title: CEMBA181008_5G_3_CEMBA181008_5G_4_G9_ad010


title: CEMBA181008_5G_3_CEMBA181008_5G_4_H1_ad002

status: Public on Sep 18 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PIR

tag: Sex

value: male

tag: age

tag: strain


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title: CEMBA181008_5G_1_CEMBA181008_5G_2_F5_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F4_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F4_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F4_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F3_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F3_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F2_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F2_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F2_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F6_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F2_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F3_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F6_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F2_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F12_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F2_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F12_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F2_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F12_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F5_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F4_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F4_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F12_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F12_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F3_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F11_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F12_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F11_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F11_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F11_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F11_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F11_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F11_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F10_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F10_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F1_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F1_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F1_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F12_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F1_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F1_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E9_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F1_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F12_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F1_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E9_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F1_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E8_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E8_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E8_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E8_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_F10_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E7_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E8_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E7_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E7_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E6_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E7_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E7_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E6_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E6_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E6_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E6_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E6_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E5_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E5_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E5_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E5_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E4_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E7_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E8_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E6_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E5_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E4_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E7_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E4_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E4_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E7_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E6_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E4_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E3_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E3_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E3_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E3_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E2_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E3_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E5_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E2_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E2_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E5_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E2_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E2_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E2_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E11_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E12_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E11_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E12_ad006


title: SDS|GDF11|Daughter [index712_507_GS2A]

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

library_source: transcriptomic

data_processing:
Raw reads were mapped to the Ensembl human genome GRCh38 using HISAT2
Gene-level counts were generated using HTSeq
All downstream analysis were performed in R using Bioconductor packages
Genome_build: GRCh38 v99
Supplementary_files_format_and_content: Normalized log2 counts

molecule: total RNA

organism: Homo sapiens

source_name: Daughter_GDF11 treated SDS-HSC

growth_protocol: Single CD34+CD38- cells were sorted into terasaki plates and cultured for 16 hrs in IMDM containing 10% FBS and cytokines GCSF, TPO and Flt3 at 10ng/ml each.  Cells were monitored every 24hrs for daughter cells.

extract_protocol:
After first division, daughter cells were separated manually, washed in PBS and processed for cDNA synthesis and amplification using SMART-Seq V4 Ultra Low Input RNA Kit from Clontech (Catalog# 634892).
Libraries were prepared using Illumina's Nextera XT DNA Library Preparation Kit (Catalog # FC 131-1096).  Briefly, 150 - 200pg of amplified cDNA was used for tagmentation followed by reduced cycle PCR amplification with indexed primers.  Libraries were quantified using an agilent bio-analyzer, pooled and subjected to next generation sequencing in a Hi-Seq 2500 under paired end 75bp sequencing conditions.

treatment_protocol: One set of cells were treated with GDF11 at a concentration of 10ng/ml.

tag: generation

value: Daughter

tag: treatment/sample group

value: GDF11 treated SDS-HSC

tag: cell type

value: Hematopoietic stem cells


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E11_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E11_ad006


title: 293T transfected with OLFM4-RET fusion plasmid

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

description: GRW-OR

data_processing:
Sequencing reads were trimmed for adapter contamination with Cutadapt
then aligned to human genome with HISAT2
read counts were produced by using featureCounts
Genome_build: GENCODE release 26

source_name: Human 293T cell

growth_protocol: HEK293 cells were grown in DMEM with 10% FBS.

extract_protocol:
Total RNA were extracted using Qiagen RNeasy Plus Mini Kit 48h after transfection
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When 70% confluence, the cells were transfected with vector, RET or OLFM4-RET plasmid with Lipofectamine 2000

tag: tissue

value: Homo sapiens embryonic kidney


title: 293T transfected with vector plasmid

description: GRW-V


title: 293T transfected with RET plasmid

description: GRW-R


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E12_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E12_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E11_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E1_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E12_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E1_ad004


title: Control|Control|Daughter [index711_505_C2B]

value: Control-HSC


title: SDS|GDF11|Daughter [index711_507_GS1B]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E12_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E11_ad010


title: Control|Control|Daughter [index712_505_C3A]


title: SDS|GDF11|Daughter [index710_507_GS1A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E11_ad002


title: SDS|SDS|Daughter [index711_506_S5B]

value: SDS-HSC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E1_ad006


title: SDS|SDS|Daughter [index710_506_S5A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E1_ad012


title: Control|Control|Daughter [index710_505_C2A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E1_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E12_ad004


title: SDS|SDS|Mother [index710_504_SM4]

value: Mother


title: SDS|SDS|Daughter [index709_506_S4B]


title: Control|Control|Daughter [index709_505_C1B]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D9_ad006


title: Control|Control|Daughter [index708_505_C1A]


title: SDS|SDS|Mother [index709_504_SM3]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D9_ad004


title: SDS|SDS|Daughter [index707_506_S2B]


title: SDS|SDS|Mother [index708_504_SM2]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D9_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D9_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D8_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D9_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E1_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D9_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D8_ad002


title: SDS|SDS|Daughter [index708_506_S4A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D8_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D8_ad004


