title: Aged_patient.6_S34

city: Galveston

first: Helen

middle: Lee

last: Hellmich

state: TX

address: 601 Harborside Dr. Bldg.21 Rm 3.202H

department: Anesthesiology

institute: University of Texas Medical Branch

data_processing:
Conversion from bcl files to fastq and demultiplexing with Illumina Bcl2fastq2 version 2.20.0.422
Adapter trimming and collapsing indentical reads with the mapper.pl function of miRDeep2.0.0.8 using the command “mapper.pl input.fastq -e -v -u -h -k AGATCGGAAGAGCACACGTCT -l 18 -m -s output.collapsed.fasta”
Quantifying miRNA reads with the miRDeep2.0.0.8 quantifier.pl function with the -W parameter, using miRBase release 21.
Genome_build: miRBase Release 21
Supplementary_files_format_and_content: tab delimited table of miRNA read counts

source_name: Serum

extract_protocol:
Total cellular RNA was extracted using  Ribopure (Ambion) according to the manufacturer’s recommendations
New England Biolabs NEBNext Small RNA library Prep following the manufacturer’s protocol

tag: phenotype

value: TBI

tag: time

value: Chronic

value: not determined

tag: race

value: ND

tag: gcs

tag: injury type

tag: subtype

tag: other injuries

tag: biofluid

value: Serum


title: 10B_2729_minus2W_LN

status: Public on Mar 09 2020

type: SRA

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

library_source: transcriptomic

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq v2.20.0.422.
The quality of raw reads was assessed with FastQC v0.11.8.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm.
Normalized expression (normalized read counts) was obtained with DESeq2 v1.22.1.
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

molecule: total RNA

organism: Macaca mulatta

source_name: Lymph Node MNCs

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kits with DNase digest and QIAcube automation stations. RNA was quantified on NanoDrop 2000 spectrophotometer and the quality was assessed by Bioanalyzer analysis.
Set A samples: Libraries were prepared using the Illumina TruSeq mRNA stranded kit, as per manufacturer’s instructions, with 400 ng of total RNA as input. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 16 million reads/sample.
Set B samples: 10 ng of total RNA was used as input for cDNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit. Amplified cDNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 25 million reads/sample.

tag: set

value: B

tag: subject id

tag: siv genotype

value: wt

tag: tissue

value: LN

tag: timepoint (weeks)

tag: infection status

value: uninfected


title: subject ID 00397-0 at diease time point 4_Male, a T1D case and 0.8980151yrs old_450K array [3998909009_R05C01]

type: genomic

city: Aurora

first: Lauren

last: Vanderlinden

state: Colorado

address: 13001 E. 17th Place, Mail Stop B119

department: Department of Biostatistics and Informatics

institute: Colorado School of Public Health

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe (v1.0.0) pipeline was used to normalize data (via Noob), perform dye bias correction and perform probe specific QC (via pOOBAH).
ComBat was used to adjust for batch effects were batch was considered to be plate and row position combination
Filtered probes with a small Beta range (range < 0.05), those with known SNPs in the CpG site, and those located on the sex chromosomes
Mvalues.normalized.*.txt contains methylation M-value

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: T1D case_Male_time point 4

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human450K or EPIC Beadchip using standard Illumina protocol

extract_protocol: Standard Illumina Protocol

tag: disease time point

tag: age

tag: Sex

value: Male

tag: t1d status

value: T1D case

value: peripheral blood sample


title: Aged_patient.3_S31

tag: phenotype

tag: time

tag: years from tbi


title: Control_repA_hyb3_red

type: RNA

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

description:
257046510045_Ary00107_2017-03-31_GE2_1105_Oct12_1_1.txt
GS6M_Ctrl-A3_Cy5

hyb_protocol: Hybridizations were performed on a rotative Agilent Hybridization Oven, for 17h at 65°C, 10g. Afterwards, slides were washed, dried, and scanned according to the manufacturer protocol

scan_protocol: Scanning was performed at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200.

data_processing: Statistical analyses were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. Data were normalized with the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple Granny Smith fruit peel, 6 months cold storage

label_protocol: 200 ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5 mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France). After purification (NucleoSpin Gel and PCR Clean-up column kits, Macherey-Nagel, GmbH & Co. KG, Germany), labelled samples were combined as 30 pmol for each dye and co-hybridized on the array.

growth_protocol: Granny Smith apples were harvested from a commercial orchard at Imathia region (North Greece).

extract_protocol: Total RNA was extracted from 1 g of frozen fruit peel tissue ground in liquid nitrogen using two successive extraction procedures with a CTAB (cetyltrimethylammonium bromide) buffer (Gasic et al., 2004) and then a SSTE buffer (Chang et al., 1993) as described by Nobile et al., 2011 and Segonne et al., 2014.

treatment_protocol:
treatment 1: Harvested apples were treated with 1-MCP (1000 ppm for 24 h at 0 °C) according to manufacturer’s instructions (SmartFresh, AgroFresh Inc., Rohm and Haas, Spring House, USA) .
treatment 2: Cold storage atmosphere was enriched with O3 at 0.3 μL.L-1 (ozone generator model COM-AD-04 and ozone analyser model MP-6060, Anseros Klaus Nonnenmacher GmbH, Tübingen, Germany)
treatment 3: Storage in cold rooms at 0°C and 95% relative humidity (RH) for 6 months.

tag: organ

value: Fruit

value: Peel

tag: genetic background

value: Granny Smith

tag: genotype

value: Wild-type

tag: tissue developmental stage

value: Harvested at physiological maturity (full ripe)

tag: treatment 1

tag: treatment 2

tag: treatment 3

value: 6 months cold storage


title: Serum_TS [TS045]

city: Catania

first: Marco

last: Ragusa

address: Via Santa sofia 87

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

hyb_protocol: Purified and labeled target/probe complexes were hybridized to the manufactuer supplied cartridge, according to the manufactuer's instructions.

scan_protocol: The cartridges were digitally imaged and analyzed using the nCounter Digital Analyzer.

data_processing: Data analysis was performed using nSolver 3.0 software. Quality of raw data was assessed through an evaluation of imaging, binding density, positive control linearity and positive control limit of detection parameters. A code-set normalization was applied to minimize technical noise (variations in purification, binding, hybridization efficiency), according to the nSolver analysis software protocol.

label: color codes

label_protocol: RNA were hybridized to color codes and washed using a two step-magnetic bead method, according to the manufactuer's instructions.

extract_protocol:
Extraction of RNA was carried out from 800 μl of serum samples by using a Qiagen miRNeasy Mini Kit (Qiagen, GmbH, Hilden, Germany), according to Qiagen Supplementary Protocol for purification of total RNA (including small RNAs) from serum and plasma.
MiRNA profiling was performed on 3 μl (approximately 150 ng) of isolated RNA of samples.

tag: subject status

value: Tourette syndromes (TS)

tag: gender

value: M

tag: tissue

value: serum

tag: molecule subtype

value: circulating RNA


title: Serum_ACTS [ACTS001]

value: ACTS

tag: age


title: Serum_TS [TS040]


title: Serum_TS [TS002]


title: Aged_patient.2_S30

value: TBI

value: Chronic

tag: Sex

value: not determined

tag: race

value: ND

tag: gcs

tag: injury type

tag: subtype

tag: other injuries

tag: biofluid

value: Serum


title: Aged_patient.1_S29

tag: phenotype

tag: time

tag: years from tbi


title: Serum_TS [TS001]


title: Control_repB_hyb2_green

description:
257046510043_Ary00106_2017-03-28_GE2_1105_Oct12_1_4.txt
GS6M_Ctrl-B2_Cy3

tag: organ

tag: genetic background

tag: genotype

tag: tissue developmental stage

tag: treatment 1

tag: treatment 2


title: X84_S20

data_processing:
Conversion from bcl files to fastq and demultiplexing with Illumina Bcl2fastq2 version 2.20.0.422
Adapter trimming and collapsing indentical reads with the mapper.pl function of miRDeep2.0.0.8 using the command “mapper.pl input.fastq -e -v -u -h -k AGATCGGAAGAGCACACGTCT -l 18 -m -s output.collapsed.fasta”
Quantifying miRNA reads with the miRDeep2.0.0.8 quantifier.pl function  with the -W parameter, using miRBase release 21.
Genome_build: miRBase Release 21
Supplementary_files_format_and_content: tab delimited table of miRNA read counts

organism: Rattus norvegicus

source_name: Rat hippocampal tissue

tag: treatment

tag: time after treatment

value: 1 year


title: Serum_NC [NC043]

tag: subject status

value: unaffected controls (NC)

tag: age

tag: gender

tag: tissue

tag: molecule subtype


title: Control_repA_hyb2_red

description:
257046510043_Ary00106_2017-03-28_GE2_1105_Oct12_1_3.txt
GS6M_Ctrl-A2_Cy5

value: Fruit

value: Peel

tag: treatment 3


title: X83_S19


title: Forelimbs of E12.5 from cultured embryo for 1 hour, biological rep3

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

institute: University Hospital of Montpellier, Inserm

description:
Gene expression data from forelimbs of E12.5 from cultured embryo for 1 hour
FB_E12.5_1h_3

hyb_protocol: 5.5 ug of cDNA simple brin were hybridized on Affymetrix GeneChip Mouse Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix Expression Console™ following standard Exon Array protocols with Robust Multi-chip Average (RMA) was used to extract probe intensity data

label: biotin

organism: Mus musculus

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

growth_protocol: The procedure for embryo culture was conducted as previously described (Martin and Cockroft 1999).

extract_protocol: RNeasy Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Swiss mouse embryos were obtained from the breeding unit of our animal facility. The experiment was run in triplicate and included the forelimbs of E10.5 mouse embryos, the forelimbs of E10.5 embryos cultured during 1, 3 or 6 hours, the forelimbs of E12.5 mouse embryos and the forelimbs of E12.5 embryos cultured during either, 1 or 3 hours. Selected forelimbs of the appropriate stage were rinsed with PBS prior to be processed RNA extraction.

