title: MRC004 Adeno_2

description: 10x Genomics

value: Tumor


title: Genomic DNA from ependymoma 1643

status: Public on Jan 31 2024

type: genomic

city: Hamburg

first: Michael

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing:
Statistical analysis was performed using the minfi package version 1.46.0 with the statistical programming language R version 4.3.0.
Average beta-values after combining arrays and normalization using the Noob method.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: ependymoma 1643

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

tag: Sex

value: F

tag: age

tag: localization

value: supratentorial

tag: resection

value: GTR

tag: patho diagnosis

value: Ependymoma III

tag: OS status

tag: os [months]

tag: pfs status

tag: pfs [months]

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1642

source_name: ependymoma 1642

value: M


title: Genomic DNA from ependymoma 1641

source_name: ependymoma 1641


title: 184_Adeno

type: SRA

city: Barcelona

first: Xavier

last: Santamaria

state: Barcelona

address: Av. Diagonal 463 Bis Pl. 4

country: Spain

institute: Bioliquid Inovative Genetics SLU

description:
Sample ID:
184

library_source: transcriptomic

data_processing:
Quality of reads was checked with FastQC software23. Preprocessing of reads was performed with fastx-toolkit24 and specific aScidea perl scripts property of aScidea S.L. (Ascidea Computational Biology Solutions, S.L., Sant Cugat, Spain) to filter regions of low quality. Raw reads with good quality  were mapped using Tophat_2.1.125 and Bowtie2_2.2.826.
The Homo sapiens genome version GRCh38 was used as reference. Genomic annotations were obtained from Illumina iGenomes27.
The transcript isoform level and gene level counts were calculated and fragments per kilobase per million reads mapped (FPKM) were normalized using Cufflinks_2.2.1 software28.
Resulting p-values were adjusted using Benjamini and Hochberg method29 to obtain false discovery rate (FDR). Lists of differentially expressed genes (DEGs) were filtered by ln(fold change)(FC) > 1 and q-value < 0.05. Main statistical analyses were performed using the Bioconductor Project30.
Different comparisons were done using CLC_Genomics Workbench 8.0.2 software31. The comparisons made were as follows: DIE (n = 4) versus control (n = 19); OE (n = 8) versus control (n = 19); Adeno (n = 6) versus control (n = 19); DOA (DIE + OE + Adeno; n = 18) versus control (n = 19).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files containing the read distribution in each sample and the bamstats per sample
Supplementary_files_format_and_content: xlsx. File contains the fragments per kilobase million (fpkm) per sample and per each transcript

molecule: total RNA

source_name: Adeno

growth_protocol: endometrial biopsies were obtained by a Cornier Pipelle

extract_protocol:
High Pure FFPET-RNA Isolation Kit (Roche) following manufacturer’s instructions.
Library preparation was obtained using TruSeq_Stranded Total_RNA_LT, w/ Ribo-Zero Gold, Set_A kit. According to standard protocols, purified amplicons were pooled in equimolar amounts and paired-end sequenced via flow cell at 2x50nt on an Illumina Hi-Seq-2000 platform

treatment_protocol: Samples were fixed with paraformaldehyd 4% ON and embedded in paraffin

tag: tissue

value: endometrium

tag: disease state

value: Adeno

tag: mesntrual cycle phase

value: PE

tag: history of endometriosis

value: no

tag: hypermenorrhea

value: yes

tag: dysmenorrhea

tag: fertility

tag: polyps

tag: myomas

tag: laparoscopy

tag: hormones

tag: smoker


title: Genomic DNA from ependymoma 1640

source_name: ependymoma 1640

tag: Sex

tag: age

tag: patho diagnosis

tag: OS status

tag: os [months]


title: Genomic DNA from ependymoma 1638

source_name: ependymoma 1638

tag: pfs status

tag: pfs [months]

tag: classification result v12

tag: classification score


title: 86_Control

description:
Sample ID:
86

source_name: Control

tag: tissue

tag: disease state

value: Control

tag: mesntrual cycle phase

value: SE

tag: history of endometriosis

tag: hypermenorrhea


title: MRC003_ADENO_4

city: Cambridge

first: Marc

last: Sze

state: MA

address: 320 Bent Street

country: USA

institute: Merck

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger Software (v3.0.0)
Single-Cell RNA-seq reads were mapped to the human genome (GRCh38) using CellRanger and then processed through Seurat v3.0. Cells with mitochondria percentage over 10% or extreme unique gene totals (less than 500 or over 5,000 per cell) were removed from the analysis. The data after QC inspection was then normalized using sctransform, and all libraries were merged after batch effect removal through Harmony. Following the standard protocol provided by Seurat authors, principal components were computed and used for the UMAP dimensionality reduction. Cell clusters were identified at resolution 0.3 and annotated based on prior knowledge. One cluster was labeled as proliferating cells due to high expression of cell-cycle regulation genes such as STMN1. Two clusters with low cell count were expressing markers of more than one primary cell type and were removed from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: .rds files

source_name: lung

extract_protocol:
All tissue samples from 9 patients for the scRNA sequencing (cohort A) were obtained from Brigham and Women’s Hospital, with patient consent approved by the Institutional Review Board protocol DFCI #98-063. LADC samples from a cohort B of 7 patients for IMC were purchased from commercial suppliers with patient informed consents. Tumors (T) or Adjacent Non-Tumor (ANT) tissues from cohort A were minced with scissors and digested with a human tumor dissociation kit (Miltenyi Biotec, 130-095-929) as per the manufacturer’s protocol with some modifications. For digesting lung samples for MRC001-005, the digestion cocktail from the kit was used, whereas the digestion cocktail with the addition of 0.8 mg/mL dispase II (Sigma, 4942078001) was used to digest the rest of samples.
Sorted viable cells were processed by Chromium Single cell 3′ Reagent v3 kits (10XGenomics, 120234) to synthesis single cell cDNAs and prepare barcoded libraries per as the manufacturer’s protocol. Sorted live cells were suspended into a cell density at around 1 million cells/mL in 0.1% BSA of PBS. To minimize doublet percentages, 4000 cells for donor MRC001-003 or 6000 cells for the remaining donors were loaded into each lane of a 10X chip. Cells were then partitioned into single-cell gel beads in emulsions (GEMs) inside the Chromium instrument, where full-length cDNA synthesis occurred. Cleaned-up cDNAs were then amplified, fragmented, and attached with 5′-adaptor and sample index. Libraries were sequenced using a 150 bp paired-end configuration.

tag: group

value: lung


title: Genomic DNA from ependymoma 1637

source_name: ependymoma 1637


title: 189_Adeno

description:
Sample ID:
189

tag: dysmenorrhea

tag: fertility

tag: polyps

tag: myomas

tag: laparoscopy

tag: hormones


title: Genomic DNA from ependymoma 1636

source_name: ependymoma 1636

tag: Sex

tag: age

tag: patho diagnosis

tag: OS status

tag: os [months]


title: MRC003_ADENO_3

description: 10x Genomics

tag: tissue


title: 100_Control

description:
Sample ID:
100

tag: disease state

tag: smoker


title: Genomic DNA from ependymoma 1930

source_name: ependymoma 1930

tag: localization

value: spinal

value: Anaplastic ependymoma III

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1635

source_name: ependymoma 1635

tag: resection

tag: pfs status

tag: pfs [months]


title: 307_Control

description:
Sample ID:
307

tag: mesntrual cycle phase

tag: history of endometriosis

tag: hypermenorrhea

tag: dysmenorrhea

tag: fertility

tag: polyps

tag: myomas


title: MRC003_ADENO_2

description: 10x Genomics

tag: group


title: Genomic DNA from ependymoma 1634

source_name: ependymoma 1634

tag: Sex

tag: age

tag: patho diagnosis

value: Ependymoma II

tag: OS status

tag: os [months]


title: Genomic DNA from ependymoma 1632

source_name: ependymoma 1632

tag: classification result v12

tag: classification score


title: 306_Control

description:
Sample ID:
306

tag: tissue

tag: disease state

tag: laparoscopy

tag: hormones

tag: smoker


title: 166_Adeno

description:
Sample ID:
166

tag: mesntrual cycle phase

tag: history of endometriosis

tag: hypermenorrhea

tag: dysmenorrhea


title: Genomic DNA from ependymoma 1631

source_name: ependymoma 1631

tag: localization

value: posterior fossa

tag: pfs status

tag: pfs [months]


title: 305_Control

description:
Sample ID:
305

tag: age

tag: fertility

tag: polyps

tag: myomas


title: MRC002_ADENO_3

description: 10x Genomics

tag: group

value: Tumor


title: 303_Control

description:
Sample ID:
303

tag: tissue


title: Genomic DNA from ependymoma 1621

source_name: ependymoma 1621

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1633

source_name: ependymoma 1633

tag: Sex

tag: patho diagnosis

tag: OS status

tag: os [months]


title: MRC003_ADENO_1

description: 10x Genomics


title: MRC004 Adeno_5

description: 10x Genomics


title: Genomic DNA from ependymoma 1616

source_name: ependymoma 1616


title: MRC002_ADENO_2

description: 10x Genomics


title: Genomic DNA from ependymoma 1617

source_name: ependymoma 1617


title: MRC002_ADENO_1

description: 10x Genomics


title: 279_Control

description:
Sample ID:
279

tag: disease state

tag: mesntrual cycle phase

tag: history of endometriosis

tag: hypermenorrhea

tag: laparoscopy

tag: hormones

tag: smoker


title: Genomic DNA from ependymoma 1613

source_name: ependymoma 1613


title: 301_Control

description:
Sample ID:
301

tag: age

tag: dysmenorrhea

tag: fertility

tag: polyps


title: Genomic DNA from ependymoma 1614

source_name: ependymoma 1614

tag: classification result v12


title: MRC002_ANT_4

description: 10x Genomics

tag: group

value: Adjacent Non-Tumor

tag: tissue


title: Genomic DNA from ependymoma 1612

source_name: ependymoma 1612

tag: classification score


title: Genomic DNA from ependymoma 1611

source_name: ependymoma 1611


title: 310_Control

description:
Sample ID:
310

source_name: Control

tag: myomas


title: Genomic DNA from ependymoma 1610

source_name: ependymoma 1610

tag: Sex

tag: localization

tag: resection

value: STR

tag: patho diagnosis

tag: OS status

tag: os [months]

tag: pfs status

tag: pfs [months]


title: Genomic DNA from ependymoma 1609

source_name: ependymoma 1609

value: F

tag: age

value: Ependymoma III


title: 308_Control

description:
Sample ID:
308

value: endometrium

tag: disease state

tag: mesntrual cycle phase

tag: history of endometriosis

tag: hypermenorrhea

tag: dysmenorrhea

tag: laparoscopy

tag: hormones

tag: smoker


title: MRC002_ANT_3

description: 10x Genomics

source_name: lung

tag: group

tag: tissue


title: Genomic DNA from ependymoma 1608

source_name: ependymoma 1608

tag: Sex

value: M

tag: localization

tag: resection

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1607

source_name: ependymoma 1607

tag: patho diagnosis

tag: OS status

tag: os [months]

tag: pfs status

tag: pfs [months]


title: MRC002_ANT_2

description: 10x Genomics


title: 304_Control

description:
Sample ID:
304

tag: disease state

tag: age

tag: mesntrual cycle phase

value: ME

tag: history of endometriosis

tag: hypermenorrhea

tag: fertility

tag: polyps

tag: myomas


title: MRC002_ANT_1

description: 10x Genomics

tag: group

tag: tissue


title: Genomic DNA from ependymoma 1606

source_name: ependymoma 1606

tag: Sex

tag: localization

value: supratentorial

tag: resection

value: GTR

tag: classification result v12


title: 278_Control

description:
Sample ID:
278

value: Control

value: PE

value: no

value: yes

tag: dysmenorrhea

tag: laparoscopy

tag: hormones

tag: smoker


title: Genomic DNA from ependymoma 1615

source_name: ependymoma 1615

tag: classification score


title: Genomic DNA from ependymoma 1605

source_name: ependymoma 1605

tag: age

tag: patho diagnosis

tag: OS status

tag: os [months]

tag: pfs status

tag: pfs [months]


title: Genomic DNA from ependymoma 1604

source_name: ependymoma 1604


title: Genomic DNA from ependymoma 1602

source_name: ependymoma 1602


title: Genomic DNA from ependymoma 1603

source_name: ependymoma 1603


title: 268_Control

description:
Sample ID:
268

tag: disease state

tag: mesntrual cycle phase

tag: history of endometriosis

tag: hypermenorrhea

tag: fertility

tag: polyps

tag: myomas


title: MRC001_ADENO_4

description: 10x Genomics

tag: group

tag: tissue

value: lung


title: Genomic DNA from ependymoma 1600

source_name: ependymoma 1600

tag: Sex

tag: localization

tag: resection

tag: classification result v12


title: MRC001_ADENO_2

description: 10x Genomics


title: Genomic DNA from ependymoma 1598

source_name: ependymoma 1598

tag: age

tag: patho diagnosis

tag: OS status

tag: classification score


title: Genomic DNA from ependymoma 1599

source_name: ependymoma 1599

tag: os [months]

tag: pfs status

tag: pfs [months]


title: MRC001_ADENO_1

description: 10x Genomics


title: 274_Control

description:
Sample ID:
274

tag: disease state

tag: mesntrual cycle phase

tag: history of endometriosis

tag: hypermenorrhea

tag: dysmenorrhea

tag: laparoscopy

tag: hormones

tag: smoker


title: Genomic DNA from ependymoma 1597

source_name: ependymoma 1597

tag: Sex

tag: localization

tag: resection

value: Ependymoma II


title: MRC001_ANT_3

description: 10x Genomics

tag: group

tag: tissue


title: 283_Control

description:
Sample ID:
283

tag: age

tag: fertility

tag: polyps

tag: myomas


title: 300_Control

description:
Sample ID:
300

tag: disease state

value: SE


title: Genomic DNA from ependymoma 1596

source_name: ependymoma 1596

value: posterior fossa

tag: patho diagnosis

tag: OS status

tag: os [months]

tag: pfs status

tag: pfs [months]

