amplified using the Whole transcript (WT) Sense Target Labeling assay (900652, Affymetrix). 5.5μg of the cDNA was fragmented and labeled with GeneChip® WT Terminal Labeling kit (900671, Affymetrix).

growth_protocol: HepaRG cells were grown in culture. After differentiation, hepatocyte-like cells were enriched by selective detachment using mild trypsinization and plated at 1.5x10-5/cm2 density in complete media plus 2% DMSO

extract_protocol: Cells were washed twice with cold PBS, and total RNA was extracted with Trizol Reagent (Life Technologies, Carlsbad, CA), following the manufacturer’s instructions.

treatment_protocol: Cell cultures were treated with four different agonists: 2 µM of GW3965  (called LXR-L in this study), 1 µM of GW4064 (FXR-L in this study), 1 µM of GW7647  (PPARa-L in this study), or 50 µM of CDCA. These agonists were purchased from Sigma-Aldrich (St. Louis, MO). All compounds were diluted in DMSO. A set of control cell cultures was treated with DMSO only and another set of control cell cultures was left untreated.

value: HepaRG (wild type)

tag: time point

tag: ligand treatment

value: Control


title: HepaRG liver cells, PPARa treatment, 24h, replicate 3

source_name: Differentiated, hepatocyte-like HepaRG cells in culture, 24h after treatment

tag: cell line

value: PPARa


title: HepaRG liver cells, DMSO treatment, 24h, replicate 2


title: HepaRG liver cells, no treatment, 4h, replicate 2

source_name: Differentiated, hepatocyte-like HepaRG cells in culture, 4h after starting experiment


title: HepaRG liver cells, no treatment, 4h, replicate 3


title: HepaRG liver cells, PPARa treatment, 24h, replicate 1


title: HepaRG liver cells, DMSO treatment, 24h, replicate 1


title: HepaRG liver cells, no treatment, 24h, replicate 1


title: HepaRG liver cells, no treatment, 4h, replicate 1


title: HepaRG liver cells, DMSO treatment, 24h, replicate 3


title: HepaRG liver cells, DMSO treatment, 4h, replicate 2

source_name: Differentiated, hepatocyte-like HepaRG cells in culture, 4h after treatment


title: HepaRG liver cells, DMSO treatment, 4h, replicate 3


title: h_Mecp2_KD2_2_41

value: LUHMES-derived neurons


title: HepaRG liver cells, PPARa treatment, 24h, replicate 2


title: HepaRG liver cells, no treatment, 24h, replicate 3


title: replicate2 ChIP IP OE4x

tag: cell type

value: MeCP2 OE4x


title: HepaRG liver cells, PPARa treatment, 4h, replicate 3


title: HepaRG liver cells, DMSO treatment, 4h, replicate 1


title: CTTATA: PDXHCI002_Palbociclib_0.1

description:
well: D18
barcode: CTTATA
PDXHCI002_Palbociclib_0.1

tag: drug treatment


title: replicate2 ChIP IP OE11x

value: MeCP2 OE11x


title: CTTAAT: PDXHCI002_Ribociclib_3.16

description:
well: D17
barcode: CTTAAT
PDXHCI002_Ribociclib_3.16

tag: concentration (um)


title: HepaRG liver cells, PPARa treatment, 4h, replicate 1


title: replicate2 ChIP input WT

value: WT


title: CTAATT: MCF7_Alvocidib_1.0

description:
well: D16
barcode: CTAATT
MCF7_Alvocidib_1.0

value: MCF7 breast cancer cell line

tag: time (hours)


title: replicate2 ChIP input KO

value: day 9


title: HepaRG liver cells, LXR-L treatment, 24h, replicate 3

value: LXR-L


title: HepaRG liver cells, LXR-L treatment, 24h, replicate 1


title: CTAAAA: MCF7_Palbociclib_0.1

description:
well: D15
barcode: CTAAAA
MCF7_Palbociclib_0.1


title: CATAAA: Hs578T_Alvocidib_1.0

description:
well: D13
barcode: CATAAA
Hs578T_Alvocidib_1.0

value: Hs578T breast cancer cell line


title: HepaRG liver cells, LXR-L treatment, 24h, replicate 2


title: replicate2 ChIP input OE4x

value: LUHMES


title: replicate1 ChIP IP WT

value: anti- MeCP2


title: replicate1 ChIP IP KO


title: replicate2 ChIP input OE11x


title: HepaRG liver cells, LXR-L treatment, 4h, replicate 2


title: ATTTTG: Hs578T_Ribociclib_3.16

description:
well: D11
barcode: ATTTTG
Hs578T_Ribociclib_3.16


title: HepaRG liver cells, PPARa treatment, 4h, replicate 2


title: CATATT: MCF7_Ribociclib_3.16

description:
well: D14
barcode: CATATT
MCF7_Ribociclib_3.16


title: replicate1 ChIP IP OE4x


title: HepaRG liver cells, LXR-L treatment, 4h, replicate 3


title: HepaRG liver cells, FXR-L treatment, 4h, replicate 2

value: FXR-L


title: HepaRG liver cells, LXR-L treatment, 4h, replicate 1


title: HepaRG liver cells, FXR-L treatment, 24h, replicate 3


title: replicate1 ChIP IP OE11x


title: HepaRG liver cells, FXR-L treatment, 4h, replicate 1


title: ATTTAC: HCC1806_Alvocidib_1.0

description:
well: D10
barcode: ATTTAC
HCC1806_Alvocidib_1.0

value: HCC1806 breast cancer cell line

value: Alvocidib


title: HepaRG liver cells, FXR-L treatment, 4h, replicate 3


title: HepaRG liver cells, FXR-L treatment, 24h, replicate 1


title: HepaRG liver cells, CDCA treatment, 24h, replicate 3

value: CDCA


title: ATTGTT: HCC1806_Palbociclib_0.1

description:
well: D09
barcode: ATTGTT
HCC1806_Palbociclib_0.1

value: Palbociclib


title: HepaRG liver cells, FXR-L treatment, 24h, replicate 2

value: HepaRG (wild type)