value: forelimbs from cultured embryo

value: cultured for 1 hours


title: Forelimbs of E12.5 from cultured embryo for 3 hours, biological rep1

description:
Gene expression data from forelimbs of E12.5 from cultured embryo for 3 hour
FB_E12.5_3h_1

value: cultured for 3 hours


title: X1592657_6

tag: phenotype

value: Control

tag: Sex

value: female

tag: race

value: black

tag: gcs

tag: injury type

tag: subtype

tag: other injuries

tag: biofluid


title: X1592656_5

tag: time

tag: years from tbi


title: Forelimbs of E12.5 from cultured embryo for 1 hour, biological rep2

description:
Gene expression data from forelimbs of E12.5 from cultured embryo for 1 hour
FB_E12.5_1h_2


title: Ozone_repA_hyb1_green

description:
257046510043_Ary00106_2017-03-28_GE2_1105_Oct12_1_3.txt
GS6M_O3-A1_Cy3

source_name: Apple Granny Smith fruit peel, 6 months cold storage with enriched ozone atmosphere

tag: organ

tag: genetic background

value: Granny Smith

tag: genotype

value: Wild-type

tag: tissue developmental stage

value: Harvested at physiological maturity (full ripe)

tag: treatment 1

tag: treatment 2

value: Enriched ozone atmosphere

value: 6 months cold storage


title: 1-MCP_ repB_red

description:
257046510043_Ary00106_2017-03-28_GE2_1105_Oct12_1_2.txt
GS6M_MCP-B_Cy5

source_name: Apple Granny Smith fruit peel, 1-MCP treated, 6 months cold storage

tag: tissue

tag: treatment 3


title: Control_repA_hyb1_red

description:
257046510043_Ary00106_2017-03-28_GE2_1105_Oct12_1_1.txt
GS6M_Ctrl-A1_Cy5


title: Forelimbs of E12.5 from cultured embryo for 3 hours, biological rep3

description:
Gene expression data from forelimbs of E12.5 from cultured embryo for 3 hour
FB_E12.5_3h_3

tag: age


title: X82_S18

tag: treatment

value: TBI

tag: time after treatment


title: Control_repB_hyb1_green

description:
257046510043_Ary00106_2017-03-28_GE2_1105_Oct12_1_2.txt
GS6M_Ctrl-B1_Cy3


title: Serum_NC [NC039]

tag: subject status

tag: gender

value: M

value: serum

tag: molecule subtype

value: circulating RNA


title: 1-MCP_repA_green

description:
257046510043_Ary00106_2017-03-28_GE2_1105_Oct12_1_1.txt
GS6M_MCP-A_Cy3

value: Fruit


title: X1592655_4

tag: phenotype

value: Chronic

tag: Sex

tag: race

value: hispanic

tag: gcs

value: ND

tag: injury type

tag: subtype

tag: other injuries

tag: biofluid

value: Serum


title: Forelimbs of E12.5 from cultured embryo for 3 hours, biological rep2

description:
Gene expression data from forelimbs of E12.5 from cultured embryo for 3 hour
FB_E12.5_3h_2

value: forelimbs from cultured embryo

tag: time

value: cultured for 3 hours


title: X1592654_3

value: Control

value: male

value: black

tag: years from tbi


title: X81_S17

value: 1 year


title: Serum_NC [NC030]

value: unaffected controls (NC)

tag: tissue


title: X1592653_2

tag: age


title: X80_S20

tag: treatment

value: Sham surgery


title: X79_S19

tag: time after treatment


title: X1592652_1


title: Serum_ACTS [ACTS010]

tag: subject status

value: ACTS

value: F


title: X77_S17


title: Serum_AC [AC004]

value: Arnold-Chiari (AC)

tag: gender

value: M

value: serum


title: X964.96h_S24

value: TBI

value: 96 hr

value: asian

value: Focal

value: NO


title: X78B_S18


title: tube.59_S16

value: 6 months


title: Forelimbs of E12.5 from non-cultured embryo, biological rep2

description:
Gene expression data from forelimbs of E12.5 from non-cultured embryo
FB_E12.5_0h_2

value: forelimbs from non-cultured embryo

value: cultured for 0 hours


title: Forelimbs of E12.5 from non-cultured embryo, biological rep3

description:
Gene expression data from forelimbs of E12.5 from non-cultured embryo
FB_E12.5_0h_3


title: Forelimbs of E12.5 from cultured embryo for 1 hour, biological rep1

description:
Gene expression data from forelimbs of E12.5 from cultured embryo for 1 hour
FB_E12.5_1h_1

value: forelimbs from cultured embryo

value: cultured for 1 hours


title: X1231.96h_S27z

value: male

value: white

value: YES

value: Serum

value: ND


title: Forelimbs of E12.5 from non-cultured embryo, biological rep1

description:
Gene expression data from forelimbs of E12.5 from non-cultured embryo
FB_E12.5_0h_1


title: X1242.96h_S28z

value: not determined


title: tube.58_S15


title: Serum_ACTS [ACTS009]

value: ACTS

value: M

value: serum

tag: molecule subtype

value: circulating RNA


title: Aged_patient.4_S32

tag: phenotype

value: TBI

value: Chronic


title: Serum_ACTS [ACTS004]


title: X1052.96h_S26

value: 96 hr

tag: Sex

value: Diffuse


title: Serum_NC [NC015]

value: unaffected controls (NC)

value: F


title: Forelimbs of E10.5 from cultured embryo for 6 hours, biological rep3

description:
Gene expression data from forelimbs of E10.5 from cultured embryo for 6 hour
FB_E10.5_6h_3

value: forelimbs from cultured embryo

value: cultured for 6 hours


title: Forelimbs of E10.5 from cultured embryo for 6 hours, biological rep2

description:
Gene expression data from forelimbs of E10.5 from cultured embryo for 6 hour
FB_E10.5_6h_2


title: Serum_NC [NC001]


title: tube.57_S15

value: 6 months


title: Forelimbs of E10.5 from cultured embryo for 3 hours, biological rep1

description:
Gene expression data from forelimbs of E10.5 from cultured embryo for 3 hour
FB_E10.5_3h_1

value: cultured for 3 hours


title: Serum_NC [NC046]


title: X964.48h_S17

value: 48 hr

value: male

tag: race

value: asian

value: Focal

value: NO

value: Serum


title: Serum_ACTS [ACTS012]

value: ACTS

value: serum

value: circulating RNA


title: Forelimbs of E10.5 from cultured embryo for 6 hours, biological rep1

description:
Gene expression data from forelimbs of E10.5 from cultured embryo for 6 hour
FB_E10.5_6h_1


title: tube.55_S14

value: Sham surgery


title: X1249.48h_S23z

value: TBI

value: female

value: white

tag: gcs

value: YES

value: ND


title: Forelimbs of E10.5 from cultured embryo for 3 hours, biological rep2

description:
Gene expression data from forelimbs of E10.5 from cultured embryo for 3 hour
FB_E10.5_3h_2

value: forelimbs from cultured embryo


title: Forelimbs of E10.5 from cultured embryo for 3 hours, biological rep3

description:
Gene expression data from forelimbs of E10.5 from cultured embryo for 3 hour
FB_E10.5_3h_3

value: cultured for 3 hours


title: Serum_ACTS [ACTS011]

value: M


title: tube.54_S13

value: 6 months


title: X1242.48h_S22z

value: 48 hr

value: not determined

tag: injury type


title: X1231.48h_S21z

value: male

tag: subtype

value: Focal


title: tube.60_S16


title: X1038.96h_S25

value: 96 hr

value: hispanic

value: Diffuse

tag: other injuries

value: Serum


title: Aged_patient.5_S33

value: TBI

value: Chronic

tag: biofluid


title: tube.53_S13

value: Sham surgery


title: Serum_ACTS [ACTS003]

value: ACTS

value: serum

value: circulating RNA


title: Serum_ACTS [ACTS008]

value: F


title: Serum_ACTS [ACTS006]

value: M


title: Forelimbs of E10.5 from cultured embryo for 1 hour, biological rep1

description:
Gene expression data from forelimbs of E10.5 from cultured embryo for 1 hour
FB_E10.5_1h_1

value: forelimbs from cultured embryo

tag: time

value: cultured for 1 hours


title: X1141.48h_S20z

value: 48 hr

value: black

value: YES

tag: years from tbi

value: ND


title: X1052.48h_S19

value: male

value: white


title: tube.56_S14

value: 6 months


title: X95_S12

value: TBI

value: 3 months


title: X1038.48h_S18

value: hispanic

value: Diffuse

value: Serum


title: Forelimbs of E10.5 from non-cultured embryo, biological rep2

description:
Gene expression data from forelimbs of E10.5 from non-cultured embryo
FB_E10.5_0h_2

tag: tissue

value: forelimbs from non-cultured embryo

value: cultured for 0 hours


title: Serum_AC [AC008]

value: Arnold-Chiari (AC)

tag: age

value: M

value: serum

value: circulating RNA


title: Serum_ACTS [ACTS007]

value: ACTS


title: X999

value: 24 hr

value: Focal


title: X52_S11

tag: treatment


title: Forelimbs of E10.5 from cultured embryo for 1 hour, biological rep3

description:
Gene expression data from forelimbs of E10.5 from cultured embryo for 1 hour
FB_E10.5_1h_3

value: forelimbs from cultured embryo

value: cultured for 1 hours


title: Forelimbs of E10.5 from non-cultured embryo, biological rep3

description:
Gene expression data from forelimbs of E10.5 from non-cultured embryo
FB_E10.5_0h_3


title: Forelimbs of E10.5 from cultured embryo for 1 hour, biological rep2

description:
Gene expression data from forelimbs of E10.5 from cultured embryo for 1 hour
FB_E10.5_1h_2


title: X60_S10

value: Sham surgery

tag: time after treatment


title: SMSC-5d

city: Chengdu

first: Xun

last: Wang

state: China

address: Huimin road 211#, Wenjiang district

country: China

institute: Sichuan agricultural university

description: micRNA-derived 5d pigeon skeletal muscle satellite cells

data_processing:
initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences were then mapped to pigeon reference genome (Columba livia, ColLiv2, GenBank assembly accession: GCA_001887795.1)  with stringent criteria (0 mismatch for full length) using Bowtie software.
Next, mappable reads were extended in the reference genome as predicted miRNA precursors. Only candidate precursors that perfectly matched to known pigeon (Columba livia) mature miRNAs annotated by miRBase (Release 22.0) were identified as known pigeon miRNAs (Kozomara A, et al. 2019). Subsequently, to identify the conserved miRNAs, we performed alignments between remaining candidate precursors and seed sequences of mature miRNAs from chicken (Gallus gallus), zebra finch (Taeniopygia guttata) and other mammals, allowing no mismatch.
Genome_build: Genome database:pigeon genome (assembly GCA_001887795.1); miRbase version: V22.0
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads

organism: Columba livia

source_name: skeletal muscle satellite cells

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
The quantity of total RNA was assessed using an Agilent 2100 Bioanalyzer with Agilent RNA 6000 nano Reagents Part 1 kit (Agilent Technologies, USA). For samples of high-throughput sequencing, the RNAs from three replicates at each differentiation stage were pooled as one RNA sample. For each library, small RNA ranging from 10-45 nt in length was purified by polyacrylamide gel electrophoresis and ligated using proprietary adaptors. The modified small RNA was then reverse-transcribed to cDNA and amplified by PCR. Finally, the libraries were sequenced on a BGIseq-500 sequencing platform.

