title: Cortex P56 CASTxB6 Cell 153


title: CTRL4_S4

status: Public on Jan 07 2021

type: SRA

city: Toronto

first: Catherine

last: O'Brien

state: ON

address: 101 College St., PMCRT, Suite 13-704

country: Canada

institute: University Health Network

library_source: transcriptomic

data_processing:
FASTQ files were first filtered using a bespoke Perl script to remove reads shorter than 36bp.
Filtered FASTQ files were aligned to Gencode v25 gene annotations and hg38 genome build using the STAR short-read aligner (v2.4.1), and in parallel
were aligned to mouse Gencode M12 and mm10 genome build.
Mouse-derived reads were filtered out using the R package XenofilteR.
Read counts were generated from filtered BAM files using HTSeq-0.6.1 and the Gencode v25 gene annotations, and all read count matrices were merged using R.
Genome_build: hg38/mm10
Supplementary_files_format_and_content: tab-delimited text read counts

molecule: total RNA

organism: Homo sapiens

source_name: Colorectal cancer

extract_protocol:
RNA was extracted from FACS-purified tumor cells was using PicoPure RNA Isolation Kit (Applied Biosystems) following the manufacturer’s instructions. RNA was quantified using NanoDrop Spectrophotometer (Thermo Scientific).
RNA sequencing libraries were prepared using Takara SMARTer Stranded Total RNA-Seq Kit v1 - Pico Input Mammalian library kit, loaded in equimolar amounts on an Illumina NextSeq500 sequencer, and sequenced to an average depth of 40M 75 base-pair paired-end reads per sample.

tag: origin

value: xenograft - DMSO

tag: treatment

value: DMSO

tag: treatment duration

value: 8 weeks


title: CTRL3_S3


title: Cortex P56 CASTxB6 Cell 152

city: Cambridge

first: Longzhi

last: Tan

state: MA

address: 12 Oxford St

department: Chemistry and Chemical Biology

country: USA

institute: Harvard University

library_source: genomic

data_processing:
Library strategy: Dip-C
Please see 00README.md
Genome_build: mm10
Supplementary_files_format_and_content: Please see 00README.md

molecule: genomic DNA

organism: Mus musculus

source_name: cortex

extract_protocol: [Isolation of cell nuclei] Cell nuclei were isolated based on protocols from (Krishnaswami et al., 2016; Lacar et al., 2016) with minor modifications. In particular, Tris buffer would react with formaldehyde, and was therefore substituted with equal molarity of HEPES buffer. See details below:  Cortex and hippocampus were dissected in ice-cold PBS, and placed in 2 mL nuclei isolation medium with Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT, 0.1% Triton X-100) in a 2 mL Dounce homogenizer (Sigma D8938). Note that DTT concentration was not specified in (Krishnaswami et al., 2016); here we used 1 uM from (Lacar et al., 2016).  Tissues were homogenized with 5 strokes of the loose (A) pestle, and 15 strokes of the tight (B) pestle. The homogenate was centrifuged for 8 min at 94 g, 4 C, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei isolation medium without Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT).  The tube was centrifuged for 8 min at 94 g, 4 C again, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei storage buffer (0.1665 M sucrose, 5 mM MgCl2, 10 mM HEPES pH 8.0), and filtered with 40 um. Note that sucrose concentration was not specified in (Krishnaswami et al., 2016); here we used 0.1665 M from (Lacar et al., 2016). Also note that the recipe in (Lacar et al., 2016) seems to have typos in some ingredient volumes; here we followed the final concentrations.  [Fixation of cell nuclei] Nuclei were fixed according to our Dip-C protocol (Tan et al., 2019) with minor modifications. In particular, nuclei were fixed directly in the 1 mL nuclei storage buffer (with HEPES instead of Tris buffer; see above) rather than switching to PBS; and centrifugation was performed at 1,000 g rather than 600 g. See detailed below:  Nuclei were directly in the nuclei storage buffer (1 mL) with the addition of 66.7 uL 32% PFA (EMS 15714) to a final concentration of 2%. The tube was rotated for 10 min at room temperature; and 200 uL 1% BSA in PBS was then added. The tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant removed. The pellet was resuspended in 1 mL ice-cold 1% BSA in PBS. Nuclei were counted and aliquoted to up to 0.5 million per tube. Each tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant was removed. The pellet was stored at -80 C.  [Diploid chromatin conformation Capture (Dip-C)] A pellet of fixed cell nuclei was thawed on ice. We then proceeded directly to the step where 50 uL 0.5% SDS was added in the Dip-C protocol (Tan et al., 2019) and followed through with no modifications. Cells were sorted on a Beckman Coulter MoFlo Astrios, and amplified with homemade Nextera.

tag: tissue

value: cortex

tag: age

tag: strain


title: Snf5f/f_Brd9_GFP_D-3

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3);
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilobase per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene.

source_name: Brown preadipocyte cell

growth_protocol: Primary brown preadipocytes were isolated from interscapular BAT of newborn Snf5f/f or Brg1AID/AID mice and immortalized with SV40T-expressing retroviruses generated from the pBabeneo-large T plasmid.

extract_protocol:
Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).

treatment_protocol: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x10e6 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

tag: cell type

value: BAT isolated brown preadipocytes

tag: stage of adipogenesis

value: Preadipocytes (D-3)

tag: chip antibody

value: anti-BRD9 (#61537, Active Motif)


title: Snf5f/f_H3K27ac_GFP_D2

value: Differentiating preadipocytes (D2)

value: anti-H3K27ac (ab4729, Abcam)


title: CTRL2_S2


title: Cortex P1 CASTxB6 Cell 142


title: CTRL1_S1


title: Cortex P1 CASTxB6 Cell 141


title: Cortex P56 CASTxB6 Cell 151


title: Cortex P1 CASTxB6 Cell 140


title: Cortex P56 CASTxB6 Cell 150


title: Snf5f/f_H3K27ac_GFP_D-3


title: CPT_3_S3

value: xenograft - CPT-11


title: Cortex P56 CASTxB6 Cell 149


title: Snf5f/f_H3K27ac_Cre_D-3


title: Cortex P56 CASTxB6 Cell 148


title: CPT_2_S2


title: Snf5f/f_H3K27ac_Cre_D2


title: CPT_1_S1


title: Cortex P1 CASTxB6 Cell 144


title: Cortex P1 CASTxB6 Cell 139


title: Cortex P56 CASTxB6 Cell 147


title: Cortex P56 CASTxB6 Cell 154


title: Snf5f/f_H3K4me1_GFP_D-3

value: anti-H3K4me1 (13-0040, EpiCypher)


title: Snf5f/f_H3K4me1_GFP_D2


title: Cortex P56 CASTxB6 Cell 145


title: Cortex P1 CASTxB6 Cell 136


title: 68_TR_8_S11

value: xenograft - CPT-11 Resistant

value: 7 months


title: Cortex P56 CASTxB6 Cell 146


title: Cortex P1 CASTxB6 Cell 134


title: Cortex P1 CASTxB6 Cell 137


title: Snf5f/f_CBP_GFP_D2

value: anti-CBP (D6C5, #7389, Cell Signaling)


title: 66_BRCD_T7-9_S8

value: xenograft - FOLFIRI Regrowth

value: FOLFIRI


title: Snf5f/f_H3K4me1_Cre_D2


title: 67_TR_7_S10


title: 66_TR_1_S9


title: 66_BRCD_T7-5_S7


title: Cortex P1 CASTxB6 Cell 135


title: Cortex P56 CASTxB6 Cell 144


title: Cortex P56 CASTxB6 Cell 142


title: 66_BRCD_T7-2_S6


title: Snf5f/f_H3K4me1_Cre_D-3


title: Snf5f/f_CBP_Cre_D-3


title: Cortex P1 CASTxB6 Cell 131


title: Cortex P56 CASTxB6 Cell 143


title: Snf5f/f_MLL4_GFP_D2

value: anti-MLL4 (Homemade, Cho YK et al., Cell Metab, 2009)


title: Cortex P1 CASTxB6 Cell 133


title: 66_BRCD_T5-4_S4

value: xenograft - CPT-11 Regrowth


title: Snf5f/f_CBP_GFP_D-3


title: Cortex P1 CASTxB6 Cell 132


title: Cortex P1 CASTxB6 Cell 138


title: 66_BRCD_T5-9_S5


title: Snf5f/f_CBP_Cre_D2


title: Cortex P56 CASTxB6 Cell 137


title: Snf5f/f_MLL4_Cre_D2


title: Cortex P56 CASTxB6 Cell 138


title: Cortex P56 CASTxB6 Cell 141


title: Cortex P1 CASTxB6 Cell 130


title: Cortex P56 CASTxB6 Cell 136


title: Cortex P56 CASTxB6 Cell 135


title: Cortex P56 CASTxB6 Cell 139


title: 66_BRCD_T3-3_S11

value: xenograft - 5-FU/LV


title: Snf5f/f_Brg1_GFP_D2

value: anti-SMARCA4/BRG1 (ab110641, Abcam)


title: Snf5f/f_MLL4_GFP_D-3


title: 66_BRCD_T5-3_S3

value: 8 weeks


title: Cortex P1 CASTxB6 Cell 129

value: cortex


title: 66_BRCD_T3-4_S1


title: Cortex P1 CASTxB6 Cell 128


title: Snf5f/f_Brg1_Cre_D-3

value: BAT isolated brown preadipocytes

value: Preadipocytes (D-3)


title: Snf5f/f_MLL4_Cre_D-3


title: Cortex P1 CASTxB6 Cell 127


title: Cortex P56 CASTxB6 Cell 140


title: Cortex P56 CASTxB6 Cell 132


title: Cortex P1 CASTxB6 Cell 123


title: Cortex P56 CASTxB6 Cell 131


title: Cortex P1 CASTxB6 Cell 126


title: 66_BRCD_T1-1_S5

value: xenograft - Saline

value: Saline


title: Snf5f/f_CEBPb_GFP_D2

value: Differentiating preadipocytes (D2)

value: anti-C/EBPbeta (C-19, sc-150X, Santa Cruz)


title: Cortex P56 CASTxB6 Cell 134


title: Cortex P1 CASTxB6 Cell 125


title: Cortex P1 CASTxB6 Cell 120


title: 66_BRCD_T2-9_S10

value: xenograft - DMSO

value: DMSO


title: Snf5f/f_Brg1_GFP_D-3


title: 66_BRCD_T3-8_S2


title: 66_BRCD_T2-4_S8


title: Cortex P56 CASTxB6 Cell 133


title: Cortex P1 CASTxB6 Cell 124


title: Mll3-/-Mll4f/f_ATAC_GFP_D2

extract_protocol:
5 × 10e4 freshly collected cells were aliquoted into a new tube and spun down at 500 × g for 5 min at 4 °C. The cell pellet was incubated in 50 µl of ATAC-RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin (Promega) on ice for 3 min and was washed out with 1 ml of ATAC-RSB buffer containing 0.1% Tween-20. Nuclei were collected by centrifugation at 500 × g for 10 min at 4 °C, then resuspended in 50 µl of transposition reaction buffer (25 µl 2x Tagment DNA buffer, 2.5 µl transposase (100 nM final; Illumina), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). The reaction was incubated at 37 °C for 30 min with mixing (1000 r.p.m.) and directly subjected to DNA purification using the MinElute Reaction Cleanup Kit (Qiagen) according to the manufacturer’s instructions.
DNA was amplified with PCR using Nextera i7- and i5-index primers for Illumina protocols.


title: CRPC24

city: LONDON

first: YONG-JIE

last: LU

address: Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: BLSMD, Queen Mary University of London

data_processing:
Unaligned reads were trimmed and aligned against mirBase mature miRNA (Release 20) within Partek® Genomics Suite®. Samples were sequenced twice and read counts from two runs were combined.
Genome_build: aligned against mirBase mature miRNA (Release 20)
Supplementary_files_format_and_content: total read counts for each miRNA from two runs for all samples are summarized in miRNA_read_counts.xlsx

source_name: castration-resistant prostate cancer patient

extract_protocol:
Plasma was isolated within 2 h of blood draw by centrifugation of the whole blood at 1200 g for 10 min, followed by another centrifugation of the supernatant at 2000 g for 10 min. The supernatant was taken as plasma and stored at -80°C for future use. 200 μl of plasma from each case was used. Prior to exosome precipitation, plasma samples were treated with RNase A to remove free circulating RNAs and then RNase A was inactivated with RNase inhibitor. Exosomes were isolated using the Total Exosome Isolation Kit (from plasma) (Invitrogen™) following the manufacturer’s instructions. Exosome pellet was re-suspended in Buffer RLT (Qiagen) with 0.25 μg/μl Proteinase K and incubated at 50°C for 30 min. Exosomal RNA was then extracted using miRNeasy Micro Kit (Qiagen) and QIAzol Lysis Reagent (Qiagen) according to the manufacturer’s protocols.
Indexed libraries were prepared from the exosomal RNA as instructed by the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) without size selection.

