title: Input DNA control for SOM-H3K4me3 ChIP rep2

description:
a fraction of the input total chromatin that was used for glp-1(q224) soma control H3K27ac ChIP
SOM-H3K4me3_ChIP-input.wig

source_name: 2% formaldehyde pre-fixed glp-1(q224) young adult animals

extract_protocol: Growth:  glp-1(q224) animals were cultured to starvation on NGM plates at 15°C. L1 worms were floated and plated on one 15-cm NGM plate. Worms were cultured at 15°C for four days until gravid. Adult worms were bleached and embryos were incubated with shaking at 15°C for  36-42 hours. L1s were plated to three peptone enriched plates with 50K L1s per plate and cultured at 25°C for 46-48 hours until adult stage. Adult glp-1(q224) animals were harvested by 3X washes with M9. Extraction:  Worms were crosslinked in 50 mL 2% formaldehyde for 30 minutes in a 50 mL conical tube at room temperature. Formaldehyde was quenched by 1 M Tris (pH 7.5) wash. Worms were then washed 2 more times with M9. Worms were transferred to a 15 mL conical tube and washed with 15 mL prechilled FA buffer. Worm pellets were frozen in liquid nitrogen and stored at -80°C. Worm pellets were thawed on ice and 750 µl of FA buffer was added to each sample. Samples were transferred to a 2 mL Kontes Dounce. Samples were Dounced 15 times with the small “A” pestle for two cycles and 15 times with the large “B” pestle for four cycles. Samples were sonicated with a SFX250 sonifier in an ice bath at 22% amplitude with 10 sec on/1 min off pulses for 34 cycles. 100-650 bp DNA fragments were enriched after sonication. 4.4 mg protein was used for each ChIP sample. 5% of lysate was removed for input sample and stocked at -20°C overnight. Library construction:  The Yale Center for Genome Analysis (YCGA) prepared the library and performed sequencing. The KAPA Hyper Library Preparation kit was used for ChIP sequencing library prep. DNA fragment ends were repaired with T4 DNA Polymerase, and Polynucleotide Kinase and “A” base added using Klenow fragment in a single reaction followed by ligation of custom adapters (IDT) using T4 ligase. Adaptor-ligated DNA fragments were purified and size selected with Agencourt AMPure XP magnetic beads.  Adaptor-ligated DNA fragments were amplified by LM-PCR using custom-made primers (IDT). During LM-PCR, unique 10 base indices were inserted at each DNA fragment and amplified products were purified.

value: none - input


title: blood_control_18

status: Public on Jun 07 2019

type: genomic

city: Wuerzburg

first: Tobias

last: Mueller

address: Am Hubland

country: Germany

institute: University of Wuerzburg

description: control

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan

data_processing: Beta values normalized by quantile normalization method as implemented in the minfi package

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: Standard Illumina Protocol

tag: gender

value: male

tag: disease state

value: control

tag: age


title: blood_patient WRN_18

description: patient with WRN mutation

extract_protocol: Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

value: classical Werner syndrome


title: SOM-H3K4me3 ChIP rep2

type: SRA

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

country: USA

institute: Yale University School of Medicine

description:
ChIP was performed with anti-H3K4me3 on glp-1(q224) which represents somatic tissues
SOM-H3K4me3_ChIP-input.wig

library_source: genomic

data_processing:
ChIP-seq:  The raw paired-end ChIP and corresponding input sequencing fastq reads were mapped to ce10 genome by mapping with Bowtie2 (v2.3.2) with default parameters.
ChIP-seq: Wig files were generated by a custom script (https://github.com/guifengwei/glib/blob/master/bam2wig.py),
ChIP-seq:  Peaks were called by MACS2 (v2.1.1)  with the key parameter (-q 0.001 --nomodel --extsize 150).
RNA-seq: The raw paired-end RNA-seq fastq reads were first mapped to rRNA build by bowtie2 (v2.1.0)
RNA-seq:  The remaining unmapped reads were further aligned to ce10 genome by HISAT2 (v2.0.4) with the mode suppressing the unpaired reads
RNA-seq:  The gene annotation was downloaded from UCSC Genome Browser, filtered to remove transcripts <50 nt, then was employed to estimate gene expression and call differential gene expression by Cuffdiff program [20] (v2.2.1) under the default parameters between VC2010 and glp-1(q224) strains.
Genome_build: ce10
Supplementary_files_format_and_content: wig or BigWig files were generated as an output

organism: Caenorhabditis elegans

extract_protocol: Growth:  glp-1(q224) animals were cultured to starvation on NGM plates at 15°C. L1 worms were floated and plated on one 15-cm NGM plate. Worms were cultured at 15°C for four days until gravid. Adult worms were bleached and embryos were incubated with shaking at 15°C for  36-42 hours. L1s were plated to three peptone enriched plates with 50K L1s per plate and cultured at 25°C for 46-48 hours until adult stage. Adult glp-1(q224) animals were harvested by 3X washes with M9. Extraction:  Worms were crosslinked in 50 mL 2% formaldehyde for 30 minutes in a 50 mL conical tube at room temperature. Formaldehyde was quenched by 1 M Tris (pH 7.5) wash. Worms were then washed 2 more times with M9. Worms were transferred to a 15 mL conical tube and washed with 15 mL prechilled FA buffer. Worm pellets were frozen in liquid nitrogen and stored at -80°C. Worm pellets were thawed on ice and 750 µl of FA buffer was added to each sample. Samples were transferred to a 2 mL Kontes Dounce. Samples were Dounced 15 times with the small “A” pestle for two cycles and 15 times with the large “B” pestle for four cycles. Samples were sonicated with a SFX250 sonifier in an ice bath at 22% amplitude with 10 sec on/1 min off pulses for 34 cycles. 100-650 bp DNA fragments were enriched after sonication. 4.4 mg protein was used for each ChIP sample. 5% of lysate was removed for input sample and stocked at -20°C overnight. 5 μg of anti-H3K4me3 was used for each SOM sample.  Library construction:  The Yale Center for Genome Analysis (YCGA) prepared the library and performed sequencing. The KAPA Hyper Library Preparation kit was used for ChIP sequencing library prep. DNA fragment ends were repaired with T4 DNA Polymerase, and Polynucleotide Kinase and “A” base added using Klenow fragment in a single reaction followed by ligation of custom adapters (IDT) using T4 ligase. Adaptor-ligated DNA fragments were purified and size selected with Agencourt AMPure XP magnetic beads.  Adaptor-ligated DNA fragments were amplified by LM-PCR using custom-made primers (IDT). During LM-PCR, unique 10 base indices were inserted at each DNA fragment and amplified products were purified.

tag: developmental stage

value: young adult (YA)

tag: tissue

value: Soma

tag: chipped factor

tag: antibody

value: H3K4me3 (61379, Active Motif)

tag: strain


title: Healthy Controls [Imipramine study][SAMPLE 6]

type: RNA

city: Rotterdam

first: Hemmo

middle: A

last: Drexhage

state: Zuid-Holland

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: ErasmusMC

description: Control

data_processing:
The software included in the Excel program to create the delta CT and normalized values as given.
Matrix normalized worksheet reports normalized signal (against housekeeping gene ABL1).
2^-dCT (normalized, linearized values)

label: FAM

molecule: total RNA

source_name: Monocytes

label_protocol: 1 ug RNA was converted into cDNA using the High Capacity cDNA synthesis kit (Applied Biosystems)

extract_protocol: Total RNA was extracted using QIAgen Rneasy Mini kit

tag: group

value: Healthy Controls


title: blood_control_49

description: control


title: Healthy Controls [Imipramine study][SAMPLE 9]

description: Control


title: blood_patient LMNA_36

description: patient with LMNA mutation

value: atypical Werner syndrome


title: blood_control_31

description: control

value: female


title: blood_patient WRN_49

description: patient with WRN mutation


title: Input DNA control for SOM-H3K4me3 ChIP rep1


title: Healthy Controls [Imipramine study][SAMPLE 5]

description: Control


title: SOM-H3K4me3 ChIP rep1


title: Healthy Controls [Imipramine study][SAMPLE 4]

description: Control


title: Healthy Controls [Imipramine study][SAMPLE 8]

description: Control


title: Input DNA control for IGN-H3K4me3 ChIP rep2

description:
a fraction of the input total chromatin that was used for isolated germ nuclei H3K27ac ChIP
IGN-H3K4me3_ChIP-input.wig

source_name: Isolated germ nuclei from 2% formaldehyde pre-fixed VC2010 wild type young adult animals

extract_protocol: Growth: VC2010 worms were grown to starvation on NGM plates. Starved L1s were floated on peptone-enriched plates, and grown until gravid at 20˚C. Gravid adults were bleached and synchronized by L1 starvation.  L1s were plated to enriched plates and grown until the young adult stage. Animals for nuclei isolation were collected from eighteen enriched plates (~1 million) per ChIP-seq experiment. Young adult animals were harvested at 54-56 hours after plating synchronized L1s when most of the animals had 4-10 embryos. Worms from every six plates (~0.3 million) were collected into one 50 mL conical tube and spun at 3100 rpm for 2 minutes and then washed 3x in M9. Extraction/nuclear preparation:  worms were crosslinked in 50 mL 2% formaldehyde for 30 minutes in three 50 mL conical tubes at room temperature. Formaldehyde was quenched by 1 M Tris (pH 7.5) wash. Worms were then washed two more times with M9. Worms were then washed in the same tubes with 10 mL of prechilled Nuclei Purification Buffer. Germ nuclei were isolated following our protocol. Most of the supernatant was removed so that ~20 µL NPB was left. The nuclei were gently pipetted to mix and then flash frozen in liquid nitrogen and stored at -80°C until sonication. IGN samples were sonicated at 2°C in a water bath sonicator (Misonix S-4000). 20% amplitude and 10 sec on/10 sec off pulses were used for a total processing time of 20 minutes, resulting in enrichment for 100-650 bp DNA fragments. 5% of lysate was removed for the input sample and stored at -20°C until the following day to prepare input DNA.  Library construction:  The Yale Center for Genome Analysis (YCGA) prepared the library and performed sequencing. The KAPA Hyper Library Preparation kit was used for ChIP sequencing library prep. DNA fragment ends were repaired with T4 DNA Polymerase, and Polynucleotide Kinase and “A” base added using Klenow fragment in a single reaction followed by ligation of custom adapters (IDT) using T4 ligase. Adaptor-ligated DNA fragments were purified and size selected with Agencourt AMPure XP magnetic beads.  Adaptor-ligated DNA fragments were amplified by LM-PCR using custom-made primers (IDT). During LM-PCR, unique 10 base indices were inserted at each DNA fragment and amplified products were purified.

value: Isolated germ nuclei


title: Healthy Controls [Imipramine study][SAMPLE 3]

description: Control


title: B_19: genomic DNA from blood belong to group highBFR

city: Malaga

first: Isabel

last: Moreno-Indias

state: Malaga

address: Virgen de la Victoria Hospital

country: Spain

institute: IBIMA

description:
201533570030_R03C01
genomic DNA from blood belong to group highBFR

hyb_protocol: Genomic DNA were bisulfite-treated using the ZymoResearch Infinitum HD FFPE Methylation kit and methylation sites were interrogated with the Infinium Methylation EPIC Bead Chip Kit (Illumina, San Diego, CA, USA) following the Infinium HD Assay Methylation protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: Signal intensities files were extracted using the minfi Bioconductor package. Normalization was performed using the Beta-Mixture Quantile function implemented in rnBeads Bioconductor package

source_name: blood highBFR

extract_protocol: DNA was extracted using Zymo ZR 96 Quick gDNA kit following manufacturer’s instructions

value: Blood


title: B_17: genomic DNA from blood belong to group highBFR

description:
201533570005_R06C01
genomic DNA from blood belong to group highBFR


title: Healthy Controls [Imipramine study][SAMPLE 2]

description: Control


title: IGN-H3K4me3 ChIP rep2

description:
ChIP was performed with anti-H3K4me3 on isolated germ nuclei
IGN-H3K4me3_ChIP-input.wig

extract_protocol: Growth: VC2010 worms were grown to starvation on NGM plates. Starved L1s were floated on peptone-enriched plates, and grown until gravid at 20˚C. Gravid adults were bleached and synchronized by L1 starvation.  L1s were plated to enriched plates and grown until the young adult stage. Animals for nuclei isolation were collected from eighteen enriched plates (~1 million) per ChIP-seq experiment. Young adult animals were harvested at 54-56 hours after plating synchronized L1s when most of the animals had 4-10 embryos. Worms from every six plates (~0.3 million) were collected into one 50 mL conical tube and spun at 3100 rpm for 2 minutes and then washed 3x in M9. Extraction/nuclear preparation:  worms were crosslinked in 50 mL 2% formaldehyde for 30 minutes in three 50 mL conical tubes at room temperature. Formaldehyde was quenched by 1 M Tris (pH 7.5) wash. Worms were then washed two more times with M9. Worms were then washed in the same tubes with 10 mL of prechilled Nuclei Purification Buffer. Germ nuclei were isolated following our protocol. Most of the supernatant was removed so that ~20 µL NPB was left. The nuclei were gently pipetted to mix and then flash frozen in liquid nitrogen and stored at -80°C until sonication. IGN samples were sonicated at 2°C in a water bath sonicator (Misonix S-4000). 20% amplitude and 10 sec on/10 sec off pulses were used for a total processing time of 20 minutes, resulting in enrichment for 100-650 bp DNA fragments. 5% of lysate was removed for the input sample and stored at -20°C until the following day to prepare input DNA. 5 μg of anti-H3K4me3 was used for each IGN sample. Library construction:  The Yale Center for Genome Analysis (YCGA) prepared the library and performed sequencing. The KAPA Hyper Library Preparation kit was used for ChIP sequencing library prep. DNA fragment ends were repaired with T4 DNA Polymerase, and Polynucleotide Kinase and “A” base added using Klenow fragment in a single reaction followed by ligation of custom adapters (IDT) using T4 ligase. Adaptor-ligated DNA fragments were purified and size selected with Agencourt AMPure XP magnetic beads.  Adaptor-ligated DNA fragments were amplified by LM-PCR using custom-made primers (IDT). During LM-PCR, unique 10 base indices were inserted at each DNA fragment and amplified products were purified.