title: replicate1 ChIP input WT


title: HepaRG liver cells, CDCA treatment, 24h, replicate 2


title: ATTCAT: HCC1806_Ribociclib_3.16

description:
well: D08
barcode: ATTCAT
HCC1806_Ribociclib_3.16

value: Ribociclib


title: HepaRG liver cells, CDCA treatment, 24h, replicate 1


title: ATTATC: PDX1258_Alvocidib_1.0

description:
well: D07
barcode: ATTATC
PDX1258_Alvocidib_1.0

value: PDX1258 breast cancer PDX


title: HepaRG liver cells, CDCA treatment, 4h, replicate 2


title: replicate1 ChIP input KO

value: LUHMES-derived neurons

value: MeCP2 KO


title: Pum2

first: Stefan

middle: A

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

data_processing:
Base-calling was performed with bcl2fastq v2.17
The PAR-CLIP sequencing data were processed by PARpipe, which handles the library pre-processing, alignment, clustering, annotation and meta-analysis. (https://ohlerlab.mdc-berlin.de/software/PARpipe_119/).
Adapters were trimmed using Cutadapt 1.12 (43) and reads were aligned to the mm10 (GRCm38) genome using Bowtie v1.1.1, allowing for up to one mismatch (44).
Aligned reads were sorted, converted to BAM files, and indexed with Samtools v0.1.19 (45). PARalyzer v1.5 (29) was used to process reads into groups and clusters via filters for (1) minimum read length, (2) minimum read count, (3) minimum unique T-to-C locations, and (4) minimum T-to-C conversions.
Reads, groups and clusters were annotated to the features in the Gencode vM9 annotation file for reference chromosomes, scaffolds, assembly patches and alternative loci.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BED : clusters called by PARalyzer for each respective PAR-CLIP replicate

source_name: 220-8 cell line, Pum2

growth_protocol: The 220-8 mouse pro-B cell line is a v-Abl-transformed clone derived from adult BALB/c bone marrow with nonproductive VDJH rearrangements on both alleles. They are cultured in RPMI-1640 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 mg/ml of penicillin, 100 mg/ml of streptomycin and 50 mM 2-mercaptoethanol at 37 °C in an atmosphere of 5% CO2

extract_protocol:
Performed as described in Hafner et al, Cell (2010) and Danan et al., Methods Mol Biol (2016).
RNA was converted into a cDNA library using a standard small RNA library protocol as described in Hafner et al., Methods (2008)

treatment_protocol: 220-8 cells were retrovirally transduced with FH-LIN28A or FH-LIN28B.

value: BALB/c

value: 220-8 cell line


title: replicate1 ChIP input OE4x

value: day 9

value: MeCP2 OE4x


title: CAAAAT: Hs578T_Palbociclib_0.1

description:
well: D12
barcode: CAAAAT
Hs578T_Palbociclib_0.1

value: Hs578T breast cancer cell line


title: ATTAAG: PDX1258_Palbociclib_0.1

description:
well: D06
barcode: ATTAAG
PDX1258_Palbociclib_0.1


title: Igf2bp3_4

source_name: 220-8 cell line, Igf2bp3


title: replicate1 ChIP input OE11x

value: LUHMES

value: MeCP2 OE11x


title: Igf2bp3_2


title: Igf2bp3_1


title: Igf2bp3_3


title: Control ATAC-seq 5

description:
Tn5 transposed chromatin
h_MeCP2_WT_112

extract_protocol:
Neurons were scraped from the plate and nuclei were isolated using hypotonic buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3mM MgCl2, 0.1% [v/v] Igepal CA-630) and counted. 50,000 nuclei were resuspended in 50 µl transposition reaction mix containing 2.5 µl Nextera Tn5 Transposase and 2x TD Nextera reaction buffer. The reaction was incubated for 30 min at 37 ºC.
DNA was purified by either MinElute PCR kit (Qiagen) or Agencourt AMPure XP (Beckman Coulter) beads and PCR amplified with NEBNext High Fidelity reaction mix (NEB) to generate a sequencing library.

value: Day 9

value: Control


title: FH-LIN28B_1

source_name: 220-8 cell line, FH-LIN28B


title: FH-LIN28B_3


title: HepaRG liver cells, CDCA treatment, 4h, replicate 1


title: ATCTTA: BT549_Alvocidib_1.0

description:
well: D04
barcode: ATCTTA
BT549_Alvocidib_1.0

value: BT549 breast cancer cell line

value: Alvocidib


title: FH-LIN28B_4


title: ATCTAT: BT549_Palbociclib_0.1

description:
well: D03
barcode: ATCTAT
BT549_Palbociclib_0.1

value: Palbociclib


title: Free Ubiquitin-2

city: suzhou

first: zhang

middle: shu

last: yu

state: Jinagsu

address: 199 Ren'ai Rd

department: Radiation Medicine

institute: soochow University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

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

source_name: Intestine

label_protocol: Standard Illumina label protocol

growth_protocol: SPF condition for the growth of C57 mice.

extract_protocol: Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.

treatment_protocol: Male C57 mice (4 weeks old) were irradiated with a single dose of 7 Gy radiation (total body radiation). Mice were then administered with PBS or free ubiquitin. Mice intestine tissues were then collected 3.5 days  after radiation.

