title: Wild Type CJ7 mESC Bru-seq rep1

description:
Bru-CJ7-1
processed data column: Bru-CJ7-WT-average

tag: cell type


title: EloAK754M mESC Bru-seq rep2

status: Public on Nov 16 2017

type: SRA

city: Boston

first: Behfar

last: Ardehali

state: Massachusetts

address: Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN7250

department: Molecular Biology

country: USA

institute: MGH, Harvard Medical School

description: processed data column: Bru-K754M-2

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the mouse genome (mm9 build) using the aligner BWA.
Sequencing reads were counted over an assembly of all putative introns for each gene and normalized by the length of the cumulative intron assembly and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: txt, bigwig: RPKM and genebrowser tracks

molecule: total RNA

organism: Mus musculus

source_name: EloAK754M mESC Bru-seq

growth_protocol: Murine CJ7 cells were grown on 0.2% gelatin-coated 6-well plates seeded with irradiated or mitomycin C treated mouse embryonic fibroblast (MEF). ES cell medium contained: 1x DMEM knockOut medium, 15% hyclone FBS, 1x GlutaMAX, 1x NEAA, 1x pen/strep, 1-1.6x103 Units/ml of mLIF (Millipore), 55μM 2BME. Media was supplemented with 1µM and 3µM of PD0325901 and CHIR99021, respectively (2i). ES cells were depleted of MEF by plating the ES cell suspension at 37oC for 30min.

extract_protocol:
Experiments were carried out on mouse ES cells gown on feeder-free, 1% gelatinized 100mm tissue culture dishes. 5-Bromouridine (BrU) was added to cells at a final concentration of 2mM (from a100mM BrU stock) and incubated in the incubator for 10 min. Media was aspirated off and cells were lysed in 4ml of Trizol. 800µl of chloroform was next added to the lysed cells in 5ml epp tubes, vortexed and spun down at 5200 g for 15min. Equal volume of isopropanol was added to the aqueous phase, mixed, left at RT for 5-10 min and spun down at 4oC for 20min at max speed (14000 g) in a tabletop centrifuge to precipitate the RNA.  Resulting RNA pellet was washed twice with 70% EtOH, air dried and resuspended in 200-400 µl Nuclease-free water. The amount of RNA was quantified using Nanodrop, and a small fraction of the total RNA was run on agarose gel to determine the quality of purified total RNA.
Bru-RNA enrichment: Mouse aBrdU antibody (SCBT, sc-32323) was coupled to Dynabeads M-280 Sheep Anti-Mouse IgG (11201D). 1ml of magnetic beads was washed 4 x with PBS-DEPC/0.1%BSA and 500ul of Ab  was incubated with 1ml of beads and yeast RNA (500ng/µl final concentration) for 2-3 hours at 4oC, washed 3x with PBS-DEPC/0.1%BSA/Tween 0.05%.The final volume was raised to 1ml. For enrichment of Bru-RNA, 25-50µg of total RNA (after preheating at 95oC and immediate cooling) was added to 50µl of Antibody-bound beads in 1 ml of PBS-DEPC/0.1%BSA/Tween 0.05% and incubated for 90 min at RT with a foil wrapped around the tube. Beads were washed 4x with PBS-DEPC/0.1%BSA/Tween 0.05%, 5-10min (last wash was done with Tween-free buffer). Enriched RNA was either eluted by addition of 25µl of DEPC-water and incubation at 95oC for 10min with occasional flicking/shaking, or Trizol extraction. The enriched RNA was depleted of ribosomal RNA and used for generation of RNA-seq library.

treatment_protocol: 5-BromoUridine (BrU) was added to CJ7 mES cells growing in plates at a final concentration of 2mM for 10min in 10mm plates. Media was aspirated off and RNA was extracted by addition of 4ml of Trizol.