title: SDS|GDF11|Mother [index706_505_GSM3]

source_name: Mother_GDF11 treated SDS-HSC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D9_ad001


title: SDS|GDF11|Mother [index707_505_GSM4]


title: SDS|SDS|Daughter [index706_506_S2A]


title: SDS|SDS|Mother [index707_504_SM1]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D8_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_E1_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D8_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D8_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D7_ad001


title: SDS|GDF11|Daughter [index705_508_GS4B]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D7_ad007


title: SDS|SDS|Daughter [index705_506_S1B]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D7_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D7_ad008


title: Control|Control|Mother [index705_504_CM4]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D7_ad004


title: SDS|SDS|Daughter [index704_506_S1A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D6_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D7_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D6_ad008


title: SDS|GDF11|Mother [index704_505_GSM1]


title: Control|Control|Mother [index704_504_CM3]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D6_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D6_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D6_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D6_ad001


title: Control|Control|Mother [index706_504_CM5]


title: Female OVX+MS

type: RNA

city: Chiyoda-ku

first: Tomohisa

last: Ootake

state: Tokyo

address: 2-9-18 Kanda-Misakicho

country: Japan

institute: Tokyo Dental College

description: Gene expression data of the mandibular condyle in the female OVX + MS group that combined the reduction of 17β-estradiol by OVX and the mechanical stress load by wearing the device.

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hr at 45 ̊C on Clariom S Array. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

label: biotin

source_name: Female mouse OVX and mechanical stress loading combined group (12 weeks old)

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit(Thermo Fisher Scientific) following the manufacturer's instructions.

growth_protocol: Eight-week old male and female mice were divided into four groups: control, gonadectomy [orchiectomy (ORX) and ovariectomy (OVX)], mechanical stress (MS), and gonadectomy plus mechanical stress (ORX+MS and OVX+MS) . Hard pellets and water were provided for ad libitum consumption.All mice were sacrificed 4 weeks into the experiment.

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

treatment_protocol: The mandibular head with cartilage/subchondral bone was collected from mice 4 weeks after the start of the experiment. All soft tissues were removed and frozen with liquid nitrogen, then stored at –80°C until RNA extraction with TRIzol reagent (Invitrogen). The frozen TMJ was placed in a mortar containing liquid nitrogen and crushed with a pestle.

value: Mandibular condyles

tag: gender

value: Female

value: 12 weeks old

tag: treatment

value: OVX+MS


title: Female OVX

description: Gene expression data of the mandibular condyle in the female OVX group whose 17β-estradiol was reduced by OVX

source_name: OVX group of female mice (12 weeks old)

value: OVX


title: Male MS

description: Gene expression data of mandibular condyle in male MS group subjected to mechanical stress loading by wearing the device

source_name: Mechanical stress loading group of male mice (12 weeks old)

value: Male

value: MS


title: Female MS

description: Gene expression data of mandibular condyle in female MS group subjected to mechanical stress loading by wearing the device

source_name: Mechanical stress loading group of female mice (12 weeks old)


title: Male ORX+MS

description: Gene expression data of the mandibular condyle in the male ORX + MS group that combined the reduction of dihydrotestosterone by ORX and the mechanical stress load by wearing the device.

source_name: Male mouse ORX and mechanical stress loading combined group (12 weeks old)

value: ORX+MS


title: Male Control

description: Gene expression data of the mandibular condyle in the male control group that underwent sham surgery

source_name: Control group of male mice (12 weeks old)

value: Control


title: Female Control

description: Gene expression data of the mandibular condyle in the female control group that underwent sham surgery

source_name: Control group of female mice (12 weeks old)


title: Male ORX

description: Gene expression data of the mandibular condyle in the male ORX group whose dihydrotestosterone was reduced by ORX

source_name: ORX group of male mice (12 weeks old)

value: ORX


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D7_ad006

value: PIR

value: male


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D6_ad004


title: Control|Control|Daughter [index703_506_C4B]

value: Daughter

value: Hematopoietic stem cells


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D5_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D6_ad010


title: SDS|GDF11|Daughter [index703_508_GS3B]

value: GDF11 treated SDS-HSC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D5_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D5_ad012


title: Control|Control|Mother [index703_504_CM2]

value: Control-HSC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D5_ad001


title: SDS|GDF11|Daughter [index702_508_GS3A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D5_ad008


title: Control|Control|Daughter [index702_506_C4A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D4_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D4_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D5_ad004


title: Control|Control|Mother [index702_504_CM1]

value: Mother


title: #10 NLC IBRUTINIB

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

description:
US22502667_251485085053_S01_GE1_107_Sep09_1_4
Gene expression data from  NLC treated with ibrutinib

hyb_protocol: Cy3-labeled cRNAs (1.65 ug) were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized for 17 hours at 65°C on 4x44K Whole Human Genome Microarray (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Fluorescence data were analyzed with Feature Extraction Software v.10.5 (Agilent Technologies) an QC Chart tool v.1.3 to obtain background subtracted, spatially detrended Processed Signal intensities and quality control analyses.