treatment_protocol: 16-day-old pigeon embryos were dissected, followed by removing bilateral pectoral muscles and soaking in PBS (Hyclone, Utah, USA). The pectoral muscles were finely minced and dissociated in Dulbecco’s modified Eagle’s medium(DMEM) containing 0.1% collagenase type IV (Sigma, MO, USA) for about 45 min. Subsequently, cell suspension was filtered twice using a 40-μm nylon mesh (BD, Falcon™) to remove debris. The cells were collected by centrifugation at 1500 r·min–1 for 5 min at room temperature and resuspended in DMEM (Hyclone, Utah, USA) containing 20% fetal bovine serum (FBS) (Natocor, Villa Carlos Paz, Argentina) with 100 U/mL penicillin and 100 μg/mL streptomycin (Solarbio, Beijing, China). Subsequently, cells were seeded in 96-well plates at a concentration of 3,000 cells per well and cultured in CO2 incubator (Thermo, USA) at 37°C and 5% CO2 with saturating humidity. The culture medium was refresh every 48 h until the fifth day.

value: pectoral muscles

tag: cell type

value: skeletal muscle satellite cells

tag: developmental stage


title: miRNA of MZdgcr8 2

city: Hong Kong

first: Christopher H.K.

last: Cheng

address: Rm604,39 zone, CUHK, Shatin

institute: The Chinese University of Hong Kong

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

organism: Danio rerio

source_name: Embryo

extract_protocol:
small RNA was extracted from MZdcgr8 and Wild-type embryos ( 50 embryos per sample) at 30% epiboly stage of early development representing 4.5 hpf using miRNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: AB

value: embryo

tag: genotype


title: X62_S11

value: TBI

value: 3 months


title: Serum_AC [AC001]

tag: subject status

tag: gender

tag: molecule subtype


title: SMSC-1d

description: micRNA-derived 1d pigeon skeletal muscle satellite cells


title: miRNA of MZdgcr8 1


title: X57_S9


title: Forelimbs of E10.5 from non-cultured embryo, biological rep1

description:
Gene expression data from forelimbs of E10.5 from non-cultured embryo
FB_E10.5_0h_1

value: forelimbs from non-cultured embryo

value: cultured for 0 hours


title: X94_S12


title: X9931

tag: phenotype

tag: Sex

value: not determined

value: ND

tag: race

tag: gcs

tag: injury type

value: UNSURE

value: Serum


title: ChIP-seq-input-for-25_29

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: ChIP-seq input

library_source: genomic

data_processing:
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg19 and mouse mm9 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, plotProfile (Ramírez et al., 2016). ChIP-seq peaks were called using MACS 2.1.0 (Zhang et al., 2008) with a q-value cutoff of 0.05. Peaks were annotated using HOMER 4.10 (Heinz et al., 2010).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg19 and fly dm3 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome. Protein coding transcripts were chosen from Ensembl version 75 database by R 3.3.3, according to the previously described protocol (Liang et al., 2018) with minor modifications. Briefly, we selected RefSeq-validated transcripts with TSSs that overlapping NELF-C ChIP-seq peaks. We filtered out transcripts that are ≤ 2 kb long and ≤ 2 kb away from the nearest genes. Next, we chose transcripts that have ≥ 2 rpm total PRO-seq coverage at the region between TSS – 100 bp and TSS + 300 bp, using 3 independent PRO-seq data in untreated NELF-C-AID cells. In these selected transcripts, the nucleotide position with maximum PRO-seq coverage in the region between TSS – 100 bp and TSS + 300 bp was assigned to the 1st pause region. Transcripts that have ≤ 0.2 rpm coverage at the 1st pause region nucleotide were excluded. The resulting transcripts with assigned the 1st pause regions were used for further analyses. The nucleotide positions with maximum PRO-seq coverage in 1h auxin-treated NELF-C-AID cells at the region from +10 to +500 bp downstream of the 1st pause region was assigned to the 2nd pause region. For Heat shock experiments, transcripts with ≥ 1.5-fold increase or decrease in PRO-seq coverage at gene bodies (the 1st pause regions +500 to +100kb or to transcription termination sites) upon heat shock were assigned to HS-upregulated or HS-downregulated genes, respectively. Heatmaps and metaplots of PRO-seq signals were generated by deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, and plotProfile (Ramírez et al., 2016). Log2 fold change of PRO-seq signals at nucleotide resolution were calculated by deepTools 3.0.0/3.1.1/3.1.2 bigwigCompare with pseudocount 0.25 rpm.
For PRO-cap, raw reads were processed as described for PRO-seq above, requiring a read length of 18–36 bp. Processed paired-end reads were aligned to a concatenated genome comprised of hg19 and dm3 assemblies using bowtie2 with options (--very-sensitive -X 1000 --no-mixed --no-discordant --no-unal) (Langmead and Salzberg, 2012). The 5’ ends of aligned R2 reads with MAPQ ≥ 40 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options. Read counts were normalized to total reads aligned to the spike-in genome. de novo transcription start sites were identified from PRO-cap data using HOMER 4.11 with findcsRNATSS option (Duttke et al., 2019; Heinz et al., 2010). TSS identified in untreated and auxin-treated samples were merged then defined as TSS regions. Distances between TSS in each sample were measured using HOMER 4.11 annotatePeaks. Raw PRO-cap reads were counted using HOMER 4.11 annotatePeaks. Read counts were normalized to spike-in counts using RUVseq with RUVg option (Risso et al., 2014) in R 3.3.3. Differential expression analysis was performed using DESeq2 (Love et al., 2014) and visualized in R 3.3.3. TSS with significant gain of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Up TSS, while TSS with significant loss of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Down TSS. Metaplots of PRO-cap and PRO-seq at Cap Up TSS or Cap Down TSS were generated using deepTools 3.1.1. For heatmaps of ChIP-seq and MNase-seq at TSS, TSS were first merged with gap of no longer than 600 bp to obtain TSS clusters, heatmaps were then generated at Cap Up TSS clusters and Cap Down TSS clusters.
Genome_build: hg19, dm3, mm9
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

growth_protocol: DLD-1 cells were grown in DMEM (Corning) supplemented with 10% FBS (Corning), 1X GlutaMAX (Gibco), 2 µg/ml puromycin (Gibco), 100 U/ml Penicillin and 100 µg/ml Streptomycin (Gibco).

extract_protocol:
For ChIP-seq, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples as described previously (Orlando et al., 2014) for NELF-C, NELF-E, SPT5, Pol II CTD Ser2P, Pol II CTD Ser5P, XRN2, DCP2 ChIP-seq in NELF-C-AID cells. Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Protein A/G-agarose beads (Santa Cruz) or Dynabeads Protein G (Invitrogen).  PRO-seq sample preparation was performed according to the previously published protocol (Mahat et al., 2016b) with minor modifications. 10 million DLD-1 nuclei were mixed with spike-in Drosophila S2 nuclei. Nuclear run-on assay was performed with 4 biotinylated nucleotides (PerkinElmer). 5’ cap was removed by RppH (NEB).  PRO-cap libraries were prepared as described previously (Kwak et al., 2013; Mahat et al., 2016b) with minor modifications. NELF-C-AID cells were treated with or without 500 µM auxin for 2 h, followed by nuclear extraction. ~10 million NELF-C-AID nuclei with 0.5 million spike-in drosophila S2 nuclei were subjected to nuclear run-on reaction.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA) and sequenced on the NextSeq 500 or NovaSeq 6000 (Illumina). For PRO-seq, adapter sequences previously described (Mahat et al., 2016) were used. DNA Libraries were size selected by PippinHT (Sage) or AMpure XP (Beckman Coulter) and sequenced on a NextSeq 500 (Illumina). For PRO-cap, PRO-seq adapter sequences were used instead of PRO-cap adapters. Libraries were then sequenced by NextSeq 500 in paired-end sequencing mode.

treatment_protocol: Cells were treated with 500 µM Auxin (3-indole-acetic acid sodium salt, abcam), 1 µM Flavopiridol (Cayman), or 250 nM NVP-2 (MedChemExpress). Heat shock treatment at 42 ˚C for 1 h was carried out as described previously (Mahat et al, 2016)

value: Colorectal adenocarcinoma

value: NELF-C-AID OsTIR1

value: Auxin

tag: cell line


title: X48_S9


title: Serum_AC [AC006]

value: Arnold-Chiari (AC)

value: F

tag: tissue

value: serum

value: circulating RNA


title: Serum_AC [AC005]

tag: age

value: M


title: miRNA of MZdgcr8 3

value: AB

value: embryo


title: X9993

value: TBI

tag: time

value: 24 hr

value: male

value: white

tag: subtype

value: Focal

tag: other injuries

tag: biofluid

tag: years from tbi


title: ChIP-seq-input-for-24_28

description: ChIP-seq input

tag: cell type

tag: genotype


title: X9911

value: female

value: hispanic

value: ND


title: X78A_S10

tag: treatment

value: Sham surgery

tag: time after treatment

value: 3 months


title: miRNA of Wild-type 3

tag: strain

value: wild type


title: X750_S28

value: 2 months


title: miRNA of Wild-type 1


title: miRNA of Wild-type 2


title: ChIP-seq-input-for-23_27

description: ChIP-seq input

value: Colorectal adenocarcinoma

value: NELF-C-AID OsTIR1

value: Auxin


title: X748_S27


title: X1027

tag: phenotype

tag: Sex

value: Serum


title: ChIP-seq-input-for-22_26

description: ChIP-seq input


title: X749_S28


title: X1022

tag: race

value: black

tag: gcs


title: X747_S27

value: TBI


title: X1028

value: 24 hr

tag: injury type


title: ChIP-seq-28-NELFC-AID-untreated-DCP2-rep2

description: ChIP-seq DCP2

tag: antibody

value: DCP2 (Bethyl, A302-597A)

tag: cell line


title: ChIP-seq-27-NELFC-AID-treated-DCP2-rep1

description: ChIP-seq DCP2


title: ChIP-seq-29-NELFC-AID-treated-DCP2-rep2

description: ChIP-seq DCP2


title: X1016

tag: time

tag: age

value: white

value: Diffuse


title: X776_S26


title: ChIP-seq-26-NELFC-AID-untreated-DCP2-rep1

description: ChIP-seq DCP2


title: X1013

value: male

tag: subtype

tag: other injuries


title: X752_S25


title: X10050

value: female

value: hispanic

tag: biofluid

tag: years from tbi


title: ChIP-seq-24-NELFC-AID-untreated-XRN2-rep2

description: ChIP-seq XRN2

tag: cell type

tag: genotype

value: XRN2 (Bethyl, A301-103A)


title: X777_S26

tag: treatment

value: Sham surgery

tag: time after treatment


title: ChIP-seq-25-NELFC-AID-treated-XRN2-rep2

description: ChIP-seq XRN2


title: X1025

tag: phenotype

value: Focal

value: ND


title: 140220-131323A_IN3_(PrimeView)

city: Guangzhou

first: Shangbiao

last: Li

address: Department of Radiation Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, China

department: Department of Radiation Oncology

institute: Southern Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Lung cancer cell lines were cultured in RPMI-1640 medium (Corning, NY, USA) containing 10% fetal bovine serum (FBS, GIBCO, South America, NY, USA) under a 5% CO2 atmosphere at 37°C.