title: Input DNA control for IGN-H3K4me3 ChIP rep1


title: Healthy Controls [Imipramine study][SAMPLE 1]

description: Control


title: B_20: genomic DNA from blood belong to group highBFR

description:
201533570037_R05C01
genomic DNA from blood belong to group highBFR


title: B_14: genomic DNA from blood belong to group highBFR

description:
201533570040_R06C01
genomic DNA from blood belong to group highBFR


title: B_16: genomic DNA from blood belong to group highBFR

description:
201533570002_R08C01
genomic DNA from blood belong to group highBFR


title: B_15: genomic DNA from blood belong to group highBFR

description:
201533570040_R07C01
genomic DNA from blood belong to group highBFR


title: blood_patient WRN_40

description: patient with WRN mutation


title: B_18: genomic DNA from blood belong to group highBFR

description:
201533570002_R01C01
genomic DNA from blood belong to group highBFR


title: IGN-H3K4me3 ChIP rep1


title: blood_control_30-2

description: control


title: blood_patient POLD1_30

description: patient with POLD1 mutation

value: MDP syndrome


title: Input DNA control for SOM-H3K27ac ChIP rep2

description:
a fraction of the input total chromatin that was used for glp-1(q224) soma control H3K27ac ChIP
SOM-H3K27ac_ChIP-input.wig


title: blood_control_36

description: control


title: blood_control_47

description: control


title: B_12: genomic DNA from blood belong to group lowBFR

description:
201533570005_R03C01
genomic DNA from blood belong to group lowBFR


title: B_13: genomic DNA from blood belong to group highBFR

description:
201533570005_R01C01
genomic DNA from blood belong to group highBFR


title: B_11: genomic DNA from blood belong to group highBFR

description:
201533570040_R05C01
genomic DNA from blood belong to group highBFR


title: blood_control_40

description: control


title: ∆admB rep 4

city: Fuchu-shi

first: Takuji

last: Kobayashi

state: Tokyo

address: 3-5-8 Saiwai-cho

country: Japan

institute: Tokyo Univ. of Agriculture and Technology

library_source: transcriptomic

data_processing:
The single-end sequencing reads were demultiplexed and the indexed adaptor sequences were trimmed using Illumina CASAVA v1.8.2 software.
The raw FASTQ format data sets generated from the above software were assessed for quality using FASTQC v0.10.1.
Poor-quality reads (Phred score <3) were trimmed from the tail end of each single-end read and only reads with lengths ≥35 bp were subjected to further analysis.
These data sets were aligned to reference genome and transcriptome sequences of Aspergillus oryzae RIB40 with TopHat v2.0.9.
Reads per kilobase of transcript per million mapped reads (RPKMs) for each experiment were calculated with Cufflinks v 2.1.1.
Genome_build: ASM18445v3 (Aspergillus oryzae RIB40 genomic DNA sequenced in "Genome sequencing and analysis of Aspergillus oryzae", Nature 438, 1157-1161, 2005 [PMID 16372010]).
Supplementary_files_format_and_content: Tab-delimited text files include gene IDs and RPKM values for each Sample.

organism: Aspergillus oryzae

source_name: admB deletion mutant cultivated in wheat bran solid culture

growth_protocol: A. oryzae mutant strains and control strain conidia of 3.8 x 10^7 were inoculated into 76.5 g of wheat bran solid medium (70 mL of water per 100 g wheat bran) in a 1 L Fernbach flask (giving 5.0 x 10^5 conidia/g wheat bran) and cultured at 30ºC for 72 h.

extract_protocol:
Wheat bran solid culture was immediately frozen with liquid N2, pulverized using a pestle and mortar, and then RNA was harvested using Sepasol®-RNA I Super G (Nacalai Tesque Inc., Kyoto, Japan).
TruSeq® RNA Sample Prep Kit (Illumina Inc., San Diego, CA, USA) was used with 4 µg of total RNA for the construction of sequencing libraries.

tag: strain/background

tag: genotype/variation

value: del-pyrG del-admB[pyrG+ ligD+]

tag: growth media

value: wheat bran solid medium

tag: incubation temperature

tag: incubation time


title: SOM-H3K27ac ChIP rep2

description:
ChIP was performed with anti-H3K27ac on glp-1(q224) which represents somatic tissues
SOM-H3K27ac_ChIP-input.wig

extract_protocol: Growth:  glp-1(q224) animals were cultured to starvation on NGM plates at 15°C. L1 worms were floated and plated on one 15-cm NGM plate. Worms were cultured at 15°C for four days until gravid. Adult worms were bleached and embryos were incubated with shaking at 15°C for  36-42 hours. L1s were plated to three peptone enriched plates with 50K L1s per plate and cultured at 25°C for 46-48 hours until adult stage. Adult glp-1(q224) animals were harvested by 3X washes with M9. Extraction:  Worms were crosslinked in 50 mL 2% formaldehyde for 30 minutes in a 50 mL conical tube at room temperature. Formaldehyde was quenched by 1 M Tris (pH 7.5) wash. Worms were then washed 2 more times with M9. Worms were transferred to a 15 mL conical tube and washed with 15 mL prechilled FA buffer. Worm pellets were frozen in liquid nitrogen and stored at -80°C. Worm pellets were thawed on ice and 750 µl of FA buffer was added to each sample. Samples were transferred to a 2 mL Kontes Dounce. Samples were Dounced 15 times with the small “A” pestle for two cycles and 15 times with the large “B” pestle for four cycles. Samples were sonicated with a SFX250 sonifier in an ice bath at 22% amplitude with 10 sec on/1 min off pulses for 34 cycles. 100-650 bp DNA fragments were enriched after sonication. 4.4 mg protein was used for each ChIP sample. 5% of lysate was removed for input sample and stocked at -20°C overnight. 5 μg of anti-H3K27ac was used for each SOM sample.  Library construction:  The Yale Center for Genome Analysis (YCGA) prepared the library and performed sequencing. The KAPA Hyper Library Preparation kit was used for ChIP sequencing library prep. DNA fragment ends were repaired with T4 DNA Polymerase, and Polynucleotide Kinase and “A” base added using Klenow fragment in a single reaction followed by ligation of custom adapters (IDT) using T4 ligase. Adaptor-ligated DNA fragments were purified and size selected with Agencourt AMPure XP magnetic beads.  Adaptor-ligated DNA fragments were amplified by LM-PCR using custom-made primers (IDT). During LM-PCR, unique 10 base indices were inserted at each DNA fragment and amplified products were purified.

value: H3K27ac (39685, Active Motif)


title: B_10: genomic DNA from blood belong to group lowBFR

description:
201533570017_R03C01
genomic DNA from blood belong to group lowBFR

source_name: blood lowBFR


title: B_09: genomic DNA from blood belong to group lowBFR

description:
201533570037_R01C01
genomic DNA from blood belong to group lowBFR


title: ∆admB rep 3


title: blood_patient POLD1_13

description: patient with POLD1 mutation


title: B_08: genomic DNA from blood belong to group lowBFR

description:
201533570002_R03C01
genomic DNA from blood belong to group lowBFR


title: B_07: genomic DNA from blood belong to group lowBFR

description:
201533570005_R05C01
genomic DNA from blood belong to group lowBFR


title: ∆admB rep 5


title: ∆admB rep 2


title: SOM-H3K27ac ChIP rep1


title: B_05: genomic DNA from blood belong to group lowBFR

description:
201533570030_R05C01
genomic DNA from blood belong to group lowBFR


title: ∆admB rep 1


title: B_04: genomic DNA from blood belong to group lowBFR

description:
201533570002_R02C01
genomic DNA from blood belong to group lowBFR


title: blood_control_39

description: control


title: Input DNA control for IGN-H3K27ac ChIP rep2

description:
a fraction of the input total chromatin that was used for isolated germ nuclei H3K27ac ChIP
IGN-H3K27ac_ChIP-input.wig


title: IGN-H3K27ac ChIP rep2

description:
ChIP was performed with anti-H3K27ac on isolated germ nuclei
IGN-H3K27ac_ChIP-input.wig

extract_protocol: Growth: VC2010 worms were grown to starvation on NGM plates. Starved L1s were floated on peptone-enriched plates, and grown until gravid at 20˚C. Gravid adults were bleached and synchronized by L1 starvation.  L1s were plated to enriched plates and grown until the young adult stage. Animals for nuclei isolation were collected from eighteen enriched plates (~1 million) per ChIP-seq experiment. Young adult animals were harvested at 54-56 hours after plating synchronized L1s when most of the animals had 4-10 embryos. Worms from every six plates (~0.3 million) were collected into one 50 mL conical tube and spun at 3100 rpm for 2 minutes and then washed 3x in M9. Extraction/nuclear preparation:  worms were crosslinked in 50 mL 2% formaldehyde for 30 minutes in three 50 mL conical tubes at room temperature. Formaldehyde was quenched by 1 M Tris (pH 7.5) wash. Worms were then washed two more times with M9. Worms were then washed in the same tubes with 10 mL of prechilled Nuclei Purification Buffer. Germ nuclei were isolated following our protocol. Most of the supernatant was removed so that ~20 µL NPB was left. The nuclei were gently pipetted to mix and then flash frozen in liquid nitrogen and stored at -80°C until sonication. IGN samples were sonicated at 2°C in a water bath sonicator (Misonix S-4000). 20% amplitude and 10 sec on/10 sec off pulses were used for a total processing time of 20 minutes, resulting in enrichment for 100-650 bp DNA fragments. 5% of lysate was removed for the input sample and stored at -20°C until the following day to prepare input DNA. 5 μg of anti-H3K27ac was used for each IGN sample. Library construction:  The Yale Center for Genome Analysis (YCGA) prepared the library and performed sequencing. The KAPA Hyper Library Preparation kit was used for ChIP sequencing library prep. DNA fragment ends were repaired with T4 DNA Polymerase, and Polynucleotide Kinase and “A” base added using Klenow fragment in a single reaction followed by ligation of custom adapters (IDT) using T4 ligase. Adaptor-ligated DNA fragments were purified and size selected with Agencourt AMPure XP magnetic beads.  Adaptor-ligated DNA fragments were amplified by LM-PCR using custom-made primers (IDT). During LM-PCR, unique 10 base indices were inserted at each DNA fragment and amplified products were purified.