source_name: Peripheral blood, CLL cells

label_protocol: High quality RNAs were amplified and Cy3-labeled using Low Input Quick Amp Labeling kit (Agilent Technologies, Palo alto, CA, USA). Agilent RNA One-Color Spike-In was added in each sample to provide positive controls for monitoring the microarray workflow from sample amplification and labelling to microarray processing. It contains 10 in vitro synthesized, polyadenylated transcripts derived from the Adenovirus E1A transcriptome that are premixed at various ratios. All cRNA products were purified using RNeasy columns (QIAGEN). Dye incorporation and cRNA yield were checked with InfiniteM200 (Tecan).Samples had to contain at least 6 pmole of cyanine dye/ug of cRNA to be considered suitable for subsequent hybridization.

growth_protocol: we will generate NLCs by culturing peripheral blood mononuclear cells (PBMCs) from 10 CLL patients for 14 days

extract_protocol: total RNAs were extracted using RNeasy Mini kit Plus (QIAGEN, Valencia, CA, USA) following the manufacturer's recommendations.  RNAs were quantified using InfiniteM200 (Tecan)

treatment_protocol: After 14 days, non-adherent cells were wash off by vigorously pipetting, then treating adherent NLC with 0.5µM ibrutinib or vehicle (control sample)

value: NLC (macrophages) derived from 14-days culture of peripheral blood mononuclear cells (PBMCs) from CLL patient


title: Control|Control|Daughter [index701_506_C3B]


title: #9 NLC CTRL

description:
US22502667_251485085053_S01_GE1_107_Sep09_1_1
Gene expression data from untreated NLC


title: #10 NLC CTRL

description:
US22502667_251485085053_S01_GE1_107_Sep09_1_3
Gene expression data from untreated NLC


title: #8 NLC IBRUTINIB

description:
US22502667_251485085052_S01_GE1_107_Sep09_1_4
Gene expression data from  NLC treated with ibrutinib


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D4_ad007


title: SDS|SDS|Mother [index712_504_SM5]

value: SDS-HSC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D4_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D4_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D4_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D4_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D3_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D4_ad004


title: #8 NLC CTRL

description:
US22502667_251485085052_S01_GE1_107_Sep09_1_3
Gene expression data from untreated NLC


title: SDS|SDS|Daughter [index712_503_SD8B]


title: SDS|SDS|Daughter [index710_505_S5B]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D3_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D3_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D3_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D3_ad002


title: #9 NLC IBRUTINIB

description:
US22502667_251485085053_S01_GE1_107_Sep09_1_2
Gene expression data from  NLC treated with ibrutinib


title: SDS|SDS|Mother [index710_504_SM3]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D3_ad012


title: SDS|SDS|Daughter [index709_505_S5A]


title: #6 NLC IBRUTINIB

description:
US22502667_251485085051_S01_GE1_107_Sep09_1_4
Gene expression data from  NLC treated with ibrutinib


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D2_ad002


title: #7 NLC CTRL

description:
US22502667_251485085052_S01_GE1_107_Sep09_1_1
Gene expression data from untreated NLC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D2_ad004


title: SDS|SDS|Daughter [index708_505_S4B]


title: #7 NLC IBRUTINIB

description:
US22502667_251485085052_S01_GE1_107_Sep09_1_2
Gene expression data from  NLC treated with ibrutinib


title: #5 NLC IBRUTINIB

description:
US22502667_251485085051_S01_GE1_107_Sep09_1_2
Gene expression data from  NLC treated with ibrutinib


title: SDS|SDS|Mother [index708_504_SM1]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D2_ad006


title: #5 NLC CTRL

description:
US22502667_251485085051_S01_GE1_107_Sep09_1_1
Gene expression data from untreated NLC


title: #6 NLC CTRL

description:
US22502667_251485085051_S01_GE1_107_Sep09_1_3
Gene expression data from untreated NLC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D2_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D2_ad010


title: #4 NLC IBRUTINIB

description:
US22502667_251485085050_S01_GE1_107_Sep09_1_4
Gene expression data from  NLC treated with ibrutinib


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D3_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D2_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D2_ad012


title: #4 NLC CTRL

description:
US22502667_251485085050_S01_GE1_107_Sep09_1_3
Gene expression data from untreated NLC


title: #3 NLC IBRUTINIB

description:
US22502667_251485085050_S01_GE1_107_Sep09_1_2
Gene expression data from  NLC treated with ibrutinib


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D12_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D12_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D2_ad008


title: #2 NLC IBRUTINIB

description:
US22502667_251485085049_S01_GE1_107_Sep09_1_4
Gene expression data from  NLC treated with ibrutinib


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D12_ad010


title: #3 NLC CTRL

description:
US22502667_251485085050_S01_GE1_107_Sep09_1_1
Gene expression data from untreated NLC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D12_ad007


title: SDS|SDS|Mother [index707_504_SM5]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D12_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D12_ad002


title: SDS|SDS|Daughter [index705_505_S3A]


title: SDS|SDS|Daughter [index706_505_S3B]


title: ChIPSeq_Control

city: Ottawa

first: Theodore

last: Perkins

state: Ontario

address: 501 Smyth Rd.