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

treatment_protocol: Lung cancer cells were transfected with antagomir-744 or antagomir-NC designed and synthesized by RiboBio (Guangzhou, China)

tag: tissue

value: Advanced lung cancer cells

tag: transfection


title: X10018

tag: Sex

tag: race

tag: gcs


title: X964.24h_S1

value: asian

tag: injury type

value: NO


title: ChIP-seq-23-NELFC-AID-treated-XRN2-rep1

description: ChIP-seq XRN2

value: Colorectal adenocarcinoma

value: NELF-C-AID OsTIR1

value: Auxin

tag: antibody

tag: cell line


title: X768_S24

value: TBI

value: 1 month


title: X1249.24h_S8z

tag: time

value: 24 hr

tag: age

value: white

tag: subtype

value: YES

value: Serum


title: X757_S23


title: ChIP-seq-22-NELFC-AID-untreated-XRN2-rep1

description: ChIP-seq XRN2


title: human_302OE3

city: Houston

first: Rachel

last: Keuls

address: One Baylor Plaza, Alkek N1020

institute: Baylor College of Medicine

description:
Chick_NormalizedCounts.xlsx
Chick_NormalizedCounts_AlignedHuman.xlsx

data_processing:
Illumina FastQ generation v1.0.0 was used to generate .fastq files from each lane of the flow cell which were subsequently concatenated for each read 1 and read2 for each sample
FastQC v0.11.5 was used to check read quality.CutAdapt was used to trim off adapters
STAR 2.7.0f was used for alignment
SummarizeOverlaps was used to produce a summarized experiment object
count matrix was constructed and CPM was normalized for read depth
Genome_build: hg38/Gal5
Supplementary_files_format_and_content: Normalized counts when alinged to either the chick or human genome to detect miR-302 deletion or overexpression respectively

organism: Gallus gallus

source_name: chicken embryo sorted cells

growth_protocol: Embryos were allowed to develop until HH4-5

extract_protocol:
Total RNA was extracted from sorted cells using the Qiagen miRNeasy Mini Kit protocol as stated except that Trizol-LS was used instead of Qiazol and RNA was eluted off the column in 11ul.
half of the toal RNA obtained was used as input for the NEXTflex® Small RNA-Seq Kit v3 from Bioo Scientific. The protocol was followed as stated and gel extraction was used for size selection

treatment_protocol: Emrbyos were electroporated with a GFP expression vector and costructs to either delete chick miR-302 or overexpress human miR-302. Cells were sorted directly into trizol and miR-302 expression of GFP positice cells was compared to tat of the GFP negative cells

value: chicken embryo sorted cells

tag: gfp

value: GFP positive

tag: genotype/variation

value: overexpress human miR-302


title: 140220-131323A_NC3_(PrimeView)

source_name: cells were transfected with antagomir-NC

value: antagomir-NC


title: X1242.24h_S7z

value: not determined

value: ND

value: Focal

tag: other injuries

tag: biofluid

tag: years from tbi


title: human_302OE3_Control

tag: cell type

value: GFP negative


title: human_302OE2_Control


title: human_302OE2


title: X769_S24

tag: treatment

tag: time after treatment


title: X1231.24h_S6z

tag: phenotype

tag: Sex

value: male


title: 140220-131323A_IN2_(PrimeView)

source_name: cells were transfected with antagomir-744

tag: tissue

value: Advanced lung cancer cells

tag: transfection


title: X751_S25

value: Sham surgery

value: 2 months


title: Dog_11_CD5-CD21+

city: Philadelphia

first: Ying

last: Wu

state: Pennsylvania

address: 3900 Spruce Street

institute: University of Pennsylvania

data_processing:
Sequence reads were trimmed using Skewer v0.1.125 to remove adaptor and achor sequences, then mapped to canine genome, CanFam3.1, using HISAT2 v2.0.0-beta.
The mapped read pairs were quantified using featureCounts v1.5.0, and annotated using the same canine genomic data.
Mapping matrics were generated using Picard Tools v1.92. The metrics and variants for assessing read distribution, biotype distribution and mapped transcripts were generated using R v3.4.2.
Read counts were all converted to transcripts per milllion (TPM).
Genome_build: CanFam3.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Canis lupus

source_name: lymph node

extract_protocol:
CD5-CD21+ cells were sorted from fine needle aspirated lymph node cells and sorted by FACS. Total RNA was extracted from cells using RNA Bee and Direct-zol RNA MicroPrep Kit.
RNA libraries were generated following standard Illumina protocols.

tag: animal

value: Dog_11_B cell lymphoma


title: Dog_10_CD5-CD21+

value: Dog_10_B cell lymphoma


title: human_302OE1_Control


title: X756_S23

value: TBI

value: 1 month


title: X1141.24h_S5z

value: 24 hr

tag: race

value: black

tag: gcs

tag: injury type

value: YES

value: Serum


title: 140220-131323A_NC1_(PrimeView)

value: antagomir-NC


title: X794_S22


title: 140220-131323A_IN1_(PrimeView)


title: Dog_9_CD5-CD21+

value: Dog_9_B cell lymphoma


title: human_302OE1

value: chicken embryo sorted cells

value: GFP positive

value: overexpress human miR-302


title: 140220-131323A_NC2_(PrimeView)


title: X1108.24h_S4

tag: time

value: not determined

tag: age

value: ND

tag: subtype

value: Focal


title: Dog_8_CD5-CD21+

value: Dog_8_B cell lymphoma


title: chick_302KO3_Control

tag: gfp

value: GFP negative

tag: genotype/variation

value: chicken miR-302 knocked-down


title: X784_S21

value: Sham surgery


title: Dog_7_CD5-CD21+

value: Dog_7_B cell lymphoma


title: X1038.24h_S2

value: TBI

value: 24 hr

value: male

value: hispanic

value: Diffuse

tag: other injuries

tag: biofluid

tag: years from tbi


title: X795_S22

tag: treatment

tag: time after treatment

value: 1 month


title: X1052.24h_S3

tag: phenotype

tag: Sex

value: white

value: YES

value: Serum


title: Dog_6_CD5-CD21+

value: Dog_6_B cell lymphoma


title: BRH.1429989_S14

value: Control

value: 0 hr

value: female

value: ND


title: Dog_5_CD5-CD21+

value: Dog_5_B cell lymphoma


title: X783_S21

value: Sham surgery


title: chick_302KO2_Control

tag: cell type

value: chicken embryo sorted cells

value: GFP negative

value: chicken miR-302 knocked-down


title: tube.23_S8

value: TBI

value: 2 weeks


title: BRH.1429988_S13

value: hispanic


title: Dog_4_CD5-CD21+

tag: animal

value: Dog_4_B cell lymphoma


title: Dog_3_CD5-CD21+

value: Dog_3_B cell lymphoma


title: tube.22_S7


title: chick_302KO1_Control


title: tube.24_S8


title: chick_302KO2

value: GFP positive


title: BRH.1429986_S11

value: male

tag: race

value: Serum


title: chick_302KO1


title: BRH.1429987_S12

value: Control


title: Dog_2_CD5-CD21+

value: Dog_2_B cell lymphoma


title: Naïve CD4 T cells, PIK3CD GOF mutant 4

city: Chongqing

first: Xiaodong

last: Zhao

state: Chongqing

address: No.136, Zhongshan 2nd Rd, Yuzhong District

institute: Chongqing Medical University

data_processing:
Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the mouse mm10 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: mm10
Supplementary_files_format_and_content: counts, FPKMs

source_name: Naïve CD4 T cells

growth_protocol: All experiments were performed with gender and aged-matched littermate controls (8 week). All mice were kept in a specific pathogen-free environment.

extract_protocol:
Naive CD4+ T cells in the spleen were negatively isolated ex vivo(Stemcell Technologies).Total RNA from isolated naive CD4+ T cells was extracted using RNeasy Plus Mini Kit according to the manufacture’s instruction and checked for RNA integrity by an Agilent Bioanalyzer 2100 . Qualified total RNA was further purified by RNeasy micro kit (QIAGEN) and RNase-Free DNase Set (QIAGEN). Paired-end libraries were constructed using the TruSeq® RNA Sample Preparation Kit (Illumina, USA)by the Shanghai Biotechnology Corporation (Shanghai, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No special treatment

tag: strain

tag: tissues

value: Spleen

value: 8-week old

tag: genotype

value: PIK3CD GOF (heterozygous)

value: Naive CD4 T cells


title: BRH.1429985_S10

tag: time

value: 0 hr

tag: age

tag: injury type

value: ND


title: X9961

value: 24 hr

value: not determined

tag: gcs

tag: subtype

value: UNSURE


title: chick_302KO3

value: chicken embryo sorted cells

tag: gfp

tag: genotype/variation

value: chicken miR-302 knocked-down


title: Naïve CD4 T cells, PIK3CD GOF mutant 3


title: tube.20_S6

tag: treatment

value: Sham surgery

value: 2 weeks


title: BRH.1429984_S9

value: male

value: black

tag: biofluid

tag: years from tbi


title: Dog_1_CD5-CD21+

value: Dog_1_B cell lymphoma


title: tube.18_S5

tag: time after treatment


title: X12256

source_name: CSF

tag: phenotype

value: TBI

tag: Sex

value: white

value: Focal

tag: other injuries

value: YES

value: CSF


title: X12176

tag: race

value: hispanic

value: Diffuse


title: Naïve CD4 T cells, Wild-type 3

tag: strain

tag: tissues

value: Spleen

value: 8-week old

value: Wild-type

tag: cell type

value: Naive CD4 T cells


title: Naïve CD4 T cells, PIK3CD GOF mutant 1

tag: age

tag: genotype

value: PIK3CD GOF (heterozygous)


title: X12108

tag: time

value: 24 hr

tag: gcs

tag: injury type

value: ND


title: Ps_ALD_M1

city: Boston

first: James

last: Galagan

state: MA

address: 44 Cummington Mall

department: Biomedical Engineering

institute: Boston University

description: Extracted from P. simplex with hormone at beginning of stationary phase