title: B_02: genomic DNA from blood belong to group lowBFR

description:
201533570050_R06C01
genomic DNA from blood belong to group lowBFR


title: blood_control_13

description: control


title: ∆admA rep 5

source_name: admA deletion mutant cultivated in wheat bran solid culture

value: del-pyrG del-admA[pyrG+ ligD+]


title: blood_patient WRN_47

description: patient with WRN mutation


title: ∆admA rep 3


title: B_01: genomic DNA from blood belong to group lowBFR

description:
201533570050_R03C01
genomic DNA from blood belong to group lowBFR


title: blood_control_45-2

description: control


title: AT_18: genomic DNA from adipose belong to group highBFR

description:
201533630046_R01C01
genomic DNA from adipose belong to group highBFR

source_name: adipose highBFR

value: Adipose


title: blood_control_9

description: control


title: blood_control_37

description: control


title: blood_patient WRN_39

description: patient with WRN mutation

value: male


title: Input DNA control for IGN-H3K27ac ChIP rep1

value: none - input


title: AT_17: genomic DNA from adipose belong to group highBFR

description:
201533630047_R06C01
genomic DNA from adipose belong to group highBFR


title: IGN-H3K27ac ChIP rep1


title: blood_patient LMNA_37

description: patient with LMNA mutation


title: AT_16: genomic DNA from adipose belong to group highBFR

description:
201533630046_R08C01
genomic DNA from adipose belong to group highBFR


title: ∆admA rep 4


title: AT_15: genomic DNA from adipose belong to group highBFR

description:
201533630040_R07C01
genomic DNA from adipose belong to group highBFR


title: blood_patient POLD1_9

description: patient with POLD1 mutation


title: mT_3-RNAseq

city: Hangzhou

first: Yisheng

last: Sun

state: Zhejiang

address: 3399# Binsheng Road, Binjiang District

department: Department of Microbiology

country: China

institute: Zhejiang Provincial Center for Disearse Control and Prevention

data_processing:
Illumina Casava1.7 software was used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
Genome_build: no reference genome
Supplementary_files_format_and_content: Read_count, FPKM

organism: Meriones unguiculatus

source_name: brainstem

growth_protocol: EV71 clinical strains EV71-58301 (Genbank ID: KX588236) were continuously  passaged with Vero cells until a cytopathogenic effect (CPE) was observed. Vero cells were grown in MEM supplemented with 10% fetal bovine serum at 37 °C.

extract_protocol:
Brainstems were obtained and RNA was extracted using the RNeasy extraction kit (Qiagen, Cat#74014) according to the manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 21-day-old gerbils were inoculated using strain EV71-58301 at a TCID50 of 106 by the intra-peritoneal route. Control animals were inoculated with PBS. After four days infection, the gerbils were sacrificed and the brainstems were collected immediately.

value: brainstem

value: 4 days post-infection

tag: agent

value: EV71 virus


title: mT_2-RNAseq


title: ∆admA rep 1


title: blood_patient WRN_45-2

description: patient with WRN mutation

value: classical Werner syndrome


title: AT_13: genomic DNA from adipose belong to group highBFR

description:
201533630047_R01C01
genomic DNA from adipose belong to group highBFR


title: AT_12: genomic DNA from adipose belong to group highBFR

description:
201533630047_R03C01
genomic DNA from adipose belong to group highBFR


title: ∆admA∆admB rep5

source_name: admA/admB deletion mutant cultivated in wheat bran solid culture

value: del-pyrG del-admA del-admB[pyrG+ ligD+]


title: ∆admA∆admB rep4


title: mC_3-RNAseq

value: control


title: B_06: genomic DNA from blood belong to group lowBFR

description:
201533570050_R04C01
genomic DNA from blood belong to group lowBFR


title: AT_14: genomic DNA from adipose belong to group highBFR

description:
201533630040_R06C01
genomic DNA from adipose belong to group highBFR


title: AT_10: genomic DNA from adipose belong to group lowBFR

description:
202110250019_R03C01
genomic DNA from adipose belong to group lowBFR

source_name: adipose lowBFR


title: AT_09: genomic DNA from adipose belong to group lowBFR

description:
201490030149_R01C01
genomic DNA from adipose belong to group lowBFR


title: ∆admA∆admB rep3


title: mC_2-RNAseq


title: AT_11: genomic DNA from adipose belong to group highBFR

description:
201533630040_R05C01
genomic DNA from adipose belong to group highBFR


title: AT_08: genomic DNA from adipose belong to group lowBFR

description:
201533630046_R03C01
genomic DNA from adipose belong to group lowBFR


title: ∆admA∆admB rep2


title: mC_1-RNAseq


title: AT_06: genomic DNA from adipose belong to group lowBFR

description:
201533630044_R04C01
genomic DNA from adipose belong to group lowBFR


title: blood_control_30-1

description: control

value: female


title: AT_05: genomic DNA from adipose belong to group lowBFR

description:
201105980147_R05C01
genomic DNA from adipose belong to group lowBFR


title: blood_patient WRN_37-1

description: patient with WRN mutation


title: Biosample_8150_4132_48365_HHKN3BGX2_S2_InSituHiC_NHS_2_ATCACG

city: Ithaca

first: Charles

last: Danko

state: NY

address: 235 Hungerford Drive

department: Computational Biology

institute: Cornell University

data_processing:
Fastq files were processed using the Aiden Lab's Juicer pipeline. The reference genome used was dm3, and the restriction enzyme was MboI
The resulting contact matices (.hic files) were produced at resolutions of 20 Mb, 10 Mb, 5 Mb, 2.5 Mb, 1 Mb, 500 Kb, 250 Kb, 100 Kb, 50 Kb, 25 Kb, 10 Kb, 5 Kb, and 1 Kb, using only high quality reads (MAPQ score >= 30)
Genome_build: dm3
Supplementary_files_format_and_content: hic files - highly compressed binary files that store contact matrices at multiple resolutions

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were grown in M3+BPYE medium with 10% FBS at 25°C  incubator.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min, quenched and permeabilized. Nuclei were digested with MboI and ends were biotinylated with biotin-14-dATP followed by in-situ ligation. Crosslinks were reversed and DNA was purified, sonicated and pulled down by streptavidin beads.
DNA was end repaired with T4 DNA polymerase, DNA polymerase I large (Klenow) polymerase and T4 polynucleotide kinase. DNA ends were adenylated by dATP and Klenow (3'-5' exo-) polymerase. Illumina Truseq adapters were ligated to the DNA ends and PCR amplified for 8 cycles. Library was purified with Qiaquick PCR purfication kit and sequenced on Illumina Nextseq 500.

treatment_protocol: Growing S2 cells were transferred to a shaking water bath maintained at room temperature (NHS) or at 36.5°C (HS). Simultaneously, an equal volume of medium (without FBS), kept at room temperature or at 48°C  was added into the NHS or HS cells respectively. Cells were incubated for 20 min.


title: ∆admA∆admB rep1


title: Deletion-control rep 5

source_name: deletion control cultivated in wheat bran solid culture

value: del-pyrG[pyrG+ ligD+]


title: blood_patient LMNA_30

description: patient with LMNA mutation

value: atypical Werner syndrome


title: AT_04: genomic DNA from adipose belong to group lowBFR

description:
201533630046_R02C01
genomic DNA from adipose belong to group lowBFR


title: AT_07: genomic DNA from adipose belong to group lowBFR

description:
201533630047_R05C01
genomic DNA from adipose belong to group lowBFR


title: Input DNA control for SOM-H3K27ac ChIP rep1

description:
a fraction of the input total chromatin that was used for glp-1(q224) soma control H3K27ac ChIP
SOM-H3K27ac_ChIP-input.wig

value: young adult (YA)

value: Soma


title: Deletion-control rep 4

value: wheat bran solid medium


title: Biosample_8150_4132_48366_HHKN3BGX2_S2_InSituHiC_HS_2_CGATGT


title: Y_1-RNAseq

data_processing:
Illumina Casava1.7 software was used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
Genome_build: no reference genome
Supplementary_files_format_and_content: Readcounts, FPKMs

growth_protocol: CA16 clinical strains CA16-193 (Genbank ID: KU854873) were continuously  passaged with Vero cells until a cytopathogenic effect (CPE) was observed. Vero cells were grown in MEM supplemented with 10% fetal bovine serum at 37 °C.

treatment_protocol: 21-day-old gerbils were inoculated using strain CA16-193 at a TCID50 of 106 by the intra-peritoneal route. Control animals were inoculated with PBS. After four days infection, the gerbils were sacrificed and the brainstems were collected immediately.

tag: infection

value: Coxsackievirus A16 (CA16)


title: Deletion-control rep 3


title: blood_control_37-1

description: control


title: Y_3-RNAseq


title: Y_2-RNAseq


title: AT_02: genomic DNA from adipose belong to group lowBFR

description:
201533630044_R06C01
genomic DNA from adipose belong to group lowBFR


title: AT_03: genomic DNA from adipose belong to group lowBFR

description:
201533630044_R02C01
genomic DNA from adipose belong to group lowBFR


title: Deletion-control rep 2


title: Con_2-RNAseq


title: Con_3-RNAseq


title: SC5314

city: Nanjing

first: Chengzhen

last: Zhang

address: 22 Han-kou road

institute: Nanjing University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (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.

organism: Candida albicans

source_name: cells

extract_protocol:
Cells of the JL01 and SC5314 were inoculated from overnight cultures by 1% into liquid YPD plus 10% serum medium at 37°C for 3 h. Cells were collected and total RNA was extracted as described. RNA-Seq analysis was performed by the company Majorbio (Shanghai, China). mRNA was purified, fragmented and used to synthesize cDNA. The library products were sequenced on the HisSeq 4000 platform using the HisSeq 4000 PE Cluster Kit and HisSeq 4000 SBS Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cells


title: Biosample_8018_4132_46901_HFYYWBGX2_S2_InSituHiC_HS_1_CGATGT


title: AT_20: genomic DNA from adipose belong to group highBFR

description:
201490030149_R05C01
genomic DNA from adipose belong to group highBFR

value: Adipose


title: Deletion-control rep 1


title: Con_1-RNAseq


title: Biosample_8018_4132_46900_HFYYWBGX2_S2_InSituHiC_NHS_1_ATCACG


title: ∆admA rep 2

value: del-pyrG del-admA[pyrG+ ligD+]


title: gDNA

status: Public on Jun 06 2019

city: Oxford

first: Florian

last: Bonkhofer

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: Oxford University

description:
Genomic control DNA was isolated from 30.000 cells using the DNeasy Blood & Tissue kit (Qiagen) and eluted with EB buffer.
ATAC-HE-91

data_processing:
Sequencing was performed on a NextSeq machine, using two 75bp paired-end chips loaded with the same Master-Library mix. Reads were combined to one raw data set. RAW data files represent the combined reads and combined lanes.
Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32).
Sequences were aligned to the Zebrafish Genome Zv10 with BWA (Version 0.7.12) with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1).
Peaks were identified using MAC2 software (Version 1.4.2), using the genomic DNA as input to define background. Differential peaks analysis was carried out using DiffBind (Bioconductor Package).  tool).
Triplicates were analysed for consistency by PCA and correlation analysis and one outlying replicate has been removed for each, DP-R1hi and DP-R1lo. Using a GLM analysis with EdgeR methods a list of DE packs between DP-R1hi and DP-R1lo population has been identified, then annotated with Homer software (Version 3.0). Further, peaks were filtered for log2 Fold Change <-0.7 and >0.7. Selecting the specific peaks for DP-R1hi   and DP-R1lo.
“De novo analysis” for transcription factor binding site has been carried out using the TSS, intergenic, and intron peaks list with “findMotifsGenome.pl” in Homer software package.
Genome_build: Zv10
Supplementary_files_format_and_content: bw files: bigwig files representing the Zv10 mapping data in bigwig format, for each tissue type and each replicates
Exp4-Wt-Flk1_S3_mergedLanes.sorted.bw  Exp5-Wt-Flk1_S5_mergedLanes.sorted.bw  Exp6-Wt-Flk1_S11_mergedLanes.sorted.bw  Exp4-Wt-High_S6_mergedLanes.sorted.bw  Exp5-Wt-High_S21_mergedLanes.sorted.bw  Exp6-Wt-High_S23_mergedLanes.sorted.bw  Exp4-Wt-Medium_S10_mergedLanes.sorted.bw  Exp5-Wt-Medium_S13_mergedLanes.sorted.bw  Exp6-Wt-Medium_S16_mergedLanes.sorted.bw  Exp4-Wt-Low_S9_mergedLanes.sorted.bw  Exp5-Wt-Low_S17_mergedLanes.sorted.bw  Exp6-Wt-Low_S15_mergedLanes.sorted.bw  Exp4-Wt-Negativ_S20_mergedLanes.sorted.bw  Exp5-Wt-Negative_S2_mergedLanes.sorted.bw  Exp6-Wt-Negative_S22_mergedLanes.sorted.bw  gDNA-DA_S7_mergedLanes.sorted.bw
Supplementary_files_format_and_content: bed files: The tab delimited file contains the result of the differential peak analysis obtained with the diffBind package using the EdgeR package for the contrast. The sample used for the analysis are the Wt DP-R1hi vs Wt DP-R1Lo. The one with positive FoldChange represent the peaks close into the  Wt DP-R1Lo population, and the one with negative FoldChange are the one with peaks close into the  Wt DP-R1Hi population.
DE_peacks_CloseIntoLow_FC_annotation_gs.bed DE_peacks_CloseIntoHigh_FC_annotation_gs.bed

organism: Danio rerio

source_name: whole embryo

growth_protocol: TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos, were raised to 28-30 hpf.