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1595

source_name: ependymoma 1595

tag: Sex


title: MRC001_ANT_2

description: 10x Genomics

value: Adjacent Non-Tumor


title: Genomic DNA from ependymoma 1594

source_name: ependymoma 1594

tag: localization


title: MRC001_ADENO_3

description: 10x Genomics

value: Tumor


title: MRC001_ANT_1

description: 10x Genomics


title: Genomic DNA from ependymoma 1593

source_name: ependymoma 1593

tag: resection


title: 299_Control

description:
Sample ID:
299

source_name: Control

tag: mesntrual cycle phase

tag: history of endometriosis

tag: hypermenorrhea

tag: dysmenorrhea

tag: laparoscopy

tag: hormones

tag: smoker


title: 302_Control

description:
Sample ID:
302

tag: tissue

tag: disease state

tag: age

tag: fertility

tag: polyps

tag: myomas


title: Genomic DNA from ependymoma 1589

source_name: ependymoma 1589

value: STR

tag: patho diagnosis

tag: OS status

tag: os [months]

tag: pfs status

tag: pfs [months]

tag: classification result v12

tag: classification score


title: 298_Control

description:
Sample ID:
298

tag: mesntrual cycle phase

tag: history of endometriosis

tag: hypermenorrhea

tag: dysmenorrhea


title: Genomic DNA from ependymoma 1588

source_name: ependymoma 1588

tag: Sex

tag: localization

tag: resection

value: Ependymoma III


title: Genomic DNA from ependymoma 1590

source_name: ependymoma 1590

value: F

tag: age


title: Genomic DNA from ependymoma 1601

source_name: ependymoma 1601

value: M


title: Genomic DNA from ependymoma 1587

source_name: ependymoma 1587


title: MM-14

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

data_processing:
Reads were mapped to the hg38 genome using HiSat2 2.0.4
Transcripts were counted against the GenCode annotation using the Rsubread package for R
Genome_build: hg38
Supplementary_files_format_and_content: Text file containing the gene name and raw count value

source_name: Bone marrow

extract_protocol:
BM mononucleated cells (MNC) were freshly-isolated by lineage depletion with RosetteSep Human MSC Enrichment Cocktail and density gradient centrifugation. PharmLyse  was used to eliminate residual erythrocytes. Cell were stained with monoclonal antibodies and FACS populations of lin-CD45-CD71-CD235a-CD31-CD271+ were directly sorted into Arcturus PicoPure RNA lysis buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue source

value: Posterior iliac crest

tag: cell type

value: Primary, freshly isolated, uncultured BMSC

tag: processing

value: Lineage depleted, FACS sorted

tag: disease

value: Multiple myeloma


title: MGUS-13

value: premalignant precursor MGUS


title: MM-15


title: Genomic DNA from ependymoma 1586

source_name: ependymoma 1586

value: GTR

tag: patho diagnosis

tag: OS status

tag: os [months]


title: Genomic DNA from ependymoma 1585

source_name: ependymoma 1585

tag: pfs status

tag: pfs [months]

tag: classification result v12


title: Genomic DNA from ependymoma 1592

source_name: ependymoma 1592

tag: classification score


title: Genomic DNA from ependymoma 1591

source_name: ependymoma 1591


title: Genomic DNA from ependymoma 1584

source_name: ependymoma 1584


title: Genomic DNA from ependymoma 1583

source_name: ependymoma 1583

value: supratentorial


title: Genomic DNA from ependymoma 1582

source_name: ependymoma 1582


title: Genomic DNA from ependymoma 1581

source_name: ependymoma 1581


title: MGUS-12


title: Genomic DNA from ependymoma 1580

source_name: ependymoma 1580


title: Genomic DNA from ependymoma 1579

source_name: ependymoma 1579


title: Genomic DNA from ependymoma 1578

source_name: ependymoma 1578


title: MM-12


title: Genomic DNA from ependymoma 1577

source_name: ependymoma 1577


title: MGUS-11


title: IgG.C.1

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

library_source: genomic

data_processing:
Cistromes were analyzed with csaw with different size windows for transcription factors or histone modifications, along with TF motif analyses (MotifDb). In order to find potential transcription factor binding enrichment within cistromes, GIGGLE was utilized to query the complete human transcription factor ChIP-seq dataset collection (10,361 and 10,031 datasets across 1,111 transcription factors and 75 histone marks, respectively) in Cistrome DB. Prostate specific filtering limited analysis to 681 datasets across 74 TFs and 238 datasets across 19 HMs. For each query dataset, we determined the overlap of each transcription factor cistrome. Putative co-enriched factors were identified by assessment of the number of time a given factor was observed in the top 200 most enriched datasets relative to the total number of datasets for that factor in the complete Cistrome DB (> 1.2 FC enrichment over background). For prostate specific analysis, overlaps across datasets were averaged for each factor.
Within each cistrome (e.g. MYC, or AR) two analsyes were undertaken. Firstly the treatments were compared to IgG, with the results indicated as the target (e.g. AR) and treatment (e.g. Enza) in the  file name. Secondly, the a design matrix was constructed to measure the effect of the combined treatment (ERb12.Enza) compared to the predicted combination of agents alone (ERb12 + Enza/2), and for this comparison IgG was not included. These results have the phrase "vs.combo" in the file name
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using RSubread
Cistromes were analyzed with Rsubread/csaw along with TF motif analyses (MotifDb) all in R
Assembly: hg38
Supplementary files format and content: bed files

source_name: prostate

growth_protocol: 22Rv1 cells in triplicate were treated with either vehicle, OSU-ERb-12 alone (100 nM) or E2 alone (100nM), Enza (1 microMolar) or the combinations for 6h and ATAC-Seq was undertaken. Cell lines were authenticated by STR profiling and confirmed mycoplasma free.  Cell lines were authenticated by STR profiling and confirmed mycoplasma free.

extract_protocol:
Briefly, approximately 20x106 cells were crosslinked with 1% formaldehyde solution, quenched with glycine (0.125 M) and harvested in cold PBS. Sonication of crosslinked chromatin was performed using a Bioruptor® UCD-200TM Sonicator (Diagenode) with optimized cycles for each cell type. Immunoprecipitation of sonicated material was performed with antibodies against VDR (D2K6W) – Cell Signaling) or IgG (Rabbit IgG sc2729 – Santa Cruz) for 16 hours, and antibody/bead complexes isolated with Magna ChIPTM Protein A+G magnetic beads (Millipore). Complexes were washed, reverse crosslinked, and treated sequentially with RNase and proteinase K prior to DNA isolation.
Sequencing libraries prepared from immunopreciptiated DNA
Briefly, approximately 20x106 cells were crosslinked with 1% formaldehyde solution, quenched with glycine (0.125 M) and harvested in cold PBS. Sonication of crosslinked chromatin was performed using a Bioruptor® UCD-200TM Sonicator (Diagenode) with optimized cycles for each cell type. Immunoprecipitation of sonicated material was performed with antibodies against VDR (D2K6W) – Cell Signaling) or IgG (Rabbit IgG sc2729 – Santa Cruz) for 16 hours, and antibody/bead complexes isolated with Magna ChIPTM Protein A+G magnetic beads (Millipore). Complexes were washed, reverse crosslinked, and treated sequentially with RNase and proteinase K prior to DNA isolation.

treatment_protocol: Cells were grown to 70% confluence and treated with either vehicle, OSU-ERb-12 alone (100 nM) or E2 alone (100nM), Enza (1 microMolar) or the combinations or EtOH in biological triplicate samples and analyzed by CUT&RUN.

tag: tissue

value: prostate

tag: cell line

tag: genotype

value: WT

tag: chip antibody

value: IgG

tag: treatment

value: Vehicle


title: K27.Z.2

value: Enzalutamide, 1microMolar, 6h


title: K27.WZ.1

value: OSU-ERb-12 plus Enzalutamide  (6h)


title: K27.WZ.2


title: IgG.C.2


title: K27.WZ.3


title: IgG.C.3


title: K27.Z.1


title: Genomic DNA from ependymoma 1576

source_name: ependymoma 1576

tag: Sex

tag: age

tag: localization

value: posterior fossa

tag: resection


title: Genomic DNA from ependymoma 1575

source_name: ependymoma 1575

value: Ependymoma III


title: MM-11

tag: tissue source

tag: cell type

tag: processing

tag: disease


title: MM-13


title: Genomic DNA from ependymoma 1574

source_name: ependymoma 1574

tag: patho diagnosis

tag: OS status

tag: os [months]

tag: pfs status


title: MM-10

source_name: Bone marrow


title: K27.Z.3

tag: tissue


title: Genomic DNA from ependymoma 1573

source_name: ependymoma 1573

value: Ependymoma II

tag: pfs [months]

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1639

source_name: ependymoma 1639

value: M


title: Genomic DNA from ependymoma 1572

source_name: ependymoma 1572

value: F


title: Genomic DNA from ependymoma 1571

source_name: ependymoma 1571


title: Genomic DNA from ependymoma 1570

source_name: ependymoma 1570

value: unclear, in evaluation


title: K27.W.1

tag: cell line

tag: genotype

tag: chip antibody

tag: treatment


title: MGUS-10

value: Posterior iliac crest

value: Primary, freshly isolated, uncultured BMSC

value: Lineage depleted, FACS sorted


title: Genomic DNA from ependymoma 1569

source_name: ependymoma 1569

tag: Sex

tag: age

tag: localization

tag: resection

value: GTR


title: MM-9

tag: tissue source

tag: cell type

tag: processing

tag: disease

value: Multiple myeloma


title: K27.W.2

value: prostate


title: Genomic DNA from ependymoma 1567

source_name: ependymoma 1567

value: STR

tag: patho diagnosis

tag: OS status

tag: os [months]

tag: pfs status


title: MGUS-9

value: premalignant precursor MGUS


title: Genomic DNA from ependymoma 1560

source_name: ependymoma 1560

tag: pfs [months]