tag: cell line background

value: Embryonic stem cells (mESC)

tag: genotype/variation

value: EloAK754M edited

tag: molecule subtype

value: BrU-labelled nascent RNA


title: EloAK754R mESC Bru-seq rep1

description: processed data column: Bru-K754R-1

source_name: EloAK754R mESC Bru-seq

value: EloAK754R edited


title: EloAK754M mESC Bru-seq rep1

description: processed data column: Bru-K754M-1


title: EloA+/+ CCE mESC rep2

description:
EloAplusplus-2
processed data file: mES_RPKM_table.txt

data_processing:
Basecalls performed using CASAVA version 1.7
Subsequent to demultiplexing and adapter trimming, fastqs were mapped to the mouse genome (build mm9) with splice-aware aligner STAR vers-2.3.0 using mm9 Ensembl gtf version 67
To calculate RPKM expression values, sequencing reads were counted over an assembly of all putative exons for each gene and normalized by the length of the exon assembly and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: txt, bigwig: RPKM and genebrowser tracks

source_name: EloA+/+ CCE mESC

growth_protocol: Murine CJ7 or CCE28 cells were grown on 0.2% gelatin-coated 6-well plates seeded with irradiated or mitomycin C treated mouse embryonic fibroblast (MEF). ES cell medium contained: 1x DMEM knockOut medium, 15% hyclone FBS, 1x GlutaMAX, 1x NEAA, 1x pen/strep, 1-1.6x103 Units/ml of mLIF (Millipore), 55μM 2BME. Media was supplemented with 1µM and 3µM of PD0325901 and CHIR99021, respectively (2i). ES cells were depleted of MEF by plating the ES cell suspension at 37oC for 30min.

extract_protocol:
MEF-depleted ES cells were lysed in Trizol and total RNA was isolated using Direct-zol RNA preparation kit (Zymo Research, R2070). On column DNase tretment was done according to manufacturer's protocol. After checking the quality and quantity of the isolated RNA, 0.5 to 1 microgram of total RNA was depleted of rRNA using RiboZero Gold magnetic kit (Illumina Inc. MRZG12324). The rRNA-depleted RNA was used for cDNA generation and library construction.
cDNA was generated using Truseq total RNA kit (Illumina Inc.) according to the manufacturer's protocol. End repair, A-tailing, adapter ligation  and PCR amplification was carried out according to manufacturer's instructions with modifications described elsewhere (Bowman et al., BMC Genomics 2013).

tag: passage

value: Wild Type


title: Wild Type mESC Bru-seq rep2

description: processed data column: Bru-WT-2

source_name: Wild Type mESC Bru-seq

value: EloA WT


title: EloA+/+ CCE mESC rep3

description:
EloAplusplus-3
processed data file: mES_RPKM_table.txt


title: EloA+/+ CCE mESC rep1

description:
EloAplusplus-1
processed data file: mES_RPKM_table.txt


title: EloA-null CCE mESC rep3

description:
EloAnull-3
processed data file: mES_RPKM_table.txt

source_name: EloA-null CCE mESC

value: EloA null


title: WT-CJ7 mESC rep2

description:
WT-2
processed data file: mES_RPKM_table.txt

source_name: WT-CJ7 mESC


title: EloAK754R-CJ7 mESC rep2

description:
K754R-2
processed data file: mES_RPKM_table.txt

source_name: EloAK754R-CJ7 mESC


title: WT-CJ7 mESC rep1

description:
WT-1
processed data file: mES_RPKM_table.txt


title: EloAK754M CJ7 mESC rep2

description:
K754M-2
processed data file: mES_RPKM_table.txt

source_name: EloAK754M CJ7 mESC


title: EloAK754M CJ7 mESC rep1

description:
K754M-1
processed data file: mES_RPKM_table.txt


title: Eed-null CJ7 mESC rep1

description:
EEDnull-1
processed data file: mES_RPKM_table.txt

source_name: Eed-null CJ7 mESC

value: Eed null


title: EZH2 ChIP mES cell replicate 1

library_source: genomic

data_processing:
Paired-end sequencing reads were mapped to the mouse genome (mm9 build) using the aligner bwa.
Duplicate fragments were removed prior to generation of input-normalized coverage files (bigwig).
Genome_build: mm9
Supplementary_files_format_and_content: Input-normalized coverage files (bigwig) were generated over 50bp bins using Deeptools v. 2.4.0