value: plasma

tag: fraction

value: exosome


title: Cortex P56 CASTxB6 Cell 127


title: 66_BRCD_T2-6_S9


title: Cortex P56 CASTxB6 Cell 128


title: Cortex P1 CASTxB6 Cell 118


title: 66_BRCD_T1-6_S6


title: Snf5f/f_Brg1_Cre_D2


title: Cortex P1 CASTxB6 Cell 122


title: Mll3-/-Mll4f/f_ATAC_Cre_D2


title: Cortex P1 CASTxB6 Cell 117


title: Cortex P56 CASTxB6 Cell 130


title: Mll3-/-Mll4f/f_ATAC_Cre_D-3


title: Mll3-/-Mll4f/f_input_GFP_D2


title: Snf5f/f_CEBPa_GFP_D2

value: anti-C/EBPalpha (144AA, sc-61X, Santa Cruz)


title: Cortex P56 CASTxB6 Cell 129


title: CRPC20


title: Cortex P1 CASTxB6 Cell 121


title: Mll3-/-Mll4f/f_input_GFP_D-3


title: Cortex P1 CASTxB6 Cell 119


title: CRPC22


title: Mll3-/-Mll4f/f_ATAC_GFP_D-3


title: Cortex P56 CASTxB6 Cell 123


title: 66_BRCD_T1-10_S7


title: Cortex P1 CASTxB6 Cell 111


title: Cortex P1 CASTxB6 Cell 114


title: CRPC21


title: Cortex P1 CASTxB6 Cell 115


title: Cortex P1 CASTxB6 Cell 116


title: Cortex P56 CASTxB6 Cell 125


title: Cortex P1 CASTxB6 Cell 112


title: Mll3-/-Mll4f/f_SS18_GFP_D2

value: anti-SS18 (D6I4Z, #21792, Cell Signaling)


title: CRPC18


title: CRPC23


title: Cortex P1 CASTxB6 Cell 110


title: Cortex P56 CASTxB6 Cell 124


title: CRPC15


title: Cortex P56 CASTxB6 Cell 126


title: Cortex P56 CASTxB6 Cell 119


title: CRPC17


title: CRPC14


title: Cortex P56 CASTxB6 Cell 118


title: Cortex P1 CASTxB6 Cell 113


title: Cortex P56 CASTxB6 Cell 122


title: Mll3-/-Mll4f/f_input_Cre_D2


title: CRPC12


title: Cortex P56 CASTxB6 Cell 116


title: CRPC11


title: Mll3-/-Mll4f/f_BAF200_GFP_D2

value: anti-ARID2/BAF200 (E-3, sc-166117X, Santa Cruz)


title: CRPC10


title: Mll3-/-Mll4f/f_SS18_Cre_D2


title: Cortex P56 CASTxB6 Cell 121


title: CRPC16


title: Cortex P1 CASTxB6 Cell 104


title: CRPC19


title: HCT116, chronic hypoxia with FAO inhibition

type: RNA

city: Tokyo

first: Masatoshi

last: Wakui

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Laboratory Medicine

country: Japan

institute: Keio University School of Medicine

description: gene expression after culture

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Scan resolution 3um Feature Extraction Software: 10.7.3.1 Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Acute culture was defined as the culture under normoxia or severe hypoxia for 2 days. Chronic culture was defined as the culture under normoxia or mild hypoxia for 7 days.

extract_protocol: Total RNAs were extracted from cultured HCT116 cells using the QIAzol reagent and the miRNeasy Mini Kit (QIAGEN) according to the manufacture’s instructions.

treatment_protocol: HCT116 cells were cultured normoxically or hypoxically with or without pharmacological inhibition of P53 signaling or fatty acid b oxidation (FAO) and then subjected to the transcriptomic analysis.

tag: cell line

value: colon cancer

value: chronic hypoxia with FAO inhibition


title: Cortex P1 CASTxB6 Cell 103


title: Mll3-/-Mll4f/f_SS18_GFP_D-3


title: Cortex P1 CASTxB6 Cell 107


title: Mll3-/-Mll4f/f_input_Cre_D-3


title: Cortex P1 CASTxB6 Cell 109


title: Mll3-/-Mll4f/f_BAF200_GFP_D-3


title: Cortex P56 CASTxB6 Cell 120


title: HCT116, chronic hypoxia without FAO inhibition

description: gene expression after culture

value: chronic hypoxia without FAO inhibition


title: Cortex P1 CASTxB6 Cell 108

value: cortex


title: CRPC13


title: Cortex P1 CASTxB6 Cell 101


title: Cortex P56 CASTxB6 Cell 117


title: Mll3-/-Mll4f/f_SS18_Cre_D-3

value: BAT isolated brown preadipocytes


title: Cortex P1 CASTxB6 Cell 106


title: Cortex P56 CASTxB6 Cell 114


title: Cortex P1 CASTxB6 Cell 105


title: Cortex P1 CASTxB6 Cell 100


title: Cortex P1 CASTxB6 Cell 099


title: Cortex P56 CASTxB6 Cell 115


title: HCT116, chronic hypoxia with FAO inhibition followed by acute hypoxia

description: gene expression after culture


title: CRPC4


title: CRPC3


title: CRPC9


title: CRPC8


title: Cortex P56 CASTxB6 Cell 113


title: Cortex P1 CASTxB6 Cell 097


title: Cortex P1 CASTxB6 Cell 102


title: HCT116, chronic normoxia without FAO inhibition

description: gene expression after culture

value: chronic normoxia without FAO inhibition


title: Cortex P56 CASTxB6 Cell 106


title: HCT116, chronic normoxia with FAO inhibition followed by acute hypoxia

description: gene expression after culture


title: Cortex P56 CASTxB6 Cell 111


title: CRPC7


title: FGF13Aoe rep 2 [RNA-seq]

city: Shanghai

first: Qiaoqiao

last: Yang

address: 320 Yue Yang Road

department: Institute of Neuroscience

country: China

institute: Chinese Academy of Sciences

description: 017 OE2 STAR_outReadsPerGene.out.tab

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence. Index of the reference genome was built using STAR, alignment of paired-end clean reads to the reference genome and counting reads umbers mapped to each gene were performed using STAR
DESeq2 online (https://usegalaxy.org/) was used to estimate normalized counts for known transcripts and analyze differentially expressed transcripts. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include normalize values for each Sample

source_name: Hippocampus

growth_protocol: The hippocampus Tissue was microdissected out from neonatal mouse followed by digestion in 0.01% (wt/vol) trypsin-EDTA buffer and then dissociation into single cells. The isolated cells from one mouse were plated into 2 wells of a 12-well tissue culture plate contains Dulbecco's modified Eagle medium (DMEM)/nutrient mixture F12 (F12), supplemented with B27, 20 ng/ml of FGF-2 and 20 ng/ml EGF. Change half of the medium every other day and the neurospheres were harvested on the seventh day.

extract_protocol:
The neurospheres were harvested using Trizol reagent.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following manufacture's recommendations.

value: neural progenitor cells

value: Hippocampus

tag: genotype

value: hGFAPCre+, ROSA26FGF13A LSL/+


title: FGF13Aoe rep 1 [RNA-seq]

description: 016 OE1 STAR_outReadsPerGene.out.tab


title: HCT116, chronic normoxia with FAO inhibition

description: gene expression after culture

value: chronic normoxia with FAO inhibition


title: Cortex P56 CASTxB6 Cell 105


title: HCT116, chronic normoxia without FAO inhibition followed by acute hypoxia

description: gene expression after culture


title: CRPC6


title: Cortex P56 CASTxB6 Cell 110


title: Control  rep 2 [RNA-seq]

description: 015 con STAR_outReadsPerGene.out.tab

value: hGFAPCre+, ROSA26FGF13A +/+


title: treatment-naive24

source_name: treatment-naïve prostate cancer patient


title: Cortex P56 CASTxB6 Cell 112


title: Cortex P56 CASTxB6 Cell 109


title: CRPC5


title: Control rep 1 [RNA-seq]

description: 011 con1 STAR_outReadsPerGene.out.tab


title: Cortex P56 CASTxB6 Cell 103


title: Cortex P56 CASTxB6 Cell 107


title: Cortex P1 CASTxB6 Cell 098


title: Cortex P1 CASTxB6 Cell 094


title: HCT116, chronic hypoxia without FAO inhibition followed by acute hypoxia

description: gene expression after culture


title: Cortex P56 CASTxB6 Cell 102


title: CRPC2


title: CRPC1


title: treatment-naive23


title: Cortex P1 CASTxB6 Cell 096


title: treatment-naive20


title: Cortex P56 CASTxB6 Cell 101


title: Cortex P56 CASTxB6 Cell 104


title: Cortex P1 CASTxB6 Cell 095


title: Cortex P56 CASTxB6 Cell 108


title: Cortex P56 CASTxB6 Cell 100


title: Cortex P1 CASTxB6 Cell 093


title: Cortex P1 CASTxB6 Cell 090


title: treatment-naive22


title: Cortex P1 CASTxB6 Cell 092


title: treatment-naive21


title: treatment-naive18


title: Cortex P1 CASTxB6 Cell 091


title: cultured organoids (CTOS, Cerv61)

city: Kyoto

first: Masahiro

last: Inoue

state: Kyoto

address: Med-Pharm Collaboration Bldg 503, Shimoadachi-cho 46, Sakyou-ku, Kyoto, 606-8304, Japan

institute: Kyoto Univ Graduate School of Medicine

description: Gene expression

hyb_protocol: 0.6ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Ver.2.0 Microarray (Agilent, G4851B) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 or 12.0.3.1 (Agilent) using default parameters (FE10.7.3.1 with protocol: GE1_107_Sep09 and grid: 039494_D_F_20120411, FE12.0.3.1 with protocol: GE1_1200_Jun14 and grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cultured organoids (CTOS, Cerv61)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the Low Input Quick Amp Labeling Kit (Agilent, 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: CTOSs were cultured in Matrigel in StemPro hESC SFM (Life Technologies, Carlsbad, CA).

extract_protocol: Total RNA was extracted from CTOSs with TRIzol reagent (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: no treatment

value: cultured organoids (CTOS)

tag: chemosensitivity


title: Cortex P56 CASTxB6 Cell 098


title: treatment-naive17

value: plasma


title: Cortex P56 CASTxB6 Cell 099


title: Cortex P1 CASTxB6 Cell 088


title: Cortex P56 CASTxB6 Cell 097


title: treatment-naive19

value: exosome


title: treatment-naive16


title: Cortex P1 CASTxB6 Cell 086


title: Cortex P56 CASTxB6 Cell 096


title: Cortex P1 CASTxB6 Cell 085


title: Cortex P1 CASTxB6 Cell 087


title: treatment-naive13


title: treatment-naive15


title: Cortex P1 CASTxB6 Cell 084


title: treatment-naive12


title: Cortex P56 CASTxB6 Cell 095


title: cultured organoids (CTOS, Cerv60)

description: Gene expression

source_name: cultured organoids (CTOS, Cerv60)


title: Cortex P56 CASTxB6 Cell 094


title: cultured organoids (CTOS, Cerv54)

description: Gene expression

source_name: cultured organoids (CTOS, Cerv54)


title: cultured organoids (CTOS, Cerv59)

description: Gene expression

source_name: cultured organoids (CTOS, Cerv59)


title: Cortex P1 CASTxB6 Cell 082


title: treatment-naive11


title: treatment-naive14


title: Cortex P56 CASTxB6 Cell 091


title: S3_WT-mitoRNA

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
QC performed usinf fastQC
Trmming applied using Cutadapt
Alignment performed using Bowtie2
samtools stats used to calculated mismatches and error rates
bcftools view and vcfutils.pl varFilter was used to generate dinucleotide transitions and transversions
The error rate calculation was performed using the CirSeq pipeline developed by Gout et al., 2017 (PMID:29062891)
Genome_build: Drosophila melanogster (DM6)
Supplementary_files_format_and_content: Tab delimited Gene Counts (chrM.gene.counts.txt) and error rate (*errors.txt, *coverages.txt)

organism: Drosophila melanogaster

source_name: Wild type mitochondria

extract_protocol:
Whole adult fly mitochondria were extracted and mitochondrial RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total mitochodnrial RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type RNA polymerase overexpression

value: Two weeks old

tag: molecule subtype

value: Total mitochondrial RNA


title: cultured organoids (CTOS, Cerv9)

description: Gene expression

source_name: cultured organoids (CTOS, Cerv9)


title: cultured organoids (CTOS, Cerv46)

description: Gene expression

source_name: cultured organoids (CTOS, Cerv46)


title: Cortex P56 CASTxB6 Cell 090


title: cultured organoids (CTOS, Cerv21)

description: Gene expression

source_name: cultured organoids (CTOS, Cerv21)


title: Cortex P1 CASTxB6 Cell 089


title: cultured organoids (CTOS, Cerv39)

description: Gene expression

source_name: cultured organoids (CTOS, Cerv39)


title: Cortex P56 CASTxB6 Cell 093


title: Cortex P1 CASTxB6 Cell 079


title: S4_E423P-mitoRNA

source_name: E423P mitochondria

value: E423P RNA polymerase overexpression


title: Cortex P56 CASTxB6 Cell 092


title: Cortex P1 CASTxB6 Cell 081


title: Cortex P1 CASTxB6 Cell 083


title: treatment-naive8


title: treatment-naive10


title: Cortex P56 CASTxB6 Cell 087


title: Cortex P1 CASTxB6 Cell 080


title: Cortex P56 CASTxB6 Cell 088


title: Cortex P1 CASTxB6 Cell 077


title: treatment-naive6


title: cultured organoids (CTOS, Cerv8)

description: Gene expression

source_name: cultured organoids (CTOS, Cerv8)


title: Cortex P56 CASTxB6 Cell 089


title: Cortex P56 CASTxB6 Cell 086


title: treatment-naive9


title: CD14+ monocytes, healthy nondiabetic control, replicate 4 [G254]