extract_protocol:
whole embryos were prepaired for FACsorting. 2000-3000 cells were FAC-sorted directly into 100 µl of 1x HBSS/10 mM HEPES/0.25% BSA buffer for Tagmentation
Tagmentation (as described by Buenrostro et al. (2013), Nat. Methods 10, 1213-1218), but with 1.5 µl Tn5 transposase (Illumina) in a 50 µl reaction volume. DNA was purified using the QIAquick PCR purification kit (Qiagen). Fragments were amplified for 16 cycles.

value: whole embryo

tag: cell isolation

value: FACS isolated cells


title: ATAC-seq_Wt DP-R1med rep3

source_name: aortic endothelium

value: aortic endothelium

tag: cell population

value: double positive runx1-medium   mCherry+Citrinemed


title: ATAC-seq_Wt DP-R1hi rep1

source_name: haemogenic endothelium

value: haemogenic endothelium

value: double positive runx1-high   mCherry+Citrinehigh


title: ATAC-seq_Wt DP-R1hi rep3


title: B_03: genomic DNA from blood belong to group lowBFR

description:
201533570050_R02C01
genomic DNA from blood belong to group lowBFR

tag: gender

tag: disease state

value: Blood


title: ATAC-seq_Wt DP-R1lo rep2

tag: age

value: double positive runx-low   mCherry+Citrinelow


title: ATAC-seq_Wt SP-kdrl rep3

source_name: non-aortic endothelioum (NAE)

tag: tissue

value: non-aortic endothelioum (NAE)

value: single positive-kdrl  mCherry+Citrine-


title: AT_01: genomic DNA from adipose belong to group lowBFR

description:
201533630044_R03C01
genomic DNA from adipose belong to group lowBFR


title: ATAC-seq_Wt DN rep2

source_name: non-endothelial tissue

value: non-endothelial tissue

value: double negative   mCherry-Citrine-


title: ATACseq in zebrafish wild type embryos at 36hpf, replicate 2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

institute: CABD/CSIC

description:
ATAC_seq
ATACseq_zebra_WT_36hpf_IDR_Peaks.bed

data_processing:
Alignment: reads were aligned against reference genome using Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: BED files with peaks called using Irreproducibility Discovery Rate (IDR) framework

growth_protocol: Embryos were cultivated at 28°C in E3 medium until desired developmental stage

extract_protocol:
Wild type or mutant embryos were dechorionated, deyolked and lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

tag: developmental stage

tag: genotype

value: WT


title: ATACseq in zebrafish tp63 mutant embryos at 36hpf, replicate 2

description:
ATAC_seq
ATACseq_zebra_p63mut_36hpf_IDR_Peaks.bed


title: ATAC-seq_Wt DP-R1med rep2


title: ATAC-seq_Wt SP-kdrl rep2


title: ATAC-seq_Wt DP-R1med rep1


title: ATAC-seq_Wt DP-R1lo rep3


title: ATAC-seq_Wt SP-kdrl rep1


title: ATAC-seq_Wt DN rep3


title: ATAC-seq_Wt DP-R1lo rep1


title: ATAC-seq_Wt DN rep1


title: ATACseq in zebrafish wild type embryos at 36hpf, replicate 1


title: JL01

tag: strain


title: ATAC-seq_Wt DP-R1hi rep2


title: ATACseq in zebrafish tp63 mutant embryos at 36hpf, replicate 1


title: mouse_pancreatic_primary_tumour_cell_line-Trp53_R175H-rep1

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

description: mouse pancreatic primary tumour cell-line, Trp53fl (null) + human mutant p53 (R175H)

hyb_protocol: cDNA probes were then hybridized to the Affymetrix mouse GeneChip 430 2.0 array as per the manufacturer’s instructions (Affymetrix Ca, USA) at the Beatson/Patterson Institute (UK).

scan_protocol: Arrays were scanned at the Beatson/Paterson institute (UK), following manufacturers instructions.

data_processing: Data was RMA normalised

label: Biotin

organism: Mus musculus

label_protocol: Total RNA was converted to cDNA. The cDNA was biotin labeled at the Beatson/Patterson insitute (UK), following manufacturers instructions.

growth_protocol: All cells were grown in DMEM + 10% FBS + 1% P/S to 60% confluency. Trp53_vec and Trp53_R175H cell culture medium was supplemented with 0.6mg/ml G418.

extract_protocol: Total RNA was isolated using Qiagen RNeasy mini (Qiagen GmbH, Germany) and measured on the 2100 Bioanalyzer (Agilent).

treatment_protocol: The experiment did not involve any drug treatments.

value: pancreatic primary tumour cell-line


title: mouse_pancreatic_primary_tumour_cell_line-Trp53flox-rep3

description: mouse pancreatic primary tumour cell-line, Trp53fl (null)

value: Trp53fl (null)


title: mouse_pancreatic_primary_tumour_cell_line-Trp53_vector-rep1

description: mouse pancreatic primary tumour cell-line, Trp53fl (null) + vector

value: Trp53fl (null) + vector


title: mouse_pancreatic_primary_tumour_cell_line-Trp53_R175H-rep2

source_name: mouse pancreatic primary tumour cell-line, Trp53fl (null) + human mutant p53 (R175H)


title: mouse_pancreatic_primary_tumour_cell_line-Trp53_R175H-rep3

value: Trp53fl (null) + human mutant p53 (R175H)


title: mouse_pancreatic_primary_tumour_cell_line-Trp53flox-rep1

source_name: mouse pancreatic primary tumour cell-line, Trp53fl (null)


title: mouse_pancreatic_primary_tumour_cell_line-Trp53_vector-rep2

source_name: mouse pancreatic primary tumour cell-line, Trp53fl (null) + vector


title: mouse_pancreatic_primary_tumour_cell_line-Trp53_R172H-rep3

description: mouse pancreatic primary tumour cell-line, Trp53 mutant (R172H)

value: Trp53 mutant (R172H)


title: mouse_pancreatic_primary_tumour_cell_line-Trp53_vector-rep3


title: mouse_pancreatic_primary_tumour_cell_line-Trp53flox-rep2


title: M3-817

city: Shanghai

first: Huaifeng

last: Li

address: NO.1665, kongjiang road, Shanghai, China

department: general surgery

institute: Xinhua hospital affiliated to Shanghai jiaotong university, school of medicine

data_processing:
base-calling was performed by Novaseq6000 V4 PE150 (Illumina, USA)
For the quality control of the reads, cutadapt (v1.11) software was used to delete the joint and inferior quality sequences.
HISAT2 (v2.1.0) software was used to compare the clean reads to the reference human genome (hg19).
RSeQC software was used to access the position of the reads on genome.
Kallisto (v0.44.0) software were used to quantitate gene expression levels of the RNA-sequencing data.
Genome_build: hg19
Supplementary_files_format_and_content: excel files include TPM values for each Sample

source_name: normal gallbladder tissue

extract_protocol:
Tissues were grinded in liquid nitrogen, total RNA was extracted using All Prep DNA/RNA/Protein Mini Kit (QIAGEN, Germany). Qubit TM RNA HS Assay Kit (Invitrogen, USA) was used for the quantitation of the total RNA.
After erasing rRNA from the total RNA by KAPA Stranded RNA-Seq Kit with RiboErase (KAPA, USA), strand specific lncRNA library were constructed. The quality and quantity of the library were detected by Qubit TM dsDNA HS Assay Kit (Invitrogen, USA), the inserts of the library were detected by High Sensitivity DNA Chip using Agilent 2100 Bioanalyzer system. The molarity of the library was detected by Step One Plus™ Real-Time PCR System.

value: normal gallbladder tissue

tag: age (years)

value: female

tag: tumor stage (tnm)

value: IV


title: M3-761

source_name: liver metastatic tissue of gallbladder cancer


title: M3-760


title: M3-759

source_name: primary gallbladder cancer tissue

value: primary gallbladder cancer tissue


title: M3-740


title: mT_1-RNAseq

value: brainstem

value: 4 days post-infection

value: EV71 virus


title: M3-819

value: liver metastatic tissue of gallbladder cancer


title: Lung, Dex_HDM 2

city: Reno

first: William

middle: T

last: Gerthoffer

state: Nevada

address: 1440 N Virginia St

department: Pharmacology

institute: University of Nevada, Reno

description:
Dexamethasone treated 2
ribosome-depleted

data_processing:
Sequencing adapters were trimmed and bases identified with Illumina Casava 1.9 base calling software
Fastq files were analyzed using a model-based method (Sailfish-cir, Li et al., Bioinformatics 2017 15:33(14):2131-2139)
Normalized abundance (TPM) was calculated for linear RNA transcripts and circularRNAs according to Li et al., 2017
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited txt files containig TPM for each transcript in each sample. First column is gene ID. First row is sample name.

source_name: lung

extract_protocol:
Lung lobes stored in RNALater solution were weighed (~25-30 mgs) and minced into 2-3 mm pieces. Total RNA was extracted with QIAzol Lysis Reagent (Qiagen, 1023537) using Zirconia beads (Biospec,11079110ZX) and a Mini-Bead Beater16™.  Total RNA, including microRNA, was isolated using a Qiagen miRNEasy kit (#217004). Three methods were used to determine RNA concentration and RNA quality -  spectrophotometry of total RNA (NanoDrop 1000), gel filtration of RNA integrity (RNA 6000 Nano Kit, Agilent 2100 Bioanalyzer), and fluorescent dye binding (Quant-iT RiboGreen Kit, Invitrogen55).  RNA quality determined by A260/280 ranged from 1.8 to 2.2, A260/230 >2 and RIN values ranged from 6.9 to 8.6.
Initial RNA quantification was performed with a Qubit RNA assay kit, followed by RIN determination with an Agilent 2100 Bioanalyzer. cDNA libraries were prepared using 2 micrograms of total RNA for ribosomal reduction, directional RNA-seq, paried-end, 150 nucleotide. Final quantification was performed with a Kapa Library Quant kit. Stranded cDNA libraries were sequenced using an Illunina HiSeq 25000 instrument (HiSeq v4 reagents) at read depth of 100M reads/sample.
Ribosome reduction, stranded, 100 nt paired-end RNA-seq

treatment_protocol: Allergic sensitization of the lungs was elicited with house dust mite extract according to Collison et al. (J Allergy Clin Immunol 2011 128(1):160-167). AntimiR-145-treated mice received 3 doses of 2 mg/kg, i.v. antisense miR-145 oligonucleotide complexed with TheraSilence lipid nanoparticles on days 13, 15 and 17. Dexamethasone-treated mice recieved 3 doses of 3 mg/kg, i.p. on days 13, 15 and 17.