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1559

source_name: ependymoma 1559

value: supratentorial


title: K27.W.3

tag: tissue

tag: cell line

tag: genotype

value: WT

tag: chip antibody


title: K27.C.2

tag: treatment

value: Vehicle


title: MM-6


title: MM-8


title: K27.C.3


title: Genomic DNA from ependymoma 1558

source_name: ependymoma 1558

tag: Sex

tag: age

tag: localization

value: posterior fossa

tag: resection


title: K27.C.1


title: HD-9

tag: tissue source

tag: cell type

tag: processing

tag: disease

value: healthy donor


title: ARv7.WZ.1

value: OSU-ERb-12 plus Enzalutamide  (6h)


title: Genomic DNA from ependymoma 1562

source_name: ependymoma 1562

tag: patho diagnosis

value: Ependymoma III

tag: OS status

tag: os [months]

tag: pfs status


title: Genomic DNA from ependymoma 1561

source_name: ependymoma 1561

value: F

tag: pfs [months]

tag: classification result v12

tag: classification score


title: MM-7


title: Genomic DNA from ependymoma 1557

source_name: ependymoma 1557

value: M


title: HD-7

value: Posterior iliac crest


title: Genomic DNA from ependymoma 1553

source_name: ependymoma 1553

value: Ependymoma II


title: ARv7.WZ.3

source_name: prostate

tag: tissue

tag: cell line

tag: genotype

tag: chip antibody


title: HD-6

value: Primary, freshly isolated, uncultured BMSC

value: Lineage depleted, FACS sorted


title: Genomic DNA from ependymoma 1554

source_name: ependymoma 1554

tag: Sex

tag: age

tag: localization

value: GTR


title: ARv7.Z.1

value: prostate

tag: treatment

value: Enzalutamide, 1microMolar, 6h


title: Genomic DNA from ependymoma 1552

source_name: ependymoma 1552

tag: resection


title: HD-5

source_name: Bone marrow

tag: tissue source

tag: cell type

tag: processing

tag: disease


title: Genomic DNA from ependymoma 1551

source_name: ependymoma 1551

tag: patho diagnosis

tag: OS status

tag: os [months]

tag: pfs status


title: Genomic DNA from ependymoma 1549

source_name: ependymoma 1549

tag: pfs [months]

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1543

source_name: ependymoma 1543


title: Genomic DNA from ependymoma 1548

source_name: ependymoma 1548


title: ARv7.Z.2

tag: tissue

tag: cell line

tag: genotype

tag: chip antibody


title: ARv7.WZ.2

tag: treatment


title: HD-4


title: Genomic DNA from ependymoma 1540

source_name: ependymoma 1540

tag: Sex

tag: age

tag: localization

tag: resection

value: STR


title: ARv7.Z.3


title: ARv7.W.2


title: Genomic DNA from ependymoma 1550

source_name: ependymoma 1550


title: Genomic DNA from ependymoma 1539

source_name: ependymoma 1539

value: supratentorial


title: Genomic DNA from ependymoma 1535

source_name: ependymoma 1535


title: HD-3

tag: tissue source

tag: cell type

tag: processing

tag: disease


title: ARv7.W.1

value: WT


title: Genomic DNA from ependymoma 1555

source_name: ependymoma 1555

tag: patho diagnosis

tag: OS status

tag: os [months]

tag: pfs status


title: Genomic DNA from ependymoma 1556

source_name: ependymoma 1556

tag: pfs [months]

tag: classification result v12

tag: classification score


title: HD-10


title: Genomic DNA from ependymoma 1530

source_name: ependymoma 1530


title: MRC004 Adeno_1

description: 10x Genomics

source_name: lung

tag: group

value: Tumor

tag: tissue

value: lung


title: Genomic DNA from ependymoma 1529

source_name: ependymoma 1529

tag: Sex


title: Genomic DNA from ependymoma 1528

source_name: ependymoma 1528

tag: age


title: 5HT_Col_4

city: New York

first: Katherine

last: Sanidad

address: 413 E69th St

institute: Weill Cornell Medicine

data_processing:
Paired-end reads were analyzed and classified into operational taxonomic units (OTUs) at > 97% identity level using Mothur v.1.35
Taxonomic assignments were determined using the SILVA 16S rRNA reference file release 132 and the Ribosomal Database Project (RDP) training set version 16
LEfSe Linear discriminant analysis (LDA) was performed by the Mothur command using all OTU reads
Assembly: SILVA 16S rRNA reference file release 132
Supplementary files format and content: OTU table xlsx file

organism: Mus musculus

source_name: Colon luminal contents

extract_protocol:
Bacterial genomic DNA was extracted from luminal contents using the E.Z.N.A stool DNA kit (Omega Biotek)
The V4-V5 region within the 16S rRNA gene was amplified and prepared for sequencing using standard Illumina 16S Metagenomic Sequencing Library Preparation protocols
Other: 16S rRNA seq

treatment_protocol: WT neonatal mice were given 50 μL of 5-HT (12.5 μg/mL) or vehicle (PBS) at P8 and P9 via oral gavage. The mice were then sacrificed at P14 and SI and colon luminal contents were collected for 16S sequencing.

value: Colon luminal contents

tag: genotype

tag: treatment


title: 5HT_Col_5


title: ARv7.W.3

source_name: prostate

tag: cell line

tag: chip antibody


title: ARv7.C.1

value: Vehicle


title: ARv7.C.2


title: Genomic DNA from ependymoma 1526

source_name: ependymoma 1526

tag: localization

value: posterior fossa

tag: resection

value: Ependymoma III


title: Genomic DNA from ependymoma 1527

source_name: ependymoma 1527

value: M

tag: patho diagnosis


title: 5HT_Col_2


title: Genomic DNA from ependymoma 1524

source_name: ependymoma 1524

tag: OS status


title: Genomic DNA from ependymoma 1522

source_name: ependymoma 1522

tag: os [months]


title: Genomic DNA from ependymoma 1525

source_name: ependymoma 1525

value: F

tag: pfs status


title: 5HT_Col_1


title: Genomic DNA from ependymoma 1523

source_name: ependymoma 1523

tag: pfs [months]


title: PBS_Col_5

value: PBS


title: Genomic DNA from ependymoma 1520

source_name: ependymoma 1520

tag: classification result v12


title: Genomic DNA from ependymoma 1541

source_name: ependymoma 1541

tag: classification score


title: Genomic DNA from ependymoma 1521

source_name: ependymoma 1521


title: Genomic DNA from ependymoma 1519

source_name: ependymoma 1519


title: PBS_Col_4


title: AR.WZ.2

value: AR

value: OSU-ERb-12 plus Enzalutamide  (6h)


title: ARv7.C.3


title: Genomic DNA from ependymoma 1518

source_name: ependymoma 1518

value: GTR


title: 5HT_Col_3


title: AR.WZ.1

value: prostate


title: PBS_Col_3


title: AR.WZ.3


title: Genomic DNA from ependymoma 1517

source_name: ependymoma 1517


title: Genomic DNA from ependymoma 1516

source_name: ependymoma 1516


title: Genomic DNA from ependymoma 1515

source_name: ependymoma 1515


title: AR.Z.2

value: Enzalutamide, 1microMolar, 6h


title: AR.Z.1


title: PBS_Col_2


title: PBS_Col_1


title: Genomic DNA from ependymoma 1514

source_name: ependymoma 1514


title: Genomic DNA from ependymoma 1513

source_name: ependymoma 1513

value: STR


title: Genomic DNA from ependymoma 1512

source_name: ependymoma 1512

value: supratentorial


title: AR.Z.3

source_name: prostate

value: WT


title: Genomic DNA from ependymoma 1511

source_name: ependymoma 1511


title: 5HT_SI_4

source_name: Small intestine luminal contents

value: Small intestine luminal contents


title: Genomic DNA from ependymoma 1509

source_name: ependymoma 1509


title: Genomic DNA from ependymoma 1510

source_name: ependymoma 1510


title: AR.W.1


title: AR.W.2


title: Genomic DNA from ependymoma 1508

source_name: ependymoma 1508


title: 5HT_SI_3


title: 5HT_SI_2


title: Genomic DNA from ependymoma 1507

source_name: ependymoma 1507


title: Genomic DNA from ependymoma 1506

source_name: ependymoma 1506


title: AR.W.3


title: Genomic DNA from ependymoma 1505

source_name: ependymoma 1505


title: AR.C.2


title: Genomic DNA from ependymoma 1504

source_name: ependymoma 1504

value: Ependymoma II


title: 5HT_SI_1


title: PBS_SI_5


title: PBS_SI_4


title: Genomic DNA from ependymoma 1501

source_name: ependymoma 1501


title: Genomic DNA from ependymoma 1503

source_name: ependymoma 1503


title: Genomic DNA from ependymoma 1502

source_name: ependymoma 1502


title: Genomic DNA from ependymoma 1500

source_name: ependymoma 1500


title: AR.C.1


title: AR.C.3


title: PBS_SI_3


title: Genomic DNA from ependymoma 1498

source_name: ependymoma 1498


title: Genomic DNA from ependymoma 1499

source_name: ependymoma 1499


title: PBS_SI_2


title: Genomic DNA from ependymoma 1497

source_name: ependymoma 1497


title: Genomic DNA from ependymoma 1496

source_name: ependymoma 1496


title: Myc.WZ.3

source_name: prostate

value: MYC


title: Genomic DNA from ependymoma 1495

source_name: ependymoma 1495


title: Genomic DNA from ependymoma 1493

source_name: ependymoma 1493


title: Genomic DNA from ependymoma 1494

source_name: ependymoma 1494


title: Myc.Z.1


title: Neonate_3

source_name: Small intestine luminal contents

treatment_protocol: Small intestine luminal contents were harvested from adult (8 weeks) and neonatal (14 days) mice.

value: 14 days


title: Neonate_4


title: Myc.Z.2


title: Genomic DNA from ependymoma 1492

source_name: ependymoma 1492


title: Genomic DNA from ependymoma 1488

source_name: ependymoma 1488

value: posterior fossa


title: Genomic DNA from ependymoma 1491

source_name: ependymoma 1491

value: Ependymoma III


title: Genomic DNA from ependymoma 1490

source_name: ependymoma 1490

value: M


title: Neonate_1


title: Myc.WZ.1


title: Myc.W.1


title: Adult_4

value: 8 weeks


title: Neonate_2


title: Myc.Z.3


title: Genomic DNA from ependymoma 1486

source_name: ependymoma 1486

value: F


title: Genomic DNA from ependymoma 1485

source_name: ependymoma 1485


title: Genomic DNA from ependymoma 1484

source_name: ependymoma 1484


title: Adult_3


title: Genomic DNA from ependymoma 1483

source_name: ependymoma 1483


title: Myc.WZ.2


title: PBS_SI_1

value: PBS


title: Myc.W.3


title: Genomic DNA from ependymoma 1482

source_name: ependymoma 1482


title: Genomic DNA from ependymoma 1489

source_name: ependymoma 1489


title: Myc.C.1

value: Vehicle


title: Genomic DNA from ependymoma 1480

source_name: ependymoma 1480


title: Genomic DNA from ependymoma 1481

source_name: ependymoma 1481

value: GTR


title: Genomic DNA from ependymoma 1479

source_name: ependymoma 1479


title: Adult_2


title: Genomic DNA from ependymoma 1487

source_name: ependymoma 1487


title: Adult_1


title: Genomic DNA from ependymoma 1478

source_name: ependymoma 1478


title: Genomic DNA from ependymoma 1459

source_name: ependymoma 1459

value: spinal

value: Ependymoma


title: Myc.C.2

source_name: prostate

value: prostate


title: Myc.W.2


title: Genomic DNA from ependymoma 1460

source_name: ependymoma 1460

value: STR

value: Anaplastic Ependymoma


title: Genomic DNA from ependymoma 1458

source_name: ependymoma 1458


title: feces, CCI, 07d, biolrep7

city: Cincinnati

first: Anthony

middle: Joseph

last: DeSana

state: Ohio

address: 231 Albert Sabin Way

department: Neurosurgery

institute: University of Cincinnati

description: Biological replicate 7 for TBI group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after TBI (controlled cortical impact) procedure

data_processing:
Illumina RTA (1.18.54.4) basecalling
dada2 package
assignTaxonomy
Rarefaction for alpha diversity only
Beta Diversity
ANCOM-BC
Assembly: Silva 138
Supplementary files format and content: OTU table
Supplementary files format and content: Taxonomy Table

source_name: feces

extract_protocol:
QIAamp PowerFecal Pro DNA kit
16S Metagenomic Sequencing Library Preparation

treatment_protocol: Frozen -80C

value: feces

tag: strain

value: CCI, 07d


title: feces, CCI, 28d, biolrep7

description: Biological replicate 7 for TBI group. 28 day (4 weeks) post injury timepoint: Sample taken 28 days (4 weeks) after TBI (controlled cortical impact) procedure

tag: tissue

value: CCI, 28d


title: Myc.C.3

value: WT

value: MYC


title: feces, CCI, 14d, biolrep7

description: Biological replicate 7 for TBI group. 14 day (2 weeks) post injury timepoint: Sample taken 14 days (2 weeks) after TBI (controlled cortical impact) procedure