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.54.1).

label: biotin

source_name: CD14+ monocytes, isolated from peripheral blood mononuclear cells obtained from a healthy nondiabetic control subject

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: For this transcriptome profiling study, 5 patients with T1D and 5 healthy nondiabetic control subjects carefully matched for age, sex and BMI were included. Patients included in the study were diagnosed with T1D at least 10 years ago and were recruited from the outpatient clinic of the Radboud University Medical Center (Radboudumc) Nijmegen. Participants provided written informed consent before start of the study.

extract_protocol: RNA was isolated using Qiagen RNeasy Micro Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by dilution of blood with pyrogen-free PBS and differential density centrifugation over Ficoll-Plaque gradient media (GE Healthcare, Eindhoven, The Netherlands). PBMCs were purified to CD14+ monocytes using indirect magnetic labelling (Miltenyi Biotec B.V., Leiden, The Netherlands), and used for RNA isolation.

tag: disease

value: healthy nondiabetic control

value: CD14+ monocytes


title: cultured organoids (CTOS, Cerv5)

description: Gene expression

source_name: cultured organoids (CTOS, Cerv5)


title: CD14+ monocytes, healthy nondiabetic control, replicate 5 [G254]


title: treatment-naive7


title: treatment-naive5


title: Cortex P1 CASTxB6 Cell 075

source_name: cortex

value: cortex


title: Cortex P1 CASTxB6 Cell 078


title: CD14+ monocytes, healthy nondiabetic control, replicate 3 [G254]


title: treatment-naive4


title: Cortex P56 CASTxB6 Cell 084


title: Cortex P56 CASTxB6 Cell 085


title: treatment-naive3


title: Cortex P1 CASTxB6 Cell 076


title: Cortex P1 CASTxB6 Cell 074


title: treatment-naive2


title: Cortex P1 CASTxB6 Cell 073


title: Cortex P1 CASTxB6 Cell 072


title: Cortex P1 CASTxB6 Cell 071


title: Cortex P56 CASTxB6 Cell 082


title: Cortex P56 CASTxB6 Cell 081


title: treatment-naive1


title: Cortex P56 CASTxB6 Cell 080


title: HeLa Wild Type AQ-seq 1

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: small RNA-seq

data_processing:
FASTQ files were generated by base-calling using Illumina RTA (v1.18) and conversion using bcl2fastq (v1.8.4).
The TruSeq 3′ adapter sequence was removed using cutadapt. For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Preprocessed reads were first aligned to the spike-in sequences by BWA with an option of -n 3. Reads mapped to spike-in sequences perfectly or with a single mismatch were considered as reliable spike-in reads.
Reads unmapped to spike-in sequences by BWA with an option of -n 3 were subsequently mapped to the human genome (hg38) with the same option. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values (tsv) files containing miRNA names and corresponding read counts.

source_name: HeLa

growth_protocol: HEK293T and HeLa cells were grown in DMEM media (Welgene) supplemented with 10% FBS (Welgene).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Total RNA was mixed with thirty synthetic miRNA-like spike-in oligos. The RNA mixture was size-fractionated by 15% urea-polyacrylamide gel electrophoresis to enrich miRNA species. Small RNA libraries were constructed using either TruSeq small RNA library preparation kit (Illumina) according to manufacturer's instructions or AQ-seq as follows: miRNA-enriched RNA was ligated to 3′ randomized adapter with 20% PEG 8000, then ligated to 5′ randomized adapter with 20% PEG 8000, reverse-transcribed, and amplified. The cDNA was sequenced using a HiSeq 2500 platform.

value: HeLa


title: CD14+ monocytes, healthy nondiabetic control, replicate 2 [G254]


title: Cortex P56 CASTxB6 Cell 083


title: CD14+ monocytes, T1D patient, replicate 5 [G254]

source_name: CD14+ monocytes, isolated from peripheral blood mononuclear cells obtained from a patient with type 1 diabetes

value: T1D patient


title: CD14+ monocytes, T1D patient, replicate 3 [G254]


title: ShZc3h10 2

city: Milan

first: Nico

last: Mitro

state: MI

address: Via Balzaretti 9

department: Pharmacological and biomolecular sciences

country: Italy

institute: Università degli studi di Milano

data_processing:
Adapter Trimming using bbduk.sh e.g. "bbduk.sh -Xmx1g threads=7 in=<<Sample.fastq>> out=<<Sample.trim.fastq>> ref=<<adapters.fa>> ktrim=r k=28 mink=13 hdist=1 tbo "
Mapping to reference mm10 using ncbiRefSeqCurated annotation 2017-11-16 e.g. "tophat2 -p 4 -G <<Refseq_Curated>> -o <<Sample_name>> --max-multihits 2 --b2-very-sensitive <<Bowtie2_Index>> <<Sample.fastq>>"
Select uniquely mapped reads e.g. "samtools view -h -F 4 <<accepted_hits.bam>> | grep -v "NH:i:2" | samtools view -b -S -"
Remove ENCODE black list reagions using the Boyle lab list https://github.com/Boyle-Lab/Blacklist e.g. "bedtools intersect -a <<Aligned.bam>> -b <<Encode_black.list.bed>> -v > <<Cleaned_Sample.bam>>"
Creationof strand specific BigWig e.g. "bamCoverage -p 20 -bs 1 --scaleFactor <<Precomputed_scale_factor>> --filterRNAstrand <<forward or Reward>> -b <<Sample.bam>> -o <<Out_folder>>"
Genome_build: mm10
Supplementary_files_format_and_content: .bw are BigWig normalised files
Supplementary_files_format_and_content: .bam are BAM format files

source_name: C3H10T1/2 preadipocytes

growth_protocol: Cells were grown in DMEM high glucosesuppemented with 10% FBS, 1% Pen/Strep, 1% Gln

extract_protocol:
For preparation of 4sU-RNAseq libraries from Scramble and ShZc3h10 36h differentiated pradipocytes. 4-thiouridine (4sU, T4509 Sigma-Aldrich) was added to the medium at a final concentration of 300uM for 10 min. before harvesting. The labeled RNA was isolated and processed as described (Austenaa et al., 2015). The nascent 4sU-labelled RNA was extracted from 50 ug of total TRIZOL-isolated RNA.
100-200 ng of the isolated nascent 4sU-labelled RNA was used for cDNA-library synthesis using the QIAseq Stranded  Total RNA Library Kit (Qiagen).

treatment_protocol: Cells were transduced 24h after congluency and induced to differentiate with DMIR cocktail (Dexamethasone 2µg/ml, 3-isobutyl-1-methylxanthine (IBMX) 0.5mM, insulin 5µg/ml and rosiglitazone 5µM)

value: Mesenchymal stem cells

tag: passage

tag: differentiated

value: Adipocytes

tag: transduced


title: ShZc3h10 1


title: ShZc3h10 3


title: Cortex P1 CASTxB6 Cell 070


title: Cortex P56 CASTxB6 Cell 079


title: CD14+ monocytes, T1D patient, replicate 2 [G254]


title: Scramble 4

value: scramble


title: CD14+ monocytes, healthy nondiabetic control, replicate 1 [G254]


title: Cortex P1 CASTxB6 Cell 069


title: Cortex P56 CASTxB6 Cell 078


title: D3_p-IFNg

first: Alice

last: Muglia Thomaz da Silva Amancio

address: Building 33, room 1W10.A3

department: Immunobiology Section

institute: National Institutes of Health (NIH)

scan_protocol: Sample Cartridges are placed in the Digital Analyzer for data collection. Color codes on the surface of the cartridge are counted and tabulated for each target molecule. The cartridge was read with maximum sensitivity (280 FOV).  The data produced by the nCounter Digital Analyzer are exported as a Reporter Code Count (RCC) file.

data_processing: Data collection is performed using epifluorescence microscopy and CCD capture technology on an nCounter instrument to yield hundreds of thousands of target molecule counts. Digital images are processed within the nCounter instrument, and the Reporter Probe counts are tabulated in a comma-separated value (CSV) format or RCC file for downstream data analysis with NanoString’s nSolverTM Analysis Software.

source_name: Monocytes

growth_protocol: Cultures were performed in RPMI 1640 medium (Life Technologies, Carlsbad, CA) supplemented with 10 % heat-inactivated FCS (HyClone, South Logan, UT), 4 mM L-glutamine, 10 mM HEPES, 1 mM sodium pyruvate, 0.1 mM MEM nonessential amino acids, 100 U/ml penicillin, 100 ug/ml streptomycin (Life Technologies), 100 mg/ml streptomycin, and 50 mM 2-ME (MilliporeSigma, Rockville, MD). Monocytes were plated at 2 x 105/0.1ml in 96-well plates (cytokine measurements) or 0.5 ml in 12-well plates (RNA analysis)

extract_protocol: Total RNA was extracted from monocytes cultured for 8 hours with or without IFN-g by adding Trizol reagent (Life Technologies) and employing the Direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions.

treatment_protocol: Cells were either kept in media or primed with IFN-g (10ng/mL) for 8 hours prior to RNA extraction

value: Peripheral blood

tag: donor

tag: monocyte subset

tag: ifn-g priming

value: Yes


title: Cortex P1 CASTxB6 Cell 068

tag: tissue

tag: age


title: CD14+ monocytes, T1D patient, replicate 1 [G254]

tag: cell type


title: HeLa Wild Type AQ-seq 2

description: small RNA-seq


title: Scramble 3


title: Cortex P56 CASTxB6 Cell 077

tag: strain


title: D3_p

value: No


title: Cortex P56 CASTxB6 Cell 076


title: Cortex P1 CASTxB6 Cell 067


title: 06.HiC.NPC.5uM.r2

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

data_processing:
Base call by bcl2fastq v. 2.17
fastq files were mapped to mm10 genome assembly with bwa
hic files were generated with Hiccup
Genome_build: mm10
Supplementary_files_format_and_content: HiC files to show chromain contact matrices using Juicebox
Supplementary_files_format_and_content: bedpe files with genomic coordinates of chromatin contact loops

source_name: NPC cultured in NPEM (5 uM CHIR) for 24 hrs

growth_protocol: NPEM (Brown et al., 2015)

extract_protocol:
Cortex of mouse embryonic kidneys were dissociaed and nephron progenitor cells (NPCs) were purified with MACS (Brown et al., 2015). Nuclei was prepared as described (Buenrostro et al., 2015).
Library construction protocol: Rao et al., 2014 Cell

value: cultured nephron progenitor cells (NPCs)

tag: developmental stage

value: 16.5 days

value: Swiss Webster


title: D3_n


title: Cortex P56 CASTxB6 Cell 073


title: Cortex P56 CASTxB6 Cell 074


title: Cortex P1 CASTxB6 Cell 066


title: 05.HiC.NPC.5uM.r1


title: 04.HiC.NPC.1.25uM.r2

source_name: NPC cultured in NPEM (1.25 uM CHIR) for 24 hrs


title: Cortex P56 CASTxB6 Cell 070


title: D3_n-IFNg


title: RNA.NPC.5uM.r3

description:
RNA_NPC_24hr_5uM_r3
RNASeq.transcripts.NPC_1.25uM-vs-NPC_5uM.xlsx

data_processing:
Base call by bcl2fastq v. 2.17
Fastq files were aligned using TopHat2.
TPM values were calculated with Partek E/M distributed on Partekflow (http://www.partek.com/partek-flow/)
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with TPM values

molecule: polyA RNA

extract_protocol:
Cortex of mouse embryonic kidneys were dissociated and nephron progenitor cells (NPCs) were purified with MACS (Brown et al., 2015).
Kapa stranded mRNA-Seq library (#KK8420)

value: nephron progenitor cells (NPCs)


title: Cortex P1 CASTxB6 Cell 064


title: Cortex P1 CASTxB6 Cell 065


title: D2_n


title: D2_p


title: Cortex P1 CASTxB6 Cell 063


title: Cortex P1 CASTxB6 Cell 060


title: Cortex P56 CASTxB6 Cell 072


title: Cortex P1 CASTxB6 Cell 062


title: 03.HiC.NPC.1.25uM.r1


title: Cortex P1 CASTxB6 Cell 061


title: D2_n-IFNg


title: 02.HiC.NPC.r2

source_name: primary NPC

value: primary nephron progenitor cells (NPCs)