value: BALB/c AnNHsd

value: lung, left lobe

value: 70 days

tag: treatment

value: Dexamethasone treated


title: Lung, Dex_HDM 3

description:
Dexamethasone treated 3
ribosome-depleted


title: Lung, Dex_HDM 4

description:
Dexamethasone treated 4
ribosome-depleted


title: M3-816


title: Lung, Dex_HDM 6

description:
Dexamethasone treated 6
ribosome-depleted

value: 71 days


title: Lung, Dex_HDM 1

description:
Dexamethasone treated 1
ribosome-depleted


title: AT_19: genomic DNA from adipose belong to group highBFR

description:
201105980147_R03C01
genomic DNA from adipose belong to group highBFR

source_name: adipose highBFR

tag: group

value: Adipose


title: mouse_pancreatic_primary_tumour_cell_line-Trp53_R172H-rep1

source_name: mouse pancreatic primary tumour cell-line, Trp53 mutant (R172H)

value: pancreatic primary tumour cell-line


title: Lung, Dex_HDM 5

description:
Dexamethasone treated 5
ribosome-depleted


title: mouse_pancreatic_primary_tumour_cell_line-Trp53_R172H-rep2


title: Lung, AM 10

description:
AntimiR-145 treated 10
ribosome-depleted

value: AntimiR-145 treated


title: M3-741


title: M3-743


title: Lung, AM 9

description:
AntimiR-145 treated 9
ribosome-depleted


title: Lung, AM 8

description:
AntimiR-145 treated 8
ribosome-depleted


title: Lung, AM 7

description:
AntimiR-145 treated 7
ribosome-depleted


title: Lung, AM 6

description:
AntimiR-145 treated 6
ribosome-depleted


title: Lung, AM 5

description:
AntimiR-145 treated 5
ribosome-depleted


title: Lung, AM 4

description:
AntimiR-145 treated 4
ribosome-depleted


title: Lung, AM 3

description:
AntimiR-145 treated 3
ribosome-depleted


title: Lung, AM 1

description:
AntimiR-145 treated 1
ribosome-depleted


title: Lung, AM 2

description:
AntimiR-145 treated 2
ribosome-depleted


title: Lung, HDM 18

description:
HDM sensitized 10
ribosome-depleted

value: HDM sensitized


title: Lung, HDM 8

description:
HDM sensitized 7
ribosome-depleted


title: Lung, HDM 5

description:
HDM sensitized 5
ribosome-depleted


title: Lung, HDM 9

description:
HDM sensitized 8
ribosome-depleted


title: Lung, HDM 3

description:
HDM sensitized 3
ribosome-depleted


title: Lung, HDM 1

description:
HDM sensitized 1
ribosome-depleted


title: Lung, HDM 7

description:
HDM sensitized 6
ribosome-depleted


title: Lung, Saline 3

description:
Unsensitized 2
ribosome-depleted

value: Unsensitized


title: Lung, HDM 2

description:
HDM sensitized 2
ribosome-depleted


title: Lung, Saline 5

description:
Unsensitized 3
ribosome-depleted


title: Lung, Saline 2

description:
Unsensitized 1
ribosome-depleted


title: B145T26 RNA-seq

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: RNA-seq

data_processing:
Quality control for PROseq: Adapter sequences were trimmed with cutadapt v1.8.2. Nucleotides with poor 3’ base quality (BAPQ < 20) were trimmed and reads of <20 bp were discarded.
Quality control for mRNAseq: First ten bases from all reads were removed, due to their low quality, using FASTX toolkit (v0.0.13).
Genome reconstruction: The VCF file (mgp.v5.merged.snps_all.dbSNP142.vcf) reporting all SNP sites from 36 mouse strains, based on mm10, was downloaded from the Sanger database. SNPsplit tool (v0.3.0) was used to reconstruct the Cast genome from the mm10 reference.
Mapping for PROseq: Ribosomal reads were first removed by alignment to the rRNA reference using bowtie1 (v1.0.0) and allowing 2 mismatches in the seed. Then, non-ribosomal reads were mapped to both parental genomes. Only random best alignments with fewer than two mismatches were kept for downstream analyses.
Mapping for mRNAseq: Reads were then mapped to both parental genomes with TopHat2 software (v2.1.0). Only random best alignments with less than two mismatches were kept for downstream analyses.
Allelic Ratio: Mapping files of both parental genomes were merged for each sample and SAMtools mpileup (v1.1) was then used to extract the base-pair information at each genomic position. Read counts mapping to the paternal and maternal genomes, respectively, were summed up across all SNPs present in the same gene.
Estimation of gene expression levels: RPKM values were calculated using gene count table, generated with Gencode annotation (M9) and HTSeq software (v0.6.1).
Genome_build: mm10

source_name: ES cells

growth_protocol: The female TX1072 cell line is a F1 hybrid ESC line derived from a cross between the  57BL/6 (B6) and CAST/EiJ (Cast) mouse strains that carries a doxycycline responsive promoter in front of the Xist gene on the B6 chromosome and an rtTA insertion in the Rosa26 locus (described in Schulz et al. (Schulz et al., 2014) ). TX1072 cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Chemicon)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901).

extract_protocol:
For PROseq samples: For each timepoint ~1 x 107 nuclei were isolated by washing the cells twice with ice-cold PBS, and once with 15 ml swelling buffer (10 mM Tris-Cl, pH 7.4, 300 mM Sucrose, 3 mM CaCl2, 2 mM MgAc2, 5 mM DTT). Then, 15 ml cell lysis buffer (10 mM Tris-Cl, pH 7.4, 300 mM Sucrose, 3 mM CaCl2, 2 mM MgAc2, 0.5% NP-40, 1 mM PMSF, EDTA-free protease inhibitors (1 tablet for 50 ml buffer; Roche), 5 mM DTT) is added and cells are scraped off the plate into a 50 ml tube and spun at 900 g and 4 °C in a swing bucket centrifuge for 5 minutes. Supernatant is removed and the cell pellet is resuspended in 5 ml cell lysis buffer, transferred to a 7 ml dounce homogenizer and dounced 50x on ice. Dounced cells are moved to 15 ml tube and spun at 1200 g and 4 °C in a swing bucket centrifuge for 5 minutes. Supernatant is removed and the nuclei are counted, snap frozen and stored in glycerol storage buffer (50 mM Tris-Cl, pH 8.3, 40% glycerol, 0.1 mM EDTA, 5 mM MgAc2, 1 mM PMSF, EDTA-free protease inhibitors (1 tablet for 50 ml buffer; Roche), 5 mM DTT).
For PROseq samples: Run-on and library preparation was performed as previously described (Mahat et al., 2016), using the single biotin-CTP nucleotide run-on protocol to prolong run-on and increase sequence length. In short, run-on was performed with 1 x 107 nuclei in 100 ml glycerol storage buffer and 100 ml pre-heated nuclear run-on mix, to get a final concentration in the run-on of 5 mM Tris-HCl, pH 8, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.025 mM biotin-11-CTP, 0.25 mM CTP, 0.125 mM ATP, UTP and GTP, 0.5% sarkosyl and RNase inhibitor. Run-on was done for 5 minutes at 37 °C and stopped by adding 500 ml Trizol LS.
For mRNAseq samples: The 32 libraries were prepared with an input of 1µg of totalRNA, using the TruSeq Stranded mRNA LT Sample Prep kit from Illumina, according to manufacturer's recommendations. Single Index kit was used, and 12 cycles of PCR were set up. Final libraries were quantified with Qubit dsDNA HS Assay Kit, and qualified with LabChip® GX system (PerkinElmer). Then 2 equimolar pools of 16 libraries each were prepared at 10nM. The exact molarity of the pools were assess by qPCR using the KAPA Library Quantification Kit Illumina on CFX96 system (Biorad).
For PROseq samples: Libraries were sequenced on the HiSeq 2000 Illumina sequencer (100bp, single-end). For each library at least 50 Mio reads were generated.
For mRNAseq samples: Each pool was sequenced on 1 flowcell of HiSeq 2500 system in PE100, in order to target ~100M cluster per sample.

treatment_protocol: Cells were seeded at a density of 105 cells/cm2 coated with gelatin two days before the experiment. Xist was induced by supplementing the medium with 1 μg/ml Doxycycline. For PRO-seq samples were collected before doxycycline treatment (0h) and at time points 0.5, 1, 2, 4, 8, 12 and 24h after treatment. Samples without doxycycline and 24 h doxycycline were collected in duplicate. For mRNA-Seq on undifferentiated TX1072 cells, samples were collected before doxycycline treatment and at time points 2, 4, 8, 12 and 24h after treatment. Also for mRNA-seq samples without doxycycline and 24 h doxycycline were collected in duplicate. For mRNA-Seq on differentiating TX1072 cells samples were collected at time points 0, 8, 16, 24 and 48h.

tag: doxycycline treatment (h)

tag: cell type

value: Differenciated ES cells


title: CTR_qNSC_2: prospectively isolated qNSCs after vehicle treatment. 2nd replica

city: Planegg

first: Jovica

last: Ninkovic

address: Grosshaderner strasse 9

institute: LMU Munich

data_processing:
FASTQ files were used for the transcript counting using kallisto pipeline (the reference transcriptome was Muss musculus full transcriptome (mm10))
Sleuth pipeline was used for statistical analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Cells isolated from subependymal zone of 3 months old mice

growth_protocol: cells are isolated from gfap:GFP transgenic animals using FACS protocol as previously described (Fischer et al., 2011)

extract_protocol:
RNA is isolated using PicoPure RNA isolation Kit (ThermoFisher; KIT0204) and cDNA was made using SMART-Seq v4 Ultra Low Input RNA Kit (Takara, Cat. No. 634888).
MicroPlex Library Preparation Kit v2 and processed according to the manufacturer ́s instruction. Deep sequencing was performed on Illumina HiSeq system with 100bp paired-end reads

treatment_protocol: intraventricular injection of miR204-specific antagoMIRs

value: brain

tag: treatment group


title: CTR_qNSC_3: prospectively isolated qNSCs after vehicle treatment. 3rd replica


title: AmiR_qNSC_1: prospectively isolated qNSCs after miR-204 specific treatment. 1st replica


title: AmiR_qNSC_3: prospectively isolated qNSCs after miR-204 specific treatment. 3rd replica


title: CTR_qNSC_1: prospectively isolated qNSCs after vehicle treatment. 1st replica


title: AmiR_qNSC_2: prospectively isolated qNSCs after miR-204 specific treatment. 2nd replica


title: Lung, HDM 4

description:
HDM sensitized 4
ribosome-depleted


title: Lung, HDM 17

description:
HDM sensitized 9
ribosome-depleted


title: B145T25 RNA-seq

description: RNA-seq


title: B145T24 RNA-seq

description: RNA-seq


title: Lung, Saline 10

description:
Unsensitized 4
ribosome-depleted


title: B145T22 RNA-seq

description: RNA-seq


title: Lung, Saline 11

description:
Unsensitized 5
ribosome-depleted


title: B145T23 RNA-seq

description: RNA-seq


title: B145T19 RNA-seq

description: RNA-seq


title: B145T17 RNA-seq

description: RNA-seq


title: B145T21 RNA-seq

description: RNA-seq


title: B145T18 RNA-seq

description: RNA-seq


title: B145T20 RNA-seq

description: RNA-seq


title: B144T11 RNA-seq

description: RNA-seq

value: Undifferenciated ES cells


title: B144T12 RNA-seq

description: RNA-seq


title: B144T10 RNA-seq

description: RNA-seq


title: B144T9 RNA-seq

description: RNA-seq


title: B144T8 RNA-seq

description: RNA-seq


title: B144T5 RNA-seq

description: RNA-seq


title: B144T2 RNA-seq

description: RNA-seq


title: B144T4 RNA-seq

description: RNA-seq


title: B144T3 RNA-seq

description: RNA-seq


title: B144T1 RNA-seq

description: RNA-seq


title: B144T6 RNA-seq

description: RNA-seq


title: stomach_P5_wt

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

data_processing:
Stranded reads were aligned to the mm9 reference genome and to the Mus Musculus transcriptome (iGenome refGene) using TopHat v2.0.13 (PMID: 23618408). The option --no-coverage-search was specified, while all the other parameters were left to default.
Reads were de-duplicated using SAMtools v0.1.18 (PMID: 19505943) and the expression of genes quantified with Cufflinks v2.2.1 (PMID: 20436464).
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63.
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression by transcript (RPKM) (refer to http://cole-trapnell-lab.github.io/cufflinks/ for details).

source_name: Stomach

growth_protocol: A 1512 bp mouse region (chr17:25175032-25176543, mm9) was replaced by loxP-Neomycin-loxP cassette in W4/129S6 mouse ES cells through homologous recombination. The neomycin cassette was subsequently removed by Cre recombinase, leaving a loxP site in place of the 1512 bp sequence. The resulting ES clones were injected into C57BL/6J blastocyst stage embryos. Chimeric mice were then crossed to C57BL/6J mice to generate mice carrying a heterozygous deletion. The deletion KO lines were maintained in 129Sv/C57 mixed background through sibling breeding. Noon of the day the vaginal plug was observed was considered as embryonic day 0.5 (E0.5). Mice and embryos were genotyped by PCR using genomic DNA extracted from ear punch and tail, respectively.

extract_protocol:
Whole gut (including stomach and intestine) were dissected from E14.5 mutant and wild type embryos. Stomach (P5 and younger: whole stomach; older mice: stomach was divided into top and bottom halves), intestine (divided into top and bottom halves), colon and rectum were dissected from postnatal mice. Gut contents were squeezed out. Tissue was snap frozen in liquid nitrogen, and was stored at -80 °C. Total RNA was extracted from tissue samples with TRIzol® Reagent (ThermoFisher Scientific).
RNA-seq libraries were generated using Illumina TruSeq® Stranded Total RNA LT - with Ribo-Zero™ Human/Mouse/Rat-Set A (Cat# RS-122-2201), following manufacture’s recommendation.