value: CCI, 14d


title: rep1_myh9_facs_unsorted

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

description: PCR of genomic DNA to recover gRNA protospacer sequences in sorted cells

data_processing:
Resulting FASTQ files were aligned to a custom reference sequence corresponding to the given gRNA library using bowtie2 and all downstream analyses were performed in R. All gRNA were verified to be represented in the baseline untreated library dat Day 8 post-transduction, and counts+1 for each gRNA were taken (to normalize for samples that dropped out in one condition) and normalized by sequencing depth for each library before downstream analysis (in counts per million reads sequenced, ‘CPM’).
Due to the highly-apparent strand bias in the positive-strand when targeting the MYH9 gene body (Supplementary Note 1) , we only included the non-interfering gRNA from the negative strand (2,863 gRNA). A ratio was taken of the CPM for each gRNA of the low MYH9 expression group to high MYH9 expression group to identify whether the gRNA perturbation led to increases in enrichment in either expression bin. Next, for each screen replicate the Z-score was calculated for each gRNA relative to the control non-targeting gRNA population using similar methodologies as previously described in 35. First, each sample’s ratio was converted to a log2 fold-enrichment, and population statistics for the negative control non-targeting gRNAs (median, standard deviation, gRNA number) were calculated. For each individual gRNA, the median of the negative control fold-enrichment was subtracted from each individual gRNA’s log2 fold-enrichment value, and this value was further divided by the standard deviation of the negative control non-targeting gRNA population to get an individual Z-score relative to the negative control population. Raw Z-score values from both replicates were pooled to calculate pRE-wide effects. Phenotype scores (t-score based) were calculated as:  Phenotype Score = U (pRE) - U CTL /  (S varNexp +S varNCTL)  Svar = Var (pRE) * (N(pRE)-1) + Var(CTL)*(Nctl -1)
Assembly: hg38
Supplementary files format and content: Tab-separated gRNA counts across conditions (high, low and unsorted bins) and replicates (2 reps).
Supplementary files format and content: Supp. Table 5 - Comma-separated values file with gRNA counts and enrichment scores
Supplementary files format and content: Supp. Table 6 - Comma-separated values file with gRNA enrichment (high vs low) results grouped by DHS
Library strategy: CRISPR gRNA recovery from genomic DNA

source_name: HFF

growth_protocol: Primary human neonatal fibroblasts (HFF cells) were acquired from ATCC (CRL-2097) and cultured in DMEM with 10% FBS, 1% AntiAnti, and 1% NEAA (Sigma) on tissue culture plastic. All work was performed within 30 doublings from the initial passage of the vial.

extract_protocol:
Cells were counted following sorting to verify enrichment, followed by DNA recovery/extraction from fixed cells using the PicoPure DNA extraction kit (ThermoFisher) according to manufacturer’s instructions. Recovery digests were performed for 20 hours at 65C using up to 1.5M HFF cells per reaction volume.
All gDNA was split between sample-indexed 100uL Q5 PCR reactions (up to ~340ng max input per 100uL reaction) to amplify out the gRNA protospacer from HFF cells. These PCRs from gDNA were run as follows [ 98C for 30s / 25x: 98C for 10s, 60C for 30s, 72C for 15s / 72C for 2 min] with primers in Supplementary Table 15, followed by individual PCRs being pooled together and subjected to a double-sided 0.65X/1X SPRI clean-up. Quality control was performed by running the amplified libraries out on a High Sensitivity D1000 Tapestation (Agilent) to confirm expected size, and Qubit dsDNA HS assays were performed to determine a final concentration.

treatment_protocol: A stable HFF line was created using a lentiviral dCas9-KRAB construct (pLV-hUbC-dCas9-KRAB-2A-Blast (pJB289)), followed by the gRNA library being transduced at an MOI of ~0.33 and Puro selection for four days at 1 ug/mL. Cells were maintained for an additional four days, prior to trypsinization and fixation at Day 10 post-transduction. Following trypsinization with 0.25% Trypsin-EDTA for 5 minutes at 37C, trypsin was neutralized with 1X volumes of complete growth media following by 300g for 5 minutes centrifugation and aspiration of the supernatant, one rinse with 1X volume PBS followed by another centrifugation and aspiration leaving 200uL of PBS above the pellet. The eBioScience ICC Fixation kit (ThermoFisher) was used to fix/permeabilize cells according to manufacturer’s instructions, with both reagents being equilibrated to room temp prior to usage. Fixation was performed through the addition of 500uL eBioSciences Fix/Perm Buffer (ThermoFisher) to the 200uL PBS and pellet, and incubation at room temperature for 20 minutes. At the end of this incubation 1X Permeabilization Buffer was added to 8mL total volume, spun at 600g for 5 minutes, followed by an additional perm buffer rinse. Following this step: HFF cells were counted, and ~2M cells were removed to be used for unsorted controls, and ~500k cells were set aside to be control samples for single channel compensation controls. Immunostaining of MYH9 was performed using a AlexaFluor-488 conjugated Rabbit monoclonal anti-NMMIIA antibody (clone EPR8965, Abcam, #ab204675) at a ratio of 0.5 uL antibody per 300k HFF cells per 100uL of Perm Buffer which was determined to be the ideal staining ratio using an antibody titration series. HFF cells were incubated for 30 minutes at room temperature in the dark on a nutating rocker, a 600g for 5 minutes spin, and two repeats of 3mL 1X Perm Buffer rinse/spin cycles. Following the last spin down, cells were resuspended in FACS Buffer [1X PBS supplemented w/ 1% BSA (Sigma) and 0.5mM EDTA (Sigma)] at density of ~9M cells/mL and sorted. A SH800 Cell Sorter (Sony Biotechnologies) was used to separate out the top/bottom-expressing MYH9 fractions following immunostaining. Compensation panels were set up using single channel expressing cell populations including untreated cells, antibody-only cells, mCherry-only cells. The top 10% and lower 10% of the MYH9 population was sorted off and used for downstream gRNA-enrichment analysis and sequencing.

value: HFF

tag: cell type

value: Human foreskin fibroblasts

value: gRNA library


title: rep1_myh9_facs_low


title: C42.WT.Enza.1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using RSubread
Read count extraction and normalization were performed featureCounts and an edgeR workflow in R
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: All cells were maintained at 37oC and 5.0% CO2 (Sanyo); LNCaP, LNCaP C4-2 and 22Rv1 cells were maintained in RPMI 1640 containing 10% FBS. All media contained 100 U/mL Penicillin-Streptomycin. 1α,25(OH)2D3 was kept as 10mM EtOH stocks. Cell lines were authenticated by STR profiling and confirmed mycoplasma free.

extract_protocol:
Total RNA was isolated via TRIzol® reagent
Sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA

treatment_protocol: Cells were grown to 70% confluence and treated with OSU-ERb-12 alone (100 nM) or E2 alone (100nM), Enza (1 microM) or the combinations for 12h or EtOH in biological triplicate samples and analyzed by RNA-Seq.

value: prostate cancer

value: WT (100nM) plus Ezalutamide (1 microMolar), 12h


title: C42.WT.Enza.2


title: C42.WT.Enza.3


title: rep2_myh9_facs_unsorted


title: feces, CCI, 02d, biolrep7

description: Biological replicate 7 for TBI group. 2 day post injury timepoint: Sample taken 2 days after TBI (controlled cortical impact) procedure

value: CCI, 02d


title: rep2_myh9_facs_low


title: rep2_myh9_facs_high


title: feces, CCI, 01d, biolrep7

description: Biological replicate 7 for TBI group. 1 day post injury timepoint: Sample taken 1 day after TBI (controlled cortical impact) procedure

value: CCI, 01d


title: Genomic DNA from ependymoma 1477

source_name: ependymoma 1477

tag: Sex

value: F

tag: age

value: posterior fossa

value: GTR

value: Ependymoma II


title: feces, CCI, 00d, biolrep7

description: Biological replicate 7 for TBI group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a TBI injured animal (controlled cortical impact)

value: feces

tag: treatment

value: CCI, 00d


title: MigLib-D0-rep2

data_processing:
Resulting FASTQ files were aligned to a custom reference sequence corresponding to the given gRNA library using bowtie2 and all downstream analyses were performed in R. All gRNA were verified to be represented in the baseline untreated library at day 8 post-transduction, and counts+1 for each gRNA were taken (to normalize for samples that dropped out in one condition) and normalized by sequencing depth for each library before downstream analysis (in counts per million reads sequenced, ‘CPM’). A ratio was taken of the CPM for each gRNA of the 2x migrated group to the 2x non-migrated group to identify migratory or non-migratory enrichment.
For each screen replicate the Z-score was calculated for each gRNA relative to the control non-targeting gRNA population using similar methodologies as previously described35. First, each sample’s ratio was converted to a log2 fold-enrichment, and population statistics for the negative control non-targeting gRNAs (median, standard deviation, gRNA number) were calculated. For each individual gRNA, the median of the negative control fold-enrichment was subtracted from each individual gRNA’s log2 fold-enrichment value, and this value was further divided by the standard deviation of the negative control non-targeting gRNA population to get an individual Z-score relative to the negative control population. Raw Z-score values from both replicates were pooled to calculate pRE-level effects. An individual gRNA was called as a “hit” if the Z-score was above 2 or below -2. pRE-level stats were generated by performing a Fisher’s exact text relative to the non-targeting gRNA population, and a pRE-level was labeled significant for follow-up if the pval was less than 0.1.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and text files.
Library strategy: CRISPR gRNA recovery from genomic DNA

extract_protocol:
Following these two rounds of migration we trypsinized and collected the cells that either migrated twice or did not migrate twice (with a similar number of cells, 24%, being found to have migrated during this second round) and isolated gDNA using DNeasy kits (Qiagen).
All gDNA was split between sample-indexed 100uL Q5 PCR reactions (up to ~340ng max input per 100uL reaction) to amplify out the gRNA protospacer from HFF cells. These PCRs from gDNA were run as follows [ 98C for 30s / 25x: 98C for 10s, 60C for 30s, 72C for 15s / 72C for 2 min] with primers in Supplementary Table 15, followed by individual PCRs being pooled together and subjected to a double-sided 0.65X/1X SPRI clean-up. Quality control was performed by running the amplified libraries out on a High Sensitivity D1000 Tapestation (Agilent) to confirm expected size, and Qubit dsDNA HS assays were performed to determine a final concentration. All libraries were pooled to an effective concentration of 4 nM and combined in equal volumes prior to sequencing on an Illumina MiSeq, using a v2 50 cycle reagent kit with Read1 being 21 cycles (protospacer) and index read 1 being 6 reads (sample barcoding).

treatment_protocol: To perform screening, 600k HFF cells were transduced with the lentiviral library virus at 10.8 MOI to achieve a coverage of ~279 cells per gRNA. 20 hours after transduction the viral media was removed and replaced with fresh media, and starting 48 hours after transduction HFF cells were selected with 1 ug/mL puromycin for 4 days. Puromycin selection media was then removed and HFF cells were grown out for two additional days until day 8. On day 8, ~11M cells were counted and split between migration and growth screens. Coverage of at least 279 cells/gRNA was maintained for each group throughout the entire experiment. On day 8, the bottoms of 8 um transwell inserts for 6WP were coated with 10 ug/mL fibronectin at room temp for 45 minutes and then rinsed 1x with PBS for 30 minutes before use. HFF cells were counted, placed into low serum conditions (0.2% FBS) and seeded at 240k cells per transwell insert across 18 inserts (~4.4M cells total). These inserts were placed into 10% serum and cells were allowed to migrate for 24 hours. Following this first day of migration, each side of the membrane was separately trypsinized and counted, where 27% of the initial cells were recovered as migratory cells (~1.2M cells) and non-migrated cells were recovered from the top of the insert. These migratory and non-migratory populations were re-seeded (separately by group) in the same way on new fibronectin-coated transwell inserts, with 4-5 inserts seeded at 240k cells/insert and allowed to migrate overnight.