tag: treatment

value: free ubiquitin following 7 Gy radiation


title: FH-LIN28B_2


title: HepaRG liver cells, CDCA treatment, 4h, replicate 3

value: HepaRG (wild type)

value: CDCA


title: ATATTC: BT549_Ribociclib_3.16

description:
well: D02
barcode: ATATTC
BT549_Ribociclib_3.16

value: Ribociclib


title: FH-LIN28A_4

source_name: 220-8 cell line, FH-LIN28A


title: PBS-3

value: PBS following 7 Gy radiation


title: Free Ubiquitin-3


title: PBS-1


title: Free Ubiquitin-1


title: MeCP2 OE 4x ATAC-seq 2

description:
Tn5 transposed chromatin
h_MeCP2_OE_E4_115

value: LUHMES-derived neurons

value: MeCP2 OE 4x


title: PBS-2


title: FH-LIN28A_3

value: BALB/c

value: 220-8 cell line


title: GATATA: T47D_DMSO_0.0

description:
well: C22
barcode: GATATA
T47D_DMSO_0.0

value: T47D breast cancer cell line

value: DMSO


title: FH-LIN28A_2


title: GATAAT: T47D_Abemaciclib_3.16

description:
well: C21
barcode: GATAAT
T47D_Abemaciclib_3.16

value: Abemaciclib


title: ATGTAA: PDX1258_Ribociclib_3.16

description:
well: D05
barcode: ATGTAA
PDX1258_Ribociclib_3.16

value: PDX1258 breast cancer PDX


title: FH-LIN28A_1


title: MeCP2 OE 4x ATAC-seq 1

description:
Tn5 transposed chromatin
h_MeCP2_OE_E4_113

value: Day 9

value: LUHMES


title: X201247480034_R08C01: genomic DNA from buccal cells 12_2

type: genomic

city: Nottingham

first: Reinhard

last: Stoger

address: Sutton Bonington Campus

department: School of Biosciences

institute: Universityf Nottingham

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
samples have been processed using minfi https://bioconductor.org/packages/release/bioc/html/minfi.html as these are from different populations where underlying genotype can affect the outcome, any probes containing known SNPs have been removed.  As all samples are female the probes on the X & Y chromosomes have been retained.
methylation beta values are normalised by SWAN https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-6-r44

label: Cy5 and Cy3

source_name: buccal cell

label_protocol: Standard Illumina Protocol

growth_protocol: adult human females age 28.1 yrs ± 5.0

extract_protocol: Buccal swabs were collected with iSWAB (Mawi DNA Technologies) and genomic DNA isolated using the DNeasy Blood & Tissue Kit (Qiagen).

treatment_protocol: different childhood environment

value: buccal cell

tag: gender

value: female

tag: environmental factor

value: born in Bangladesh


title: MeCP2 KO ATAC-seq 4

description:
Tn5 transposed chromatin
h_MeCP2_KO_H4_113

value: MeCP2 KO


title: X201247480034_R07C01: genomic DNA from buccal cells 36


title: X201247480034_R06C01: genomic DNA from buccal cells 33


title: X201247480034_R05C01: genomic DNA from buccal cells 32


title: CTTTAA: PDXHCI002_DMSO_0.0

description:
well: C19
barcode: CTTTAA
PDXHCI002_DMSO_0.0

extract_protocol:
RNA was extracted using TCL lysis buffer, samples were using universal adapters, barcodes, unique molecular identifiers, and a template switching reverse transcriptase.
Libraries were prepared using Nextera DNA kit (Illumina).
Digitial gene expression (DGE)

value: PDXHCI002 breast cancer PDX


title: GAAATT: T47D_Ribociclib_3.16

description:
well: C20
barcode: GAAATT
T47D_Ribociclib_3.16

value: Ribociclib


title: CTATTA: PDXHCI002_Abemaciclib_3.16

description:
well: C18
barcode: CTATTA
PDXHCI002_Abemaciclib_3.16


title: MeCP2 KO ATAC-seq 3

description:
Tn5 transposed chromatin
h_MeCP2_KO_D10_115


title: MeCP2 KO ATAC-seq 1

description:
Tn5 transposed chromatin
h_MeCP2_KO_115


title: X201247480036_R08C01: genomic DNA from buccal cells 27


title: X201247480034_R02C01: genomic DNA from buccal cells 29


title: CTATAT: PDXHCI002_Ribociclib_3.16

description:
well: C17
barcode: CTATAT
PDXHCI002_Ribociclib_3.16


title: X201247480036_R06C01: genomic DNA from buccal cells 25

value: born in UK to Banlgadeshi parents


title: X201247480034_R01C01: genomic DNA from buccal cells 28


title: X201247480036_R07C01: genomic DNA from buccal cells 26


title: Control ATAC-seq 4

description:
Tn5 transposed chromatin
h_MeCP2_ctr_F6_115

value: LUHMES-derived neurons

value: Control


title: CATTTA: MCF7_DMSO_0.0

description:
well: C16
barcode: CATTTA
MCF7_DMSO_0.0

value: MCF7 breast cancer cell line


title: Control ATAC-seq 3

description:
Tn5 transposed chromatin
h_MeCP2_ctr_F6_113


title: X201247480036_R05C01: genomic DNA from buccal cells 24


title: X201247480036_R04C01: genomic DNA from buccal cells 23


title: CATTAT: MCF7_Abemaciclib_3.16

description:
well: C15
barcode: CATTAT
MCF7_Abemaciclib_3.16


title: X201247480036_R03C01: genomic DNA from buccal cells 22


title: Control ATAC-seq 2

description:
Tn5 transposed chromatin
h_MeCP2_ctr_E10_115


title: X201247480036_R02C01: genomic DNA from buccal cells 21


title: CAATAA: MCF7_Ribociclib_3.16

description:
well: C14
barcode: CAATAA
MCF7_Ribociclib_3.16


title: X201247480036_R01C01: genomic DNA from buccal cells 20


title: Control ATAC-seq 1

description:
Tn5 transposed chromatin
h_MeCP2_ctr_E10_113


title: CAAATA: Hs578T_DMSO_0.0

description:
well: C13
barcode: CAAATA
Hs578T_DMSO_0.0

value: Hs578T breast cancer cell line


title: X201247480031_R08C01: genomic DNA from buccal cells 19


title: X201247480034_R03C01: genomic DNA from buccal cells 30


title: X201247480034_R04C01: genomic DNA from buccal cells 31


title: MeCP2 KO ATAC-seq 2

description:
Tn5 transposed chromatin
h_MeCP2_KO_D10_113


title: X201247480031_R07C01: genomic DNA from buccal cells 18


title: ATTTGT: Hs578T_Abemaciclib_3.16

description:
well: C12
barcode: ATTTGT
Hs578T_Abemaciclib_3.16


title: X201247480031_R06C01: genomic DNA from buccal cells 17


title: RBM25.KD_GRO_rep1_HepG2_batch3

city: Wuhan

first: Rui

last: Xiao

state: Hubei

address: Medical Research Institute, Wuhan University

department: Medical Research Institute

institute: Wuhan University

description:
Nascent RNA
GRO-seq data (SE)