tag: strain background

value: Mixed 129SvEv and C57BL/6

tag: genotype/variation

value: wild type

value: Stomach

tag: library type

value: Stranded (first-strand synthesis)


title: wholegut_E14.5_wt

source_name: Whole gut

value: Whole gut


title: wholegut_E14.5_ko


title: stomach_P5_ko


title: stomach-bottom_P20_wt

source_name: Stomach (Bottom)

value: Stomach (Bottom)


title: stomach_P1_ko


title: stomach-bottom_P20_ko


title: stomach_P1_wt


title: stomach-bottom_P15_wt


title: stomach-bottom_P10_ko


title: rectum_P5_ko

source_name: Rectum

value: Rectum


title: rectum_P5_wt


title: intestine-top_P5_ko

source_name: Intestine (Top)

value: Intestine (Top)


title: intestine-top_P1_ko


title: stomach-bottom_P15_ko


title: intestine-top_P15_wt


title: intestine-top_P1_wt


title: intestine-top_P15_ko


title: intestine-bottom_P10_wt

source_name: Intestine (Bottom)

value: Intestine (Bottom)


title: intestine-bottom_P20_wt


title: B144T7 RNA-seq

description: RNA-seq


title: intestine-bottom_P20_ko


title: intestine-bottom_P5_ko


title: intestine-bottom_P1_wt


title: intestine-bottom_P5_wt


title: intestine-bottom_P10_ko


title: stomach-bottom_P10_wt


title: intestine-top_P5_wt


title: colonrectum_P1_ko

source_name: Colon Rectum

value: Colon Rectum


title: colon_P5_wt

source_name: Colon

value: Colon


title: colonrectum_P1_wt


title: colon_P5_ko


title: 16164T

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Basecalling was performed with Illumina RTA 1.18.64. Bcl conversions into Fastq were performed using bcl2fastq version 1.8.3.
Reads were mapped to mm10 genome with STAR version 2.4.0g1 using Ensembl annotation (GRCm38, release 78)
Duplicate reads were removed using the function MarkDuplicates from Picard tools and a filtering for uniquely mapped reads was performed.
We quantified read counts for all genes annotated in Ensembl release 78 with HTSeqcount version 0.6.1
Differential gene expression analysis was performed with the Bioconductor package DESeq2 version 1.6.3 and SARTools version 1.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including differential expression results from DESeq2

molecule: polyA RNA

source_name: Thymic lymphoma

extract_protocol:
RNA was prepared from single-cell suspensions of mouse tumor thymus using the RNeasy Mini Kit (Qiagen).
Libraries were generated according to the TruSeq Stranded mRNA Library Preparation kit protocol (Illumina)

value: mixed background C57BL/6 and 129S6/SvEv


title: 16152T


title: 16248T


title: 16166T


title: intestine-bottom_P1_ko


title: 16499T


title: TTTTGA

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

description: R1 fastq file: cDNA; R2 fastq file: barcode/UMI

data_processing:
Dropseq (v1.0) – see Macosko et al., PMID: 26000488.
Genome_build: GRCm38
Supplementary_files_format_and_content: Lgp130-Bcell-RawCounts.txt: Tab-delimited text file includes raw read counts for each sample.
Supplementary_files_format_and_content: Lgp130-Bcell-Eset.rds: ExpressionSet containing raw counts and metadata.

extract_protocol:
Qiagen RNeasy plus mini Kit.
Generation of barcoded cDNA using Maxima RT polymerase. Application of template switch oligo. Library preparation with Nextera XT kit (Illumina).

tag: strain/background

value: Myc

value: Bone marrow

tag: phenotype

value: immature

tag: purified

value: N

tag: transplantation

value: Y


title: ACTTAT

tag: tissue

value: Spleen


title: CGCCCT


title: ACGGGG

value: Lymph node


title: ACAATA


title: ACCGGC

value: mature


title: CAAATA


title: GGTGGC


title: TTTCTT


title: TATAGA

value: Tumor


title: GCCCTC


title: AATTCT

value: plasma cell


title: GCCAGG


title: GGGTCG


title: TATGAA


title: CATTAT


title: GGGGAC


title: GCACGG


title: GTACCG


title: CCTGGC


title: TTTACA


title: AATCTT


title: ATTTCA


title: TAGTAA


title: CCGTCG


title: GAGCGG


title: CCAACC


title: CGAGGC


title: TTGAAA


title: GACCGC


title: AATACA


title: TACTAT


title: AAGATT


title: TTATTG


title: CCGGAC


title: TAATGA


title: TCTGCA


title: CTGCGG


title: GGCCAC


title: ATTACT


title: GTTCGA


title: CCCTGG


title: TAAGAT


title: ATGAAT


title: AAATTG


title: GGGCAG


title: GGAGCC


title: CGTGGG


title: CCCCGT


title: TTAATC


title: TAAAGT


title: GGGATT


title: GGCGTC


title: ATTCTA


title: AAAGTT

value: B cells


title: GCTCGC


title: ATCAAA


title: CGGTGG


title: GCTAGA

value: L-gp


title: ATATAG


title: GTTTAT


title: AAAACT


title: progenitor_Sp3KO_RNAseq_rep1

city: Birmingham

first: Christopher

last: Middleton

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
Alignment HiSat2 v2.1.0 default parameters
FPKM quantification: StringTie 1.3.3 stringtie --G mm10_refGene.gtf -e -o  -A
Coverage track generation: bedtools genomecov (2.19), using bedtools genomecov -ibam <bam> -g mm10.chrom.sizes -bg -split -trackline -trackopts ‘name=<name> description=<description>’
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph format representing read depth coverage, tsv format representing normalized FPKM values

source_name: Progenitor

growth_protocol: ESC were cultured in ESC maintenance media as previously described (Gilmour et al 2014). Flk1 cells were purified from embryoid bodies using MACS columns, using biotinylated Flk1 antibody and anti-biotin microbeads and subsequently seeded into blast culture media as previously described (Gilmour et al 2014). HE1, HE2 and Progenitor cells were sorted from the blast culture cell populations at D2 after seeding of Flk1 cells.

extract_protocol:
RNA was isolated using Trizol, then treated with Ambion Dnase before clean up using Macherey Nagel RNA purification kits.
RNA Sequencing libraries were produced in duplicate using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina).

value: Progenitor

tag: cell line

tag: genotype


title: HE2_Sp3KO_RNAseq_rep1


title: progenitor_Sp1_deltaDBD_RNAseq_rep1


title: HE2_Sp3KO_RNAseq_rep2


title: progenitor_WT_RNAseq_rep2

value: WT


title: HE2_Sp1_deltaDBD_RNAseq_rep2


title: TTAGTT


title: HE2_WT_RNAseq_rep2


title: HE2_WT_RNAseq_rep1


title: HE1_Sp3KO_RNAseq_rep2


title: progenitor_Sp3KO_RNAseq_rep2


title: progenitor_WT_RNAseq_rep1


title: progenitor_Sp1_deltaDBD_RNAseq_rep2


title: HE1_Sp1_deltaDBD_RNAseq_rep2


title: HE1_Sp1_deltaDBD_RNAseq_rep1


title: HE1_WT_RNAseq_rep2


title: Flk1_Sp3KO_RNAseq_rep2


title: TGTTTA


title: CCCACG


title: HE2_Sp1_deltaDBD_RNAseq_rep1


title: HE1_Sp3KO_RNAseq_rep1


title: Flk1_Sp3KO_RNAseq_rep1


title: Flk1_Sp1_deltaDBD_RNAseq_rep1


title: Flk1_Sp1_deltaDBD_RNAseq_rep2


title: Flk1_WT_RNAseq_rep2


title: HE1_WT_RNAseq_rep1


title: ESC_Sp1_deltaDBD_RNAseq_rep2

source_name: ESC

value: ESC


title: ESC_Sp3KO_RNAseq_rep1


title: ESC_Sp3KO_RNAseq_rep2


title: ESC_WT_RNAseq_rep2


title: ESC_WT_RNAseq_rep1


title: ESC_Sp1_deltaDBD_RNAseq_rep1


title: A17Lox_Sp1het1_Flk1_Sp3_ChIPseq

data_processing:
Reads were aligned to the mouse genome (version mm10) using Bowtie v2.3.1 with default parameters
Regions of enrichment corresponding to regions of open chromatin (Peaks) were identified using MACS v1.4.2 using the parameters --keep-dup=all -w -S
Genome_build: mm10
Supplementary_files_format_and_content: WIG files generated by MACS version 1.4.2

growth_protocol: ESC were cultured in ESC maintenance media as previously described (Gilmour et al 2014). Flk1 cells were purified from embryoid bodies using MACS columns, using biotinylated Flk1 antibody and anti-biotin microbeads.

extract_protocol:
Cells were harvested and washed with PBS prior to a 2-step crosslinking procedure. Proteins were crosslinked by incubating cells for 45min at RT in PBS supplemented with 0.83 mg/ml Di(N-succinimidyl) glutarate (DSG, Sigma). Cells were then washed 4 times with PBS, prior to formaldehyde crosslinking of proteins and DNA for 10min at RT using 1% formaldehyde (Pierce) in IMDM with 10% FCS. Formaldehyde was quenched by adding 1/10th volume 2M glycine and crosslinked cells were washed twice in ice-cold PBS. Single crosslinked samples were treated with 1% formaldehyde crosslinking only. Nuclei were prepared essentially as described in Lefevre et al 2003. Antibody incubated with chromatin 2-4hrs at 4 degrees.
Kapa Hyper-prep kit

tag: chip antibody

value: Sp3 (Santa Cruz sc644X)


title: A17Lox_Sp1het2_Flk1_Sp3_ChIPseq


title: A17Lox_Sp1deltaDBD_Flk1_Sp3_ChIPseq


title: A17Lox_Sp1het1_Flk1_Sp1_ChIPseq

value: Sp1 (Millipore 17-601)


title: A17Lox_WT_Flk1_Sp3_ChIPseq


title: A17Lox_Sp1het2_ESC_Sp3_ChIPseq


title: A17Lox_Sp1het2_Flk1_Sp1_ChIPseq


title: A17Lox_Sp1deltaDBD_Flk1_Sp1_ChIPseq


title: A17Lox_WT_Flk1_Sp1_ChIPseq


title: A17Lox_Sp1KO_ESC_Sp3_ChIPseq


title: A17Lox_Sp1deltaDBD_ESC_Sp3_ChIPseq


title: A17Lox_Sp1het1_ESC_Sp3_ChIPseq


title: A17Lox_Sp1KO_ESC_Sp1_ChIPseq


title: E14_Sp1_deltaDBD_Flk_ATACseq_Rep2

growth_protocol: ESC were cultured in ESC maintenance media as previously described (Gilmour et al 2014). Flk1 cells were purified from embryoid bodies using MACS columns, using biotinylated Flk1 antibody and anti-biotin microbeads and subsequently seeded into blast culture media as previously described (Gilmour et al 2014).

extract_protocol:
50,000 cells were washed with PBS and resuspended in transposition reaction buffer with Tn5 transposase and digitonin and incubated at 37degrees for 30mins with shaking. DNA was subsequently purified using the Qiagen Enzymatic Reaction Clean-up kit.
Nextera PCR primers were added during PCR amplification of transposed DNA fragments for an appropriate number of cycles determined for each library. Samples were purified using Qiagen Minelute clean-up kit and Ampure beads.