department: Regenerative Medicine Program

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
ChIP-seq and control reads mapped to mm10 genome using bowtie v 1.1.0 with parameters: -l 32 --strata --best -y --chunkmbs 3072 -a -n 2 -m 1 -p 4
Fragment length for Myf6 was estimated using the MaSC programming (with result 127)
Peaks were called comparing the Myf6 reads against the control using MACS version 2.1.0.20140616 with parameters --gsize=mm --keep-dup=1 --qval=0.05 --nomodel --extsize=127
RNA-seq reads were mapped to mm10 gene definitions GENCODE M12 (GRCm38.p5) using hisat 2.1.0 with parameters -p 1 --dta
Mapped RNA-seq sam file was sorted, indexed and converted to BAM using samtools
Read counts per gene were obtained using featureCounts with mm10 gene definitions GENCODE M12 (GRCm38.p5)
Differential expression was assessed using DESeq2 (WT vs KO, for both uninjured and injured conditions) using parameters
Genome_build: mm10
Supplementary_files_format_and_content: Myf6 peak calls and two differential expression analyses

source_name: Primary myotubes

extract_protocol:
Chromatin was sheered by sonication in a water bath bioruptor (UCD-200, Diagenode) to an average fragment length of 200 bp. ChIP was performed as described previously (Soleimani et al., 2013). ChIP library construction was performed from 10 ng of ChIP DNA using TruSeq ChIP Library Preparation Kit (Illumina) and as described previously (Soleimani et al., 2013). Sequencing was performed on GAIIx (Illumina) sequencing platform.
Soleimani, V.D., Palidwor, G.A., Ramachandran, P., Perkins, T.J., and Rudnicki, M.A. (2013). Chromatin tandem affinity purification sequencing. Nature protocols 8, 1525-1534.

value: adult mouse muscle satellite cells


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D1_ad008


title: SDS|SDS|Daughter [index702_505_S1B]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D1_ad004


title: SDS|SDS|Daughter [index704_505_S2B]


title: SDS|GDF11|Daughter [index705_504_SG3A]


title: Myf6_ChIPSeq

tag: antibody

value: Flag


title: #2 NLC CTRL

description:
US22502667_251485085049_S01_GE1_107_Sep09_1_3
Gene expression data from untreated NLC


title: #1 NLC IBRUTINIB

description:
US22502667_251485085049_S01_GE1_107_Sep09_1_2
Gene expression data from  NLC treated with ibrutinib


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D1_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D1_ad012


title: SDS|GDF11|Daughter [index706_504_SG3B]


title: SDS|GDF11|Daughter [index702_504_SG1B]


title: #1 NLC CTRL

description:
US22502667_251485085049_S01_GE1_107_Sep09_1_1
Gene expression data from untreated NLC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D1_ad007


title: SDS|SDS|Daughter [index701_505_S1A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C9_ad006


title: CFPAC1.MYRF-KO #03

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to human genome build GRCh38/hg38 using using START version 2.6.0c. Only uniquely mapped reads were retained
Gene expression counts were estimated using featureCounts  v0.6.1 (Rsubread version 1.6.1) , summarized across all exons , with option “largestOverlap”.
Differentially expressed genes were identified using EdgeR R-package v3.2.2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: The file gene.counts.txt contains the raw read counts for each samples. The file edgeR_results.txt contains differentially expressed genes in biological triplicates of wild type and MYRF-KO CFPAC1 clones.

source_name: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

growth_protocol:
IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep
See additional columns of the SAMPLES section

extract_protocol: 10^6 cells are lysed and processed according to SMART-Seq2 protocol. Briefly, 5 ng of poly-A containing mRNA molecules are copied into first strand cDNA by reverse transcription and template-switching using oligo(dt) primers and LNA-containing template-switching oligo (TSO). cDNA is pre-amplified using limited number of cycles, purified and tagmented with Tn5 transposase. cDNA fragments generated after tagmentation are gap-repaired, enriched by PCR and purified to create the final cDNA library for Trueseq Illumina sequencing.

treatment_protocol:
Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting MYRF gene
See additional columns of the SAMPLES section

value: CFPAC1 genome-edited clonal cell line


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C9_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D12_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C9_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C9_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C9_ad004


title: SDS|GDF11|Mother [index712_517_GFM3]


title: SDS|GDF11|Daughter [index701_504_SG1A]


title: CFPAC1.MYRF-KO #01


title: SDS|SDS|Daughter [index712_502_SD2B]


title: CFPAC1.MYRF-KO #02


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C9_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C8_ad010


title: CFPAC1.WT #03

treatment_protocol:
Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961)
See additional columns of the SAMPLES section

value: CFPAC1 clonal cell line


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C8_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C9_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C8_ad007


title: SDS|SDS|Daughter [index711_503_SD8A]


title: CFPAC1.WT #01


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C8_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_D1_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C8_ad001


title: SDS|SDS|Daughter [index711_502_SD2A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C8_ad006