data_processing:
Library strategy: GRO-seq
GRO-seq reads were mapped on the human reference genome using the Bowtie2 local model
Non-redundant reads were determined and kept for downstream analysis by using Samtools
DEseq2 package was used to search for differentially expressed genes (DEGs), which was defined with the following cutoff: adjusted p-value of ≤0.05 and fold change of ≤2/3 or ≥3/2.
Genome_build: GRCh37 (hg19)
processed data files format and content: BED and BigWig

growth_protocol: ENCODE cell culture protocols

extract_protocol:
Nuclei were isolated and applied for global nuclear run-on experiment in the present of BrUTP; BrUTP labeled nascent RNAs were purified with BrdU antibody conjugated agarose beads.
Purified nascent RNAs were polyadenylated and reversely transcribed; cDNAs were circulated and relinearized; the GRO-seq libraries were finally obtained by barcoded PCR amplification and PAGE purification.

treatment_protocol: siRNA transfection with RNAiMAX

value: Hepatocellular carcinoma


title: RBM25.KD_GRO_rep2_HepG2_batch3

description:
Nascent RNA
GRO-seq data (SE)


title: ATTTCA: Hs578T_Ribociclib_3.16

description:
well: C11
barcode: ATTTCA
Hs578T_Ribociclib_3.16

data_processing:
barcode and Unique moelcular identifiers (UMIs) were identified for all reads and reads not within one edit distance of a well known barcode were discarded
surviving reads were quasialigned using RapMap.
Reads per well were counted using UMI's, duplicate UMIs were discarded. Mutimapped reads were weighted by  the number of transcirpts they aligned to
Reads counts were collapsed to gene counts by adding all counts for each transcript of a gene.
Genome_build: GRch38
Supplementary_files_format_and_content: .csv file of counts for all gene identifiers that mapped to a mRNA across all 335 samples


title: YY1.KD_GRO_rep2_HepG2_batch3

description:
Nascent RNA
GRO-seq data (SE)


title: X201247480031_R03C01: genomic DNA from buccal cells 14


title: ATTGAA: HCC1806_DMSO_0.0

description:
well: C10
barcode: ATTGAA
HCC1806_DMSO_0.0

value: HCC1806 breast cancer cell line

value: DMSO


title: X201247480031_R01C01: genomic DNA from buccal cells 12


title: X201247480032_R08C01: genomic DNA from buccal cells 10


title: X201247480031_R02C01: genomic DNA from buccal cells 13


title: X201247480031_R04C01: genomic DNA from buccal cells 15


title: ATTCTA: HCC1806_Abemaciclib_3.16

description:
well: C09
barcode: ATTCTA
HCC1806_Abemaciclib_3.16

value: Abemaciclib


title: ATTAGA: HCC1806_Ribociclib_3.16

description:
well: C08
barcode: ATTAGA
HCC1806_Ribociclib_3.16


title: YY1.KD_GRO_rep1_HepG2_batch3

description:
Nascent RNA
GRO-seq data (SE)


title: X201247480032_R07C01: genomic DNA from buccal cells 8


title: X201247480032_R06C01: genomic DNA from buccal cells 7


title: X201247480032_R05C01: genomic DNA from buccal cells 6


title: ATTACT: PDX1258_DMSO_0.0

description:
well: C07
barcode: ATTACT
PDX1258_DMSO_0.0

value: PDX1258 breast cancer PDX


title: Control_GRO_rep1_HepG2_batch3

description:
Nascent RNA
GRO-seq data (SE)


title: X201247480032_R03C01: genomic DNA from buccal cells 4


title: X201247480032_R04C01: genomic DNA from buccal cells 5


title: ATGATA: PDX1258_Abemaciclib_3.16

description:
well: C06
barcode: ATGATA
PDX1258_Abemaciclib_3.16


title: X201247480032_R01C01: genomic DNA from buccal cells 1


title: X201247480031_R05C01: genomic DNA from buccal cells 16


title: ATGAAT: PDX1258_Ribociclib_3.16

description:
well: C05
barcode: ATGAAT
PDX1258_Ribociclib_3.16


title: XRCC5.KD_GRO_rep1_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: X201247480032_R02C01: genomic DNA from buccal cells 2


title: ATCATT: BT549_DMSO_0.0

description:
well: C04
barcode: ATCATT
BT549_DMSO_0.0

value: BT549 breast cancer cell line


title: RBM22.KD_GRO_rep2_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: ATATCT: BT549_Ribociclib_3.16

description:
well: C02
barcode: ATATCT
BT549_Ribociclib_3.16


title: RBM25.KD_GRO_rep1_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: Control_GRO_rep2_HepG2_batch3

description:
Nascent RNA
GRO-seq data (SE)


title: AGTTAA: T47D_Ribociclib_0.3

description:
well: B20
barcode: AGTTAA
T47D_Ribociclib_0.3

value: T47D breast cancer cell line


title: PTBP1.KD_GRO_rep1_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: ATAAGT: T47D_Abemaciclib_0.3

description:
well: B21
barcode: ATAAGT
T47D_Abemaciclib_0.3


title: ATCAAA: BT549_Abemaciclib_3.16

description:
well: C03
barcode: ATCAAA
BT549_Abemaciclib_3.16


title: PCBP2.KD_GRO_rep2_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: PCBP2.KD_GRO_rep1_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: AGATAT: PDXHCI002_Abemaciclib_0.3