data_processing:
Adaptor sequences were removed from reads and low quality bases trimmed from both ends using Cutadapt
Reads were aligned to the reference genome with Bowtie2
BAM files were sorted and indexed using Samtools
Transcript assembly and expression quantification was performed using Cufflinks
All resulting raw expression counts were normalized as a group using deseq
A custom MATLAB script was then used to calculate fold changes of normalized counts for each gene between each sterol exposure experiment and its corresponding vehicle control.
Genome_build: CP009896.1 (GenBank)
Supplementary_files_format_and_content: custom MATLAB script output and .xlsx file containing deseq, fpkm, tpm, counts, fold change, and log fold change values

organism: Pimelobacter simplex

source_name: purified RNA

growth_protocol: 6 mL M3 media inoculated with OD 0.005 P. simplex

extract_protocol:
P. simplex total RNA was extracted using RNeasy Protect Bacteria Mini Kit (Qiagen) by enzymatic lysis
ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina)

treatment_protocol: Inoculations done with and without hormone and incubated for 17 hours at 26oC, 150 RPM

tag: hormone

value: yes


title: Naïve CD4 T cells, Wild-type 2


title: X460_S4

tag: treatment


title: X454_S3


title: Ps_PRG_M1


title: X12104

value: male

tag: subtype

tag: biofluid


title: X12190

value: NO

tag: years from tbi


title: mRNA of MZdgcr8 3

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

extract_protocol:
Total RNA was extracted from MZdcgr8 and Wild-type embryos ( 50 embryos per sample) at 30% epiboly stage of early development representing 4.5 hpf using RNeasy Mini Kit(Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB

tag: tissue

value: embryo


title: BRH.1386873

tag: phenotype

value: Control

value: 0 hr

tag: Sex

value: female


title: X593_S4

value: TBI

tag: time after treatment


title: Ps_ESL_M1

tag: strain


title: mRNA of MZdgcr8 2


title: Ps_CRT_M1


title: BRH.1386872

tag: race

value: hispanic

tag: other injuries

value: CSF


title: tube.19_S6

value: Sham surgery

value: 2 weeks


title: Ps_ESE_M1


title: mRNA of MZdgcr8 1

tag: age


title: tube.17_S5


title: BRH.1386871

value: black


title: X461_S1


title: Naïve CD4 T cells, PIK3CD GOF mutant 2

tag: tissues

value: Spleen

value: 8-week old

tag: genotype

value: PIK3CD GOF (heterozygous)

tag: cell type

value: Naive CD4 T cells


title: mRNA of Wild-type 3

value: wild type


title: Psim_WM

data_processing:
Reads aligned to GenBank ID CP009896.1 using bowtie2 and samtools
Coverage displayed using igvtools and genomeview
Determined peak regions visually on genome browser
Took coordinates for peak calls in region of interest
Top peaks compiled in .xlsx file
Genome_build: CP009896.1 (GenBank)
Supplementary_files_format_and_content: .xlsx file containing identified peak region and coordinates

source_name: purified genomic DNA

growth_protocol: P. simplex grown in M3 broth for 3 days.

extract_protocol:
P. simplex genomic DNA was extracted using GenElute Bacteria Kit (Sigma). protein was purified from Ecoli 10G cells using Qiagen Ni-NTA Fast Start Kit
Standard NEBNext library prep protocol for Illumina

treatment_protocol: Extracted genomic DNA was sheared using Covaris to optimal length.

value: VKM Ac-2033D

tag: antibody

value: 6x-His Tag Monoclonal Antibody (HIS.H8)/ThermoFIsher/MA1-21315

tag: genotype/variation

value: control


title: mRNA of Wild-type 2

value: AB

value: embryo


title: Naïve CD4 T cells, Wild-type 1

value: Wild-type


title: BRH.1425634_S16

data_processing:
Conversion from bcl files to fastq and demultiplexing with Illumina Bcl2fastq2 version 2.20.0.422
Adapter trimming and collapsing indentical reads with the mapper.pl function of miRDeep2.0.0.8 using the command “mapper.pl input.fastq -e -v -u -h -k AGATCGGAAGAGCACACGTCT -l 18 -m -s output.collapsed.fasta”
Quantifying miRNA reads with the miRDeep2.0.0.8 quantifier.pl function with the -W parameter, using miRBase release 21.
Genome_build: miRBase Release 21
Supplementary_files_format_and_content: tab delimited table of miRNA read counts

value: Control

tag: time

value: 0 hr

value: female

value: white

tag: gcs

value: ND

tag: injury type


title: Psim_AIY

value: with SRTF1


title: X457_S1

tag: treatment

value: Sham surgery


title: BRH.1425633_S15

value: male

value: hispanic

tag: subtype

tag: biofluid

value: CSF

tag: years from tbi


title: mRNA of Wild-type 1

tag: tissue

value: wild type


title: P15_post_T

status: Public on Mar 08 2020

first: Dongqiang

last: Zeng

state: Guangdong

address: NO.1838 North Guangzhou Avenue

department: Medical oncology

description:
Patient 15 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt

data_processing:
FASTQ files were mapped by Hisat2
Hisat BAMs were quantified using HTSeq v0.6.0
Genome_build: GRCh37
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

source_name: Tumor biopsy_liver metastatic_colorectal cancer

extract_protocol:
Total RNA was extracted from tissue specimens using Trizol and digested with DNase I. Then mRNA was purified from total RNA using oligo(dT)-attached magnetic beads and then fragmented.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s protocols.

treatment_protocol: mFOLFOX6 ± Bevacizumab

tag: study site

value: UCLA

value: colorectal cancer liver metastasis tumor

tag: biopsy time

tag: bor

value: PR

tag: subject id

value: Patient 15


title: P15_pre_T

description:
Patient 15 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt


title: P14_pre_T

description:
Patient 14 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt

value: Baseline

value: Patient 14


title: P14_post_T

description:
Patient 14 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt

value: SD


title: X594_S2

extract_protocol:
Total cellular RNA was extracted using  Ribopure (Ambion) according to the manufacturer’s recommendations
New England Biolabs NEBNext Small RNA library Prep following the manufacturer’s protocol

tag: time after treatment


title: tube.21_S7

value: TBI

value: 2 weeks


title: Ps_CNTL_M1

description: Extracted from P. simplex without hormone at beginning of stationary phase

tag: strain

tag: hormone

value: no


title: P13_pre_T

description:
Patient 13 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt

value: Patient 13


title: P12_post_T

description:
Patient 12 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt

value: Patient 12


title: P13_post_T

description:
Patient 13 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt


title: MyH3delta/delta replicate6 Dia

city: Faridabad

first: Sam

middle: J

last: Mathew

state: Haryana

address: NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway,

department: Developmental Genetics

country: India

institute: Regional Centre for Biotechnology

data_processing:
Reads were aligned to mm10 + splice junctions using pysano (Alignments/Raw)
Spliced alignments were converted back to space, poor quality and repetitive alignments were dropped using USeq's SamTranscriptomeParser (Alignments/Processed)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Normalized coverage tracks (coverage per million mapped reads) were created using Sam2USeq and USeq2UCSCExe (CoverageTracks).
Differential expression was determined using USeq's DefinedRegionDifferentialSeq (Analysis/Tables).
Counts were extracted and used in a paired-sample differential expression analysis.
RNASeq metrics were generated using Picard's CollectRnaSeqMetrics.
Samples were clustered using custom R scripts (Analysis/Plots).
Signficiant genes were run in IPA to generate pathway analyses.
Genome_build: mm10
Supplementary_files_format_and_content: excel files with counts, 0-5 represents replicate 1-6, respectively

source_name: Diaphragm muscle

extract_protocol:
Muscles were isolated from P0 stage neonates, flash frozen in liquid nitrogen, and RNA was harvested using the Qiagen RNEasy Lipid Tissue Mini kit.
Library preparation was performed using the Illumina TruSeq Stranded mRNA sample preparation kit with oligo dT selection

value: Skeletal Muscle

tag: age

value: Postnatal day 0

tag: genotype


title: MyH3delta/delta replicate6 Quad

source_name: Quadriceps muscle


title: X453_S3


title: X599_S2

value: Sham surgery


title: MyH3+/+ replicate 6 Dia


title: MyH3delta/delta replicate6 Gastroc

source_name: Gastrocnemius muscle


title: P10_pre_T

description:
Patient 10 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt

value: Patient 10


title: P07_post_T

description:
Patient 7 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt

value: PD

value: Patient 7


title: P11_post_T

description:
Patient 11 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt

value: UCLA

value: colorectal cancer liver metastasis tumor

value: Patient 11


title: MyH3delta/delta replicate6 TA

source_name: Tibialis Anterior muscle


title: MyH3delta/delta replicate5 Dia


title: P14_3rd_T

description:
Patient 14 liver metastatic colorectal cancer, post mFOLFOX treatment, 3rd biopsy
matrix file.txt


title: MyH3+/+ replicate 6 TA

value: wild type


title: P06_pre_T

description:
Patient 6 liver metastatic colorectal cancer, pret mFOLFOX treatment, 1st biopsy
matrix file.txt

value: Baseline

value: Patient 6


title: MyH3+/+ replicate 6 Gastroc


title: P08_post_T

description:
Patient 8 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt

value: SD

value: Patient 8


title: MyH3delta/delta replicate5 Gastroc


title: P06_post_T

description:
Patient 6 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt


title: P10_post_T

description:
Patient 10 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt


title: P04_post_T

description:
Patient 4 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt

value: PR

value: Patient 4


title: MyH3+/+ replicate 5 Dia


title: P04_3rd_T

description:
Patient 4 liver metastatic colorectal cancer, post mFOLFOX treatment, 3rd biopsy
matrix file.txt


title: P03_pre_T

description:
Patient 3 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt

value: Patient 3


title: MyH3+/+ replicate 5 Gastroc

value: Skeletal Muscle


title: MyH3+/+ replicate 5 Quad

value: Postnatal day 0


title: P03_post_T

description:
Patient 3 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt


title: P03_3rd_T

description:
Patient 3 liver metastatic colorectal cancer, post mFOLFOX treatment, 3rd biopsy
matrix file.txt


title: MyH3+/+ replicate 5 TA


title: P07_pre_T

description:
Patient 7 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt


title: MyH3+/+ replicate 6 Quad


title: MyH3delta/delta replicate4 Dia


title: P02_pre_T

description:
Patient 2 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt

value: Patient 2


title: MyH3delta/delta replicate4 Gastroc


title: MyH3delta/delta replicate4 TA


title: MyH3delta/delta replicate4 Quad


title: LISHU-KO-2-INPUT

city: Wuhan

first: Shu

state: Hubei

address: Donghu Road 185

department: Department of Immunology

institute: liver

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using …; Scores represent …

source_name: liver cells

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

treatment_protocol: The C57 and FCNAKO of mouse liver 0.3g, grinding, cracking obtain mouse liver protein. DNA was crosslinked with protein by 1.5% formaldehyde. The protein was digested by micrococcal nuclease and broken into fragments about 200 bp in size by ultrasound. Then the antibodies were incubated, DNA fragments were enriched and sequenced.