molecule: genomic DNA

source_name: EZH2 ChIP mES cell

extract_protocol:
mESC were MEF depleted, crosslinked with 1% formaldehyde in PBS for 10min in conical tubes while gently rotating at RT and quenched by adding Glycine to a final concentration of 0.125M and left at RT for 5min on rotator. Crosslinked cells were spun down for 3min at 3500 rpm (2850 rcf) and lysed in cell lysis buffer  (50mM Tris PH 8.0, 50mM NaCl, 1mM EDTA, 5mM MgCl2, 0.25% NP-40, Roche complete EDTA-free protease inhibitor tablet(PI)* 0.2% PMSF* and 0.2% DTT*(*freshly-added)) at 2-2.5x107 cells/ml. Cells were left on ice for 10 min and dounced 10x using the tight pestle. Nuclei was spun down at 2850 rcf in 15ml conical tubes and the supernatnant was completely removed and nuclei was resuspended in sonication buffer (20mM Tris PH 8.0, 1% SDS, 2mM EDTA, 0.5mM EGTA, 0.5mM PMSF*, PI*(freshly added) at 5.0x107 nuclei/ml. Resuspended nuclei was left on ice for 10min and sonicated using the Bioruptor sonicator, at high setting 30’’ on 45’’ off twice for 15min. Water and ice was changed in between each sonication. IP was performed with using rabbit anti EZH2 (CST,D2C9), 1-2.5x106 nuclei were used per IP reaction, by adding 20-50 µl of sonicated chromatin to 1-1.25ml of IP buffer (20mM Tris PH 8.0, 0.5% Triton X-100, 150mM NaCl, 10% glycerol, 2mM EDTA) with the respective antibodies and after 4 hours of incubation protein A (40-50 µl) was added to the IP reaction and incubated for 4 more hours. Each wash was done on the rotator at RT for 5min as follows: x1 low salt wash (20mM Tris PH 7.8, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 150mM NaCl), x3 high salt wash (20mM Tris PH 7.8, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl), x1 LiCl wash (20mM Tris PH 7.8, 1% NP-40, 1% NaDeoxycholate, 2mM EDTA, 250mM LiCl), x2 TE wash.Elution was done on the IPed samples in 2x250µl of elution buffer (1% SDS, 0.1M NaHCO3) on the rotator at RT. To the 500µl elution buffer, 20 µl of 5M NaCl was added and samples were incubated in a thrmomixer for 4hr-O/N at 65oC to reverse the crosslink (same was done for the Input material). Next, 15µl of 1M Tris PH 7.8, 1-2 µl glycoblue (Ambion) and 2 µl of proteinase K was added to the reaction mix and incubated at 65oC for 30-60min. DNA was extracted from the reversed crosslink material using phenol/chloroform extraction and EtOH precipitation.
Library constructing for sequencing was prepared as described elsewhere (Bowman et al., BMC Genomics 2013).

tag: cell line

value: wild type

tag: chip antibody

value: Ezh2(D2C9 XP Rabbit mAb, 5246S, Cell Signaling Technology)


title: Eed-null CJ7 mESC rep2

description:
EEDnull-2
processed data file: mES_RPKM_table.txt


title: EloAK754R mESC Bru-seq rep2

description: processed data column: Bru-K754R-2


title: EloAK754R-CJ7 day5 EB rep2

description:
EB-K754R-2
processed data file: EB_RPKM_table.txt

source_name: EloAK754R-CJ7 day5 EB

value: Day 5 post LIF withdrawl embryoid body(EB)