description:
well: B18
barcode: AGATAT
PDXHCI002_Abemaciclib_0.3


title: AGTATA: PDXHCI002_Palbociclib_1.0

description:
well: B19
barcode: AGTATA
PDXHCI002_Palbociclib_1.0

value: Palbociclib


title: HNRNPLL.KD_GRO_rep2_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: HNRNPLL.KD_GRO_rep1_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: ACTATT: MCF7_Palbociclib_1.0

description:
well: B16
barcode: ACTATT
MCF7_Palbociclib_1.0


title: XRCC5.KD_GRO_rep2_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: ACTAAA: MCF7_Abemaciclib_0.3

description:
well: B15
barcode: ACTAAA
MCF7_Abemaciclib_0.3


title: HNRNPK.KD_GRO_rep1_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: HNRNPH1.KD_GRO_rep2_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: HNRNPH1.KD_GRO_rep1_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: AATTAG: Hs578T_Abemaciclib_0.3

description:
well: B12
barcode: AATTAG
Hs578T_Abemaciclib_0.3


title: HNRNPK.KD_GRO_rep2_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: ACAAAT: MCF7_Ribociclib_0.3

description:
well: B14
barcode: ACAAAT
MCF7_Ribociclib_0.3


title: Control_GRO_rep2_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: RBM25.KD_GRO_rep2_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: RBM22.KD_GRO_rep1_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: ATAATG: T47D_Palbociclib_1.0

description:
well: B22
barcode: ATAATG
T47D_Palbociclib_1.0


title: PTBP1.KD_GRO_rep2_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: Control_GRO_rep1_HepG2_batch2

description:
Nascent RNA
GRO-seq data (SE)


title: AATGTA: Hs578T_Ribociclib_0.3

description:
well: B11
barcode: AATGTA
Hs578T_Ribociclib_0.3


title: AATCAA: HCC1806_Palbociclib_1.0

description:
well: B10
barcode: AATCAA
HCC1806_Palbociclib_1.0


title: U2AF2.KD_GRO_rep2_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AATATG: HCC1806_Abemaciclib_0.3

description:
well: B09
barcode: AATATG
HCC1806_Abemaciclib_0.3


title: AATTTC: Hs578T_Palbociclib_1.0

description:
well: B13
barcode: AATTTC
Hs578T_Palbociclib_1.0


title: U2AF1.KD_GRO_rep2_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AATAAC: HCC1806_Ribociclib_0.3

description:
well: B08
barcode: AATAAC
HCC1806_Ribociclib_0.3


title: AAGTTA: PDX1258_Palbociclib_1.0

description:
well: B07
barcode: AAGTTA
PDX1258_Palbociclib_1.0


title: U2AF2.KD_GRO_rep1_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: U2AF1.KD_GRO_rep1_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AACATA: PDX1258_Ribociclib_0.3

description:
well: B05
barcode: AACATA
PDX1258_Ribociclib_0.3


title: SRSF4.KD_GRO_rep2_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)

data_processing:
Library strategy: GRO-seq
GRO-seq reads were mapped on the human reference genome using the Bowtie2 local model
Non-redundant reads were determined and kept for downstream analysis by using Samtools
DEseq2 package was used to search for differentially expressed genes (DEGs), which was defined with the following cutoff: adjusted p-value of ≤0.05 and fold change of ≤2/3 or ≥3/2.
Genome_build: GRCh37 (hg19)
processed data files format and content: BED and BigWig
processed data files format and content: BED and BigWig


title: SRSF4.KD_GRO_rep1_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AGAATT: PDXHCI002_Ribociclib_0.3

description:
well: B17
barcode: AGAATT
PDXHCI002_Ribociclib_0.3


title: HNRNPL.KD_GRO_rep2_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AAATCA: BT549_Abemaciclib_0.3

description:
well: B03
barcode: AAATCA
BT549_Abemaciclib_0.3


title: HNRNPL.KD_GRO_rep1_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AGO2.KD_GRO_rep2_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AAATGT: BT549_Palbociclib_1.0

description:
well: B04
barcode: AAATGT
BT549_Palbociclib_1.0


title: AAACTA: BT549_Ribociclib_0.3

description:
well: B02
barcode: AAACTA
BT549_Ribociclib_0.3


title: ATAACA: T47D_Palbociclib_3.16

description:
well: A22
barcode: ATAACA
T47D_Palbociclib_3.16


title: AGO2.KD_GRO_rep1_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AGO1.KD_GRO_rep2_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: ATAAAC: T47D_DMSO_0.0

description:
well: A21
barcode: ATAAAC
T47D_DMSO_0.0


title: AGO1.KD_GRO_rep1_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AGTAAT: T47D_Palbociclib_0.3

description:
well: A20
barcode: AGTAAT
T47D_Palbociclib_0.3


title: AACTAA: PDX1258_Abemaciclib_0.3

description:
well: B06
barcode: AACTAA
PDX1258_Abemaciclib_0.3


title: Control_GRO_rep2_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: AGATTA: PDXHCI002_Palbociclib_3.16

description:
well: A19
barcode: AGATTA
PDXHCI002_Palbociclib_3.16


title: ACTTTA: PDXHCI002_DMSO_0.0

description:
well: A18
barcode: ACTTTA
PDXHCI002_DMSO_0.0


title: Microphyll

city: shanghai

first: luoyan

last: zhang

address: songhu Road 2005

institute: fudan university

data_processing:
Illumina HiSeqTM2000 software used for basecalling. Raw reads were processed to remove adaptors, low-quality reads and reads with unknown bases.
The clean reads of S. moellendorfii were aligned to the genome sequence of S. moellendorfii at JGI database (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Smoellendorffii/annotation/) using the assembling program SOAPaligner/SOAP2 from Li et al, Bioinformatics, 2009.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nucleic Acids Research, 2008.
Fold changes in gene expression were determined from RPKM ratios. Genes were considered to be differentially expressed if they had an FDR < 0.05, P-value < 0.05, and the absolute value of log2Ratio ≥ 1.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Selaginella moellendorffii