tag: genotype/variation

value: ficolinA ko

tag: chip antibody


title: P01_pre_T

description:
Patient 1 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt

value: Patient 1


title: MyH3+/+ replicate 4 Gastroc


title: MyH3delta/delta replicate5 TA


title: P01_post_T

description:
Patient 1 liver metastatic colorectal cancer, post mFOLFOX treatment, 2nd biopsy
matrix file.txt


title: P04_pre_T

description:
Patient 4 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt


title: LISHU-KO-2-H3K27ME3

value: H3K27me3 (Cell Signaling Technology, Cat# 9733)


title: MyH3+/+ replicate 4 Dia


title: LISHU-KO-1-H3K27ME3


title: MyH3delta/delta replicate3 Dia


title: MyH3delta/delta replicate3 Gastroc


title: LISHU-KO-2-H3K9ME3

value: H3K9me3 (Active Motif, Cat# 61013)


title: P08_pre_T

description:
Patient 8 liver metastatic colorectal cancer, pre mFOLFOX treatment, 1st biopsy
matrix file.txt

value: UCLA

value: colorectal cancer liver metastasis tumor


title: MyH3+/+ replicate 4 Quad

value: wild type


title: MyH3delta/delta replicate3 Quad


title: MyH3delta/delta replicate3 TA


title: LISHU-KO-1-H3K9ME3


title: MyH3+/+ replicate 3 Dia


title: shock-1

city: Lanzhou

first: Yuan

last: Song

address: the south of Tianshui road

institute: Lanzhou university

description: mRNA sequencing

data_processing:
Prior to assembly, we removed the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) in the raw data.Reference genome  http://www.mbkbase.org/Pinku1/  alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.Tophat build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.  Transcript abundance estimation and differentially expressed testing  The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the tianscripts. The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).The feference GTF annotation file used in Cufflinks was downloaded from the JGI database. Cufflink was used to de novo assemble the transcripiome at first; The second ,Cuffmerge was used to comerge all transcripts of sample A and B to generate unique transcripts. The downloaded JGI GTF file was passed to Cuffdiff along with the original alinment (SAM) files produced by Tophat. Cuffdiff re-estimates the abundance of the transcripts listed in the GTF file using aligments from the SAM file and concurrently test for different expression. Only the comparisons with “q_value”less than 0.05 and status marked as “OK” in the Cuffdiff output were regarded as showing differential expression.
Genome_build: Tartary Buckwheat (Pinku1) Genome
Supplementary_files_format_and_content: FPKM,expression profiles

organism: Fagopyrum tataricum

source_name: Fagopyrum tataricum Dingku 1

growth_protocol: The three leaf age seedlings were cultivated in pots of nutritious soil

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp).

treatment_protocol: The seedlings were in a growth chamber (12/12h light/dark; light intensity 300 μmol m−2 s−1), the control group was at a constant temperature 16-21 ºC; the momery group with cold acclimation (4ºC 6h repeat 4 times ) then 0  ºC 6h;  the shock group without cold acclimation  0 ºC 6h directly.

value: plants stems and leaves

tag: group

value: shock


title: LISHU-KO-2-H3K4ME3

value: H3K4me3 (Cell Signaling Technology Cat# 9751)


title: MyH3+/+ replicate 3 Gastroc


title: shock-2

description: mRNA sequencing


title: memory-3

description: mRNA sequencing

value: memory


title: MyH3+/+ replicate 3 TA


title: MyH3+/+ replicate 3 Quad


title: memory-2

description: mRNA sequencing


title: MyH3+/+ replicate 4 TA


title: LISHU-KO-1-H3K4ME3


title: memory-1

description: mRNA sequencing


title: shock-3

description: mRNA sequencing


title: LISHU-C57-1-INPUT


title: MyH3delta/delta replicate5 Quad


title: MyH3delta/delta replicate2 TA


title: MyH3delta/delta replicate2 Quad


title: control-3

description: mRNA sequencing

value: control


title: MyH3+/+ replicate 2 Dia


title: MyH3+/+ replicate 2 Gastroc


title: control-2

description: mRNA sequencing


title: MyH3+/+ replicate 2 TA


title: control-1

description: mRNA sequencing


title: MyH3+/+ replicate 2 Quad


title: LISHU-KO-1-INPUT


title: MyH3delta/delta replicate2 Dia


title: MyH3delta/delta replicate2 Gastroc


title: MyH3delta/delta replicate1 Gastroc


title: MyH3delta/delta replicate1 TA


title: LISHU-C57-2-INPUT


title: MyH3delta/delta replicate1 Quad


title: MyH3+/+ replicate 1 Gastroc


title: shock

data_processing:
Briefly, as protocol shown below, the Adaptase step is a highly efficient, proprietary reaction that simultaneously performs end repair, tailing of 3’ ends, and ligation of the first truncated adapter complement to 3’ ends.
The Extension step is used to incorporate truncated adapter 1 by a primer extension reaction. The Ligation step is used to add the second truncated adapter to the bottom strand only. The Indexing PCR step increases yield and incorporates full length adapters.
Bead-based SPRI clean-ups are used to remove both oligonucleotides and small fragments, as well as to change enzymatic buffer composition. Finally, we performed the pair-end 2×150bp sequencing on an illumina Hiseq 4000 platform housed in the LC Sciences.
Genome_build: Tartary Buckwheat (Pinku1) Genome
Supplementary_files_format_and_content: Scores represent the peak of riches, WinRAR

extract_protocol:
Total DNA was extracted using QIAamp Fast DNA Tissue Kit (Qiagen, Dusseldorf, Germany) following the manufacturer's procedure
The Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI, USA) was utilized for attaching adapters to single-stranded DNA fragments and library construction.
The fragmented DNA samples by using sonication were subjected to bisulfite conversion. The  Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI, USA) was utilized for attaching adapters to  single-stranded DNA fragments.


title: LISHU-C57-2-H3K4ME3

value: H3K4me3 (Cell Signaling Technology, Cat# 9751)


title: MyH3+/+ replicate 1 Dia


title: MyH3+/+ replicate 1 TA


title: control


title: memory


title: LISHU-C57-1-H3K9ME3


title: LISHU-C57-1-H3K27ME3


title: LISHU-C57-1-H3K4ME3


title: MyH3+/+ replicate 1 Quad


title: MyH3delta/delta replicate1 Dia


title: anti-LTbR_6_Hours [RVS_007]

status: Public on Mar 07 2020

city: La Jolla

first: Richard

last: Virgen-Slane

state: CA

address: 10901 North Torrey Pines Rd

department: Infectious and Inflammatory Diseases Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Reads were aligned using RNA-Seq Alignment (BaseSpace Workflow) version 1.0.0
Gene counts were normalized using DESeq2
Genome_build: Homo sapiens (UCSC hg19)
Supplementary_files_format_and_content: Counts were rlog normalized using DESeq2

source_name: Normal human dermal fibroblasts undergoing LTbR stimulation for 6 Hours

growth_protocol: 620,000 fibroblasts were plated on 10 cm plates in DMEM with 10% FBS at 37ºC.

extract_protocol:
Following stimulation for the indicated times, monolayers were washed with warm PBS, detached using TrypLE express. Cell pellets were split and processed for western blot analysis or lysed with QIAGEN RLT buffer. RNA was isolated using QIAGEN RNA easy extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The following day cells were stimulated with 2 µg/ml agonistic goat anti-human LTBR antibody for 0, 2, 6, or 20 hours

tag: time point (hours)

tag: agent

value: agonistic goat anti-human LTBR antibody

tag: cell type

value: Normal human dermal fibroblasts


title: anti-LTbR_2_Hours [RVS_006]

source_name: Normal human dermal fibroblasts undergoing LTbR stimulation for 2 Hours


title: Control_pituitary_pool samples CPm

city: Jinan

first: Jiajia

last: Liu

state: Shandong

address: No 336, West Road of Nan Xinzhuang,

institute: University of Jinan

description:
Control_pituitary_pool samples
Gene expression data in pituitary of mouse in control group

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) software using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Other mice in control group

growth_protocol: Ten pairs of 6 weeks old female BABL/c mice with same parents were chosen in this experiment. Each pair of littermates were distributed into control and stress groups randomly and fed until 9 weeks old before performing superovulation

treatment_protocol: Mice in stress group were performed with transportation stress by transporting for a long-term distance of 1000km, nearly 10 h, at an average speed of 50 km/h from and back to the laboratory. Control and transported animals were housed in the same laboratory before and after transportation.

value: pituitary gland

tag: ovulation

value: Other mice in control group


title: anti-LTbR_0_Hours [RVS_005]

source_name: Normal human dermal fibroblasts undergoing LTbR stimulation for 0 Hours


title: Stress_pituitary_pool samples SPm

description:
Stress_pituitary_pool samples
Gene expression data in pituitary of mouse after 1000 km transportation stress

source_name: Other mice in stress group

tag: tissue

value: Other mice in stress group


title: anti-LTbR_6_Hours [RVS_003]


title: Control_pituitary_low ovulation CPl

description:
Control_pituitary_low ovulation
Gene expression data in pituitary of mouse in control group

source_name: Mouse with lowest oocytes in control group

value: Mouse with lowest number of oocytes among the mice in control group


title: LISHU-C57-2-H3K9ME3


title: Stress_pituitary_low ovulation SPl

description:
Stress_pituitary_low ovulation
Gene expression data in pituitary of mouse after 1000 km transportation stress

source_name: Mouse with lowest oocytes in stress group

value: Mouse with lowest number of oocytes among the mice in stress group


title: Stress_hypothalamus_high ovulation SHh

description:
Stress_hypothalamus_high ovulation
Gene expression data in hypothalamus of mouse after 1000 km transportation stress

source_name: Mouse with highest oocytes in stress group

value: hypothalamus

value: Mouse with largest number of oocytes among the mice in stress group


title: anti-LTbR_2_Hours [RVS_002]


title: Stress_ovary_low ovulation SOl

description:
Stress_ovary_low ovulation
Gene expression data in ovary of mouse after 1000 km transportation stress

value: ovary


title: Stress_pituitary_high ovulation SPh

description:
Stress_pituitary_high ovulation
Gene expression data in pituitary of mouse after 1000 km transportation stress


title: Control_pituitary_high ovulation CPh

description:
Control_pituitary_high ovulation
Gene expression data in pituitary of mouse in control group