title: 01.HiC.NPC.r1


title: RNA.NPC.5uM.r2

description:
QG180806RNA08.NPC.5uM.r2
RNASeq.transcripts.NPC_1.25uM-vs-NPC_5uM.xlsx


title: CD14+ monocytes, T1D patient, replicate 4 [G254]


title: Cortex P56 CASTxB6 Cell 071


title: D1_p-IFNg


title: D1_n-IFNg


title: Cortex P56 CASTxB6 Cell 067


title: D1_n


title: RNA.NPC.1.25uM.r3

description:
QG180806RNA06.NPC.1.25uM.r3
RNASeq.transcripts.NPC_1.25uM-vs-NPC_5uM.xlsx
RNASeq.transcripts.NPC_1.25uM-vs-NPC_0uM.xlsx
RNASeq.transcripts.NPC_1.25uM-vs-NPC.xlsx


title: Cortex P56 CASTxB6 Cell 069


title: Hi-C, primary Naïve CD4+ T cells

city: Manchester

first: chenfu

last: shi

address: AV Hill Building, Upper Brook Street, room 1.023

institute: the university of manchester

description: 3 Biological replicates combined in one sample

data_processing:
The sequencing data was filtered and adapters were removed using fastp v0.19.4 (S. Chen et al., 2018). The reads were then mapped to the GRCh38 genome with Hi-C Pro v2.11.0 (Servant et al., 2015), using default settings. The Hi-C interaction matrices were normalised within Hi-C Pro using iterative correction and eigenvector decomposition (ICE). TADs were identified using OnTAD v1.2 (An et al., 2019), a novel Optimized Nested TAD caller for Hi-C data, using Hi-C data binned at a 40 kb resolution and a maximum TAD size of 4 mb. Files for visualisation were created using the hicpro2juicebox.sh utility and visualised in Juicebox (Durand et al., 2016).
Sequencing data for the HiChIP libraries was filtered and the adapters were removed using fastp v0.19.4 (S. Chen, Zhou, Chen, & Gu, 2018). The reads were then mapped to the GRCh38 genome with Hi-C Pro v2.11.0 (Servant et al., 2015), using default settings. Enriched regions (H3K27ac peaks) were identified using HiChIP-peaks v 0.1.1 (Shi, Rattray, & Orozco, 2019) with default settings and FDR < 0.01. Loops were identified using FitHiChIP (Bhattacharyya, Chandra, Vijayanand, & Ay, 2019) using the following settings: Coverage normalization, stringent background with merging enabled, peaks generated from HiChIP-peaks and 5 kb bin size.
RNA-seq: Reads were quality trimmed using Trimmomatic v0.38 using a sliding window of 5 with a mean minimum quality of 20. Adapters and poly A/poly G tails were removed using Cutadapt v1.18 and then UMIs were extracted from the 5’ of the reads using UMI-tools v0.5.5. Reads were then mapped using STAR v2.5.3a on the GRCh38 genome with GENCODE annotation v29. Reads were de-duplicated using UMIs with UMI-tools and then counted using HTSeq v0.11.2. Count matrixes were analysed in R 3.5.1 and normalisation and differential expression analysis was conducted using DESeq2 v1.22.2.
Genome_build: hg38
HiC/*.hic files: Hi-C files for juicebox
HiC/OnTAD*.bed.gz: TAD calls from OnTAD
HiChIP/*WashU.bed.gz: washu files containing significant interactions from FitHiChIP
HiChIP/*peaks.bed peak calls from HiChIP-peaks
HiChIP/*bedgraph.bdg HiChIP enrichment signal from HiChIP-peaks
RNA/DEgenes_HAC_STvsUNST.csv: DESeq2 results from contrast HaCaT stimulated vs unstimulated
RNA/hacat_myla_norm_counts.csv: Normalized counts from DESeq2 with all samples

source_name: Primary Naïve CD4+ T cells

growth_protocol: PBMCs were isolated from a buffy coat using a ficoll gradient. T-cells were isolated using an EasySep T-cell isolation kit according to the manufacturer's instructions.

extract_protocol:
Hi-C libraries were generated using the Arima Hi-C kit following manufacture's instructions.
Sequencing was performed on a NovaSeq platform with 150bp paired end reads at a target depth of 300 million reads per sample.

treatment_protocol: 3 million cells were fixed with 2% formaldehyde for 10 minutes. Fixation was quenched by the addition of cold 1M glycine to a final concentration of 0.125M. Pelleted cells were frozen on dry ice and stored at -80C.

value: Primary Naive CD4+ T cells

tag: stimulation

tag: restriction enzyme

value: Arima


title: Cortex P1 CASTxB6 Cell 056


title: Cortex P56 CASTxB6 Cell 066


title: Cortex P1 CASTxB6 Cell 057


title: D1_p


title: Cortex P56 CASTxB6 Cell 065


title: RNA.NPC.1.25uM.r1

description:
QG180806RNA04.NPC.1.25uM.r1
RNASeq.transcripts.NPC_1.25uM-vs-NPC_5uM.xlsx
RNASeq.transcripts.NPC_1.25uM-vs-NPC_0uM.xlsx
RNASeq.transcripts.NPC_1.25uM-vs-NPC.xlsx


title: Cortex P1 CASTxB6 Cell 059


title: Cortex P1 CASTxB6 Cell 058


title: D2_p-IFNg


title: RNA.NPC.0uM.r3

description:
QG180806RNA03.NPC.0uM.r3
RNASeq.transcripts.NPC_1.25uM-vs-NPC_0uM.xlsx

source_name: NPC cultured in NPEM (0 uM CHIR) for 24 hrs


title: Cortex P56 CASTxB6 Cell 068


title: Cortex P1 CASTxB6 Cell 054


title: RNA.NPC.1.25uM.r2

description:
QG180806RNA05.NPC.1.25uM.r2
RNASeq.transcripts.NPC_1.25uM-vs-NPC_5uM.xlsx
RNASeq.transcripts.NPC_1.25uM-vs-NPC_0uM.xlsx
RNASeq.transcripts.NPC_1.25uM-vs-NPC.xlsx


title: Cortex P1 CASTxB6 Cell 055


title: Cortex P56 CASTxB6 Cell 063


title: Cortex P56 CASTxB6 Cell 064


title: BP1664855 Chromatin Interaction Calls

city: Mississauga

first: James

middle: R

last: Hawley

state: Ontario

address: 7070 Mississauga Road

department: Computational Sciences

institute: Roche Canada

data_processing:
Paired-end Hi-C FASTQ files were pre-processed with HiCUP (v0.7.2). Reads were truncated at MboI ligation junction sites prior to alignment with `hicup_digester`. Each mate was independently aligned to the hg38 genome and were then paired and assigned to MboI restriction sites by `hicup_map`. `hicup_map` uses Bowtie2 (v2.3.4) as the underlying aligner which has the following parameters: `--very-sensitive --no-unal --reorder`. Reads that reflect technical artefacts were filtered out with `hicup_filter`. Duplicate reads were removed with `hicup_deduplicator`. Reads that came from different sequencing batches were then aggregated for each tumour sample at this stage using `sambamba merge` (v0.6.9).
Aggregated Hi-C binary alignment map (BAM) files were converted to the pairs format using pairtools (v0.2.2) and then the cooler format using the cooler package (v0.8.5). The pairs files were generated with the following command: `pairtools parse -c {genome} --assembly hg38 -o {output_pairs} {input_bam}`. The cooler files were generated at an initial matrix resolution of 1000 bp with the following command: `cooler cload pairs --assembly hg38 -c1 2 -p1 3 -c2 4 -p2 5 {genome}:1000 {input_pairs} {output_cooler}`. The raw contact matrices stored in the cooler file format were balanced using cooler’s implementation of the ICE algorithm using the `cooler balance` command. Contact matrices at different resolutions were created with the `cooler zoomify` command.
Contact matrices were binned at a resolution of 40 kbp. To remove sequencing depth as a confounding factor, contact matrices for all samples were first downsampled to match the sequencing depth of the shallowest sample. For comparisons only involving primary samples, this was 300x10^6 contacts. This was achieved with Cooltools (v0.3.2) with the following command: `cooltools random-sample -c 120000000 {input}::/resolutions/40000 {output}`. TADs were identified using TopDom on the downsampled, ICE-normalized contact matrices. To identify domains at multiple length scales, similar in concept to Artamus’ gamma parameter, TopDom was run multiple times per sample, with the window size parameter set at values between 3 and 40, inclusive (corresponding to 120 kbp and 1.6 Mbp). The lower bound for the window size parameter allowed for the identification of domains multiple megabases in size at the upper end and domains < 100 kbp at the lower end without being dominated by false calls due to sparsity of the data. Given the stochasticity of Hi-C sequencing, boundaries called at one window size may not correspond to the exact same location at a different window size. To attempt to resolve these different boundary calls and leverage power from multiple window sizes, boundaries for a given patient were considered at all window sizes. Boundaries within one bin (40 kbp) of each other and called at  different window sizes were marked as conflicting calls. If only two boundaries were in conflict and all the window sizes where the first boundary was called are smaller than the window sizes where the second boundary was called, the second boundary was selected since larger smoothing windows are less sensitive to small differences in contact counts. If only two boundaries were in conflict but there is no proper ordering of the window sizes, the boundary that was identified most often between the two was selected. If three boundaries are in conflict, the middle boundary was selected. If four or more boundaries were in conflict, the boundary that was identified most often was selected. To determine the maximum window size for TAD calls, TAD calls were compared across window sizes for the same patient using the BPscore metric. TAD calls are identical when the BPscore is 0, and divergent when 1. The cut-off window size for a single patient was determined when the difference between TAD calls at consecutive window sizes was < 0.005, twice in a row. The maximum window size was determined by the maximum window size cut-off across all samples in a comparison. For comparisons involving only primary samples, the maximum window size was determined to be w = 20 x 40 kbp. The persistence of a TAD boundary was calculated as the number of window sizes where this region was identified as a boundary.
Chromatin interactions were identified in all 17 primary samples with Mustache. Using the Cooler files from above, Mustache was run on the ICE-normalized 10 kbp contact matrix for each chromosome with the following command: `mustache -f {input} -r 10000 -ch {chromosome} -p 8 -o {output}`. Interaction calls on each chromosome were merged for each sample to create a single table of interaction calls across the entire genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: TAD calls: tab-delimited BED format. Columns: chr, start, end, persistence_left, persistence_right, domain type, window size
Supplementary_files_format_and_content: Chromatin interaction calls: tab-delimited BEDPE format. Columns: chr_from, start_from, end_from, chr_to, start_to, end_to, interaction_ID, anchor_from_ID, anchor_to_ID, detection_scale, FDR

source_name: Primary prostate benign, Hi-C

extract_protocol:
Phenol-chloroform extraction columns were spun down at 17,000 x g for 1 minute at 4°C to get gel down to the bottom of the tube. The samples incubated overnight were then added to the column. Next, an equal volume (~325 µL) of phenol-chloroform-isoamyl alcohol mixture (25:24:1) (Sigma) was also added to the column. The column was then inverted for thorough mixing and spun down at 17,000 x g for 5 minutes at 4 °C. The surface layer on top of the gel upon spinning contains the sample and is transferred to a clean 1.5 mL tube (~325 µL). Each sample was mixed with 31.5 µL of 3M sodium acetate, 2 µL of GlycoBlue (ThermoFisher Scientific), and 504 µL of 100% ethanol for DNA precipitation. The samples were inverted several times for mixing and incubated at -80 °C for 20 minutes, followed by a centrifuge spin at 17,000 x g for 45 minutes at 4 °C. The supernatant was carefully discarded and the pellet was washed with 800 µL of ice-cold 70% ethanol followed by a centrifuge spin at 17,000 x g for 5 minutes at 4 °C. The supernatant was then discarded and the tube was air-dried until no traces of ethanol was left prior to dissolving the DNA pellet with 30 µL of Elution Buffer (Qiagen PCR Clean-Up Kit). 1 µL of RNase A (ThermoFisher Scientific) was added to each sample followed by incubation at 37 °C for 15 minutes. A mix of 5 µL of 10X NEB2.1 buffer (New England Biolabs), 1.25 µL of 1 mM dATP, 1.25 µL of 1 mM dCTP, 1.25 µL of 1 mM dGTP, 1 mM of dTTP, 0.5 µL of 10 mg/mL BSA, 5 µL of water, 3.5 µL of 3 U/µL T4 DNA Polymerase (New England Biolabs) was added to each sample. The samples were mixed thoroughly by gentle pipetting, and then incubated at 20 °C for 4 hours.
The beads containing the Hi-C samples were separated on a magnetic rack to remove the supernatant. The beads were then resuspended in a total volume of 10 µL for library preparation using the SMARTer ThruPLEX DNA-seq library preparation kit (Takara Biosciences) per manufacturer’s protocol with an adjustment on the last step, a PCR reaction for library amplification. Upon reaching that step, the reaction was carried out on a regular PCR for two cycles to amplify the Hi-C samples off the streptavidin beads. Next, the samples were transferred onto a new tube where 20X SYBR was added. The samples were then subject to real-time qPCR and pulled out from the qPCR machine mid-exponential phase. Ultimately, this is done to reduce PCR duplication rates, a huge limitation for low-input Hi-C protocols. The Hi-C libraries were then double size-selected for 300-700 bp using Ampure XP beads and sent for BioAnalyzer analysis prior to sequencing.