source_name: Young microphyll

extract_protocol:
Total RNAs of a series of sporangia at different developmental stages and young leaves were extracted using the TRIzol solution.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stge

value: Young microphyll

value: wild type


title: Sporangium_s_6

source_name: Sporophyll

value: Sporangium big

tag: genotype/variation


title: Control_GRO_rep1_HepG2_batch1

description:
Nascent RNA
GRO-seq data (SE)


title: ACTTAT: PDXHCI002_Palbociclib_0.3

description:
well: A17
barcode: ACTTAT
PDXHCI002_Palbociclib_0.3

value: PDXHCI002 breast cancer PDX


title: ACATAA: MCF7_Palbociclib_3.16

description:
well: A16
barcode: ACATAA
MCF7_Palbociclib_3.16


title: input_Control_K562_batch11

description: input DNA control (SE)

data_processing:
ChIP-seq data were processed in accordance with ENCODE uniform transcription factor ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/transcription_factor/).
Briefly, ChIP-seq reads were aligned to the GRCh37 human genome using BWA;
PCR duplicates and reads of low quality were filtered;
Peak-calling was performed with SPP and IDR with 0.02 IDR threshhold;
Signal tracks were generated with MACS2 and bigWig applications from UCSC genome browser (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Peak files were narrowPeak files generated by SPP; column information of narrowPeak file is explicated at the link (https://genome-euro.ucsc.edu/FAQ/FAQformat.html#format12).

extract_protocol:
Nuclei were isolated and sonicated and lysates were cleared-up and applied for purification of RBP-DNA complexes with antibodies.
Libraries were constructed according to the instruction of the Illumina Preparing Samples for ChIP Sequencing.


title: input_Control_K562_batch10

description: input DNA control (SE)


title: Wild type B6(Cg)-Tyrc-2J/J (p16+/+) mice treated with cigarette smoke

city: Gaithersburg

first: Christopher

middle: Travis

last: Cottage

address: 1 Medimmune Way

institute: AstraZeneca

description: Test

data_processing:
Qiagen’s Data Analysis software was used to analyze results and construct a heatmap. Lysates were collected from 5 treated lungs (4 lungs for p16 KO room air group) and were averaged.   All genes are normalized to 5 housekeeping genes within the array
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.  Values from the different treated lungs were averaged within
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e.,Room air wt/ experimental CS) ratios.

label: SYBR Green

source_name: Jackson Mice

label_protocol: QIAGEN PAMM030 RT2 Profiler PCR Arrays were used to determine the genes altered in the insulin signaling pathway.  Fast SYBR Green master max (ThermoFisher) was used during the reaction.  Qiagen’s Data Analysis software was used to analyze results and construct a heatmap.  All genes are normalized to 5 housekeeping genes within the array

extract_protocol: Total RNA was extracted with Zymo RNA isolation Kit followed by DNase I treatment.

tag: tissue

value: lung lysate

tag: activation agent

value: WT CS

tag: time

value: 8 weeks + 16 weeks CS

value: WT


title: Wild type B6(Cg)-Tyrc-2J/J (p16+/+) mice

description: Control

value: control

value: 24 weeks old

tag: genotype


title: Sporangium_s_4


title: p16Luc mice (Strain Code 01XBT -- B6.Cg-Cdkn2a tm3.1Nesh Tyr c-2J/Nci)

description: Test

value: p16(-/-) room air


title: p16Luc mice (Strain Code 01XBT -- B6.Cg-Cdkn2a tm3.1Nesh Tyr c-2J/Nci) mice treated with cigarette smoke

description: Test


title: ACAATA: MCF7_DMSO_0.0

description:
well: A15
barcode: ACAATA
MCF7_DMSO_0.0

value: MCF7 breast cancer cell line

value: DMSO


title: Sporangium_s_5


title: input_Control_K562_batch9

description: input DNA control (SE)

value: Hepatocellular carcinoma


title: Gametophyte_young

data_processing:
Illumina HiSeqTM2000 software used for basecalling. Raw reads were processed to remove adaptors, low-quality reads and reads with unknown bases.
The RNA-Seq reads of P. aloides were assembled into denovo transcripts using SOAPdenovo v1.04 (http://soap.genomics.org.cn/soapdenovo.html) with default settings.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nucleic Acids Research, 2008.
Fold changes in gene expression were determined from RPKM ratios. Genes were considered to be differentially expressed if they had an FDR < 0.05, P-value < 0.05, and the absolute value of log2Ratio ≥ 1.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Pogonatum aloides

source_name: Seedlings of  P.aloides

extract_protocol:
Total RNAs were extracted using the TRIzol solution.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Seedlings


title: Gametophyte seedling_capsula_transcriptome_l1

data_processing:
Illumina HiSeqTM2000 software used for basecalling.
Pair-end raw reads were processed to remove adaptors, low-quality reads and reads with unknown bases.
De novo assembled unigene sequences were used for BLAST searches and annotation against public databases (NR, Swiss-Prot, COSMOSS, KEGG and COG) with an E-value threshold of 10-10. Proteins with the highest sequence similarity with the given sequences along with the functional annotations for their protein.
Supplementary_files_format_and_content: Unigene and Contig sequences

source_name: Capsules at different developmental stages and young gametophytes

extract_protocol:
Total RNAs of  young gametophytes and capsules at different developmental stages were extracted using the TRIzol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: input_Control_K562_batch8

description: input DNA control (SE)


title: Sporangium_s_2

value: Sporangium small


title: AATTGA: MCF7_Palbociclib_0.3

description:
well: A14
barcode: AATTGA
MCF7_Palbociclib_0.3

value: Palbociclib


title: Capsule_s_5

source_name: Capsula of  P.aloides

value: Big capsula


title: input_Control_K562_batch7

description: input DNA control (SE)