title: Flk1_WT_RNAseq_rep1


title: E14_Sp1_deltaDBD_Flk_ATACseq_Rep1


title: A17Lox_WT_ESC_Sp1_ChIPseq


title: A17Lox_Sp1het2_ESC_Sp1_ChIPseq


title: A17Lox_Sp1deltaDBD_ESC_Sp1_ChIPseq


title: E14_WT_Flk1_ATACseq_Rep2


title: E14_WT_Flk1_ATACseq_Rep1


title: E14_Sp1_deltaDBD_ESC_ATACseq_Rep1


title: E14_WT_ESC_ATACseq_Rep2


title: E14_Sp1_deltaDBD_ESC_ATACseq_Rep2


title: E14_WT_ESC_ATACseq_Rep1


title: A17Lox_Sp1KO_Flk1_ATACseq_Rep2


title: A17Lox_WT_ESC_Sp3_ChIPseq


title: A17Lox_Sp1het1_Flk1_ATACseq_Rep1


title: A17Lox_Sp1het2_Flk1_ATACseq_Rep1


title: A17Lox_Sp1het1_Flk1_ATACseq_Rep2


title: A17Lox_Sp1het2_ESC_ATACseq_Rep1


title: A17Lox_Sp1het2_ESC_ATACseq_Rep2


title: A17Lox_Sp1_deltaDBD_Flk1_ATACseq_Rep2


title: A17lox_WT_Flk1_ATACseq_Rep2


title: A17lox_Sp1KO_ESC_ATACseq_Rep2


title: A17lox_Sp1KO_ESC_ATACseq_Rep1


title: A17Lox_Sp1_deltaDBD_ESC_ATACseq_Rep1


title: A17Lox_Sp1het1_ESC_ATACseq_Rep2


title: A17Lox_WT_ESC_ATACseq_Rep2


title: A17lox_WT_Flk1_ATACseq_Rep1


title: A17Lox_Sp1het1_ESC_Sp1_ChIPseq


title: RNA-Seq_CD8_TIM_S3

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

description:
Truseq Ribo zero gold kit
RNA-Seq_CD8_TIMvsNaive.xlsx

data_processing:
reads were filtered using FastX 0.0.13 and ShortRead 1.16.3, polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N), low quality reads (more than 50% of the bases < Q25) and artifact reads (all but 3 bases in the read equal one base type) were removed
reads were aligned to the reference genome mm10 using Tophat v2.0.13 with the following parameters: --library-type fr-firststrand --min-intron-length 50 --max-intron-length 500000 --no-coverage-search --no-mixed --read-realign-edit-dist 3
reads from the alignment that are non-primary mappings or have a mapping quality ≤20 were removed
read counts were estimated using featureCounts v1.4.6 with the following parameters: -Q 0 -s 2 -t exon -g gene_id and genes that have less than 1 counts-per-million were removed
raw read  counts were normalised with the EDASeq package and FPKM values were obtained
differential expression analysis was performed with edgeR 3.4.0 package by applying a corrected p value FDR<0.05 and absolute log2-ratio larger than 1.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing raw read counts and FPKM normalized counts (TIM vs Naive) and  tab-delimited text files containing normalized read counts (such as total read count=20M)  for each sample and gene and differential analysis results (EomesTG vs WT)

source_name: Thymus

extract_protocol:
RNA from 106 sorted CD8SP populations was extracted using RNeasy Plus Mini kit according to manufacturer’s instructions
RNA library was prepared using Truseq Ribo zero gold kit for TIM and Naive, and Truseq kit for CD8SP WT and CD8SP EomesTg following manufacturer's instruction.

value: Thymocytes

tag: Stage

value: CD8SP Innate Memory

tag: strain

value: BALB/c

value: wild type


title: RNA-Seq_CD8_Naive_S1

value: CD8SP Naive


title: RNA-Seq_CD8_Naive_S2


title: A17Lox_Sp1het1_ESC_ATACseq_Rep1


title: A17Lox_Sp1_deltaDBD_ESC_ATACseq_Rep2


title: RNA-Seq_CD8_TIM_S2


title: RNA-Seq_CD8_TIM_S1


title: RNA-Seq_CD8_Naive_S3


title: A17Lox_Sp1KO_Flk1_ATACseq_Rep1


title: Input_CD8SP-WT

data_processing:
Reads were aligned to mm10 by Bowtie2
Reads with quality lesser than 1 (=mapping to multiple locations) were filtered out with samtools view
Reads in ENCODE blacklist were removed with bedtools intersect
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Peak calling was performed with MACS2 callpeak, using standard parameters, except for : H3K4me3, H3K4me1, H3K27ac for which we used a q-value threshold=0.01 ; Eomes for which we used a p-value threshold=0.001 ; Runx3 for which we used a p-value threshold=0.01
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal

extract_protocol:
CD8SP from pooled thymus were isolated and crosslinked with formaldehyde 1% for 10min at room temperature before staining. Crosslinking was stopped with 0.125 M glycine. Cells then were washed twice by ice-cold PBS and sorted. Each sorted cell-population was resuspended with ChIP-lysis buffer (10mM Tris pH8, 140mM NaCl, 1mM EDTA, 1% Triton x-100, 0.5% SDS, 0.1% Na-Deoxycholate) for 10min on ice supplemented with PIC (proteinase inhibitors cocktail) and sheared to have a fragments size range between 200-600bp. After clearance by centrifugation at 4°C, sheared chromatin used for each immunoprecipitation of histone marks or transcription factors.
For histones marks, library preparation was performed using TruSeq ChIP library Preparation kit using 3-6ng of ChIPed DNA. For transcription factors, the library preparation was done with MicroPlex Library Preparation kit with 0.5ng od ChIPed DNA

value: CD8SP WT


title: Input_CD8SP-EomesTG

value: CD8SP EomesTG


title: A17Lox_Sp1het2_Flk1_ATACseq_Rep2


title: Input_Naive


title: Input_TIM


title: Runx3_Naive

value: RUNX3 (Prof Yoram GRONER)


title: Runx3_TIM


title: A17Lox_Sp1_deltaDBD_Flk1_ATACseq_Rep1


title: A17Lox_WT_ESC_ATACseq_Rep1


title: H3K4me1_CD8SP-WT

value: H3K4me1 (Abcam, ab8895)


title: H3K4me1_CD8SP-EomesTG


title: H3K27ac_Naive

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_TIM


title: H3K27ac_CD8SP-EomesTG


title: H3K4me3_Naive


title: H3K4me3_CD8SP-WT


title: H3K4me1_TIM


title: ATAC_TIM

data_processing:
Reads were aligned to mm10 by Bowtie2
Reads with quality lesser than 1 (=mapping to multiple locations) were filtered out with samtools view
Reads in ENCODE blacklist were removed with bedtools intersect
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads from Naive sample were randomly distributed into 2 subsamples
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Highly reproducible peaks were selected using an IDR cut-off=10%
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal

extract_protocol:
20000 (Naïve/TIM) or 50000 sorted cells washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl,3 mM MgCl2, 0.1% (v/v) Igepal CA-630).
Nuclei were subject to transposition reaction in 1x TD Buffer containing 2.5 μl transposase Nextera enzyme and DNA was purified. Purified DNA was amplified by PCR with 10-12 cycles. Amplified libraries were purified and quality controlled.


title: Eomes_TIM

value: TBR2/Eomes (Abcam, ab23345)


title: H3K4me3_TIM


title: H3K27ac_CD8SP-WT


title: H3K4me1_Naive


title: H3K4me3_CD8SP-EomesTG


title: RA_TCZ treated9__CD4-Tem cells

city: sinjuku-ku

first: Masaru

last: Takeshita

address: 35 shinanomachi

department: Division of Rheumatology

institute: Keio University

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4.0).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

source_name: Tem CD4 cell

growth_protocol: Healthy volunteers and rheumatoid arthritis patients

extract_protocol:
Total RNA from were extracted using RNeasy Micro kit (Qiagen).
0.2 or 1 ng of total RNA from each dose and biological replicate were reverse transcribed to cDNA with SuperScript® VILO™ cDNA Synthesis Kit. Then cDNA is amplified using Ion AmpliSeq™ technology. After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. Libraries were then diluted to 75 pM and pooled equally, with eighteen individual samples per pool.

treatment_protocol: Peripheral mononuclear cells were isolated by density gradient centrifugation, and CD4 and CD8 T cell were purified from them using MojoSort (Biolegend). Cells were sorted by FACS Aria Ⅲ. Tn, Tcm, Tem, and Temra cells were defined as CD45RA+CCR7+, CD45RA-CCR7+, CD45RA-CCR7-, and CD45RA+CCR7-, respectively.

value: blood

value: Tem CD4 cell

tag: disease status

value: RA TCZ treatment

tag: age

tag: gender

value: F


title: ATAC_Naive

tag: cell type


title: SJDMNORM011389_G1-6WKO3-3

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

institute: St Jude Children's Research Hospital

description:
O3 old (6 weeks old)
RNA-Seq Stranded mRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to dm3 whole genome using an internal pipeline that employs bwa and STAR.
HTSeq was used to extract raw counts.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *_merged.txt: Gene symbols and raw count values in 2-column tab-delimited txt file, one for each sample.

source_name: skeletal muscles

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NA, genotype based.

value: Skeletal muscles

value: Old (6 weeks old)


title: RA_TCZ treated9__CD4-Tcm cells

source_name: Tcm CD4 cell

value: Tcm CD4 cell


title: RA_TCZ treated9__CD4-Tn cells

source_name: Tn CD4 cell

value: Tn CD4 cell


title: RA_TCZ treated9__CD8-Tcm cells

source_name: Tcm CD8 cell

value: Tcm CD8 cell


title: RA_TCZ treated9__CD8-Tn cells

source_name: Tn CD8 cell

value: Tn CD8 cell


title: RA_TCZ treated8__CD8-Tn cells


title: SJDMNORM011388_G1-6WKO3-2


title: Eomes_Naive

value: Thymocytes

value: CD8SP Naive

value: BALB/c


title: RA_TCZ treated8__CD8-Tem cells

source_name: Tem CD8 cell

value: Tem CD8 cell


title: RA_TCZ treated8__CD4-Tn cells


title: SJDMNORM011386_G1-1WKO3-3

description:
O3 young (1 week old)
RNA-Seq Stranded mRNA

value: Young (1 week old)


title: SJDMNORM011384_G1-1WKO3-1


title: RA_TCZ treated7__CD8-Tn cells


title: RA_TCZ treated9__CD8-Tem cells


title: SJDMNORM011382_G1-6WKO1-2

description:
O1 old (6 weeks old)
RNA-Seq Stranded mRNA


title: SJDMNORM011380_G1-1WKO1-3

description:
O1 young (1 week old)
RNA-Seq Stranded mRNA


title: RA_TCZ treated7__CD8-Tcm cells


title: RA_TCZ treated7__CD4-Tn cells


title: RA_TCZ treated9__CD8-Temra cells

source_name: Temra CD8 cell

value: Temra CD8 cell


title: RA_TCZ treated7__CD8-Tem cells


title: SJDMNORM011383_G1-6WKO1-3


title: SJDMNORM011381_G1-6WKO1-1


title: SJDMNORM011379_G1-1WKO1-2


title: SJDMNORM011378_G1-1WKO1-1


title: RA_TCZ treated7__CD4-Tem cells


title: RA_TCZ treated6__CD8-Temra cells


title: RA_TCZ treated6__CD8-Tem cells


title: RA_TCZ treated6__CD8-Tn cells


title: RA_TCZ treated7__CD4-Tcm cells


title: RA_TCZ treated6__CD8-Tcm cells


title: SJDMNORM011387_G1-6WKO3-1


title: RA_TCZ treated8__CD4-Tcm cells


title: SJDMNORM011377_G1-6WKB3-3

description:
B3 parental old (6 weeks old)
RNA-Seq Stranded mRNA

value: B3 parental


title: RA_TCZ treated8__CD4-Tem cells

value: blood


title: SJDMNORM011376_G1-6WKB3-2


title: SJDMNORM011374_G1-1WKB3-3

description:
B3 parental young (1week old)
RNA-Seq Stranded mRNA


title: RA_TCZ treated6__CD4-Tn cells


title: SJDMNORM011385_G1-1WKO3-2


title: RA_TCZ treated6__CD4-Tem cells

value: Tem CD4 cell


title: RA_TCZ treated6__CD4-Tcm cells

value: RA TCZ treatment


title: SJDMNORM011373_G1-1WKB3-2


title: SJDMNORM011372_G1-1WKB3-1


title: RA_TCZ treated5__CD8-Tn cells

value: F


title: sample_1618532_mhctim2_zt18_rep3

description:
mhc>timeless_ZT18
RNA-Seq Stranded mRNA

value: mhc>timeless

value: Skeletal muscles

tag: time point


title: sample_1618529_mhctim2_zt12_rep3

description:
mhc>timeless_ZT12
RNA-Seq Stranded mRNA

tag: genotype/variation


title: RA_TCZ treated5__CD8-Temra cells


title: RA_TCZ treated5__CD8-Tem cells


title: sample_1618531_mhctim2_zt18_rep2

description:
mhc>timeless_ZT18
RNA-Seq Stranded mRNA


title: sample_1618530_mhctim2_zt18_rep1

description:
mhc>timeless_ZT18
RNA-Seq Stranded mRNA


title: sample_1618527_mhctim2_zt12_rep1

description:
mhc>timeless_ZT12
RNA-Seq Stranded mRNA


title: SJDMNORM011375_G1-6WKB3-1

value: Old (6 weeks old)