title: CFPAC1.MYRFKO.H3K27Ac.Rep2

description: Chromatin IP against H3K27ac

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38),  then reads were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 200” and “--qvalue 0.05” flags and arguments. Each IP was compared to input DNA.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

extract_protocol: ChIP lysates were generated from 50x10^6 cells. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by AMPure XP SPRI (Beckman Coulter) and quantified using Quantifluor (Promega). ChIP DNA was prepared for HiSeq2000 or NextSeq500 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

value: Anti-H3K27ac (Abcam ab4729 Lot. GR3187597-1)


title: SDS|SDS|Daughter [index710_503_SD7B]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C8_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C7_ad010


title: Colon_crypt_epithelial_cell_naive_control

city: Bunkyo-ku

first: Kana

last: MINAMIDE

department: Medical Research Institute

institute: Tokyo Medical and Dental University

description: Gene expression of sorted EpCAM+ cells of colonic crypt of naïve Irf2fl/fl mice.

hyb_protocol: 2.0 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: sorted colonic crypt epithelial cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20 ng Total RNA using the SureTag Comlete DNA labeling Kit(Nugen, San Carlos, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the Ovation Pico WTA system V2 (Nugen, San Carlos, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain background

tag: genotype/variation

value: Colon

value: sorted EpCAM+ cells of colonic crypt


title: Colon_crypt_epithelial_cell_naive_cKO

description: Gene expression of sorted EpCAM+ cells of colonic crypt of naïve Irf2fl/fl-VilCre mice.


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C7_ad004


title: SDS|SDS|Daughter [index710_502_SD1B]


title: CFPAC1.WT #02


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C7_ad012


title: CFPAC1.MYRFWT.H3K27Ac.Rep2

description: Chromatin IP against H3K27ac


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C7_ad001


title: SDS|GDF11|Mother [index711_517_GFM2]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C7_ad008


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C7_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C7_ad006


title: CFPAC1.MYRFWT.H3K27Ac.Rep1

description: Chromatin IP against H3K27ac


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C8_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C7_ad007


title: SDS|SDS|Daughter [index709_502_SD1A]


title: SDS|SDS|Mother [index709_517_SM4]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C6_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C6_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C6_ad004


title: CFPAC1.MYRFKO.H3K27Ac.Rep1

description: Chromatin IP against H3K27ac


title: Control|Control|Daughter [index708_502_C4B]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C6_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C6_ad008


title: CtIPA_XRCC4_DKO_3

city: New York

first: Xiaobin

middle: Summer

last: Wang

state: NEW YORK

address: 1130 Siant Nicholas Ave, Room 501

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

data_processing:
Library strategy: high-throughput genome translocation sequencing (HTGTS)
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 genome using Bowtie2. The best-path searching algorithm (related to YAHA; ref. 50) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads are then filtered to exclude mispriming events, germ-line (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. To plot all of the S-region junctions, including those in the repeats but unequivocally mapped to an individual switch region, we combined the ones filtered by a mappability filter but unequivocally mapped to S regions with “good” reads passing both the mappability (both deduplicated) filters (please see ref. 28 for simulation and details on plotting). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait and prey-break site. Blunt junctions are considered to have no MHs or insertions.
Genome_build: mm9
Supplementary_files_format_and_content: .xlsx files generated from tab-delimited text files after analysis for reads distribution

source_name: B cells

growth_protocol: Purified splenic B (CD43-) cells from mice carrying preassembled IgH and IgK loci (BL6 background) were cultured in RPMI mediume with cytokines (anti-CD40 (1 ng/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
Genomic DNA was extracted from day 4 cultured B cells.
Libraries were prepared according to protocol in (Hu J, et al. Nat Protoc 11:853–871.(2016)) Linear amplifications were performed using Sμ-specific biotin primer  5′/5BiosG/CAGACCTGGGAATGTATGGT3′) and followed by nesting PCR with (5′CACACAAAGACTCTGGACCTC3′)  AflII is used to remove germ-line sequence.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: Cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

value: anti-CD40 and Il4 activated B cells

tag: genotype


title: CtIPA_XRCC4_DKO_2


title: CtIPA_XRCC4_DKO_1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C6_ad010

source_name: C57BL/6J Male P56 Mouse Brain

value: PIR


title: CtIP_XRCC4_DKO_4


title: SDS|SDS|Daughter [index709_503_SD7A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C6_ad012

value: male


title: CtIP_XRCC4_DKO_3


title: SDS|SDS|Daughter [index707_503_SD6A]

value: Daughter


title: SDS|SDS|Mother [index708_517_SM3]

value: Hematopoietic stem cells


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C5_ad008


title: CtIP_XRCC4_DKO_2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C5_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C5_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C5_ad007


title: SDS|SDS|Mother [index706_517_SM1]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C5_ad006


title: Control|Control|Daughter [index707_502_C4A]


title: CtIP_XRCC4_DKO_1


title: XRCC4AiD4_3


title: SDS|SDS|Daughter [index706_503_SD5B]


title: XRCC4AiD4_2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C4_ad004


title: Control|Control|Daughter [index706_502_C3B]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C4_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C4_ad002