title: AATTCT: Hs578T_Palbociclib_3.16

description:
well: A13
barcode: AATTCT
Hs578T_Palbociclib_3.16

value: Hs578T breast cancer cell line


title: AATCTT: Hs578T_Palbociclib_0.3

description:
well: A11
barcode: AATCTT
Hs578T_Palbociclib_0.3


title: input_Control_K562_batch6

description: input DNA control (SE)


title: Sporangium_s_1

value: wild type


title: Sporangium_s_3


title: Capsule_s_2

value: Small capsula


title: input_Control_K562_batch5

description: input DNA control (SE)


title: Capsule_s_3


title: AATAGT: HCC1806_Palbociclib_3.16

description:
well: A10
barcode: AATAGT
HCC1806_Palbociclib_3.16

value: HCC1806 breast cancer cell line


title: AATGAT: Hs578T_DMSO_0.0

description:
well: A12
barcode: AATGAT
Hs578T_DMSO_0.0


title: Capsule_s_4

value: Middle capsula


title: P20

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

description: Total RNA including miRNA.

hyb_protocol: The expression profile of mouse miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Data was quantile normalized and log2 transformed using respective R packages.

label_protocol: miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456), Cyanine 3-pcp.

extract_protocol: Total RNA including miRNAs was isolated using miRNeasy Kit (Qiagen) after manufacturer's recommendations.

tag: strain/background

tag: group

value: Union

value: Callus


title: input_Control_K562_batch4

description: input DNA control (SE)

tag: cell line


title: P19

description: Total RNA including miRNA.


title: P17

description: Total RNA including miRNA.


title: AAGTAT: HCC1806_Palbociclib_0.3

description:
well: A08
barcode: AAGTAT
HCC1806_Palbociclib_0.3

tag: cell type


title: 5’Tag-seq  Mut_3

city: Noda, Chiba

first: Kazushige

last: Shiraishi

address: Yamasaki 2669

country: Japan

institute: Tokyo University of Science

data_processing:
Adapter trimming and quality filtering of fastq files were performed by using Cutadapt-v1.18. Trimmed reads were mapped to the Refseq hg38 RNA by using Bowtie2-2.2.5 with the following parameters: -t -p 16 -N 1 -D 200 -R 20 -L 20 -i S,1,0.50 --nofw.
Total tag number was normalized using R-3.4.0 and TCC package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw tag-count values for each sample

source_name: Lung alveolar epithelial cells

extract_protocol:
Cultured alveolar epithelial cells were first stained with APC conjucated anti-human LNGFR antibody. Cells were next stained with anti-APC microbeads (Miltenyi). Labeled cells were magnetically sorted twice.
Whole transcript amplification for cultured alveolar epithelial type II cells was performed using 5’Tag-seq method according to a previous report with modifications (Shichino et al., 2019). 5’ regions of amplified cDNA were enriched using NEBNext UltraII FS library prep kit (New England Biolabs) according to the manufacturer’s protocol except using CS1 adapter, trP1 primer, and IonA-BC[N]-CS1-primer for adding sequencing adapters and barcodes. Library concentration was quantified by using the KAPA Library Quantification Kit for Ion Torrent (KAPA Biosystems) according to the manufacture’s instructions.

value: LNGFR positive alveolar epithelial cells

value: lung

tag: transfection

value: mutant surfactant protein C


title: 5’Tag-seq  Mut_1


title: AAGATT: PDX1258_Palbociclib_3.16

description:
well: A07
barcode: AAGATT
PDX1258_Palbociclib_3.16

value: PDX1258 breast cancer PDX

tag: drug treatment

tag: concentration (um)


title: 5’Tag-seq  Mut_2


title: AATACA: HCC1806_DMSO_0.0

description:
well: A09
barcode: AATACA
HCC1806_DMSO_0.0

value: DMSO

tag: time (hours)


title: P18

description: Total RNA including miRNA.


title: P15

description: Total RNA including miRNA.

value: Non-union


title: P14

description: Total RNA including miRNA.


title: input_Control_K562_batch3

description: input DNA control (SE)

value: Hepatocellular carcinoma


title: Capsule_s_1


title: AAATTG: PDX1258_Palbociclib_0.3

description:
well: A05
barcode: AAATTG
PDX1258_Palbociclib_0.3


title: 5’Tag-seq  Ctrl_2

value: control


title: AACAAT: PDX1258_DMSO_0.0

description:
well: A06
barcode: AACAAT
PDX1258_DMSO_0.0


title: AAAGTT: BT549_DMSO_0.0

description:
well: A03
barcode: AAAGTT
BT549_DMSO_0.0

value: BT549 breast cancer cell line


title: AAATAC: BT549_Palbociclib_3.16

description:
well: A04
barcode: AAATAC
BT549_Palbociclib_3.16

value: Palbociclib


title: AAAATC: BT549_Palbociclib_0.3

description:
well: A02
barcode: AAAATC
BT549_Palbociclib_0.3


title: Sample 2: yeast form of S. schenckii

city: Shenyang

first: fangliang

last: zheng

state: Liaoning

address: No. 66 Chongshan Middle Road, Huanggu District

institute: liaoning university

data_processing:
The raw data were filtered using in-house Perl scripts to obtain high-quality clean reads. Adapter sequences were removed from the raw reads. Short or low-quality reads, reads containing an adaptor, reads containing >5% unknown nt “N,” and reads in which >20% of quality values were ≤10 were removed from the raw data to obtain more reliable results. The Q20, Q30, and GC contents of the clean data were calculated. Next, the clean reads were de novo assembled using Trinity software (version v2013-02-25) (Trinity Software, Inc., Plymouth, MA, United States) and clustered with the TGICL clustering tool (Version 2.1) (Institute for Genomic Research, Rockville, MD, United States)
The reference genome and gene model annotation files were downloaded directly from NCBI. The FM index of the reference genome was constructed using Bowtie (Broad Institute, Cambridge, MA). The clean reads were then aligned to the reference genome using TopHat (Broad Institute). During the alignment of reads, seven mismatches and a gap length of 7 bp were allowed. Functional annotations of genetic variants were generated using ANNOVAR.
Gene expression levels were measured through RNA-seq analysis in units of expected number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM). DESeq software was used to identify differentially expressed genes (DEGs). DESeq analysis was performed by fitting normalized count data to a generalized linear model (GLM) and estimating a negative binomial distribution of the calculated mean values of three biologically independent samples. Sequences with fold change >2 and Padj<0.05 (P-values adjusted for multiple testing with the Benjamini–Hochberg procedure) were deemed DEGs.