value: primary prostate benign


title: RNA.NPC.0uM.r2

description:
QG180806RNA02.NPC.0uM.r2
RNASeq.transcripts.NPC_1.25uM-vs-NPC_0uM.xlsx


title: BP3320942 Chromatin Interaction Calls


title: BP3330581 Chromatin Interaction Calls


title: BP1595983 Chromatin Interaction Calls


title: Cortex P1 CASTxB6 Cell 053

value: cortex


title: RNA.NPC.5uM.r1

description:
QG180806RNA07.NPC.5uM.r1
RNASeq.transcripts.NPC_1.25uM-vs-NPC_5uM.xlsx


title: Cortex P56 CASTxB6 Cell 062


title: Cortex P1 CASTxB6 Cell 052


title: RNA.NPC.0uM.r1

description:
QG180806RNA01.NPC.0uM.r1
RNASeq.transcripts.NPC_1.25uM-vs-NPC_0uM.xlsx


title: Cortex P1 CASTxB6 Cell 051


title: BP1648133 Chromatin Interaction Calls


title: Cortex P1 CASTxB6 Cell 050


title: Cortex P56 CASTxB6 Cell 061


title: RNA.cortex.r3

description:
NPC_RNA06_20160526
RNASeq.transcripts.NPC-vs-NFC.xlsx
NFC

source_name: kidney cortical cells depleted of NPC (NFC)

value: kidney cortical cells


title: CPCG0345 Chromatin Interaction Calls

source_name: Primary prostate tumour, Hi-C

value: primary prostate cancer


title: Cortex P56 CASTxB6 Cell 059


title: RNA.cortex.r2

description:
NPC_RNA05_20160526
RNASeq.transcripts.NPC-vs-NFC.xlsx
NFC


title: Cortex P56 CASTxB6 Cell 060


title: CPCG0365 Chromatin Interaction Calls


title: Cortex P1 CASTxB6 Cell 049


title: RNA.cortex.r1

description:
NPC_RNA04_20160526
RNASeq.transcripts.NPC-vs-NFC.xlsx
NFC


title: CPCG0331 Chromatin Interaction Calls


title: Cortex P56 CASTxB6 Cell 057


title: Cortex P1 CASTxB6 Cell 048


title: CPCG0339 Chromatin Interaction Calls


title: RNA.NPC.r2

description:
NPC_RNA02_20160526
RNASeq.transcripts.NPC-vs-NFC.xlsx
RNASeq.transcripts.NPC_1.25uM-vs-NPC.xlsx


title: CPCG0336 Chromatin Interaction Calls


title: RNA.NPC.r3

description:
NPC_RNA03_20160526
RNASeq.transcripts.NPC-vs-NFC.xlsx
RNASeq.transcripts.NPC_1.25uM-vs-NPC.xlsx


title: RNA.NPC.r1

description:
NPC_RNA01_20160526
RNASeq.transcripts.NPC-vs-NFC.xlsx
RNASeq.transcripts.NPC_1.25uM-vs-NPC.xlsx


title: Cortex P56 CASTxB6 Cell 056


title: Cortex P1 CASTxB6 Cell 046


title: 60.NPC.input.r2.sorted

data_processing:
Base call by bcl2fastq v. 2.17
Fastq files were aligned using Bowtie 2.
Aligned reads were sorted with samtools (Li et al., 2009).
Duplicate reads were removed with Picard (http://broadinstitute.github.io/picard/index.html).
ChIP-Seq peaks were called using MACS2 (Feng et al., 2012).
wig profiles were generated using QuEST
Genome_build: mm10
Supplementary_files_format_and_content: wiggle files represents ChIP-Seq tags; peak files are available in tar archive on series record.

extract_protocol:
Cortex of moue embryonic kidneys were dissociated and nephron progenitor cells (NPCs) were purified with MACS (Brown et al., 2015). NPCs were fixed in AutoMACS running buffer with 1% formaldeyde for 30 min in room temperature. Chromatin was extracted with SimpleChIP® Sonication Cell and Nuclear Lysis Buffers (Cell Signaling Technology #81804) following manufacturer’s instruction. Sonicated chromatin was immuno-precipitated with the indicated antibodies. The precipitated DNA was subsequently collected with Qiagen minElute reaction cleanup kit (Qiagen, #28204).
Libraries were constructed using ThruPLEX-FD Prep Kit (Clontech, # R400523), and subsequently sequenced by Illumina NextSeq 500.

value: nephron progenitor cells

tag: chip antibody


title: Cortex P56 CASTxB6 Cell 055

extract_protocol: [Isolation of cell nuclei] Cell nuclei were isolated based on protocols from (Krishnaswami et al., 2016; Lacar et al., 2016) with minor modifications. In particular, Tris buffer would react with formaldehyde, and was therefore substituted with equal molarity of HEPES buffer. See details below:  Cortex and hippocampus were dissected in ice-cold PBS, and placed in 2 mL nuclei isolation medium with Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT, 0.1% Triton X-100) in a 2 mL Dounce homogenizer (Sigma D8938). Note that DTT concentration was not specified in (Krishnaswami et al., 2016); here we used 1 uM from (Lacar et al., 2016).  Tissues were homogenized with 5 strokes of the loose (A) pestle, and 15 strokes of the tight (B) pestle. The homogenate was centrifuged for 8 min at 94 g, 4 C, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei isolation medium without Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT).  The tube was centrifuged for 8 min at 94 g, 4 C again, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei storage buffer (0.1665 M sucrose, 5 mM MgCl2, 10 mM HEPES pH 8.0), and filtered with 40 um. Note that sucrose concentration was not specified in (Krishnaswami et al., 2016); here we used 0.1665 M from (Lacar et al., 2016). Also note that the recipe in (Lacar et al., 2016) seems to have typos in some ingredient volumes; here we followed the final concentrations.  [Fixation of cell nuclei] Nuclei were fixed according to our Dip-C protocol (Tan et al., 2019) with minor modifications. In particular, nuclei were fixed directly in the 1 mL nuclei storage buffer (with HEPES instead of Tris buffer; see above) rather than switching to PBS; and centrifugation was performed at 1,000 g rather than 600 g. See detailed below:  Nuclei were directly in the nuclei storage buffer (1 mL) with the addition of 66.7 uL 32% PFA (EMS 15714) to a final concentration of 2%. The tube was rotated for 10 min at room temperature; and 200 uL 1% BSA in PBS was then added. The tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant removed. The pellet was resuspended in 1 mL ice-cold 1% BSA in PBS. Nuclei were counted and aliquoted to up to 0.5 million per tube. Each tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant was removed. The pellet was stored at -80 C.  [Diploid chromatin conformation Capture (Dip-C)] A pellet of fixed cell nuclei was thawed on ice. We then proceeded directly to the step where 50 uL 0.5% SDS was added in the Dip-C protocol (Tan et al., 2019) and followed through with no modifications. Cells were sorted on a Beckman Coulter MoFlo Astrios, and amplified with homemade Nextera.


title: CPCG0246 Chromatin Interaction Calls


title: Cortex P1 CASTxB6 Cell 047


title: 59.NPC.input.r1.sorted


title: Cortex P1 CASTxB6 Cell 045


title: Cortex P56 CASTxB6 Cell 054


title: CPCG0324 Chromatin Interaction Calls


title: Cortex P56 CASTxB6 Cell 058


title: 58.NPC.H3K27ac.r2.sorted

value: Histone H3K27ac (Abcam, ab4729)


title: CPCG0258 Chromatin Interaction Calls


title: Cortex P56 CASTxB6 Cell 052


title: Cortex P1 CASTxB6 Cell 043


title: Cortex P56 CASTxB6 Cell 053


title: Cortex P1 CASTxB6 Cell 042


title: 56.NPC.Tcf7.r2.sorted

description:
201805ChIP09
peak coordinates:
peak18.NPC.Tcf7.txt

value: Tcf7 (Cell Signaling Technology, 2203)


title: 57.NPC.H3K27ac.r1.sorted


title: CPCG0366 Chromatin Interaction Calls


title: Cortex P56 CASTxB6 Cell 050


title: CPCG0342 Chromatin Interaction Calls


title: 55.NPC.Tcf7.r1.sorted

description:
201805ChIP05
peak coordinates:
peak18.NPC.Tcf7.txt


title: CPCG0255 Chromatin Interaction Calls


title: Cortex P1 CASTxB6 Cell 041


title: Cortex P56 CASTxB6 Cell 051


title: Cortex P56 CASTxB6 Cell 075


title: Cortex P1 CASTxB6 Cell 039


title: BP3330581 TAD Calls


title: BP3320942 TAD Calls


title: Cortex P1 CASTxB6 Cell 044


title: 54.NPC.Lef1.r2.sorted

description:
201805ChIP10
peak coordinates:
peak17.NPC.Lef1.txt

value: Lef1 (Cell Signaling Technology, 2230)


title: 52.NPC.Tcf7l2.r2.sorted

description:
201805ChIP20
peak coordinates:
peak16.NPC.Tcf7l2.txt

value: Tcf7l2 (Cell Signaling Technology, 2569)


title: Cortex P56 CASTxB6 Cell 045


title: 51.NPC.Tcf7l2.r1.sorted

description:
201805ChIP01
peak coordinates:
peak16.NPC.Tcf7l2.txt


title: Cortex P56 CASTxB6 Cell 046


title: Cortex P1 CASTxB6 Cell 040


title: Cortex P1 CASTxB6 Cell 036


title: CPCG0268 Chromatin Interaction Calls


title: Cortex P1 CASTxB6 Cell 035


title: Cortex P56 CASTxB6 Cell 049


title: Cortex P56 CASTxB6 Cell 048


title: 53.NPC.Lef1.r1.sorted

description:
201805ChIP06
peak coordinates:
peak17.NPC.Lef1.txt


title: CPCG0345 TAD Calls


title: Cortex P56 CASTxB6 Cell 044


title: Cortex P1 CASTxB6 Cell 034


title: 48.NPC.Six2.r2.sorted

description:
201805ChIP18
peak coordinates:
peak14.NPC.Six2.txt

value: Six2 (ProteinTech, 11562-1-AP)


title: BP1648133 TAD Calls


title: 49.NPC.Tcf7l1.r1.sorted

description:
201805ChIP04
peak coordinates:
peak15.NPC.Tcf7l1.txt

value: Tcf7l1 (Thermo Scientific, PA5-40327)


title: Cortex P56 CASTxB6 Cell 043


title: CPCG0365 TAD Calls


title: Cortex P56 CASTxB6 Cell 047


title: Cortex P56 CASTxB6 Cell 042


title: Cortex P1 CASTxB6 Cell 033


title: BP1664855 TAD Calls


title: Cortex P1 CASTxB6 Cell 032


title: 47.NPC.Six2.r1.sorted

description:
201805ChIP02
peak coordinates:
peak14.NPC.Six2.txt

value: 16.5 days


title: CPCG0331 TAD Calls


title: Cortex P1 CASTxB6 Cell 031


title: BP1595983 TAD Calls


title: Cortex P1 CASTxB6 Cell 038


title: Cortex P1 CASTxB6 Cell 037


title: 46.NPC.Ctnnb1.r2.sorted

description:
201805ChIP11
peak coordinates:
peak13.NPC.Ctnnb1.txt

value: Swiss Webster

value: β-catenin (ThermoFisher, 71-2700)


title: Cortex P56 CASTxB6 Cell 040


title: 50.NPC.Tcf7l1.r2.sorted

description:
201805ChIP19
peak coordinates:
peak15.NPC.Tcf7l1.txt


title: CPCG0339 TAD Calls


title: Cortex P56 CASTxB6 Cell 041


title: Cortex P56 CASTxB6 Cell 039


title: 45.NPC.Ctnnb1.r1.sorted

description:
201805ChIP07
peak coordinates:
peak13.NPC.Ctnnb1.txt


title: 44.NPC-5uM.input.r2.sorted


title: Cortex P1 CASTxB6 Cell 028


title: Cortex P1 CASTxB6 Cell 027


title: Cortex P1 CASTxB6 Cell 029


title: CPCG0336 TAD Calls


title: 42.NPC-5uM.Ser7P.r2.sorted

value: Ser7P-RNAPII (Active Motif, 61088)


title: 41.NPC-5uM.Ser7P.r1.sorted


title: CPCG0324 TAD Calls


title: Cortex P56 CASTxB6 Cell 038


title: Cortex P56 CASTxB6 Cell 037


title: Cortex P56 CASTxB6 Cell 035


title: 40.NPC-5uM.Ser5P.r2.sorted

value: Ser5P-RNAPII (Millipore, 05-623)


title: Cortex P1 CASTxB6 Cell 024


title: Cortex P56 CASTxB6 Cell 034


title: Cortex P1 CASTxB6 Cell 025


title: CPCG0366 TAD Calls


title: Cortex P56 CASTxB6 Cell 036


title: 39.NPC-5uM.Ser5P.r1.sorted


title: Cortex P1 CASTxB6 Cell 026


title: Cortex P56 CASTxB6 Cell 033


title: CPCG0255 TAD Calls


title: Cortex P56 CASTxB6 Cell 032


title: 43.NPC-5uM.input.r1.sorted


title: CPCG0268 TAD Calls


title: 38.NPC-5uM.K27me3.r2.sorted

value: Histone H3K27me2me3 (Active Motif, 39536)


title: Cortex P1 CASTxB6 Cell 023


title: CPCG0342 TAD Calls


title: CPCG0258 TAD Calls


title: CPCG0246 TAD Calls


title: 37.NPC-5uM.K27me3.r1.sorted


title: Conjunctival cells, Fangchinoline rep3

first: keting

last: bao

address: 130 Mei Long Road

institute: East China University of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample

source_name: conjunctival cells

extract_protocol:
CM-AS16 cells were removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CM-AS16 cells were cultured in 10 cm dishes, and treated with DMSO or 8 μM fangchinoline.