tag: cell line

tag: genotype


title: MigLib-D21


title: C42.E.Enza.1

value: prostate

value: Estradiol (100nM) plus Ezalutamide (1 microMolar), 12h


title: MigLib-D0-rep1


title: feces, CCI, 28d, biolrep6

description: Biological replicate 6 for TBI group. 28 day (4 weeks) post injury timepoint: Sample taken 28 days (4 weeks) after TBI (controlled cortical impact) procedure

value: CCI, 28d


title: C42.E.Enza.2

value: WT


title: C42.WT.3


title: feces, CCI, 03d, biolrep7

description: Biological replicate 7 for TBI group. 3 day post injury timepoint: Sample taken 3 days after TBI (controlled cortical impact) procedure

value: CCI, 03d


title: MigLib-D2-non-migrated-rep1

value: HFF

value: Human foreskin fibroblasts


title: feces, CCI, 14d, biolrep6

description: Biological replicate 6 for TBI group. 14 day (2 weeks) post injury timepoint: Sample taken 14 days (2 weeks) after TBI (controlled cortical impact) procedure

value: CCI, 14d


title: rep1_myh9_facs_high

value: gRNA library


title: MigLib-D2-migrated-rep2


title: MigLib-D2-CTL-rep2


title: C42.WT.1

value: prostate cancer


title: C42.WT.2


title: C42.E.Enza.3


title: C42.Enza.3

value: Enzalutamide, 1microMolar


title: feces, CCI, 07d, biolrep6

description: Biological replicate 6 for TBI group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after TBI (controlled cortical impact) procedure

value: CCI, 07d


title: feces, CCI, 03d, biolrep6

description: Biological replicate 6 for TBI group. 3 day post injury timepoint: Sample taken 3 days after TBI (controlled cortical impact) procedure


title: MigLib-D22


title: feces, CCI, 02d, biolrep6

description: Biological replicate 6 for TBI group. 2 day post injury timepoint: Sample taken 2 days after TBI (controlled cortical impact) procedure

value: CCI, 02d


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, PP7-TadA-7.10 (V82G)_Replicate-2

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

data_processing:
remove adapter with Cutadapt
align to genome using bowtie2 or bwa-mem
generate count tables along reporter sequence using Pysamstats
Assembly: 6X MS2 and 6X PP7 stem-loop-bearing mRNAs (alternating):  6X MS2 and 6X PP7 alternating and 50 bp apart mRNA.fa, 6X MS2 and 6X PP7 alternating and 50 bp apart mRNA features.txt
Assembly: 2X MS2 and 2X PP7 stem-loop-bearing mRNAs (alternating):  2X MS2 and 2X PP7 alternating and 50 bp apart mRNA.fa, 2X MS2 and 2X PP7 alternating and 50 bp apart mRNA features.txt
Assembly: 2X MS2 and 2X PP7 stem-loop-bearing mRNAs (50bp apart):  2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart) mRNA.fa, 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart) mRNA features.txt
Supplementary files format and content: count tables with called edits along reporter sequences

source_name: Kidney

extract_protocol:
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Nextera XT DNA Library Preparation Kit (Illumina, Cat # FC-131-2002 or Cat # FC-131-1024)

value: Kidney

value: immortalized cell line

tag: reporter

tag: enzyme fusion/s

tag: replicate

value: doxycycline-induced expression


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, Replicate-1

value: No Enzyme Fusions


title: MigLib-D2-CTL-rep1


title: C42.Enza.2

value: prostate


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, Replicate-2


title: MigLib-D2-non-migrated-rep2


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, PP7-TadA-7.10 (V82G)_Replicate-1


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, PP7-TadA-8e_Replicate_2


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, PP7-TadA-8e_Replicate_1


title: feces, CCI, 01d, biolrep6

description: Biological replicate 6 for TBI group. 1 day post injury timepoint: Sample taken 1 day after TBI (controlled cortical impact) procedure

value: feces

value: CCI, 01d


title: MigLib-D2-migrated-rep1


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, MCP-APOBEC1_Replicate-1


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, MCP-APOBEC1_Replicate-2


title: feces, CCI, 28d, biolrep5

description: Biological replicate 5 for TBI group. 28 day (4 weeks) post injury timepoint: Sample taken 28 days (4 weeks) after TBI (controlled cortical impact) procedure

value: CCI, 28d


title: feces, CCI, 00d, biolrep6

description: Biological replicate 6 for TBI group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a TBI injured animal (controlled cortical impact)

value: CCI, 00d


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, MCP-APOBEC1, PP7-TadA-7.10 (V82G)_Replicate-2

value: MCP-APOBEC1 and PP7-TadA-7.10 (V82G)


title: feces, CCI, 14d, biolrep5

description: Biological replicate 5 for TBI group. 14 day (2 weeks) post injury timepoint: Sample taken 14 days (2 weeks) after TBI (controlled cortical impact) procedure


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, MCP-APOBEC1, PP7-TadA-7.10 (V82G)_Replicate-1


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, MCP-APOBEC1, PP7-TadA-8e_Replicate-2

value: MCP-APOBEC1 and PP7-TadA-8e


title: C42.E.1

value: WT

value: Estradiol (100nM, 12h)


title: C42.E.2

value: prostate cancer


title: 6X MS2 and 6X PP7 alternating and 50 bp apart, MCP-APOBEC1, PP7-TadA-8e_Replicate-1


title: feces, CCI, 07d, biolrep5

description: Biological replicate 5 for TBI group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after TBI (controlled cortical impact) procedure


title: 2X MS2 and 2X PP7 alternating and 50 bp apart_Replicate-2


title: C42.C.3

value: Vehicle


title: feces, CCI, 03d, biolrep5

description: Biological replicate 5 for TBI group. 3 day post injury timepoint: Sample taken 3 days after TBI (controlled cortical impact) procedure

value: CCI, 03d


title: 2X MS2 and 2X PP7 alternating and 50 bp apart, PP7-TadA-7.10 (V82G)_Replicate-2


title: C42.Enza.1

value: Enzalutamide, 1microMolar


title: 2X MS2 and 2X PP7 alternating and 50 bp apart, PP7-TadA-8e_Replicate-2

value: Kidney


title: feces, CCI, 02d, biolrep5

description: Biological replicate 5 for TBI group. 2 day post injury timepoint: Sample taken 2 days after TBI (controlled cortical impact) procedure

value: CCI, 02d


title: C42.C.2


title: 2X MS2 and 2X PP7 alternating and 50 bp apart, PP7-TadA-7.10 (V82G)_Replicate-1

value: immortalized cell line

value: doxycycline-induced expression


title: C42.C.1

value: prostate


title: 2X MS2 and 2X PP7 alternating and 50 bp apart, PP7-TadA-8e_Replicate-1


title: 2X MS2 and 2X PP7 alternating and 50 bp apart, MCP-APOBEC1_Replicate-2


title: C42.E.3


title: 2X MS2 and 2X PP7 intertwined and 50 bp apart, MCP-APOBEC1, PP7-TadA-7.10 (V82G)_Replicate-2

value: 2X MS2 and 2X PP7 alternating and 50 bp apart


title: RV1.WT.Enza.3

value: WT (100nM) plus Ezalutamide (1 microMolar), 12h


title: feces, CCI, 14d, biolrep4

description: Biological replicate 4 for TBI group. 14 day (2 weeks) post injury timepoint: Sample taken 14 days (2 weeks) after TBI (controlled cortical impact) procedure

value: feces

value: CCI, 14d


title: feces, CCI, 01d, biolrep5

description: Biological replicate 5 for TBI group. 1 day post injury timepoint: Sample taken 1 day after TBI (controlled cortical impact) procedure

value: CCI, 01d


title: RV1.WT.Enza.1


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart)_Replicate-2

value: No Enzyme Fusions


title: feces, CCI, 07d, biolrep4

description: Biological replicate 4 for TBI group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after TBI (controlled cortical impact) procedure

value: CCI, 07d


title: feces, CCI, 00d, biolrep5

description: Biological replicate 5 for TBI group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a TBI injured animal (controlled cortical impact)

value: CCI, 00d


title: feces, CCI, 28d, biolrep4

description: Biological replicate 4 for TBI group. 28 day (4 weeks) post injury timepoint: Sample taken 28 days (4 weeks) after TBI (controlled cortical impact) procedure

value: CCI, 28d


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), PP7-TadA-7.10 (V82G)_Replicate-2


title: 2X MS2 and 2X PP7 alternating and 50 bp apart, MCP-APOBEC1, PP7-TadA-8e_Replciate-1

value: MCP-APOBEC1 and PP7-TadA-8e


title: 2X MS2 and 2X PP7 intertwined and 50 bp apart, MCP-APOBEC1, PP7-TadA-7.10 (V82G)_Replicate-1

value: MCP-APOBEC1 and PP7-TadA-7.10 (V82G)


title: RV1.WT.Enza.2

value: prostate cancer

value: WT


title: 2X MS2 and 2X PP7 alternating and 50 bp apart, MCP-APOBEC1, PP7-TadA-8e_Replciate-2

value: Kidney


title: RV1.E.Enza.3

value: Estradiol (100nM) plus Ezalutamide (1 microMolar), 12h


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart)_Replicate-1

value: immortalized cell line

value: doxycycline-induced expression


title: 2X MS2 and 2X PP7 alternating and 50 bp apart_Replicate-1


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), PP7-TadA-8e_Replicate-2


title: RV1.E.Enza.1

value: prostate


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), MCP-APOBEC1_Replicate-2


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), MCP-APOBEC1_Replicate-1


title: feces, CCI, 01d, biolrep4

description: Biological replicate 4 for TBI group. 1 day post injury timepoint: Sample taken 1 day after TBI (controlled cortical impact) procedure


title: 2X MS2 and 2X PP7 alternating and 50 bp apart, MCP-APOBEC1_Replicate-1


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), MCP-APOBEC1, PP7-TadA-7.10 (V82G)_Replicate-2


title: RV1.E.Enza.2


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), PP7-TadA-7.10 (V82G)_Replicate-1


title: RV1.WT.3


title: feces, CCI, 02d, biolrep4

description: Biological replicate 4 for TBI group. 2 day post injury timepoint: Sample taken 2 days after TBI (controlled cortical impact) procedure

value: CCI, 02d


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), MCP-APOBEC1, PP7-TadA-7.10 (V82G)_Replicate-1


title: RV1.WT.2


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), MCP-APOBEC1, PP7-TadA-8e_Replicate-1


title: RV1.WT.1


title: feces, CCI, 00d, biolrep4

description: Biological replicate 4 for TBI group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a TBI injured animal (controlled cortical impact)

value: feces


title: feces, CCI, 03d, biolrep4

description: Biological replicate 4 for TBI group. 3 day post injury timepoint: Sample taken 3 days after TBI (controlled cortical impact) procedure

value: CCI, 03d


title: feces, CCI, 28d, biolrep3

description: Biological replicate 3 for TBI group. 28 day (4 weeks) post injury timepoint: Sample taken 28 days (4 weeks) after TBI (controlled cortical impact) procedure


title: feces, CCI, 14d, biolrep3

description: Biological replicate 3 for TBI group. 14 day (2 weeks) post injury timepoint: Sample taken 14 days (2 weeks) after TBI (controlled cortical impact) procedure

value: CCI, 14d


title: RV1.Enza.2

value: Enzalutamide, 1microMolar


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), MCP-APOBEC1, PP7-TadA-8e_Replicate-2


title: 2X MS2 (50 bp apart)-350 bp-2X PP7 (50 bp apart), PP7-TadA-8e_Replicate-1


title: MCP-AID (truncated)_Replicate-2

data_processing:
remove adapter with Cutadapt
align to genome using bowtie2 or bwa-mem
generate count tables along reporter sequence using Pysamstats
Assembly: 12X MS2 stem-loop reporter mRNA
Supplementary files format and content: pysamstats tables that contain the read counts for RNA bases  at each position along the reporter mRNA sequence

tag: rbp-rbe fusion

value: MCP-AID (truncated)


title: No Enzyme_Replicate-6

value: No Enzyme


title: RV1.Enza.1


title: No Enzyme_Replicate-5


title: MCP-APOBEC3G_Replicate-2


title: feces, CCI, 07d, biolrep3

description: Biological replicate 3 for TBI group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after TBI (controlled cortical impact) procedure

value: CCI, 07d


title: RV1.E.3

value: Estradiol (100nM, 12h)


title: MCP-APOBEC3A (Y132G/G188A/R189A/L190A)_Replicate-1


title: MCP-APOBEC3A (Y132G/G188A/R189A/L190A)_Replicate-2


title: MCP-APOBEC3G_Replicate-1


title: feces, CCI, 02d, biolrep3

description: Biological replicate 3 for TBI group. 2 day post injury timepoint: Sample taken 2 days after TBI (controlled cortical impact) procedure