title: sample_1618528_mhctim2_zt12_rep2

description:
mhc>timeless_ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated5__CD4-Tn cells

value: Tn CD4 cell


title: sample_1618526_mhctim2_zt6_rep3

description:
mhc>timeless_ZT6
RNA-Seq Stranded mRNA


title: sample_1618525_mhctim2_zt6_rep2

description:
mhc>timeless_ZT6
RNA-Seq Stranded mRNA


title: sample_1618524_mhctim2_zt6_rep1

description:
mhc>timeless_ZT6
RNA-Seq Stranded mRNA


title: RA_TCZ treated4__CD8-Temra cells


title: RA_TCZ treated5__CD4-Tem cells


title: RA_TCZ treated4__CD8-Tem cells


title: RA_TCZ treated4__CD8-Tn cells


title: RA_TCZ treated5__CD4-Tcm cells

value: Tcm CD4 cell


title: RA_TCZ treated4__CD8-Tcm cells

value: Tcm CD8 cell


title: RA_TCZ treated4__CD4-Tem cells


title: RA_TCZ treated4__CD4-Tn cells


title: sample_1618522_mhctim2_zt0_rep2

description:
mhc>timeless_ZT0
RNA-Seq Stranded mRNA


title: sample_1618519_mhc_zt18_rep2

description:
mhc_ZT18
RNA-Seq Stranded mRNA

value: mhc


title: sample_1618518_mhc_zt18_rep1

description:
mhc_ZT18
RNA-Seq Stranded mRNA


title: sample_1618520_mhc_zt18_rep3

description:
mhc_ZT18
RNA-Seq Stranded mRNA


title: RA_TCZ treated5__CD8-Tcm cells


title: sample_1618516_mhc_zt12_rep2

description:
mhc_ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated3__CD8-Tem cells


title: sample_1618517_mhc_zt12_rep3

description:
mhc_ZT12
RNA-Seq Stranded mRNA


title: sample_1618514_mhc_zt6_rep3

description:
mhc_ZT6
RNA-Seq Stranded mRNA


title: RA_TCZ treated3__CD8-Temra cells


title: RA_TCZ treated3__CD8-Tcm cells


title: RA_TCZ treated3__CD4-Tn cells


title: sample_1618515_mhc_zt12_rep1

description:
mhc_ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated3__CD4-Tem cells


title: sample_1618511_mhc_zt0_rep3

description:
mhc_ZT0
RNA-Seq Stranded mRNA


title: sample_1618523_mhctim2_zt0_rep3

description:
mhc>timeless_ZT0
RNA-Seq Stranded mRNA


title: RA_TCZ treated4__CD4-Tcm cells


title: RA_TCZ treated3__CD4-Tcm cells


title: sample_1618510_mhc_zt0_rep2

description:
mhc_ZT0
RNA-Seq Stranded mRNA


title: RA_TCZ treated2__CD8-Tn cells

value: Tn CD8 cell


title: 1381452_ZT18-O3-B_S35

description:
O3_ZT18
RNA-Seq Stranded mRNA


title: RA_TCZ treated2__CD8-Tem cells


title: RA_TCZ treated2__CD8-Temra cells


title: sample_1618509_mhc_zt0_rep1

description:
mhc_ZT0
RNA-Seq Stranded mRNA


title: 1381451_ZT18-O3-A_S34

description:
O3_ZT18
RNA-Seq Stranded mRNA


title: RA_TCZ treated2__CD8-Tcm cells


title: 1381448_ZT18-O1-A_S31

description:
O1_ZT18
RNA-Seq Stranded mRNA


title: 1381447_ZT18-B3-C_S30

description:
B3 parental _ZT18
RNA-Seq Stranded mRNA


title: RA_TCZ treated2__CD4-Tn cells


title: RA_TCZ treated3__CD8-Tn cells


title: RA_TCZ treated2__CD4-Tcm cells


title: 1381444_ZT12-O3-C_S27

description:
O3__ZT12
RNA-Seq Stranded mRNA


title: 1381446_ZT18-B3-B_S29

description:
B3 parental _ZT18
RNA-Seq Stranded mRNA


title: sample_1618513_mhc_zt6_rep2

description:
mhc_ZT6
RNA-Seq Stranded mRNA


title: 1381443_ZT12-O3-B_S26

description:
O3__ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated10__CD8-Tn cells


title: sample_1618512_mhc_zt6_rep1

description:
mhc_ZT6
RNA-Seq Stranded mRNA


title: 1381442_ZT12-O3-A_S25

description:
O3__ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated10__CD8-Tem cells


title: 1381441_ZT12-O1-C_S24

description:
O1__ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated10__CD8-Tcm cells


title: RA_TCZ treated10__CD8-Temra cells


title: RA_TCZ treated10__CD4-Tn cells


title: RA_TCZ treated10__CD4-Tem cells


title: 1381439_ZT12-O1-A_S22

description:
O1__ZT12
RNA-Seq Stranded mRNA


title: 1381453_ZT18-O3-C_S36

description:
O3_ZT18
RNA-Seq Stranded mRNA


title: RA_TCZ treated1__CD8-Tn cells


title: 1381440_ZT12-O1-B_S23

description:
O1__ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated2__CD4-Tem cells


title: 1381437_ZT12-B3-B_S20

description:
B3 parental _ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated1__CD8-Temra cells


title: RA_TCZ treated10__CD4-Tcm cells


title: 1381435_ZT6-O3-C_S18

description:
O3__ZT6
RNA-Seq Stranded mRNA


title: RA_TCZ treated1__CD8-Tcm cells


title: 1381433_ZT6-O3-A_S16

description:
O3__ZT6
RNA-Seq Stranded mRNA


title: 1381438_ZT12-B3-C_S21

description:
B3 parental _ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated1__CD4-Tn cells


title: 1381431_ZT6-O1-B_S14

description:
O1__ZT6
RNA-Seq Stranded mRNA


title: 1381432_ZT6-O1-C_S15

description:
O1__ZT6
RNA-Seq Stranded mRNA


title: RA_TCZ treated1__CD4-Tem cells


title: RA_TCZ treated1__CD4-Tcm cells


title: 1381430_ZT6-O1-A_S13

description:
O1__ZT6
RNA-Seq Stranded mRNA


title: RA_SF4__CD4-Tcm cells

value: synovial fluid

value: RA synovial fluid


title: RA_SF4__CD4-Tem cells


title: 1381427_ZT6-B3-A_S10

description:
B3 parental _ZT6
RNA-Seq Stranded mRNA


title: RA_SF3__CD4-Tcm cells

value: M


title: RA_SF3__CD8-Tcm cells


title: 1381426_ZT0-O3-C_S9

description:
O3__ZT0
RNA-Seq Stranded mRNA


title: RA_SF2__CD4-Tem cells


title: 1381424_ZT0-O3-A_S7

description:
O3__ZT0
RNA-Seq Stranded mRNA


title: RA_SF2__CD4-Tcm cells


title: 1381436_ZT12-B3-A_S19

description:
B3 parental _ZT12
RNA-Seq Stranded mRNA


title: RA_TCZ treated1__CD8-Tem cells

value: Tem CD8 cell


title: 1381423_ZT0-O1-C_S6

description:
O1__ZT0
RNA-Seq Stranded mRNA


title: RA_SF1__CD8-Temra cells

value: Temra CD8 cell


title: RA_SF1__CD8-Tem cells


title: 1381420_ZT0-B3-C_S3

description:
B3 parental _ZT0
RNA-Seq Stranded mRNA

value: B3 parental


title: RA_SF1__CD8-Tcm cells


title: 1381422_ZT0-O1-B_S5

description:
O1__ZT0
RNA-Seq Stranded mRNA


title: 1381419_ZT0-B3-B_S2

description:
B3 parental _ZT0
RNA-Seq Stranded mRNA


title: RA_SF1__CD4-Tem cells

value: Tem CD4 cell


title: RA_SF1__CD4-Tcm cells


title: 1381418_ZT0-B3-A_S1

description:
B3 parental_ZT0
RNA-Seq Stranded mRNA


title: 1381429_ZT6-B3-C_S12

description:
B3 parental _ZT6
RNA-Seq Stranded mRNA


title: RA_non treated9__CD8-Temra cells

value: blood

value: RA non treatment


title: RA_non treated9__CD8-Tem cells


title: RA_non treated9__CD8-Tn cells


title: RA_non treated9__CD8-Tcm cells


title: MG63-3-GFP: Whole Genome Sequencing

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

data_processing:
Library strategy: Whole Genome Sequencing
The FASTX-Toolkit v0.0.13 was used to remove adapter sequences and trim reads with the quality cutoff of 20, excluding any reads shorter than 25bp. ChIP-seq reads were aligned to hg19 with Bowtie 2 v2.0.649, searching for multiple alignments but reporting the one with the best mapping quality score. PCR duplicates were removed using SAMtools 1.2. Peaks were detected with MACS2 2.1.1.20160309 with an input DNA sample as control, scaling the input dataset to match the read depth of the ChIP dataset. MACS2 peaks with a q-value of greater than 0.001 and overlapping ENCODE blacklisted regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were filtered out. BigWIGs were generated with DeepTools v3.0.1-2-2fa58e8 and normalized to 1x average coverage (RPGC option)
Cutadapt v1.14 was used to trim 3’ adapters, discarding trimmed reads shorter than 20bp. Sickle v1.33 was then used to trim reads with the quality cutoff of 20. RNA-Seq reads were aligned to hg19 assembly plus ERCC RNA Spike-In DNA sequences with STAR v2.5.3a. Cufflinks v2.0.2 was run with genomic bias correction to quantify the levels of transcripts in the hg19 reFLAT annotations file as well as the ERCC transcripts file. Scatter plots of ERCC transcript FPKMs versus their expected concentrations in the spike-in mix were constructed to aid in quality control assessment of the data. The FPKM table was then floored to the background noise level of 0.3. Differential expression analysis between E9-treated and untreated samples was performed by calculating the fold change of mean E9 FPKM over mean DMSO FPKM.
After removing adapter sequences using cutadapt v1.8.1,1 the DNA FASTQ files were aligned to the hg19 reference genome using BWA-mem (v0.7.17-r1188).2,3 The aligned files were then indexed and had PCR duplicates removed using samtools (v0.1.18).4 Each BAM file underwent base quality score recalibration using GATK(v4.0.1.1).5
Refseq hg19 genes underwent the following filtering steps prior to use in downstream analyses for each pair of treated and untreated samples to ensure 1-to-1 mapping of genes to TSS’s: 1:Retrieve RNA-Pol RPKM within 1KB of each TSS and calculate the minimum of E9 and DMSO RPKMs. In case of the same gene with multiple TSS’s, only retain the gene record with the max RNA-Pol RPKM minimum. 2:In case of multiple genes with the same TSS, calculate the minimum FPKM between E9 and DSMO for each gene and only retain the gene with the max FPKM minimum
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq and whole genome sequencing WIG tracks were generated with deeptools v3.1.3 and normalized with the RPGC option

source_name: highly metastatic osteosarcoma cell line

growth_protocol: Human osteosarcoma cell lines (MG63.3-GFP, 143B-GFP) were grown in DMEM 1x (Gibco, 11965-092) supplemented with 10% FBS (Corning, 35-010-CV) and 1% penicillin/streptomycin.

extract_protocol:
For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-Seq samples, cells were lysed and RNA extracted with TRIzol according to the manufacturer’s protocol.
ChIP-Seq libraries were prepared as previously described (Schmidt et al. 2009). For RNA-seq, Total RNA was treated with DNase I (Invitrogen, Carlsbad, CA). RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, Foster City, CA) and analyzed on an Agilent Bioanalyzer 2100 for integrity. PolyA+ RNA was isolated using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s protocol. For Whole Genome Sequencing, PCR-free libraries were prepared from MG63.3-GFP and 143B-GFP cells using TruSeq DNA PCR-Free High Throughput Library Prep Kit (Illumina, 20015963) and following the manufacturer’s instructions.

treatment_protocol: For ChIP-seq and RNA-seq, 143B-GFP and MG63.3-GFP cells were treated for 6 hours with E9 at 200nM or DMSO. Cells prepared for ChIP-seq were crosslinked with formalin.


title: 143B-GFP: Whole Genome Sequencing

value: highly metastatic osteosarcoma cell line