value: conjunctiva

tag: cell line

tag: treatment

value: Fangchinoline 8 μM


title: Cortex P56 CASTxB6 Cell 031

data_processing:
Library strategy: Dip-C
Please see 00README.md
Genome_build: mm10
Supplementary_files_format_and_content: Please see 00README.md

value: cortex


title: 36.NPC-5uM.K27ac.r2.sorted


title: Cortex P56 CASTxB6 Cell 030


title: Conjunctival cells, Fangchinoline rep2


title: Cortex P1 CASTxB6 Cell 030


title: Cortex P1 CASTxB6 Cell 022


title: Conjunctival cells, Fangchinoline rep1


title: 34.NPC-5uM.Lef1.r2.sorted

description:
201812ChIP23
peak coordinates:
peak12.NPC-5uM.Lef1.txt


title: Cortex P1 CASTxB6 Cell 021


title: Cortex P1 CASTxB6 Cell 018


title: Cortex P1 CASTxB6 Cell 020


title: 33.NPC-5uM.Lef1.r1.sorted

description:
201812ChIP09
peak coordinates:
peak12.NPC-5uM.Lef1.txt


title: Conjunctival cells, DMSO rep2

value: DMSO


title: Conjunctival cells, DMSO rep3


title: Cortex P56 CASTxB6 Cell 029


title: Cortex P56 CASTxB6 Cell 028


title: Cortex P1 CASTxB6 Cell 019


title: Cortex P1 CASTxB6 Cell 017


title: 32.NPC-5uM.Tcf7.r2.sorted

description:
201812ChIP22
peak coordinates:
peak11.NPC-5uM.Tcf7.txt

value: nephron progenitor cells


title: Conjunctival cells, DMSO rep1


title: Cortex P56 CASTxB6 Cell 026


title: Cortex P1 CASTxB6 Cell 016


title: 31.NPC-5uM.Tcf7.r1.sorted

description:
201812ChIP08
peak coordinates:
peak11.NPC-5uM.Tcf7.txt


title: 30.NPC-5uM.Tcf7l2.r2.sorted

description:
201812ChIP21
peak coordinates:
peak10.NPC-5uM.Tcf7l2.txt


title: Cortex P56 CASTxB6 Cell 025


title: Cortex P1 CASTxB6 Cell 015


title: 15_Ac_D_1

city: Wuhan

first: Gong

last: zhiyong

address: Xuefunan Road 68

institute: Wuhan Polytechnic University

description:
Sample 10
15 Ac D vs control deg.anno.txt

data_processing:
bcl2fastq software used for basecalling
fastp software used for filtering the original data, delete reads that do not meet the analysis criteria, and obtain clean reads that can be used for subsequent comparison, statistics, and subsequent analysis
FastQC was used to control the quality of  original offline data, get clean data, and evaluate the clean data to check the quality control effect
Hisat2/Tophat was used to alignment genome sequence and RseQC was used to analyze the uniformity
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Caco-2 cells

growth_protocol: Caco-2 cells were cultured in RPMI1640 medium at 37 ℃ in a humidified atmosphere containing 5 % CO2 in a CO2 incubator (Memmert, Germany).

extract_protocol:
Total RNA was extracted from Caco-2 cells using Trizol reagent. The concentration and purity of the RNA samples were examined at 260/280 nm ratio by Nanodrop. RNA degradation and contamination were monitored on 1% agarose gel electrophoresis (AGE) by Mini-Sub Cell GT System.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sample4-6 were treated with DON for 24 hours, Sample7-9 were treated with 3-ADON for 24h, Sample10-12 were treated with 15-ADON for 24h

value: Human cloned colon adenocarcinoma

value: 15-ADON for 24 hours


title: 15_Ac_D_2

description:
Sample 11
15 Ac D vs control deg.anno.txt


title: 15_Ac_D_3

description:
Sample 12
15 Ac D vs control deg.anno.txt


title: Cortex P56 CASTxB6 Cell 021


title: Cortex P56 CASTxB6 Cell 023


title: Cortex P1 CASTxB6 Cell 014


title: Cortex P1 CASTxB6 Cell 012


title: 26.NPC-5uM.Six2.r2.sorted

description:
201812ChIP19
peak coordinates:
peak08.NPC-5uM.Six2.txt


title: 29.NPC-5uM.Tcf7l2.r1.sorted

description:
201812ChIP07
peak coordinates:
peak10.NPC-5uM.Tcf7l2.txt


title: 35.NPC-5uM.K27ac.r1.sorted

value: Histone H3K27ac (Abcam, ab4729)


title: 3_Ac_D_1

description:
Sample 7
3 Ac D vs control deg.anno.txt

value: 3-ADON for 24 hours


title: 25.NPC-5uM.Six2.r1.sorted

description:
201812ChIP05
peak coordinates:
peak08.NPC-5uM.Six2.txt

value: Six2 (ProteinTech, 11562-1-AP)


title: 3_Ac_D_3

description:
Sample 9
3 Ac D vs control deg.anno.txt


title: Cortex P56 CASTxB6 Cell 027


title: 27.NPC-5uM.Tcf7l1.r1.sorted

description:
201812ChIP06
peak coordinates:
peak09.NPC-5uM.Tcf7l1.txt

value: Tcf7l1 (Thermo Scientific, PA5-40327)


title: Cortex P56 CASTxB6 Cell 022


title: DON_3

description:
Sample 6
DON vs control deg.anno.txt

value: DON for 24 hours


title: Cortex P1 CASTxB6 Cell 010


title: 3_Ac_D_2

description:
Sample 8
3 Ac D vs control deg.anno.txt


title: DON_2

description:
Sample 5
DON vs control deg.anno.txt


title: Cortex P1 CASTxB6 Cell 009


title: Cortex P56 CASTxB6 Cell 017


title: Cortex P1 CASTxB6 Cell 011


title: Cortex P56 CASTxB6 Cell 024


title: Cortex P56 CASTxB6 Cell 020


title: 28.NPC-5uM.Tcf7l1.r2.sorted

description:
201812ChIP20
peak coordinates:
peak09.NPC-5uM.Tcf7l1.txt

value: 16.5 days

value: Swiss Webster


title: Cortex P1 CASTxB6 Cell 013


title: Cortex P56 CASTxB6 Cell 019


title: 24.NPC-5uM.Ctnnb1.r2.sorted

description:
201812ChIP24
peak coordinates:
peak07.NPC-5uM.Ctnnb1.txt

value: β-catenin (ThermoFisher, 71-2700)


title: 22.NPC-1.25uM.input.r2..sorted


title: Cortex P56 CASTxB6 Cell 018


title: KB_3

description: Sample 3

value: untreated


title: DON_1

description:
Sample 4
DON vs control deg.anno.txt


title: 23.NPC-5uM.Ctnnb1.r1.sorted

description:
201812ChIP10
peak coordinates:
peak07.NPC-5uM.Ctnnb1.txt


title: Cortex P1 CASTxB6 Cell 008


title: Cortex P1 CASTxB6 Cell 007


title: Cortex P56 CASTxB6 Cell 016


title: KB_1

description: Sample 1


title: KB_2

description: Sample 2


title: 20.NPC-1.25uM.Ser7P.r2.sorted

value: Ser7P-RNAPII (Active Motif, 61088)


title: Cortex P56 CASTxB6 Cell 015


title: 21.NPC-1.25uM.input.r1..sorted


title: Cortex P1 CASTxB6 Cell 006


title: Cortex P56 CASTxB6 Cell 014


title: Cortex P1 CASTxB6 Cell 005


title: Cortex P56 CASTxB6 Cell 013


title: Cortex P1 CASTxB6 Cell 003


title: Hippocampus P180 B6 Plate 002

data_processing:
Please see 00README.md
Genome_build: mm10
Supplementary_files_format_and_content: * `do_filter.r`: R code for filtering out cells and genes.
Supplementary_files_format_and_content: * `UMIcount_mouse_decon_allGenes_ERCC.txt.gz`: Gene expression (UMI count) matrix before filtering.
Supplementary_files_format_and_content: * `UMIcount_mouse_decon_filtered_ERCC.tsv.gz`: Gene expression (UMI count) matrix for ERCC spike-in RNA, after filtering.
Supplementary_files_format_and_content: * `UMIcount_mouse_decon_filtered_genes.tsv.gz`: Final gene expression (UMI count) matrix for mouse genes, after filtering.

source_name: hippocampus

extract_protocol:
Cell nuclei were isolated based on protocols from (Krishnaswami et al., 2016; Lacar et al., 2016).
MALBAC-DT

tag: cell tissue

value: hippocampus


title: 18.NPC-1.25uM.Ser5P.r2.sorted

value: Ser5P-RNAPII (Millipore, 05-623)


title: Cortex P56 CASTxB6 Cell 012

value: cortex


title: 17.NPC-1.25uM.Ser5P.r1.sorted


title: Cortex P1 CASTxB6 Cell 004


title: Cortex P1 CASTxB6 Cell 002


title: Hippocampus P180 B6 Plate 003


title: Cortex P56 CASTxB6 Cell 011


title: Hippocampus P56 B6 Plate 003


title: Cortex P1 CASTxB6 Cell 001


title: 19.NPC-1.25uM.Ser7P.r1.sorted


title: Hippocampus P180 B6 Plate 001


title: enok_KD_H3K23_2

city: Taipei

first: Fu

last: Huang

address: 128, Academia Road Sec. 2, Nankang

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

data_processing:
Adapter trimming was done with Trimmomatic (Bolger et al., 2014. PMID: 24695404).
Fastq files were aligned to UCSC dm3 with Bowtie2-2.2.1 (Langmead et al., 2012. PMID: 22388286).
Genome_build: UCSC dm3 (Release 5)
Supplementary_files_format_and_content: The multicov tool from bedtools was used to acquire histone H3 and histone H3K23 unique reads in 142 piRNA clusters (Quinlan et al., 2010. PMID: 20110278).
Supplementary_files_format_and_content: Histone H3 and histone H3K23 reads in transposable elements were analyzed by TEtranscripts. (Jin Y. et al., 2015. PMID: 26206304).

source_name: ovary

growth_protocol: Gal4 driven RNAi was carried out at 29C for 2-3 days. Females were conditioned with wet yeast for 1-2 days before ovary dissection.

extract_protocol:
Lysates were prepared from sonicated nuclei and Histone H3-DNA complexes and Histone H3K23ac-DNA complexes were isolated with the anti-Histone H3 (ab1791, Abcam) and anti-acetyl-Histone H3 (Lys23) Antibody (07-355, Millipore), respectively.
Libraries were prepared according to Illumina's instructions. Barcodes used for each sample are as follows: GFP_KD_IN_1—ATGTCA, GFP_KD_IN_2—CCGTCC, enok_KD_IN_1—GTCCGC, enok_KD_IN_2—GTGAAA, GFP_KD_H3_1—ATCACG, GFP_KD_H3_2—TTAGGC, enok_KD_H3_1—ACTTGA, enok_KD_H3_2—GATCAG, GFD_KD_H3K23_1—TAGCTT, GFD_KD_H3K23_2—GGCTAC, enok_KD_H3K23_1—GTGGCC, enok_KD_H3K23_2—GTTTCG.