title: Control|Control|Mother [index705_517_CM5]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C4_ad007


title: XRCC4AiD4_1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C4_ad008


title: SDS|SDS|Daughter [index705_503_SD5A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C3_ad001


title: XRCC4D4_5


title: XRCC4D4_4


title: Control|Control|Mother [index704_517_CM3]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C3_ad012


title: mouse127_liver_15sec_RiboSeq

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

description: ribosome footprints

data_processing:
Library strategy: Ribo-seq
To remove illumina adapter from Ribo-seq libraries run "cutadapt -u 1 -m 23 -a AGATCGGAAGAGCACACGTCT --discard-untrimmed -o output.fastq input.fastq"
mRNA-seq sequences were aligned with TopHat 2.1.0 using following settings: tophat --transcriptome-index --no-discordant --no-mixed --no-novel-juncs
The NCBI mouse genome build GRCm38.p3 and the Mus musculus Annotation Release 105 were used as a reference. When aligning mRNA-seq and ribosome profiling reads for expression and translation efficiency estimation we used the following strategy. Only full chromosomes were left and all non-chromosomal and mitochondrial records removed. Furthermore, only RefSeq and BestRefSeq records were left in the transcriptome annotation, while Gnomon predictions were discarded along with pseudogenes. Read count per gene was accessed by HTseq-count software
To plot time-dependent ribosome occupancy, we employed a different strategy. First, using a gene bank (gbk) file, which comes in a package with the genome assembly and annotation, we extracted RefSeq and BestRefSeq records for every gene including CDS, 5’-UTR and 3’-UTR lengths and sequences. Among them, we identified the longest isoform for every gene, prioritized as CDS > 5’UTR > 3’UTR. 5’-UTRs were trimmed by 100 nucleotides. If either or UTRs were shorter than 100 nucleotides, we filled it with up to 100 based on genomic coordinates. The full list of sequences is collected in the mRNA_100.fna file. To prepare a list of non-redundant genes, we run blast of all vs. all (blastall -p blastn -m 8 -b 500 -v 500 -e 0.001). Gene pairs that are too similar at the level of nucleotide sequence were excluded. In addition to the e-score, we enforced a requirement of the high-homology stretch being at least 50 nt long, and if it was longer, the similarity had to be at least 90% to treat these genes as homologous and redundant. A total of 13,685 genes passed every threshold. This reference set ensured unambiguous alignment of ribosome footprints. Resulting sequences are collected in the mRNA_100unique.fna file.
Custom Perl and R scripts were used to calculate the footprint coverage profiles of individual genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts contain raw read count of individual genes; footprint coverage contains gene coverage profiles

source_name: liver

extract_protocol:
Frozen tissue was lysed a glass-Teflon Dounce homogenizer: 20 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 1 mM DTT, 1% Triton-X100, 0.1 mg/ml cycloheximide. The lysate was incubated with 4:1 mixture of ribonucleases T1 and S7 for 30 min at room temperature with gentle agitation. Lysate fractionation was performed by ultracentrifugation for 3 h at 35.000 rpm in an SW41 rotor (Beckman, Optima L-20K) at 4⁰ C in 10-50% sucrose, 20 mM Tris-HCl pH 7.5, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide. After the centrifugation, gradients were passed through a UV detector (Bio-Rad) and the absorption at 254 nm was recorded. The fraction containing monosomes was collected in a single tube. The volume of the sample was brought to 50 ul by concentrating it using 100 kDa filters (Amicon Ultra, Millipore). Then, the sample was diluted to 500 ul with a buffer containing 10 mM Tris-HCl pH 7.5, 2 mM EDTA, 1% SDS. RNA was extracted by hot acid phenol (Ambion) and precipitated by the glycogen-ethanol method (1/10 volume of 3 M sodium acetate, 1/100 volume of glycogen, 2.5 volumes of pure ethanol, 1-hour incubation at -20 followed by centrifugation). RNA was loaded on a 15% polyacrylamide TBE-urea gel and the band containing ribosomal footprints around 28-30 nucleotides was cut.
DNA adapter (rApp-AGATCGGAAGAGCACACGTCT- ddC) was ligated to the 3' end of RNA footprint. Illumina flanking sequences were added through reverse transcription and consequent Circligation technique.

value: 72 weeks old mouse

tag: inhibitors

value: harringtonine 15 sec cycloheximide

tag: injection route

value: tail-vein

tag: internal animal id


title: mouse125_liver_45sec_RiboSeq

description: ribosome footprints

value: harringtonine 45 sec cycloheximide


title: XRCC4D4_2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C4_ad006

tag: brain region


title: Control|Control|Mother [index703_517_CM2]

value: Mother

value: Control-HSC


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C3_ad004

tag: Sex


title: XRCC4D4_1


title: mouse120_liver_45sec_RiboSeq

description: ribosome footprints

tag: age


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C4_ad001

tag: strain


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C3_ad006


title: mouse113_liver_45sec_RiboSeq

description: ribosome footprints


title: XRCC4D3_3


title: SDS|SDS|Daughter [index703_503_SD4A]