source_name: Mouse with highest oocytes in control group

value: Mouse with largest number of oocytes among the mice in control group


title: anti-LTbR_20_Hours [RVS_008]

source_name: Normal human dermal fibroblasts undergoing LTbR stimulation for 20 Hours


title: Stress_hypothalamus_pool samples SHm

description:
Stress_hypothalamus_pool samples
Gene expression data in hypothalamus of mouse after 1000 km transportation stress


title: Stress_hypothalamus_low ovulation SHl

description:
Stress_hypothalamus_low ovulation
Gene expression data in hypothalamus of mouse after 1000 km transportation stress


title: Control_ovary_pool samples COm

description:
Control_ovary_pool samples
Gene expression data in ovary of mouse in control group


title: Stress_ovary_pool samples SOm

description:
Stress_ovary_pool samples
Gene expression data in ovary of mouse after 1000 km transportation stress


title: Control_hypothalamus_pool samples CHm

description:
Control_hypothalamus_pool samples
Gene expression data in hypothalamus of mouse in control group


title: Control_ovary_high ovulation COh

description:
Control_ovary_high ovulation
Gene expression data in ovary of mouse in control group


title: Control_ovary_low ovulation COl

description:
Control_ovary_low ovulation
Gene expression data in ovary of mouse in control group


title: Control_hypothalamus_low ovulation CHl

description:
Control_hypothalamus_low ovulation
Gene expression data in hypothalamus of mouse in control group


title: Control_hypothalamus_high ovulation CHh

description:
Control_hypothalamus_high ovulation
Gene expression data in hypothalamus of mouse in control group


title: Input_HP1_3'RI_B3_1

city: Granada

first: Carlos

last: Cordon-Obras

address: Av del Conocimiento

country: Spain

institute: Instituto Parasitologia Lopez Neyra

description:
Input_HP1_3'RI_B3_1
3prime_RI_B3_HP1_1.FE.bedgraph

data_processing:
Demultiplexing with bcl2fastq (Illumina) software v2.19.1.403
ChIP-Seq reads aligned to the genome using BWA v0.7.10-r789 with default parameters
Data sorted, indexed and PCR duplicates filteres using samtools v1.3
Peak calling (callpeak option) and calculation of fold enrichment over input (bdgcmp option) performed with MACS2 (v2.1.1.20160309) software using -BAMPE and --SPMR options.
Genome_build: PlasmoDB-29_Pfalciparum3D7_modified
Supplementary_files_format_and_content: BigWig files obtained using bedGraphToBigWig software v4

organism: Plasmodium falciparum

source_name: In vitro cultured blood stage cells

growth_protocol: Blood stage P. falciparum parasites were cultured in human O+ red blood cells in RPMI-1640 medium supplemented with Albumax II (10% v/v), hypoxanthine (200 μM) and gentamycin (50 μg/ml) in 3% CO2 and 5% O2 at 37 °C.

extract_protocol:
ChIP was performed as previously described (Zanghi et al, 2018 Cell. Rep.) with parasites synchronised at 36 hpi. Sonicated chromatin (500 ng DNA content) was immunoprecipitated overnight with 0.5 μg of anti-HP1 polyclonal rabbit antibodies. and incubated after with 25 μl of Dynabeads Protein G (Invitrogen) for two hours. Subsequent washing, cross-link reversion and DNA extraction were carried out as described before.
Sequencing libraries were produced with the immunoprecipitated DNA using the MicroPlex Library Preparation Kit v2 (Diagenode) with the KAPA HiFi polymerase (Kapa Biosystems) for the PCR amplification. For each ChIP sample, a control DNA corresponding to the ChIP input was processed in parallel.

tag: clone


title: Input_HP1_3'RI_B3_2

description:
Input_HP1_3'RI_B3_2
3prime_RI_B3_HP1_2.FE.bedgraph


title: Input_HP1_3'RI_E1_2

description:
Input_HP1_3'RI_E1_2
3prime_RI_E1_HP1_2.FE.bedgraph


title: anti-LTbR_0_Hours [RVS_001]


title: Input_HP1_3'RI_E1_1

description:
Input_HP1_3'RI_E1_1
3prime_RI_E1_HP1_1.FE.bedgraph


title: ChIP_HP1_3'RI_B3_2

description:
ChIP_HP1_3'RI_B3_2
3prime_RI_B3_HP1_2.FE.bedgraph

value: Rabbit anti-HP1 (Genscript Customized, see Chen et al 2016 Sci. Rep.)


title: ChIP_HP1_3'RI_E1_2

description:
ChIP_HP1_3'RI_E1_2
3prime_RI_E1_HP1_2.FE.bedgraph


title: LISHU-C57-2-H3K27ME3

value: wild type

value: H3K27me3 (Cell Signaling Technology, Cat# 9733)


title: B89

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr

department: Surgery

institute: Stanford University

description: Recruited progenitors

data_processing: Cycle Theshold (CT) values from PCR on Fluidigm C1

label: FAM

source_name: Dorsal wound

label_protocol: FACS as lin-, GFP+

growth_protocol: Primary harvest

extract_protocol: Primary harvest

treatment_protocol: Cells 1-48 are WT mice, Cells 49-96 are EKO mice on each chip

value: EKO


title: B88

description: Recruited progenitors


title: B92

description: Recruited progenitors


title: B95

description: Recruited progenitors


title: B96

description: Recruited progenitors


title: B90

description: Recruited progenitors


title: B93

description: Recruited progenitors


title: B91

description: Recruited progenitors


title: B84

description: Recruited progenitors


title: B82

description: Recruited progenitors


title: B87

description: Recruited progenitors


title: B86

description: Recruited progenitors


title: B83

description: Recruited progenitors


title: ChIP_HP1_3'RI_B3_1

description:
ChIP_HP1_3'RI_B3_1
3prime_RI_B3_HP1_1.FE.bedgraph


title: Stress_ovary_high ovulation SOh

description:
Stress_ovary_high ovulation
Gene expression data in ovary of mouse after 1000 km transportation stress


title: B78

description: Recruited progenitors


title: B75

description: Recruited progenitors


title: B74

description: Recruited progenitors


title: B77

description: Recruited progenitors


title: B76

description: Recruited progenitors


title: ChIP_HP1_3'RI_E1_1

description:
ChIP_HP1_3'RI_E1_1
3prime_RI_E1_HP1_1.FE.bedgraph


title: B73

description: Recruited progenitors


title: B94

description: Recruited progenitors


title: B72

description: Recruited progenitors


title: B79

description: Recruited progenitors


title: B81

description: Recruited progenitors


title: B80

description: Recruited progenitors


title: B85

description: Recruited progenitors


title: B69

description: Recruited progenitors


title: B68

description: Recruited progenitors


title: B66

description: Recruited progenitors


title: B70

description: Recruited progenitors


title: B67

description: Recruited progenitors


title: B65

description: Recruited progenitors


title: B55

description: Recruited progenitors


title: B64

description: Recruited progenitors


title: B62

description: Recruited progenitors


title: B61

description: Recruited progenitors


title: B63

description: Recruited progenitors


title: B52

description: Recruited progenitors


title: B58

description: Recruited progenitors


title: B59

description: Recruited progenitors


title: B57

description: Recruited progenitors


title: B56

description: Recruited progenitors


title: B49

description: Recruited progenitors


title: B50

description: Recruited progenitors


title: B54

description: Recruited progenitors


title: B60

description: Recruited progenitors


title: B51

description: Recruited progenitors


title: B42

description: Recruited progenitors

value: WT


title: B43

description: Recruited progenitors


title: B45

description: Recruited progenitors


title: B48

description: Recruited progenitors


title: B46

description: Recruited progenitors


title: B53

description: Recruited progenitors


title: B44

description: Recruited progenitors


title: B47

description: Recruited progenitors


title: B41

description: Recruited progenitors


title: B39

description: Recruited progenitors


title: B38

description: Recruited progenitors


title: B40

description: Recruited progenitors


title: B34

description: Recruited progenitors


title: B35

description: Recruited progenitors


title: B33

description: Recruited progenitors


title: B32

description: Recruited progenitors


title: B37

description: Recruited progenitors


title: B36

description: Recruited progenitors


title: B30

description: Recruited progenitors


title: B31

description: Recruited progenitors


title: B29

description: Recruited progenitors


title: B25

description: Recruited progenitors


title: B28

description: Recruited progenitors


title: B26

description: Recruited progenitors


title: B23

description: Recruited progenitors


title: B17

description: Recruited progenitors


title: B16

description: Recruited progenitors


title: B14

description: Recruited progenitors


title: B15

description: Recruited progenitors


title: B18

description: Recruited progenitors


title: B19

description: Recruited progenitors


title: B22

description: Recruited progenitors


title: B20

description: Recruited progenitors


title: B21

description: Recruited progenitors


title: B27

description: Recruited progenitors


title: B10

description: Recruited progenitors


title: B12

description: Recruited progenitors


title: B13

description: Recruited progenitors


title: B09

description: Recruited progenitors


title: B08

description: Recruited progenitors


title: B07

description: Recruited progenitors


title: B02

description: Recruited progenitors


title: B06

description: Recruited progenitors


title: B04

description: Recruited progenitors


title: A96

description: Recruited progenitors


title: A94

description: Recruited progenitors


title: B03

description: Recruited progenitors


title: A95

description: Recruited progenitors


title: B01

description: Recruited progenitors


title: anti-LTbR_20_Hours [RVS_004]


title: A93

description: Recruited progenitors


title: B11

description: Recruited progenitors


title: A91

description: Recruited progenitors


title: B05

description: Recruited progenitors


title: A92

description: Recruited progenitors


title: A89

description: Recruited progenitors


title: A86

description: Recruited progenitors


title: A84

description: Recruited progenitors


title: A87

description: Recruited progenitors


title: A85

description: Recruited progenitors


title: A90

description: Recruited progenitors


title: A78

description: Recruited progenitors


title: A77

description: Recruited progenitors


title: B24

description: Recruited progenitors


title: A83

description: Recruited progenitors


title: A82

description: Recruited progenitors


title: A80

description: Recruited progenitors


title: A79

description: Recruited progenitors


title: A81

description: Recruited progenitors


title: A75

description: Recruited progenitors


title: A76

description: Recruited progenitors


title: A74

description: Recruited progenitors


title: A72

description: Recruited progenitors


title: A71

description: Recruited progenitors


title: A73

description: Recruited progenitors


title: A88

description: Recruited progenitors


title: A70

description: Recruited progenitors


title: A68

description: Recruited progenitors


title: A67

description: Recruited progenitors


title: A63

description: Recruited progenitors


title: A62

description: Recruited progenitors


title: A53

description: Recruited progenitors


title: A66

description: Recruited progenitors


title: A52

description: Recruited progenitors


title: A51

description: Recruited progenitors


title: A69

description: Recruited progenitors


title: A61

description: Recruited progenitors


title: A43

description: Recruited progenitors


title: A42

description: Recruited progenitors


title: A55

description: Recruited progenitors


title: A56

description: Recruited progenitors


title: A58

description: Recruited progenitors


title: A57

description: Recruited progenitors


title: A54

description: Recruited progenitors


title: A59

description: Recruited progenitors


title: RF_ZFP3_plus_dox_Rep1

city: Buffalo

first: Laurie

last: Read

state: NY

address: 955 Main St

department: Microbiology and Immunology

institute: Jacobs School of Medicine and Biomedical Sciences

data_processing:
Basecalls performed by Illumina MiSeq
Adapters removed and quality trimming performed with TrimGalore, a cutadapt and FastQC wrapper.
Reads were aligned to the Trypanosoma brucei TREU927 reference genome using Spliced Transcripts Alignment to a Reference (STAR) v2.7.
Transcript expression was calculated with RNA-Seq by Expectation-Maximization (RSEM) v1.3.1.
Expression abundances were normalized with DESeq2 v1.26.
Genome_build: TbruceiTREU927
Supplementary_files_format_and_content: Isoform abundance results files were generated with DESeq2 v1.26.