value: ovary

tag: Sex

value: female

value: 2-3 day old adult

tag: genotype

value: tj-GAL4/+; P{w[+mC]=GAL4::VP16-nos.UTR}CG6325[MVD1] / P{TRiP.HMS02634}attP2

value: anti-acetyl-Histone H3 (Lys23)


title: Hippocampus P56 B6 Plate 002

first: Longzhi

last: Tan

address: 12 Oxford St

institute: Harvard University


title: Cortex P56 CASTxB6 Cell 009

source_name: cortex


title: enok_KD_H3K23_1


title: Cortex P56 CASTxB6 Cell 010


title: Hippocampus P56 B6 Plate 001


title: GFP_KD_H3K23_2

value: tj-GAL4/+; P{w[+mC]=GAL4::VP16-nos.UTR}CG6325[MVD1] / P{VALIUM20-EGFP.shRNA.1}attP2


title: 15.NPC-1.25uM.K27me3.r1.sorted

value: nephron progenitor cells

value: Histone H3K27me2me3 (Active Motif, 39536)


title: 13.NPC-1.25uM.H3K27ac.r1.sorted

value: Histone H3K27ac (Abcam, ab4729)


title: Hippocampus P28 B6 Plate 003


title: Cortex P56 CASTxB6 Cell 008


title: 14.NPC-1.25uM.H3K27ac.r2.sorted

value: 16.5 days


title: 12.NPC-1.25uM.Lef1.r3.sorted

description:
201803Tcf12
peak coordinates:
peak06.NPC-1.25uM.Lef1.txt

value: Swiss Webster

value: Lef1 (Cell Signaling Technology, 2230)


title: GFP_KD_H3K23_1


title: Hippocampus P28 B6 Plate 002


title: Cortex P56 CASTxB6 Cell 006


title: 11.NPC-1.25uM.Lef1.r2.sorted

description:
201805ChIP15
peak coordinates:
peak06.NPC-1.25uM.Lef1.txt


title: enok_KD_H3_2

value: anti-Histone H3


title: Hippocampus P28 B6 Plate 001


title: 16.NPC-1.25uM.K27me3.r2.sorted


title: enok_KD_H3_1


title: Cortex P56 CASTxB6 Cell 005


title: GFP_KD_H3_2


title: 09.NPC-1.25uM.Tcf7.r1.sorted

description:
201712tcf03+201803Tcf02
peak coordinates:
peak05.NPC-1.25uM.Tcf7.txt

value: Tcf7 (Cell Signaling Technology, 2203)


title: 10.NPC-1.25uM.Tcf7.r2.sorted

description:
201801ChIP01+201803Tcf10
peak coordinates:
peak05.NPC-1.25uM.Tcf7.txt


title: Cortex P56 CASTxB6 Cell 004


title: Hippocampus P21 B6 Plate 002

value: hippocampus


title: Cortex P56 CASTxB6 Cell 003


title: 08.NPC-1.25uM.Tcf7l2.r2.sorted

description:
201803Tcf11
peak coordinates:
peak04.NPC-1.25uM.Tcf7l2.txt

value: Tcf7l2 (Cell Signaling Technology, 2569)


title: Cortex P56 CASTxB6 Cell 007

value: cortex


title: enok_KD_input_2

value: ovary


title: Cortex P56 CASTxB6 Cell 002


title: 07.NPC-1.25uM.Tcf7l2.r1.sorted

description:
201712tcf04
peak coordinates:
peak04.NPC-1.25uM.Tcf7l2.txt


title: enok_KD_input_1

value: female


title: Hippocampus P14 B6 Plate 003


title: Cortex P56 CASTxB6 Cell 001


title: Hippocampus P21 B6 Plate 001


title: 06.NPC-1.25uM.Tcf7l1.r2.sorted

description:
201812ChIP15
peak coordinates:
peak03.NPC-1.25uM.Tcf7l1.txt

value: Tcf7l1 (Thermo Scientific, PA5-40327)


title: 05.NPC-1.25uM.Tcf7l1.r1.sorted

description:
201805ChIP14
peak coordinates:
peak03.NPC-1.25uM.Tcf7l1.txt


title: Hippocampus P21 B6 Plate 003


title: GFP_KD_input_1

value: 2-3 day old adult


title: GFP_KD_input_2


title: RNA-seq lepA::zeo/ L5-empty-Kan rep1

city: College Station

first: Thomas

last: Ioerger

state: TX

address: 3112 TAMUS

department: Department of Computer Science

institute: Texas A&M University

data_processing:
sequencer: Illumina HiSeq 2500
150x150 bp paired-end
base calling: HCS 2.2.68 and RTA 1.18.66.3
mapping to reference genome: BWA 0.7.12
tabulating counts in ORFs: in-house scripts
statistical analysis of differential expression: DeSeq2
Supplementary_files_format_and_content: smeg_LepA_RNAseq_counts.tsv: counts of reads mapping to each ORF for all 9 samples
Supplementary_files_format_and_content: smeg_LepA_DeSeq2_KO_vs_WT.tsv: output of DeSeq2 analysis for comparing LepA KO to WT; significant differentially-expressed genes are those with p.adj<0.05

organism: Mycolicibacterium smegmatis MC2 155

source_name: 7H9 culture

growth_protocol: grown in 7H9 culture

extract_protocol: none provided by the submitter

value: complemented

tag: replicate


title: Hippocampus P7 B6 Plate 003


title: 04.NPC-1.25uM.Six2.r2.sorted

description:
201803Tcf09
peak coordinates:
peak02.NPC-1.25uM.Six2.txt

value: Six2 (ProteinTech, 11562-1-AP)


title: RNA-seq lepA::zeo/ L5-empty-Kan rep2


title: Hippocampus P14 B6 Plate 002


title: enok_KD_IP

data_processing:
Adapter trimming was done with Trimmomatic. (Bolger et al., 2014. PMID: 24695404)
Fastq files were aligned to UCSC dm3 with Bowtie2-2.2.1. (Langmead et al., 2012. PMID: 22388286)
MACS2 was used to call peaks with default settings (callpeak), additional parameters (--p-value 5e-2), and PCR duplicates were removed. An additional cutoff of p-value less than 1e-15 was applied. (Zhang et al., 2008. PMID: 18798982)
Rhino input and IP were mapped to RD_SL as defined perviously. (PMID: 24906153)
Genome_build: UCSC dm3
Supplementary_files_format_and_content: The tab-delimited text files include peak information (position, -LOG10(pvalue) and -LOG10(qvalue), and fold enrichment) of GFP_KD_IP and enok_KD_IP.
Supplementary_files_format_and_content: The tab-delimited text files include reads information (position, piRNA cluster, normalized reads) of GFP_KD_IN, enok_KD_IN, GFP_KD_IP and enok_KD_IP.

growth_protocol: MTD-Gal4 driven RNAi was carried out at 29C for 2-3 days. Females were conditioned with wet yeast for 1-2 days before ovary dissection.

extract_protocol:
Lysates were prepared from sonicated nuclei and Rhino-DNA complexes were isolated with the anti-Rhino antibody (PMID: 24906153).
Libraries were prepared according to Illumina's instructions. Barcodes used for each sample are as follows: GFP_KD_IN—CGATGT, enok_KD_IN—GCCAAT, GFP_KD_IP—CAGATC, enok_KD_IP—AGTTCC


title: RNA-seq lepA::zeo/ L5-lepA-Kan rep3

value: knock-out


title: Hippocampus P7 B6 Plate 002


title: RNA-seq lepA::zeo/ L5-lepA-Kan rep2


title: 02.NPC-1.25uM.Ctnnb1.r2.sorted

description:
201803Tcf19
peak coordinates:
peak01.NPC-1.25uM.Ctnnb1.txt

value: nephron progenitor cells

value: β-catenin (ThermoFisher, 71-2700)


title: Hippocampus P7 B6 Plate 001


title: GFP_KD_H3_1

value: tj-GAL4/+; P{w[+mC]=GAL4::VP16-nos.UTR}CG6325[MVD1] / P{VALIUM20-EGFP.shRNA.1}attP2


title: GFP_KD_IP


title: RNA-seq lepA::zeo/ L5-empty-Kan rep3


title: 01.NPC-1.25uM.Ctnnb1.r1.sorted

description:
201801ChIP02+201803Tcf17
peak coordinates:
peak01.NPC-1.25uM.Ctnnb1.txt

value: 16.5 days

value: Swiss Webster


title: RNA-seq lepA::zeo/ L5-lepA-Kan rep1


title: GFP_KD_Input


title: RNA-seq mc2155/L5-empty-kan rep3

value: wild-type


title: enok_KD_Input


title: Hippocampus P1 B6 Plate 002


title: Hippocampus P1 B6 Plate 003


title: ATAC.NPC.5uM.r3

description:
mm10_201812ATAC01.5
peak coordinates:
peaks05.ATAC.NPC.5uM.txt

data_processing:
Base call by bcl2fastq v. 2.17
Fastq files were aligned using Bowtie 2.
Aligned reads were sorted with samtools (Li et al., 2009).
Duplicate reads were removed with Picard (http://broadinstitute.github.io/picard/index.html).
ATAC-Seq peaks were called using MACS2 (Feng et al., 2012).
wig profiles were generated using QuEST
Genome_build: mm10
Supplementary_files_format_and_content: wiggle files represents ATAC-Seq tags; peak files

extract_protocol:
Cortex of moue embryonic kidneys were dissociated and nephron progenitor cells (NPCs) were purified with MACS (Brown et al., 2015). Nuclei was prepared as described (Buenrostro et al., 2015).
ATAC-Seq libraries were constructed using as described (Buenrostro et al., 2015).


title: Enok_IP_3

data_processing:
Adapter trimming was done with Trimmomatic. (Bolger et al., 2014. PMID: 24695404)
Fastq files were aligned to UCSC dm3 with Bowtie2-2.2.1. (Langmead et al., 2012. PMID: 22388286)
Genome_build: UCSC dm3
Supplementary_files_format_and_content: Bigwig files were generated with bam2wig, additional parameters (-m) (https://github.com/MikeAxtell/bam2wig), and with wigToBigWig (UCSC). Then the bigwigCompare tool from deeptools was used to compare the Enok distribution between Enok_IP and Enok_IN. (Ramirez F et al., 2014. PMID: 24799436)

growth_protocol: Flies were grown at 25C. Females were collected after 24-48 hr after eclosure and conditioned with wet yeast paste for 24 hr before ovary dissection.

extract_protocol:
Lysates were prepared from sonicated nuclei and Enok-DNA complexes were isolated with the anti-Enok antibody (PMID: 25512562).
Libraries were prepared according to Illumina's instructions. Barcodes used for each sample are as follows: Enok_IN_3—CGTACG, Enok_IP_3—GAGTGG.

value: Oregon-R


title: Hippocampus P14 B6 Plate 001

value: hippocampus


title: RNA-seq mc2155/L5-empty-kan rep2


title: RNA-seq mc2155/L5-empty-kan rep1


title: ATAC.NPC.5uM.r2

description:
mm10_ATAC_NPC_5uM.r2
peak coordinates:
peaks05.ATAC.NPC.5uM.txt


title: ATAC.NPC.5uM.r1

description:
mm10_ATAC_NPC_5uM.r1
peak coordinates:
peaks05.ATAC.NPC.5uM.txt


title: Cortex P180 B6 Plate 003


title: Hippocampus P1 B6 Plate 001


title: Enok_Input_3


title: enok[2]_3

data_processing:
Adapter trimming was done with Trimmomatic. (Bolger et al., 2014. PMID: 24695404)
The levels of piRNA mapped to genic regions and piRNA clusters were calculated with piPipes, using the default small RNA-seq pipeline. (Han et al., 2015. PMID: 25342065)
Genome_build: UCSC dm3
Supplementary_files_format_and_content: The output data of genic and piRNA cluster aboundance from piPipes.