title: Wild Type mESC Bru-seq rep1

description: processed data column: Bru-WT-1


title: EloAK754M-CJ7 day5 EB rep2

description:
EB-K754M-2
processed data file: EB_RPKM_table.txt

source_name: EloAK754M-CJ7 day5 EB


title: EloA+/+ CCE day5 EB rep2

description:
EB-EloAWT-2
processed data file: EB_RPKM_table.txt

source_name: EloA+/+ CCE day5 EB


title: EloAK754M-CJ7 day5 EB rep1

description:
EB-K754M-1
processed data file: EB_RPKM_table.txt


title: EloAK754R-CJ7 day5 EB rep1

description:
EB-K754R-1
processed data file: EB_RPKM_table.txt


title: EloA+/+ CCE day5 EB rep1

description:
EB-EloAWT-1
processed data file: EB_RPKM_table.txt


title: EloA+/- CCE day5 EB rep1

description:
EB-EloAnull-1
processed data file: EB_RPKM_table.txt

source_name: EloA+/- CCE day5 EB

value: EloA het


title: EloA+/- CCE day5 EB rep2

description:
EB-EloAnull-2
processed data file: EB_RPKM_table.txt


title: EloA-null CCE mESC rep2

description:
EloAnull-2
processed data file: mES_RPKM_table.txt


title: EloA-null CCE mESC rep1

description:
EloAnull-1
processed data file: mES_RPKM_table.txt


title: EloA-null CCE day5 EB rep1

description:
EB-EloAhet-1
processed data file: EB_RPKM_table.txt

source_name: EloA-null CCE day5 EB


title: Eed null-CJ7 day5 EB rep2

description:
EB-EEDnull-2
processed data file: EB_RPKM_table.txt

source_name: Eed null-CJ7 day5 EB


title: Eed null-CJ7 day5 EB rep1

description:
EB-EEDnull-1
processed data file: EB_RPKM_table.txt


title: EloAK754R-CJ7 mESC rep1

description:
K754R-1
processed data file: mES_RPKM_table.txt


title: WT-CJ7 day5 EB rep1

description:
EB-CJ-1
processed data file: EB_RPKM_table.txt

source_name: WT-CJ7 day5 EB


title: EloA-null CCE day5 EB rep2

description:
EB-EloAhet-2
processed data file: EB_RPKM_table.txt


title: 18 Month SVZ 1

city: Rensselaer

first: Thomas

middle: R

last: Kiehl

state: NY

address: One Discovery Drive

institute: Neural Stem Cell Institute

description:
18moSVZ1
svz.18.1

data_processing:
Mapped with SHRiMP 2.2.3
DESeq2 was used to normalize reads and gauge differential expression
Novel Time series analysis and comparisons following as described in associated publication.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data in XLSX files contains normalized read counts.

source_name: 18 Month SVZ

growth_protocol: Aged male wild-type mice wer sacrificed and SVZs dissected and dissociated to single cells

extract_protocol: Trizol-based protocol used to isolate RNA from dissociated SVZ cells

tag: age

value: 18 months

tag: Sex

value: male

value: subventricular zone (SVZ) cells


title: 22 Month SVZ 3

description:
22moSVZ3
svz.22.3

source_name: 22 Month SVZ

value: 22 months


title: 18 Month SVZ 2

description:
18moSVZ2
svz.18.2


title: 18 Month SVZ 3

description:
18moSVZ3
svz.18.3


title: 6 Month SVZ 3

description:
6moSVZ3
svz.6.3

source_name: 6 Month SVZ

value: 6 months


title: 6 Month SVZ 2

description:
6moSVZ2
svz.6.2


title: 22 Month SVZ 2

description:
22moSVZ2
svz.22.2


title: 2 Month SVZ 3

description:
2moSVZ3
svz.2.3

source_name: 2 Month SVZ

tag: strain

value: 2 months


title: 6 Month SVZ 1

description:
6moSVZ1
svz.6.1


title: 2 Month SVZ 1

description:
2moSVZ1
svz.2.1


title: 2 Month SVZ 2

description:
2moSVZ2
svz.2.2


title: scRNAseq_EB_noDrug

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
library strategy: scRNA-seq
Cell-barcodes and unique molecular identifiers were extracted using the CellRanger software
Reads were aligned using STAR against mm10.
Cloupe files containing read counts for visualization in the 10X Loop Browser
Barcodes files contain the DNA sequence barcodes per cell
Genes files contain the Ensembl gene identifiers and their gene names
Genome_build: mm10
Supplementary_files_format_and_content: Cloupe files containing read counts for visualization in the 10X Loop Browser
Supplementary_files_format_and_content: csv files contain per-gene, per-cell expression and were created using cellranger mat2csv

source_name: embryoid body

growth_protocol: V6.5 (C57BL/6-129)-YY1-FKBP knock-in murine ES cells were grown on irradiated mouse embryonic fibroblasts (MEFs) in KO DMEM with serum and LIF. YY1 was depleted by addition of dTAG-47 and then LIF was withdrawn to stimulate EB formation.