title: MCP-AID (truncated)_Replicate-1


title: MCP-APOBEC3A (Y132G/K30R)_Replicate-2

value: MCP-APOBEC3A (Y132G/K30R)


title: MCP-APOBEC3A (Y132G/K30R)_Replicate-1


title: RV1.E.1

value: prostate cancer


title: MCP-APOBEC3A_Replicate-1


title: MCP-APOBEC3A_Replicate-2


title: RV1.Enza.3

value: WT


title: feces, CCI, 03d, biolrep3

description: Biological replicate 3 for TBI group. 3 day post injury timepoint: Sample taken 3 days after TBI (controlled cortical impact) procedure


title: MCP-AID-C12*_Replicate-2

value: Kidney


title: MCP-AID-C12*_Replicate-1


title: feces, CCI, 28d, biolrep2

description: Biological replicate 2 for TBI group. 28 day (4 weeks) post injury timepoint: Sample taken 28 days (4 weeks) after TBI (controlled cortical impact) procedure

value: CCI, 28d


title: MCP-evoAPOBEC1_Replicate-2

value: immortalized cell line


title: MCP-evoAPOBEC1_Replicate-1

value: doxycycline-induced expression


title: RV1.C.2

value: prostate

value: Vehicle


title: feces, CCI, 14d, biolrep2

description: Biological replicate 2 for TBI group. 14 day (2 weeks) post injury timepoint: Sample taken 14 days (2 weeks) after TBI (controlled cortical impact) procedure

value: feces


title: MCP-TadA-7.10 (V82G)_Replicate-2


title: RV1.C.1


title: MCP-TadA-7.10 (V82G)_Replicate-1


title: LNC.WT.Enza.3

value: LNCaP

value: WT (100nM) plus Ezalutamide (1 microMolar), 12h


title: RV1.E.2


title: MCP-TadA (L84F/D108N)_Replicate-2 (10)

value: MCP-TadA (L84F/D108N)


title: feces, CCI, 07d, biolrep2

description: Biological replicate 2 for TBI group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after TBI (controlled cortical impact) procedure


title: feces, CCI, 01d, biolrep3

description: Biological replicate 3 for TBI group. 1 day post injury timepoint: Sample taken 1 day after TBI (controlled cortical impact) procedure

value: CCI, 01d


title: feces, CCI, 02d, biolrep2

description: Biological replicate 2 for TBI group. 2 day post injury timepoint: Sample taken 2 days after TBI (controlled cortical impact) procedure

value: CCI, 02d


title: MCP-TadA-TadA-7.10_Replicate-1


title: LNC.WT.Enza.2


title: feces, CCI, 00d, biolrep3

description: Biological replicate 3 for TBI group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a TBI injured animal (controlled cortical impact)

value: CCI, 00d


title: feces, CCI, 03d, biolrep2

description: Biological replicate 2 for TBI group. 3 day post injury timepoint: Sample taken 3 days after TBI (controlled cortical impact) procedure

value: CCI, 03d


title: MCP-TadA (V82G)_Replicate-2 (8)

value: MCP-TadA (V82G)


title: MCP-TadA (L84F/D108N)_Replicate-1 (9)


title: LNC.WT.Enza.1

value: prostate cancer


title: feces, CCI, 01d, biolrep2

description: Biological replicate 2 for TBI group. 1 day post injury timepoint: Sample taken 1 day after TBI (controlled cortical impact) procedure


title: MCP-TadA (V82G)_Replicate-1 (7)


title: MCP-APOBEC1 (STAMP)_Replicate-4

value: MCP-APOBEC1 (STAMP)


title: RV1.C.3

value: WT


title: LNC.E.Enza.3

value: Estradiol (100nM) plus Ezalutamide (1 microMolar), 12h


title: feces, CCI, 00d, biolrep2

description: Biological replicate 2 for TBI group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a TBI injured animal (controlled cortical impact)


title: MCP-APOBEC1 (STAMP)_Replicate-3

value: Kidney

value: immortalized cell line


title: MCP-ADARcd (E488Q) (hyperTRIBE)_Replicate-2

value: MCP-ADARcd (E488Q) (hyperTRIBE)

value: doxycycline-induced expression


title: LNC.E.Enza.2

value: prostate


title: feces, CCI, 28d, biolrep1

description: Biological replicate 1 for TBI group. 28 day (4 weeks) post injury timepoint: Sample taken 28 days (4 weeks) after TBI (controlled cortical impact) procedure

value: feces

value: CCI, 28d


title: MCP-ADARcd (E488Q) (hyperTRIBE)_Replicate-1


title: MCP-TadA-TadA-7.10_Replicate-2


title: MCP-TadA-7.10_Replicate-2


title: LNC.E.Enza.1

value: LNCaP


title: MCP-TadA-7.10_Replicate-1


title: feces, CCI, 14d, biolrep1

description: Biological replicate 1 for TBI group. 14 day (2 weeks) post injury timepoint: Sample taken 14 days (2 weeks) after TBI (controlled cortical impact) procedure

value: CCI, 14d


title: No Enzyme_Replicate-4

value: No Enzyme


title: LNC.WT.3


title: No Enzyme_Replicate-3


title: MCP-TadA-TadA (V82G/D108N)_Replicate-2

value: MCP-TadA-TadA (V82G/D108N)


title: feces, CCI, 03d, biolrep1

description: Biological replicate 1 for TBI group. 3 day post injury timepoint: Sample taken 3 days after TBI (controlled cortical impact) procedure

value: CCI, 03d


title: LNC.WT.2


title: MCP-TadA-TadA (V82G/D108N)_Replicate-1


title: feces, CCI, 07d, biolrep1

description: Biological replicate 1 for TBI group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after TBI (controlled cortical impact) procedure

value: CCI, 07d


title: feces, CCI, 02d, biolrep1

description: Biological replicate 1 for TBI group. 2 day post injury timepoint: Sample taken 2 days after TBI (controlled cortical impact) procedure

value: CCI, 02d


title: MCP-TadA (V82G/D108N)_Replicate-2

value: MCP-TadA (V82G/D108N)


title: LNC.Enza.3

value: prostate cancer

value: WT

value: Enzalutamide, 1microMolar


title: MCP-TadA (L84F/D108N)_Replicate-2 (D8)

value: Kidney

value: immortalized cell line

value: MCP-TadA (L84F/D108N)


title: feces, CCI, 01d, biolrep1

description: Biological replicate 1 for TBI group. 1 day post injury timepoint: Sample taken 1 day after TBI (controlled cortical impact) procedure

value: CCI, 01d


title: LNC.WT.1

value: prostate


title: MCP-TadA-TadA (V82G)_Replicate-2

value: MCP-TadA-TadA (V82G)

value: doxycycline-induced expression


title: MCP-TadA-TadA (V82G)_Replicate-1


title: MCP-TadA (V82G/D108N)_Replicate-1


title: MCP-TadA (L84F/D108N)_Replicate-1 (D5)


title: LNC.Enza.2

value: LNCaP


title: MCP-TadA (V82G)_Replicate-1 (D1)

value: MCP-TadA (V82G)


title: MCP-TadA-TadA (L84F)_Replicate-2

value: MCP-TadA-TadA (L84F)


title: feces, Sham, 28d, biolrep6

description: Biological replicate 6 for sham group. 28 day (4 week) post injury timepoint: Sample taken 28 days (4 week) after sham (craniotomy only) procedure

value: feces

value: Sham, 28d


title: feces, CCI, 00d, biolrep1

description: Biological replicate 1 for TBI group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a TBI injured animal (controlled cortical impact)

value: CCI, 00d


title: MCP-TadA-TadA (L84F)_Replicate-1


title: LNC.E.3

value: Estradiol (100nM, 12h)


title: MCP-TadA (L84F)_Replicate-2

value: MCP-TadA (L84F)


title: LNC.Enza.1

value: prostate cancer

value: WT


title: LNC.E.2


title: LNC.C.3

value: Vehicle


title: MCP-TadA (L84F)_Replicate-1

value: Kidney

value: immortalized cell line


title: MCP-TadA-TadA (TadA-d)_Replicate-2

value: MCP-TadA-TadA (TadA-d)


title: LNC.E.1

value: prostate


title: feces, Sham, 14d, biolrep6

description: Biological replicate 6 for sham group. 14 day (2 week) post injury timepoint: Sample taken 14 days (2 week) after sham (craniotomy only) procedure

value: Sham, 14d


title: feces, Sham, 03d, biolrep6

description: Biological replicate 6 for sham group. 3 day post injury timepoint: Sample taken 3 days after sham (craniotomy only) procedure

value: Sham, 03d


title: feces, Sham, 02d, biolrep6

description: Biological replicate 6 for sham group. 2 day post injury timepoint: Sample taken 2 days after sham (craniotomy only) procedure

value: Sham, 02d


title: LNC.C.2

value: LNCaP


title: MCP-TadA (V82G)_Replicate-2 (D2)

value: MCP-TadA (V82G)

value: doxycycline-induced expression


title: MCP-TadA-TadA (TadA-d)_Replicate-1


title: feces, Sham, 01d, biolrep6

description: Biological replicate 6 for sham group. 1 day post injury timepoint: Sample taken 1 day after sham (craniotomy only) procedure

value: feces

value: Sham, 01d


title: MCP-TadA-8e_Replicate-2


title: MCP-TadA-WT_Replicate-2

value: MCP-TadA-WT


title: MCP-TadA-8e_Replicate-1


title: MCP-TadA (D108N)_Replicate-1

value: MCP-TadA (D108N)


title: feces, Sham, 00d, biolrep6

description: Biological replicate 6 for sham group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a sham (craniotomy only)

value: Sham, 00d


title: feces, Sham, 28d, biolrep5

description: Biological replicate 5 for sham group. 28 day (4 week) post injury timepoint: Sample taken 28 days (4 week) after sham (craniotomy only) procedure

value: Sham, 28d


title: LNC.C.1

value: prostate cancer

value: WT

value: Vehicle


title: feces, Sham, 07d, biolrep6

description: Biological replicate 6 for sham group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after sham (craniotomy only) procedure

value: Sham, 07d


title: MCP-TadA (D108N)_Replicate-2

value: Kidney

value: immortalized cell line


title: feces, Sham, 14d, biolrep5

description: Biological replicate 5 for sham group. 14 day (2 week) post injury timepoint: Sample taken 14 days (2 week) after sham (craniotomy only) procedure

value: Sham, 14d


title: SNU449 cells, siOXTR-3

city: xinxing

first: huijie

last: yang

address: Hongqi District, Xinxiang City

country: China

institute: Xinxiang Medical University

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
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.

source_name: Liver cancer

growth_protocol: SNU449 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Lysis of cells with Trizol regent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using BGISEQ-500 protocols.

treatment_protocol: SNU449 cells were transfected with siControl and siOXTR for 48 h.