growth_protocol: Larvae were heat shocked twice at 37C for 40 min, with 30 min break at 25C in between, for two consecutive days starting from the second day after hatching. Females were conditioned with wet yeast for 2-3 days before ovary dissection.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) followed by DNase treatment (Invitrogen).
Libraries were generated using the default directional Illumina protocol, TruSeq Adapters. A 2S blocking DNA oligo was added to remove small rRNA. Small RNAs of 18-30 nt were cut on page gel and were used as the insert. Barcodes used for each sample are as follows: WT_1—ATCACG, WT_2—CGATGT, WT_3—TTAGGC, enok[1]_1—TGACCA, enok[1]_2—ACAGTG, enok[1]_3—GCCAAT, enok[2]_1—CAGATC, enok[2]_2—ACTTGA, enok[2]_3—GATCAG

value: 3-5 day old adult

value: hs-Flp / +; FRTG13, enok[2] / FRTG13, ovo[D1-18]


title: H3K27ac Day 4 TMZ

city: Madison

first: Jack

middle: M

last: Shireman

state: WI

address: 1500 Highland Ave

department: Neurological Surgery

institute: UW-Madison

data_processing:
raw data was aligned using Bowtie2 standard settings to Hg38 reference genome acquired from NCBI repository
once aligined bam files were processed using macs2 to call peaks with standard setting and q value set to .05
visualization was done using both IGV and pygenometracks with bdg files as well as narrow peak files for visualizaration and BED files marking peak intensity and locations as wlel as providing statisitics
Genome_build: HG38
Supplementary_files_format_and_content: .bdg and narrowPeak files are standard macs2 outputs containing peak location and intensity used for visualization

source_name: Human Tumor Cells

growth_protocol: cells cultured in DMEM supplemented with 1% FBS and P/S as described in manuscript. Scraperd off t-75 flasks and pelletted and sent to zymogen for G-DNA collection and library preperation according to their established protocols

extract_protocol:
Zymogen
Zymogen (for ChIP)

treatment_protocol: 50um TMZ (or equimolar DMSO contorl) for indicated time length

value: TMZ

tag: line type

value: GBM Patient Derived Xenograft

tag: molecular subtype

value: Proneural

tag: antibody

value: Anti-H3K27ac (Abcam)


title: Cortex P180 B6 Plate 002

value: cortex


title: 03.NPC-1.25uM.Six2.r1.sorted

description:
201712tcf01
peak coordinates:
peak02.NPC-1.25uM.Six2.txt

value: Six2 (ProteinTech, 11562-1-AP)


title: enok[2]_2

tag: tissue

value: ovary


title: Cortex P180 B6 Plate 001


title: H3K27ac Day 4 DMSO

value: DMSO

value: Anti-H3k27ac (Abcam)


title: ATAC.NPC.1.25uM.r2

description:
mm10_ATAC_NPC_1_25uM.r2
peak coordinates:
peaks04.ATAC.NPC.1.25uM.txt

value: nephron progenitor cells


title: enok[2]_1


title: ATAC.NPC.1.25uM.r1

description:
mm10_ATAC_NPC_1_25uM.r1
peak coordinates:
peaks04.ATAC.NPC.1.25uM.txt

value: 16.5 days


title: H3K27me3 Day 4 TMZ

value: TMZ Day 4

value: Anti-H3k27me3 (Abcam)


title: enok[1]_3

value: hs-Flp / +; FRTG13, enok[1] / FRTG13, ovo[D1-18]


title: ATAC.NPC.0uM.r3

description:
mm10_ATAC_NPC_0uM.r3
peak coordinates:
peaks03.ATAC.NPC.0uM.txt

value: Swiss Webster


title: Cortex P56 B6 Plate 002


title: H3K27me3 Day 1 TMZ

value: TMZ Day 1

value: Anti-H3K27me3 (Abcam)


title: Cortex P56 B6 Plate 003


title: ATAC.NPC.0uM.r2

description:
mm10_ATAC_NPC_0uM.r2
peak coordinates:
peaks03.ATAC.NPC.0uM.txt


title: EZH2 Day 4 TMZ

value: Anti_EZH2 (Abcam)


title: EZH2 Day1 TMZ

value: GBM Patient Derived Xenograft

value: Anti-EZH2 (Abcam)


title: enok[1]_2

value: 3-5 day old adult


title: ATAC.NPC.1.25uM.r3

description:
mm10_ATAC_NPC_1_25uM.r3
peak coordinates:
peaks04.ATAC.NPC.1.25uM.txt


title: enok[1]_1


title: Cortex P56 B6 Plate 001

value: cortex


title: WT_3

value: hs-Flp / +; FRTG13 / FRTG13, ovo[D1-18]


title: ATAC.NPC.0uM.r1

description:
mm10_ATAC_NPC_0uM.r1
peak coordinates:
peaks03.ATAC.NPC.0uM.txt


title: Cortex P28 B6 Plate 003


title: FGF13cko rep3 [RNA-seq]

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using STAR, alignment of paired-end clean reads to the reference genome and counting reads umbers mapped to each gene were performed using STAR
DESeq2 online (https://usegalaxy.org/) was used to estimate normalized counts for known transcripts and analyze differentially expressed transcripts.Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include normalize values for each Sample

source_name: Hippocampus

extract_protocol:
The neurospheres were harvested using Trizol reagent.
The library construction and sequencing was performed by Illumina Xten at Novogene Corporation. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following manufacture's recommendations.

value: neural progenitor cells

value: Hippocampus

tag: age

value: hGFAPCre+, Fgf13 flox/y


title: Cortex P28 B6 Plate 002


title: WT_2

value: ovary


title: FGF13cko rep2 [RNA-seq]

tag: cell type


title: WT_1


title: ATAC.cortex.r1

description:
mm10_NPC_ATAC04_20160520
peak coordinates:
peaks02.ATAC.cortex.txt

source_name: kidney cortical cells depleted of NPC

value: kidney cortical cells depleted of NPC

value: 16.5 days

tag: strain


title: ATAC.cortex.r2

description:
mm10_NPC_ATAC05_20160520
peak coordinates:
peaks02.ATAC.cortex.txt

tag: developmental stage


title: CTRL rep3 [RNA-seq]

value: hGFAPCre+, Fgf13+/y


title: ATAC.cortex.r3

description:
mm10_NPC_ATAC06_20160520
peak coordinates:
peaks02.ATAC.cortex.txt


title: Cortex P21 B6 Plate 003


title: Cortex P21 B6 Plate 002


title: FGF13cko rep1 [RNA-seq]


title: ATAC.NPC.r3

description:
mm10_NPC_ATAC03_20160520
peak coordinates:
peaks01.ATAC.NPC.txt

value: nephron progenitor cells


title: Cortex P28 B6 Plate 001


title: enok_KD_IP_2

data_processing:
Adapter trimming was done with Trimmomatic. (Bolger et al., 2014. PMID: 24695404)
Fastq files were aligned to UCSC dm3 with Bowtie2-2.2.1. (Langmead et al., 2012. PMID: 22388286)
Genome_build: UCSC dm3
Supplementary_files_format_and_content: Bigwig files were generated with bam2wig, additional parameters (-m) (https://github.com/MikeAxtell/bam2wig), and with wigToBigWig (UCSC). Then the bigwigCompare tool from deeptools was used to compare the RNA Pol II distribution between enok_KD and GFP_KD. (Ramirez F et al., 2014. PMID: 24799436)

extract_protocol:
Lysates were prepared from sonicated nuclei and RNA Pol II-DNA complexes were isolated with the anti-Pol II CTD antibody (4H8, Abcam, ab5408).
Libraries were prepared according to Illumina's instructions. Barcodes used for each sample are as follows: GFP_KD_IN_1—CGATGT, GFP_KD_IN_2—TGACCA, enok_KD_IN_1—ACAGTG, enok_KD_IN_2—GCCAAT, GFP_KD_IP_1—CAGATC, GFP_KD_IP_2—CTTGTA, enok_KD_IP_1—AGTCAA, enok_KD_IP_2—CCGTCC

value: 2-3 day old adult

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody [4H8]/Abcam/ab5408/GR106949-12


title: CTRL rep2 [RNA-seq]


title: Cortex P21 B6 Plate 001


title: ATAC.NPC.r2

description:
mm10_NPC_ATAC02_20160520
peak coordinates:
peaks01.ATAC.NPC.txt

value: Swiss Webster


title: GFP_KD_IP_2


title: CTRL rep1 [RNA-seq]


title: ATAC.NPC.r1

description:
mm10_NPC_ATAC01_20160520
peak coordinates:
peaks01.ATAC.NPC.txt


title: GFP_KD_IP_1


title: Cortex P14 B6 Plate 003


title: Fgf13cko rep2 [ATAC-seq]

data_processing:
Sequencing reads were mapped to mouse genome assembly (mm10) from the UCSC genome browser (http://genome.ucsc.edu/) using Bowtie2.
Duplicate reads were marked and removed by PICARD Tools (http://broadinstitute.github.io/picard/).
Open chromatin peaks were analyzed using MACS2 software. We merged peaks of 2 replicated samples of Fgf13cko and control mice sepereatly for following analysis.
Differential peaks between Fgf13cko and control mice samples were generated by DESeq2.
HOMER (Heinz et al., 2010) was used to annotate those peaks and for motif discovery analysis.
Genome_build: mm10
Supplementary_files_format_and_content: BroadPeak files were generated using MACS2; Differential peaks between FGF13cko and control mice samples were generated by DESeq2.

extract_protocol:
Neurospheres cultured for 7 days were digested by trypsin and dissociated. The suspended cells (5*10^5/sample) were washed with cold PBS, collected by centrifugation then resuspended in resuspension buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). After collection, cells were lysed in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and collected before incubating in transposition mix containing Tn5 transposase.
The Tn5 transposase reaction and library construction is prepared using TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, TD501).The purified library was analyzed on an Agilent Bioanalyzer, and single-read sequencing was performed using Illumina HiseqXten-PE150 platform according to standard operating procedures.


title: Cortex P14 B6 Plate 002


title: enok_KD_Input_2


title: Fgf13cko rep1 [ATAC-seq]


title: Cortex P14 B6 Plate 001


title: CTRL rep2 [ATAC-seq]


title: Cortex P7 B6 Plate 003


title: GFP_KD_Input_2


title: CTRL rep1 [ATAC-seq]


title: Cortex P7 B6 Plate 002


title: ARID1Bhe_rep3 [RNA-seq]

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using STAR, alignment of paired-end clean reads to the reference genome and counting reads umbers mapped to each gene were performed using STAR.
DESeq2 online (https://usegalaxy.org/) was used to estimate normalized counts for known transcripts and analyze differentially expressed transcripts.Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include normalize values for each Sample

value: hGFAPCre+, Arid1b flox/+


title: GFP_KD_Input_1


title: Enok_IP_2

data_processing:
Adapter trimming was done with Trimmomatic. (Bolger et al., 2014. PMID: 24695404)
Fastq files were aligned to UCSC dm3 with Bowtie2-2.2.1. (Langmead et al., 2012. PMID: 22388286)
MACS2 was used to call peaks with default settings (callpeak), additional parameters (--p-value 5e-2), and PCR duplicates were removed. An additional cutoff of p-value less than 1e-15 was applied. (Zhang et al., 2008. PMID: 18798982)
Genome_build: UCSC dm3
Supplementary_files_format_and_content: The tab-delimited text files include peak information (position, -LOG10(pvalue) and -LOG10(qvalue), and fold enrichment) of Enok_IP_1 and Enok_IP_2.

extract_protocol:
Lysates were prepared from sonicated nuclei and Enok-DNA complexes were isolated with the anti-Enok antibody.
Libraries were prepared according to Illumina's instructions. Barcodes used for each sample are as follows: Enok_IN_1—AGTTCC, Enok_IN_2—ATCACG, Enok_IP_1—GTGGCC, Enok_IP_2—TAGCTT

value: Oregon-R

value: Enok, Lab-purified, PMID:25512562


title: UUO4

city: Saitama

first: Shohei

last: Kaneko

state: Saitama

address: 1-847 Amanuma-cho, Omiya-ku

institute: Saitama Medical Center, Jichi Medical University

hyb_protocol: The hybridization mixture was denatured at 100°C for 5 minutes in a reaction volume of 45 ul containing 2x Agilent GE hybridization buffer HI-RPM and 10x Agilent blocking agent following the manufacturers instructions and immediately transferred to ice water bath. Each sample was hybridized to SurePrint G3 Mouse miRNA microarray 8 x 60K Rel.21.0 (Agilent, G4859C) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using miRNA setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters(protocol miRNA_107_Sep09 and Grid 070155_D_F_20141006). The 90th percentile shift normalization was performed by the GeneSpring GX software using Agilent.miRNA.70155_v21_0 technology. Data were baseline shifted to the median of all samples.

source_name: UUO surgery 4

label_protocol: RNA labeling was performed using miRNA Complete Labeling Reagent & Hybridization Kit (Agilent, 5190-0456) following the Agilent protocols v.2.3. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. After adding DMSO, the reaction mixture was incubated at 100°C for 7 minutes and immediately transferred to ice water bath.Ligation was performed with pCp-Cy3 at 16 °C for 2 hours.The labeled RNA were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen , NV, Venlo, The Netherlands) according to the manufacturer’s instructions.

value: Kidney tissue

tag: gender

value: male

value: 8 week


title: ARID1Bhe_rep2 [RNA-seq]

first: Qiaoqiao

last: Yang

address: 320 Yue Yang Road

institute: Chinese Academy of Sciences

value: neural progenitor cells


title: UUO3

source_name: UUO surgery 3


title: UUO2

source_name: UUO surgery 2


title: enok_KD_IP_1


title: Enok_IP_1


title: ARID1Bhe_rep1 [RNA-seq]

value: Hippocampus


title: Cortex P1 B6 Plate 003

city: Cambridge

value: cortex


title: Cortex P1 B6 Plate 002


title: Ctrl rep2 [RNA-seq]

value: hGFAPCre+, Arid1b+/+


title: Sham8

source_name: Sham surgery 8


title: UUO1

source_name: UUO surgery 1


title: enok_KD_Input_1

value: ovary


title: Enok_Input_2


title: Ctrl rep1 [RNA-seq]


title: Sham2

source_name: Sham surgery 2


title: Sham3

source_name: Sham surgery 3


title: Sham1

source_name: Sham surgery 1


title: Cortex P7 B6 Plate 001


title: Cortex P1 B6 Plate 001