organism: Trypanosoma brucei

growth_protocol: Procyclic form (PF) T. brucei strain 29-13, which expresses the T7 RNA polymerase under the control of a tetracycline (tet)-inducible promoter, and all other PF strains were grown under standard conditions (Pelletier and Read, 2003; Wirtz et al., 1999).

extract_protocol:
PF T. brucei Plew100-ZFP3-TY cells were grown in the presence or absence of 4 µg/ml doxycycline for 3 days and PF T. brucei P2T7-177-ZFP3 cells were grown in the presence or absence of 4 µg/mL doxycycline for 2 days, followed by isolation of RNA using TRIzol per manufacturer’s instructions.
The total RNA for two biological replicates of each cell line was treated with DNase, and treated RNA was submitted for Illumina sequencing at the University at Buffalo Genomics and Bioinformatics Core.

tag: strain background

value: ZFP3 variants R68/71F

tag: sample type

value: procyclic form (PF) whole cell

tag: treatment

value: 4 µg/ml doxycycline


title: RNAi_ZFP3_plus_dox_Rep2

value: ZFP3 RNAi knockdown


title: RNAi_ZFP3_minus_dox_Rep2


title: RF_ZFP3_minus_dox_Rep2


title: RK_ZFP3_minus_dox_Rep2

value: ZFP3 variants R68/71K


title: RF_ZFP3_plus_dox_Rep2


title: RK_ZFP3_minus_dox_Rep1


title: RNAi_ZFP3_plus_dox_Rep1


title: RNAi_ZFP3_minus_dox_Rep1


title: RF_ZFP3_minus_dox_Rep1


title: WT_ZFP3_minus_dox_Rep2

value: wild type ZFP3


title: RK_ZFP3_plus_dox_Rep2


title: WT_ZFP3_plus_dox_Rep1


title: WT_ZFP3_plus_dox_Rep2


title: RK_ZFP3_plus_dox_Rep1


title: WT_ZFP3_minus_dox_Rep1


title: A41

description: Recruited progenitors


title: A40

description: Recruited progenitors


title: RN46A cells, Control rep 3

city: Christchurch

first: Martin

last: Kennedy

state: Canterbury

address: 2 Riccarton Avenue

department: Pathology and Biomedical Science

country: New Zealand

institute: University of Otago

data_processing:
illumina Casava 1.8 used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor6 whole genome using STAR v2.5.1.b with parameters --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --alignEndsType EndToEnd
Cleaned reads were also aligned with kallisto v0.42.4 with parameters -b 100 -t 4, and salmon v0.6.1 with parameters -p 4 --numBootstraps 100 --biasCorrect -l IU --geneMap
Differential gene expression was done with DESeq2, Cufflinks 2.2.1 for STAR-alinged reads, and with sleuth for kallisto and salmon aligend reads.
Genome_build: Rnor6
Supplementary_files_format_and_content: tab-delimited counts and DEGs from DESeq2, cufflinks2.2.1, kallisto-sleuth and Salmon-sleuth

growth_protocol: The RN46A cells were maintained at 33oC in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F12; ThermoFisher Scientific, MA, USA) containing glutamine (GlutaMAX™-I; ThermoFisher Scientific, MA, USA) and supplemented with 5% fetal bovine serum (FBS) and 250 µg/ml Geneticin G418 (ThermoFisher Scientific, MA, USA). For differentiation, RN46A cells were seeded in plates coated with 100µg/cm2 collagen (Sigma-Aldrich, St. Louis, MO, USA) and 1µg/cm2 fibronectin (Sigma-Aldrich, St. Louis, MO, USA), and confluent RN46A cultures were shifted to 39oC and supplemented with DMEM/F-12 containing 1% FBS, 1% BSA, 1% N2 supplement, 0.75 g/L sodium pyruvate and 0.073 g/L L-glutamine. RN46A cells were differentiated for 72 h and then drug exposed for 72 h.

extract_protocol:
Total RNA was isolated using Trizol reagent. RNA samples with 260/280 and 260/230 ratios of ~2 and RIN score greater than 7. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiated RN46A cells were treated with 0.5mM each of Lithium and VPA.

tag: cell line

value: serotonergic cell line RN46A

value: Control

tag: exposure

value: 72 hours

tag: concentration


title: RN46A cells, VPA rep 3

value: VPA


title: RN46A cells, Control rep 2


title: RN46A cells, VPA rep 2


title: RN46A cells, Lithium rep 3

value: Lithium


title: RN46A cells, Control rep 1


title: A65

description: Recruited progenitors


title: A60

description: Recruited progenitors


title: A49

description: Recruited progenitors


title: A50

description: Recruited progenitors


title: A44

description: Recruited progenitors


title: A45

description: Recruited progenitors


title: A64

description: Recruited progenitors


title: A48

description: Recruited progenitors


title: A46

description: Recruited progenitors


title: A47

description: Recruited progenitors


title: A36

description: Recruited progenitors


title: A38

description: Recruited progenitors


title: A39

description: Recruited progenitors


title: RN46A cells, Lithium rep 2


title: RN46A cells, VPA rep 1


title: RN46A cells, Lithium rep 1


title: CLF RIP-seq rep1

city: Beijing

first: Jingrui

state: Beijing

address: Medicine Building

institute: Tsinghua University

description: CLF-associated RNA

data_processing:
The adapter or low quality reads were removed by Trimmomatic( Bolger, 2014) .Clean reads were aligned to the Arabidopsis reference genome (TAIR10) by using TopHat version 2.0.10(Trapnell,2009) with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: The processed files contain three columns transcript_id, transcript location and expression level respectively. The abundance of transcripts expression is estimated by FPKM.

organism: Arabidopsis thaliana

source_name: 3-week-old plants

growth_protocol: Plants were grown on 1/2 MS medium with 30 g/L sucrose in long-day (LD, 16-hour light, 22°C / 8-hour dark, 18°C) condition. The Myc-tagged CLF can rescue the defective phenotype of clf-28, which shows a normal phenotype as Col-0.

extract_protocol:
Briefly, 2 g of crosslinked plant materials were ground into fine powder and suspended in Chromatin Extraction Buffer. The nuclear pellets were collected by centrifugation and washed for 4-5 times with NRBT Buffer. The pellet was resuspended in 150 μL Lysis Buffer and sonicated for 10 minutes. The supernatant was diluted with ChIP Dilution Buffer. Anti-Myc antibody and protein-A beads were added and incubated for 3 hours. Then, the beads were collected and washed with RIP Washing Buffer for 3 times. The CLF-RNA complex was eluted by RIP Elution Buffer. After de-crosslinking, the CLF-associated RNA was purified by TRIzol.
Libraries were prepared according to NEBNext Ultra II RNA Library Prep Kit. Briefly, the CLF-associated RNA was fragmented by alkaline hydrolysis. Then, the first-strand cDNA was synthesized by using Random primers. After the synthesis of the second-strand cDNA, the end-repaired reagents were used to yield a protruding 3- ‘A’ base for ligation of Illumina’s adaptors. After ligation, the libraries were amplified and ~200 bp PCR products were collected for sequencing.

tag: ecotype

value: Columbia

tag: cultivar


title: A37

description: Recruited progenitors

tag: genotype


title: RIP-seq control rep2

description: Random RNA


title: A35

description: Recruited progenitors


title: A34

description: Recruited progenitors


title: vehicle3

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

data_processing:
CASAVA v1.8.2 was used to demultiplex pooled samples and convert BCL to FASTQ.
Multiple fastq files were combined into one file for the forward reads and one file for the reverse reads.
RNA-Seq data were aligned to the mouse genome build mm9 by STAR-2.5.2a.
Data were normalized at the gene-level, using a resampling strategy PORT (v0.8.2-beta), the code is available at https://github.com/itmat/Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: vehicle, aorta thoracica

growth_protocol: Mice were housed in groups on a 12 hour light, 12 hour dark schedule. feed type : regular chow; diet availability : ad libitum; diet supplements : none; water supply type : bottle; water type : tap

extract_protocol:
Aorta were homogenized using magnetic beads and a TissueLyzer. RNA was extracted using Trizol and Qiagen Rneasy Mini kit.
Library construction was carried out using TruSeq RNA Sample Prep kit Set B. In line controls were not used, and samples were barcoded using kit adapters. Library construction was carried out over three days. Selection strategy: polyA; PCR cycles: 13

treatment_protocol: Mice were treated with 100 uL of celecoxib (30 mg/Kg), rofecoxib (10 mg/Kg), or vehicle (PEG-400) by gavage and were sacrified 6hrs later.

tag: strain

tag: developmental stage

value: adult

tag: Sex

value: male

tag: age

value: 10 to 12 week

tag: genetic alteration

value: wildtype

tag: dose

tag: collection time

value: aorta


title: vehicle4

tag: agent

tag: tissue


title: vehicle2


title: rofecoxib4

source_name: rofecoxib, aorta thoracica

value: NSAID rofecoxib

value: 10 mg/kg


title: vehicle1


title: A33

description: Recruited progenitors

value: WT


title: A32

description: Recruited progenitors


title: A28

description: Recruited progenitors


title: rofecoxib1


title: A29

description: Recruited progenitors


title: A30

description: Recruited progenitors


title: celecoxib4

source_name: celecoxib, aorta thoracica

value: NSAID celecoxib

value: 30 mg/kg


title: celecoxib3


title: celecoxib2


title: A27

description: Recruited progenitors


title: CLF RIP-seq rep2

description: CLF-associated RNA