organism: Sporothrix schenckii

source_name: yeast form of S. schenckii

growth_protocol: To obtain a mycelial culture, the ATCC10268 isolate was inoculated onto Sabouraud dextrose agar (SDA) solid medium and incubated at 25°C. The mycelial colonies thus obtained were inoculated in liquid Sabouraud medium and cultured with shaking at 100 rpm at 25°C for 48 h. To induce the switch of S. schenckii from the mycelial phase to the yeast phase, mycelial culture was enriched and transferred to brain–heart infusion (BHI) liquid medium (Hyclone; GE Healthcare Life Sciences, Logan, UT, USA), which was incubated at 37°C and shaken at 100 rpm for 36 h.

extract_protocol: Not provided

value: yeast


title: Sample 1: hyphal form of S. schenckii

source_name: hyphal form of S. schenckii

value: hyphae


title: P13

description: Total RNA including miRNA.


title: 5’Tag-seq  Ctrl_1


title: 5’Tag-seq  Ctrl_3


title: P16

description: Total RNA including miRNA.


title: genomic DNA from SELENON patients muscles [S4]

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

institute: University of Basel

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina HumanMethylation850 BeadChip using standard Illumina protocol.

data_processing: Data was normalized using preprocessQuantile method using Biconductor package minfi.

source_name: skeletal muscle

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions.

tag: disease state

value: multiminicore disease

tag: mutation

value: SELENON

tag: gender

value: female


title: HEK293T.Cascade_IL1RN_crRNA_26.ctrl.rep3

status: Public on Jun 26 2019

city: Durham

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned using Bowtie v1.0.0 (Langmead et al., 2009), reporting the best alignment with up to 2 mismatches (parameters --best --strata -v 2).
Duplicates were removed using Picard MarkDuplicates v1.130
Low mappability or blacklisted regions identified by the ENCODE project (Consortium, 2012) were filtered out from the final BAM files
Using the sequenced input controls, binding regions were identified using the callpeak function in MACS2 v2.1.0.20151222 (Zhang et al., 2008).
For the differential binding analysis, first, a union peakset was computed merging individual peak calls using bedtools2 v2.25.0 (Quinlan and Hall, 2010). Then, reads in peaks were estimated using featureCounts and the difference in binding was assessed with DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: peaks in narrowPeak format
Supplementary_files_format_and_content: RPKM signal in bigWig format

source_name: HEK293T Cells

growth_protocol: HEK293T cells were acquired from the ATCC and maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were plated into 15 cm dishes prior to transfection.

extract_protocol:
Cells were fixed with formaldehyde and lysed to isolate nuclei. Chromatin was sonicated and immunoprecipitated using an anti-FLAG antibody (M2, Sigma F3165).
Libraries were prepared using the Hyper Prep kit (Kapa Biosystems) and samples were barcoded with Illumina Truseq indexes.

treatment_protocol: HEK293T cells were transfected with 40 µg total plasmid in 15cm dishes and harvested 72 hours later for ChIP.

value: transformed human embryonic kidney cells

tag: chip antibody


title: HEK293T.Cascade_IL1RN_crRNA_26.ctrl.rep1

tag: tissue


title: genomic DNA from SELENON patients muscles [S1]


title: genomic DNA from RYR1 patients muscles [R1]

value: male


title: genomic DNA from RYR1 patients muscles [R7]


title: genomic DNA from SELENON patients muscles [S5]


title: HEK293T.Cascade_IL1RN_crRNA_26.antiFlag.rep3

value: FLAG (M2, Sigma F3165)


title: hAECs + placental basal medium _day0_1

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

description: Gene expression data from untreated control hAECs on day 0

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the top 3000 DEGs between T7 and D0 hAECs and for all DEGs between T7 and D7 hAECs to test whether a priori-defined groups of genes associated with neural differentiation were significantly related to the DEGs between RA-treated and control cells on day 0 and day 7
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HG-U219
program-name = Expression Console
program-version = 1.4.1.46

source_name: Untreated control hAECs on day0

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: AECs were isolated from delivered term placenta and were maintained in Placenta Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) in 2D culture plate. Finally, 3D spheroids were formed by seeding 1×106 AECs in Placenta Basal Epithelial Cell Medium into each well of the 24-well plate.

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour culture, the medium was changed with 20 μM of RA every 48 hours for three times (7days) for the treatment samples. Control samples were maintained in Placental medium that was also changed every 48 hours. Finally, we collected the treatment and control samples from one-week culture. Day 0 control samples were collected after the initial treatment.

value: human amnion epithelial cells (hAECs)

tag: treatment

value: none on day0


title: hAECs + placental basal medium _day7_3

description: Gene expression data from untreated control hAECs on 7th day

source_name: Untreated control hAECs on day7

value: none on day7


title: genomic DNA from normal muscles [C2]

value: normal

value: wild type SELENON and RYR1


title: genomic DNA from SELENON patients muscles [S2]


title: hAECs + placental basal medium _day7_2


title: genomic DNA from SELENON patients muscles [S3]


title: hAECs + placental basal medium _day0_2


title: genomic DNA from normal muscles [C1]


title: genomic DNA from RYR1 patients muscles [R2]


title: genomic DNA from normal muscles [C3]


title: hAECs + placental basal medium _day7_1