tag: generation

value: SDS-HSC


title: XRCC4D3_2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C3_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C5_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C3_ad002


title: SDS|GDF11|Mother [index702_502_GFM5]

tag: treatment/sample group

value: GDF11 treated SDS-HSC


title: mouse111_liver_15sec_RiboSeq

description: ribosome footprints


title: XRCC4D3_1

tag: cell type


title: XRCC4D4_3


title: mouse109_liver_30sec_RiboSeq

description: ribosome footprints

value: harringtonine 30 sec cycloheximide


title: CtIP_KO_5


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C3_ad008


title: mouse122_liver_30sec_RiboSeq

description: ribosome footprints


title: SDS|GDF11|Mother [index701_502_GFM4]


title: Control|Control|Daughter [index703_502_C2A]


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C2_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C2_ad012


title: CtIP_KO_4


title: WTS-55966

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 Pine Ave West

department: Institut de recherches cliniques de Montréal (IRCM)

institute: Université de Montréal

data_processing:
Basecalls performed using CASAVA version 1.4
Data were analysed using the Lexogen's proprietary Bluebee sequence analysis platform. Trimming using Bbduk and quality control with FASTQC. Alignment on the reference genome mm10 with STAR.
Raw counts for each feature from GRCm38 ENSEMBL v98 annotation file  including custom genes (AK142197, AK153586, Gm39552, C030026M15) were extracted using FeatureCounts v1.6.0
DESeq2 version 1.22.2 was used to normalize gene readcounts and compute differential expression between uty and b6 experimental conditions correctinf for batch effect.
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file including normalized readcounts values for each sample from DESeq2 analysis

source_name: cardiac left ventricle tissue

growth_protocol: adult male mice were used at 40 days of age to harvest cardiac tissues

extract_protocol:
Qiagen Rneasy microRNA kit with Dnase treatment
3′ end RNA sequencing libraries were prepared using the Lexogen QuantSeq 3′ mRNA-Seq   Library Prep Kit FWD library.

tag: tissue

value: cardiac left ventricle


title: CtIP_KO_3


title: Control|Control|Mother [index702_517_CM1]


title: prp39a_2

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

country: France

institute: CNRS

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq preprocessing included the trimming of library adapters and quality controls with Trimmomatic. Paired-end reads with a Phred Quality Score Qscore > 20 and a read length > 30 bases were retained, and ribosomal RNA sequences were removed with SortMeRNA. Processed reads were aligned using Tophat2 with the following arguments: --max-multihits 1 -i 20 --min-segment-intron 20 --min-coverage-intron 20 --library-type fr-firststrand --microexon-search -I 1000 --max-segment-intron 1000 --max-coverage-intron 1000 --b2-very-sensitive.
Reads overlapping exons were counted per gene with the FeatureCounts function of the Rsubreads package, using the GTF annotation files from the Araport11 repository (https://www.araport.org/downloads/Araport11_Release_201606/annotation/Araport11_GFF3_genes_transposons.201606.gff.gz). Read counts were normalized with DESeq2
Genome_build: tair10
Supplementary_files_format_and_content: TPM Normalized read counts for each isoforms

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Seedling

extract_protocol:
Total RNA was extracted using RNeasy plant mini kit (Qiagen) from whole 14-day-old Col-0, prp39a-3 (SAIL_1249A03), smd1b-3 (Elvirat-Matelot et al., 2016) and Col-0 plants grown on 1/2MS medium. Three independent biological replicates were produced per genotype. For each biological repetition and each point. After RNA extraction, polyA RNAs were purified using Dynabeads mRNA direct micro kit (Ambion). Libraries were constructed using the Tru-Seq Stranded mRNA Sample Prep kit (Illumina®).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Seedling

value: 14 days


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C2_ad006


title: prp39a_3


title: CtIP_KO_2

value: anti-CD40 and Il4 activated B cells


title: WTS-55965


title: WTS-55962


title: prp39a_1


title: smd1b_3

value: smd1b-3 (Elvirat-Matelot et al., 2016)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C2_ad008

value: PIR

value: male


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C2_ad007


title: CtIP_KO_1


title: SDS|SDS|Daughter [index701_503_SD3A]

value: Daughter

value: Hematopoietic stem cells


title: WTS-55961


title: smd1b_2


title: WTS-58114


title: WTCTV2_IV

value: wild type


title: WTS-55959


title: WTS-58092


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C2_ad001


title: WTCTV2_III


title: KOS-58122


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C2_ad004


title: WTCTV2_II


title: smd1b_1


title: KOS-58123


title: WT1


title: WT3


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C12_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C2_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C12_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C12_ad004


title: WT2


title: WTCTV1_IV


title: WTCTV1_II


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C12_ad012


title: KOS-55980


title: WTCTV1_I


title: WTCTV1_III


title: WTCTV2_I


title: 10-4A d

first: Manfred

last: Frick

address: Albert-Einstein Allee 11

country: Cote d'Ivoire

data_processing:
Sequenced read quality was checked with FastQC v0.11.2
RNA-Seq reads from all samples were aligned to the genome using the STAR Aligner v2.5.2a11
Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment
The gene expression profiles were quantified using Cufflinks software version 2.2.1 to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) as well as read counts from the feature counts software package
Genome_build: ensembl84
Supplementary_files_format_and_content: tab-delimited text files contain RPKM values for each sample