value: Liver cancer

value: SNU449 cells

value: Human HepatocarcinomaCells

value: siOXTR


title: SNU449 cells, siOXTR-2


title: MCP-RESCUE-S ADAR2dd_Replicate-2

value: MCP-RESCUE-S ADAR2dd

value: doxycycline-induced expression


title: MCP-TadA-WT_Replicate-1

value: MCP-TadA-WT


title: MCP-TadA-8.20_Replicate-2


title: feces, Sham, 07d, biolrep5

description: Biological replicate 5 for sham group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after sham (craniotomy only) procedure

value: feces


title: MCP-RESCUE ADAR2dd_Replicate-2

value: MCP-RESCUE ADAR2dd


title: MCP-TadA-8.20_Replicate-1


title: MCP-RESCUE-S ADAR2dd_Replicate-1


title: MCP-RESCUE ADAR2dd_Replicate-1


title: SNU449 cells, siOXTR-1


title: SNU449 cells, siControl-3

value: siControl


title: SNU449 cells, siControl-2


title: feces, Sham, 03d, biolrep5

description: Biological replicate 5 for sham group. 3 day post injury timepoint: Sample taken 3 days after sham (craniotomy only) procedure

value: Sham, 03d


title: MCP-ADARcd (TRIBE)_Replicate-2

value: MCP-ADARcd (TRIBE)


title: feces, Sham, 02d, biolrep5

description: Biological replicate 5 for sham group. 2 day post injury timepoint: Sample taken 2 days after sham (craniotomy only) procedure

value: Sham, 02d


title: MCP-ADARcd (TRIBE)_Replicate-1


title: MCP-SECURE rAPOBEC1 (R33A/K34A)_Replicate-2

value: MCP-SECURE rAPOBEC1 (R33A/K34A)


title: SNU449 cells, siControl-1


title: MCP-SECURE rAPOBEC1 (R33A/K34A)_Replicate-1

value: Kidney


title: MCP-APOBEC1 (STAMP)_Replicate-2

value: immortalized cell line

value: MCP-APOBEC1 (STAMP)


title: MCP-SECURE rAPOBEC1 (R33A)_Replicate-2

value: MCP-SECURE rAPOBEC1 (R33A)


title: L4_CDS2_CTRL_Rep1

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

data_processing:
Single-end reads were trimmed using TrimGalore v 0.6.4 and aligned to the human genome and transcriptome assembly GRCh37 (hg19) using STAR v 2.5.0a.
Transcript quantification was done using rsem v 1.3.0. The resulting counts matrix was used for subsequent analysis.
Significantly enriched genomic regions for TF and histone mark ChIP-seq were detected using MACS2 v 2.2.6. FDR cutoff was set to 5.00e-02
gene filtering based on the rule of 1 count per M (cpm) in at least 1 sample, library size scaling using TMM normalization (EdgeR package v 3.32.1, Robinson Bioinformatics 2010) and log-transformation using the Limma voom function
Normalized data were batch corrected using the Limma removeBatchEffect function and uwanted variation was removed with RUVr (RUVseq package v 1.24.0).
Differentially expressed genes were identified using Limma by fitting a linear model on the selected samples. Batch and RUVr-computed factors were added in the design matrix.
Assembly: Hg19
Supplementary files format and content: All_samples_data_counts.tsv (tab-delimited text file that includes raw counts for each sample)

growth_protocol: CDS1 and CDS2 cells were grown in RPMI medium (Gibco) supplemented with 10% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin (PenStrep, Gibco) in adherent cell culture conditions. Cells were passed in RPMI medium (Gibco) supplemented with 20% KO serum (Gibco) one week prior experimentations. All cells were cultured at 37°C with 5% CO2. Cells were maintained and split every 2-4 days (at approximately 80% confluence).

extract_protocol:
RNA was extracted using the RNeasy RNA isolation kit (Qiagen), a minimum of 100 ng RNA was used for preparing sequencing libraries
RNA libraries for RNA-seq were prepared using the TruSeq mRNA stranded kit (Illumina) following manufacturer's protocol.

treatment_protocol:
Knock-down of CIC-DUX4 by siRNA : SiRNAs for depletion of CIC-DUX4 were purchased from Qiagen (Hs_DUX4_11, sequence: CAGGCGCAACCTCTCCTAGAA) or from Sigma-Aldrich (SASI_Hs02_0036094, sense sequence: CCGGCGCCCUGGUCUGCAC[dT][dT], antisense sequence: GUGCAGACCAGGGCGCCGG[dT][dT]). Negative control siRNA (AllStars) was purchased from Qiagen. Oligonucleotides were transfected with INTERFERin siRNA transfection reagent (Polyplus) in 150 mm plates using siRNA duplexes at a final concentration of 12 nM and  a reverse transfection protocol according to manufacturer recommandtions. Cells were harvested 3 days after transfection.
p300 degrader : dGBP1 P300 degrader was obtained (MedChemExpress USA https://doi.org/10.1016/j.chembiol.2020.12.004) . Cells were cultured for 1-3 days in RPMI containing 20% KnockOut™ Serum Replacement, 1% penistrep, then stimulated with 50 or 100 nM dGBP1 or vehicle (DMSO)

value: Human CIC-DUX4 sarcoma cell line

value: DMSO


title: MCP-SECURE rAPOBEC1 (R33A)_Replicate-1


title: L4_CDS2_CIC_DUX4_KDS_Rep1

value: siRNAS against CIC-DUX4


title: feces, Sham, 00d, biolrep5

description: Biological replicate 5 for sham group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a sham (craniotomy only)

value: Sham, 00d


title: MCP-evoA3A (N57G)_Replicate-2

value: MCP-evoA3A (N57G)

value: doxycycline-induced expression


title: feces, Sham, 28d, biolrep4

description: Biological replicate 4 for sham group. 28 day (4 week) post injury timepoint: Sample taken 28 days (4 week) after sham (craniotomy only) procedure

value: feces

value: Sham, 28d


title: feces, Sham, 01d, biolrep5

description: Biological replicate 5 for sham group. 1 day post injury timepoint: Sample taken 1 day after sham (craniotomy only) procedure

value: Sham, 01d


title: feces, Sham, 07d, biolrep4

description: Biological replicate 4 for sham group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after sham (craniotomy only) procedure

value: Sham, 07d


title: MCP-evoA3A (N57G)_Replicate-1


title: L4_CDS2_CIC_DUX4_KDQ_Rep1

value: siRNAQ against CIC-DUX4


title: MCP-evoFERNY_Replicate-1

value: MCP-evoFERNY


title: MCP-evoCDA1_Replicate-1


title: MCP-evoCDA1_Replicate-2


title: MCP-evoFERNY_Replicate-2


title: L3_CDS1_CTRL_Rep1


title: feces, Sham, 01d, biolrep4

description: Biological replicate 4 for sham group. 1 day post injury timepoint: Sample taken 1 day after sham (craniotomy only) procedure


title: feces, Sham, 02d, biolrep4

description: Biological replicate 4 for sham group. 2 day post injury timepoint: Sample taken 2 days after sham (craniotomy only) procedure

value: Sham, 02d


title: L3_CDS1_CIC_DUX4_KDS_Rep1


title: No Enzyme_Replicate-2

value: Kidney

value: No Enzyme


title: No Enzyme_Replicate-1

value: immortalized cell line


title: L3_CDS1_CIC_DUX4_KDQ_Rep1


title: NSTEMI_15_reanalyzed

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

data_processing:
We used XSQTools (Applied Biosystems) with default parameters to remove reads with low quality base values and to generate .csfasta and .QV.qual files for each samples. Fiannly, cs.fasta and .QV.qual files were converted into .fastq format.
Sequential aligning of raw reads was performed against the GRCh38 Human Genome reference (release 99) with the “Spliced Transcripts Alignment to a Reference” (STAR v. 2.7.5c) software, and with “Bowtie2” (v. 2.4.1) to align locally any reads not mapped by STAR. We excluded 'haplotypes' and 'patches' sequences from the reference, in order to focus on primary assembly and to avoid under-estimation of gene expression.
We implemented the reference annotation based transcript (RABT) procedure, using StringTie suite v2.1.4 to create a new assembly for downstream analysis, integrating the information about known genes and transcripts position in the genome (Ensemble GTF release 99) with those reads mapped in intergenic or intronic regions.
Gene expression quantification were computed by “featureCounts” (v.2.0.1) grouping meta-features by 'gene name'.
Assembly: HG38/GRCh38.99
Supplementary files format and content: Tab-delimited text files include raw counts values for each Sample. The header of the files reports gene name, Ensemble gene ID, chromosome location, gene length, biotype, biotype class and sample identifiers.

source_name: Whole blood

growth_protocol: Blood samples were collected and mantained into Tempus Blood RNA tubes at -80 °C until processing, following manufacturer's instructions.

extract_protocol:
Total RNA was isolated using the Tempus Spin RNA Isolation Kit (Applied Biosystems) and was treated with RNase-free DNase-I to eliminate genomic contamination, following the manufacturer’s instructions.
Five µg of total RNA were precipitated, α- and β-globin mRNAs were depleted with GLOBINclear Whole Blood Globin Reduction kit (Applied Biosystems), and poly(A)+ RNA was enriched following MicroPoly(A) Purist kit protocol (Applied Biosystems). Libraries were prepared and pooled together using the multiplex SOLiD System Sequencing and Barcoding kits. Complementary DNA (cDNA) amplification reaction was conducted with 20 µL template in 100 µl end-volume reaction and with 16 PCR cycles. Clonally amplification of library templates was performed on SOLiD p1 DNA beads by emulsion PCR (ePCR) using 0.5 pM library template and E120 EZbeads scale.

value: Whole blood

value: Female

tag: acs

value: NSTEMI

tag: avsc

value: No


title: feces, Sham, 00d, biolrep4

description: Biological replicate 4 for sham group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a sham (craniotomy only)

value: Sham, 00d


title: NSTEMI_13_reanalyzed

value: Male


title: NSTEMI_14_reanalyzed


title: CDS2_Degrader_Exp_B_control

value: Human CIC-DUX4 sarcoma cell line

value: dGBP1 P300 degrader from MedChemExpress


title: feces, Sham, 14d, biolrep3

description: Biological replicate 3 for sham group. 14 day (2 week) post injury timepoint: Sample taken 14 days (2 week) after sham (craniotomy only) procedure

value: feces

value: Sham, 14d


title: feces, Sham, 28d, biolrep3

description: Biological replicate 3 for sham group. 28 day (4 week) post injury timepoint: Sample taken 28 days (4 week) after sham (craniotomy only) procedure

value: Sham, 28d


title: NSTEMI_6_reanalyzed


title: NSTEMI_9_reanalyzed

value: Yes


title: NSTEMI_4_reanalyzed


title: feces, Sham, 07d, biolrep3

description: Biological replicate 3 for sham group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after sham (craniotomy only) procedure

value: Sham, 07d


title: CDS2_Degrader_Exp_A_100_mM


title: CDS2_Degrader_Exp_B_100_mM


title: NSTEMI_3_reanalyzed


title: NSTEMI_2_reanalyzed


title: NSTEMI_7_reanalyzed


title: NSTEMI_5_reanalyzed


title: CDS2_Degrader_Exp_A_control

value: DMSO


title: NSTEMI_1_reanalyzed


title: feces, Sham, 02d, biolrep3

description: Biological replicate 3 for sham group. 2 day post injury timepoint: Sample taken 2 days after sham (craniotomy only) procedure

value: Sham, 02d


title: feces, Sham, 03d, biolrep3

description: Biological replicate 3 for sham group. 3 day post injury timepoint: Sample taken 3 days after sham (craniotomy only) procedure

value: Sham, 03d


title: CDS2_MN_Input_2

data_processing:
Single-end reads were trimmed using TrimGalore version (v) 0.6.4 (https://github.com/FelixKrueger/TrimGalore) and aligned to the human genome assembly GRCh37 (hg19) using STAR v 2.5.0a.
Multiple matches, as well as regions present in the ENCODE project DAC Exclusion List Regions (data set ENCSR636HFF), were removed and maximum three redundant reads kept for subsequent analyses.
Significantly enriched genomic regions for TF and histone mark ChIP-seq were detected using MACS2 v 2.2.6. FDR cutoff was set to 5.00e-02
False-positive rate was reduced by intersecting MACS peaks with enriched genomic bins defined as described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9046276/
Assembly: Hg19
Supplementary files format and content: CPM-normalized BigWig files were generated using bamCoverage

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Branson sonifier SFX250 sonicator followed by chromatin immunoprecipitation using desired antibodies.
ChIp-seq libraries were prepared using the Illumina Truseq ChIP Library Preparation Kit. 5 ng of DNA was used as a starting material for input and samples. Libraries were amplified using 16 cycles on the thermocycler. Post amplification libraries were size selected at 200-500bp in lenght using SPRI beads from Beckman Coulter.