organism: Rattus norvegicus

source_name: Lung cells

growth_protocol: 10-4A cells and primary fibroblasts were seeded on 38 µg/ml rat tail collagen I solution (Advanced BioMatrix Inc., San Diego, US) coated plastic in MucilAir™ medium (Epithelix, Genève, Switzerland). Seeding density of the primary fibroblasts was 5 x 10^5 cells / cm2, seeding density of the 10-4A cells was 40 x 10^3 cells / cm2. For alveolar type 2 cells, 1 x 10^6 cells / cm2 were seeded apically on 0.4 µm transparent Transwell® filter inserts in MucilAir cell culture medium.

extract_protocol:
RNA was harvested using my-Budget RNA Mini Kit (Bio-Budget Technologies GmbH, Krefeld, Germany). The Sequencing library preparation has been done using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122–2002, Illumina Inc, San Diego, CA) producing a 275 bp fragment including adapters in average size.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 10-4A immortalized cell line

value: Sprague-Dawley

value: Lung


title: 10-4A c


title: KOS-55979


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C12_ad006


title: KOS-58106


title: KOS-55976


title: 10-4A b


title: Lung fibroblasts d

value: Primary lung fibroblasts


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C12_ad010


title: KOS-55973


title: WTAiD4_4


title: B6_AGTCAA_L006

city: Toronto

first: Patrick

middle: O

last: McGowan

state: ON

address: 1265, Military Trail

department: Biological Sciences

institute: University of Toronto

data_processing:
FastQ files were trimmed to remove low quality reads (q < 30) and adaptors, and later aligned to RGD Rnor_6.0
The average reads per sample was 20.8X106 with a mapping efficiency of 50-60 %
Differentially methylated regions (DMRs) were identified using a dynamic sliding window approach and annotated using the methylPipe 49 and compEpiTools R packages
The bisulfite conversion rate was >99 % for all samples
Regions were declared to be differentially methylated if the average methylation of at least 10 consecutive CpG sites within a 1 Kb region was ≥ 5 % between mHFD and mCHD with FDR < 0.05
Genome_build: Rnor6
Supplementary_files_format_and_content: The data are the methylation calls from the BAM files - specifically, the data is filtered out to only get reads that have 4X coverage in the CpG context of each subject. These methylation calls are then used for formal analysis via methylPipe R package, where they pool all of the respective calls together (ie. aP90 subjects are pooled together, and all P7 subjects are pooled together), to obtain the appropriate methylation level in each group. These methylation files are in .txt format.

source_name: High fat diet, adulthood (P90)

extract_protocol:
gDNA was extracted using the ZR-Duet™DNA/RNA MiniPrep (D7005; Zymo Research) according to manufacturing instructions
Libraries were constructed using Ovation RRBS Methyl-Sequencing Kit (0553-32; NuGEN) as per the manufacturer's instructions.

treatment_protocol: Dams were on a high fat diet 4 weeks prior to pregnancy, during gestation, and lactation. The offspring were not directly on a high fat diet. Offspring used in the P90 condition was weaned off to a control diet. All animals were euthanized swiftly and brains were collected and stored at -80C. Brains were cryosectioned into 50 uM sections using Research Cryostat Leica CM3050 S (CM3050 S; Leica Biosystems) and the amygdala was microdissected using stereotaxic coordinates (P7: bregma: -0.20mm to -1.60 mm 38; P90 bregma: −1.72mmto −3.00mm

value: Amygdala

value: LongEvans

tag: diet

value: high fat


title: Lung fibroblasts c


title: 10-4A a


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C11_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C12_ad007


title: WTAiD4_3


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C12_ad008


title: Lung fibroblasts b


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C11_ad002


title: WTAiD4_2


title: B5_GTGAAA_L006


title: WTAiD4_1


title: WTD4_4


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C11_ad001


title: B3_GCCAAT_L006


title: WTD4_3


title: Lung fibroblasts a


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C11_ad010


title: B2_ACAGTG_L006

source_name: Control diet, adulthood (P90)

value: control diet


title: Alveolar type 2 c

value: Primary alveolar type 2 cells


title: B1_CGATGT_L005


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C11_ad006


title: WTD4_2


title: Alveolar type 2 b


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C11_ad004


title: SDS|SDS|Mother [index707_517_SM2]

value: Mother

value: SDS-HSC


title: B4_CTTGTA_L006


title: WTD4_1

value: anti-CD40 and Il4 activated B cells


title: 4_P90_GGAGAA


title: 3_P90_AAGAGG


title: WTD3_3


title: 17_FO_P7_GCACTA

source_name: High fat diet,earlylife (P7)


title: WTD3_2


title: 18_FO_P7_AAGCCT


title: Alveolar type 2 a


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C11_ad012

value: PIR