value: human CIC-DUX4 sarcoma cell line

tag: chip antibody


title: STEMI_12_reanalyzed

value: Whole blood

value: STEMI


title: feces, Sham, 00d, biolrep3

description: Biological replicate 3 for sham group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a sham (craniotomy only)


title: STEMI_9_reanalyzed


title: STEMI_11_reanalyzed


title: STEMI_8_reanalyzed


title: feces, Sham, 01d, biolrep3

description: Biological replicate 3 for sham group. 1 day post injury timepoint: Sample taken 1 day after sham (craniotomy only) procedure

value: Sham, 01d


title: STEMI_6_reanalyzed


title: CDS2_MN_DUX4_2

value: DUX4 C-term (Origene, #AP51343PU-N)


title: CDS2_MN_DUX4_1


title: feces, Sham, 14d, biolrep2

description: Biological replicate 2 for sham group. 14 day (2 week) post injury timepoint: Sample taken 14 days (2 week) after sham (craniotomy only) procedure


title: feces, Sham, 28d, biolrep2

description: Biological replicate 2 for sham group. 28 day (4 week) post injury timepoint: Sample taken 28 days (4 week) after sham (craniotomy only) procedure


title: CDS2_Input_2


title: STEMI_5_reanalyzed


title: STEMI_13_reanalyzed

value: No


title: CDS2_Input_1


title: CDS2_MN_Input_1


title: CDS2_H3K4me3_2

value: H3K4me3 (Merck/Millipore, #04-745)


title: STEMI_1_reanalyzed

value: Male


title: feces, Sham, 07d, biolrep2

description: Biological replicate 2 for sham group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after sham (craniotomy only) procedure


title: feces, Sham, 03d, biolrep2

description: Biological replicate 2 for sham group. 3 day post injury timepoint: Sample taken 3 days after sham (craniotomy only) procedure


title: STEMI_10_reanalyzed


title: CDS2_H3K4me3_1


title: STEMI_2_reanalyzed

value: Female


title: STEMI_AVSc_15


title: feces, Sham, 02d, biolrep2

description: Biological replicate 2 for sham group. 2 day post injury timepoint: Sample taken 2 days after sham (craniotomy only) procedure

value: feces


title: NSTEMI_noAVSc_19

value: NSTEMI


title: NSTEMI_AVSc_20


title: NSTEMI_AVSc_18


title: CDS2_H3K4me1_1

value: H3K4me1 (Abcam, #ab8895)


title: feces, Sham, 01d, biolrep2

description: Biological replicate 2 for sham group. 1 day post injury timepoint: Sample taken 1 day after sham (craniotomy only) procedure


title: NSTEMI_AVSc_19

value: Yes


title: STEMI_7_reanalyzed


title: STEMI_4_reanalyzed


title: NSTEMI_noAVSc_18


title: CDS2_H3K4me1_2


title: STEMI_noAVSc_31


title: STEMI_3_reanalyzed


title: STEMI_noAVSc_32


title: feces, Sham, 00d, biolrep2

description: Biological replicate 2 for sham group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a sham (craniotomy only)

value: Sham, 00d


title: feces, Sham, 14d, biolrep1

description: Biological replicate 1 for sham group. 14 day (2 week) post injury timepoint: Sample taken 14 days (2 week) after sham (craniotomy only) procedure

value: Sham, 14d


title: CDS2_H3K27ac_1

value: H3K27ac (Active Motif, #39134)


title: STEMI_AVSc_14


title: feces, Sham, 07d, biolrep1

description: Biological replicate 1 for sham group. 7 day (1 week) post injury timepoint: Sample taken 7 days (1 week) after sham (craniotomy only) procedure

value: Sham, 07d


title: STEMI_noAVSc_29


title: STEMI_noAVSc_28


title: STEMI_AVSc_12


title: MCP-APOBEC1 (STAMP)_Replicate-1

value: Kidney

value: immortalized cell line

value: MCP-APOBEC1 (STAMP)

value: doxycycline-induced expression


title: NSTEMI_noAVSc_17

value: Whole blood


title: STEMI_AVSc_13

value: STEMI


title: CDS1_MN_Input_1

value: human CIC-DUX4 sarcoma cell line


title: CDS1_MN_DUX4_2

value: DUX4 C-term (Origene, #AP51343PU-N)


title: CDS1_MN_Input_2


title: feces, Sham, 02d, biolrep1

description: Biological replicate 1 for sham group. 2 day post injury timepoint: Sample taken 2 days after sham (craniotomy only) procedure

value: Sham, 02d


title: NSTEMI_AVSc_16

value: Male


title: feces, Sham, 01d, biolrep1

description: Biological replicate 1 for sham group. 1 day post injury timepoint: Sample taken 1 day after sham (craniotomy only) procedure

value: feces

value: Sham, 01d


title: CDS2_H3K27ac_2


title: NSTEMI_noAVSc_15

value: Female

value: NSTEMI

value: No


title: NSTEMI_AVSc_17

value: Yes


title: feces, Sham, 28d, biolrep1

description: Biological replicate 1 for sham group. 28 day (4 week) post injury timepoint: Sample taken 28 days (4 week) after sham (craniotomy only) procedure

value: Sham, 28d


title: NSTEMI_noAVSc_16


title: STEMI_noAVSc_27


title: CDS1_MN_DUX4_1


title: CDS1_Input_2


title: STEMI_noAVSc_30


title: NSTEMI_AVSc_15


title: feces, Sham, 00d, biolrep1

description: Biological replicate 1 for sham group. Pre-injury timepoint: Sample taken prior to surgical procedure for animal that would become a sham (craniotomy only)

value: Sham, 00d


title: STEMI_AVSc_11


title: SSTC3-1_R1.fq.gz_

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using Featurecounts
Assembly: mm10 (mouse)
Supplementary files format and content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: TREX1-KO BMDM

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen) and prepared into cDNA library according to the standard Illumina RNA-seq instruction.
The cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2500 by a 2X150 bp run.

value: TREX1-KO BMDM

value: SSTC3 treatment


title: feces, Sham, 03d, biolrep1

description: Biological replicate 1 for sham group. 3 day post injury timepoint: Sample taken 3 days after sham (craniotomy only) procedure

value: Sham, 03d


title: NSTEMI_AVSc_14

value: Whole blood


title: NSTEMI_AVSc_13


title: STEMI_AVSc_10

value: STEMI


title: STEMI_noAVSc_26


title: CDS1_H3K4me1_2

value: human CIC-DUX4 sarcoma cell line

value: H3K4me1 (Abcam, #ab8895)


title: SENS (exposed to sensory detection of food), rep5

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

institute: Centre Médical Universitaire de Genève

description:
1103-SENS-5
exposed to sensory detection of food (SENS; standard chow in a wire mesh so that it could be seen and smelled but not consumed) for 10 minutes

data_processing:
Data quality was checked by FastQC software.
Reads were mapped to murine genome sequence (GRCm38 from Genome Reference Consortium) by HiSAT2
Gene counts were acquired by applying featureCounts. Expression reads matrix  cutoff was setup at 10 reads
Read counts were normalized to CPMs (count per million) using the R package, EdgeR
Assembly: Mouse reference genome mm10
Supplementary files format and content: txt file containing all the gene expressions (CPM) for all the samples. Each column is a sample. Each row is a gene.

source_name: Hypothalamus

growth_protocol: Mice were maintained on a 12h-light/12h-dark cycle with free access to water and food

extract_protocol:
Nucleus arcuate (ARC)-enriched microdissections were ice-cold homogenized in 0.25 ml homogenization buffer (50 mM Tris, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 200 U/mL Promega RNasin, 1 mg/mL heparin, 100 mg/mL cycloheximide, Sigma protease inhibitor mixture at pH 7.5). To pull down, 2 ml of mouse monoclonal anti-HA antibody (HA.11, ascites fluid; Covance) was added to the homogenate and allowed to rotate for 2 h at 4°C. Then, 200 ml of Dynabead protein G magnetic beads (Invitrogen) were added and further incubated for 2 h at 4°C with rotation. Immunoprecipitates (IPs) were washed 3 times for 10 min with gentle rotation at 4°C in high-salt buffer (50 mM Tris, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 100 mg/mL cycloheximide at pH 7.5). After the final wash, RNA was stripped from the beads with Quiagen RLT buffer and total RNA was prepared according to manufacturer’s instructions using the RNeasy-plus Mini kit (Qiagen). Yield and concentration were measured with the Quant-iT™ RiboGreen™ RNA assay kit (Invitrogen). RNA integrity was assessed on a 2100 Bioanalyzer device (Agilent Technologies) using the RNA 6000 Pico kit (Agilent Technologies). Only samples with RIN > 8 were used for RNA-Seq analysis.
cDNA libraries were synthetized from 0.5 ng RNA with the SMARTer Ultra Low Input RNA kit v4 (Clontech). Sequencing libraries were prepared with the NexteraXT kit (Illumina)

treatment_protocol: Mice were fasted overnight (16 h) with free access to water and allowed to habituate to experimental room for 1 h before food presentation. Then, either  caged food pellet (SENS) or caged nonedible object (NEO) were introduced in the home cage. food pellets and nonedible object (consisting of wood sticks of the same size and color as food pellets) were caged using a metal mesh. Mice were housed in pairs or triplets. To minimize circadian clock interference, food perception paradigm was performed on the same time of day (around ZT6±1 h).

value: Hypothalamus

value: POMC neurons

value: POMCRiboTag mice

value: SENS

tag: antibody

tag: fraction

value: Translating RNA from ribosomes


title: SENS (exposed to sensory detection of food), rep4

description:
1070-SENS-4
exposed to sensory detection of food (SENS; standard chow in a wire mesh so that it could be seen and smelled but not consumed) for 10 minutes

value: anti-HA antibody (HA.11, ascites fluid; Covance)


title: STEMI_noAVSc_25

value: Male

value: No


title: CDS1_H3K4me1_1


title: STEMI_noAVSc_24


title: SENS (exposed to sensory detection of food), rep2

description:
1062-SENS-2
exposed to sensory detection of food (SENS; standard chow in a wire mesh so that it could be seen and smelled but not consumed) for 10 minutes


title: STEMI_AVSc_8

value: Female

value: Yes


title: NSTEMI_noAVSc_13

value: NSTEMI


title: SENS (exposed to sensory detection of food), rep3

description:
1068-SENS-3
exposed to sensory detection of food (SENS; standard chow in a wire mesh so that it could be seen and smelled but not consumed) for 10 minutes


title: CDS1_Input_1


title: NSTEMI_AVSc_12


title: SENS (exposed to sensory detection of food), rep6

description:
1104-SENS-6
exposed to sensory detection of food (SENS; standard chow in a wire mesh so that it could be seen and smelled but not consumed) for 10 minutes


title: STEMI_AVSc_9


title: NSTEMI_noAVSc_14


title: SENS (exposed to sensory detection of food), rep1

description:
1046-SENS-1
exposed to sensory detection of food (SENS; standard chow in a wire mesh so that it could be seen and smelled but not consumed) for 10 minutes


title: NSTEMI_AVSc_11


title: CDS1_H3K4me3_2

value: H3K4me3 (Merck/Millipore, #04-745)


title: CDS1_WT_soni_p300

value: p300 D2X6N (Cell Signaling, #54062)


title: CDS1_H3K4me3_1


title: NEO (exposed to an inaccessible nonedible object), rep 6

description:
1116-NEO-6
exposed to an inaccessible nonedible object (NEO; wooden dowel pins in a wire mesh)

value: NEO


title: STEMI_AVSc_6

value: Whole blood

value: STEMI


title: CDS1_WT_soni_Input

value: human CIC-DUX4 sarcoma cell line


title: NSTEMI_AVSc_9


title: STEMI_noAVSc_23


title: CDS1_siS_Input


title: STEMI_AVSc_7


title: NEO (exposed to an inaccessible nonedible object), rep 4

description:
1074-NEO-4
exposed to an inaccessible nonedible object (NEO; wooden dowel pins in a wire mesh)

value: Hypothalamus


title: CDS1_H3K27ac_1

value: H3K27ac (Active Motif, #39134)


title: NSTEMI_noAVSc_12


title: STEMI_noAVSc_21


title: NEO (exposed to an inaccessible nonedible object), rep 3

description:
1065-NEO-3
exposed to an inaccessible nonedible object (NEO; wooden dowel pins in a wire mesh)

value: POMC neurons

value: POMCRiboTag mice


title: STEMI_noAVSc_20


title: NSTEMI_AVSc_8


title: NEO (exposed to an inaccessible nonedible object), rep 2

description:
1064-NEO-2
exposed to an inaccessible nonedible object (NEO; wooden dowel pins in a wire mesh)

value: Translating RNA from ribosomes


title: STEMI_noAVSc_19


title: NSTEMI_AVSc_10


title: CDS1_siS_H3K27ac


title: STEMI_noAVSc_18


title: NEO (exposed to an inaccessible nonedible object), rep 1

description:
1050-NEO-1
exposed to an inaccessible nonedible object (NEO; wooden dowel pins in a wire mesh)

value: anti-HA antibody (HA.11, ascites fluid; Covance)


title: CDS1_siCTRL_Input


title: STEMI_AVSc_5

value: Male


title: NSTEMI_AVSc_7