extract_protocol:
Embryoid bodies were dissociated into a single cell suspension with accutase, and then single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell Kit
10X Chromium Single Cell Kit


title: HiChIP_mES_C3_WO_H3K27ac_rep1

data_processing:
library strategy: Hi-ChIP
Mate pairs were mapped independently to either hg19 or mm9 using bowtie (parameters: -n 1 -m 1 -p 6)
After alignment, paired reads were re-linked with an in-house script using read identifiers. To avoid potential artifacts arising from PCR bias, redundant PETs with identical genomic mapping coordinates and strand information were collapsed into a single PET. Potential interaction anchors were determined by identifying regions of local enrichment in the individually mapped reads using MACS with options “-g mm -p 1e-9 --nolambda --nomodel --shiftsize=100” (Zhang et al., Genome Biology, 2008). PETs with two mapped reads that each overlapped a different potential interaction anchor by at least 1 bp were used to identify putative interactions between the overlapped interaction anchors. Each putative interaction was then assigned an observed PET count representing the number of PETs in the dataset that connected the two anchors of the interaction.
From the set of putative interactions, we sought to identify the interactions that represent specific chromatin contacts, defined as chromatin contacts that are detected with greater frequency than expected given the linear genomic distance between the two contacting regions. In contrast, we sought to filter out putative interactions that likely result from PETs arising from non-specific chromatin contacts, defined as contacts resulting from the close linear genomic proximity of the two contacting regions, and from technical artifacts of the ChIA-PET protocol. To this end, we developed and utilized Origami, a statistical method to identify high confidence interactions, representing specific chromatin contacts, among all putative interactions. Conceptually, Origami uses a semi-Bayesian two-component mixture model to estimate the probability that a putative interaction corresponds to one of two groups: specific chromatin contacts or non-specific chromatin contacts and technical artifacts. Origami estimates this probability score for each putative interaction by modeling the relationship between PET count, linear genomic distance between interaction anchors, and read depth at the interaction anchors for each of the two groups. High confidence interactions are then identified as the subset of putative interactions that are highly likely to result from specific chromatin contacts.
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: CSV files: File contains all putative interactions. Columns 1-3 represent the left end of the putative interaction in 25 kb bins, colums 4-6 are the right end of the putative interaction. Column 7 is the number of PETs supporting that putative interaction. Column 8 is the hypergeometric score (a la ChIA-PET tool). Column 9 is the Origami score

growth_protocol: Cells were grown on as specified by provider (HCT116 in DMEM/10% FBS, Jurkat in RPMI/10%FBS, K562 in RPMI/10%FBS, V6.5 in 2i)

extract_protocol:
Cells were fixed with formaldehyde and then the genome was digested with restriction enzyme. Proximity ligation was carried out, followed by sonication and immunoprecipitation with an antibody (abcam #4729) directed towards H3K27Ac.
Library was prepared by Tn5 transposition per nextera instructions

value: mESC

tag: treated with

value: dTAG-47 @ 500 nM for 24 hours, then washout for 120 hrs


title: HiChIP_mES_C3_WO_H3K27ac_rep2

value: dTAG-47 @ 500 nM for 24 hours


title: WT-CJ7 day5 EB rep2

description:
EB-CJ-2
processed data file: EB_RPKM_table.txt

value: Wild Type


title: HiChIP_mES_C3_TR_H3K27ac_rep2


title: HiChIP_mES_C3_UT_H3K27ac_rep3

value: dTAG-47 @ 0 nM for 0 hours


title: HiChIP_mES_C3_TR_H3K27ac_rep1


title: HiChIP_K27ac_C3_YY1-degraded_24_rep3

data_processing:
Library strategy: Hi-ChIP
Mate pairs were mapped independently to mm9 using bowtie (parameters: -n 1 -m 1 -p 6)
After alignment, paired reads were re-linked with an in-house script using read identifiers. To avoid potential artifacts arising from PCR bias, redundant PETs with identical genomic mapping coordinates and strand information were collapsed into a single PET. Potential interaction anchors were determined by identifying regions of local enrichment in the individually mapped reads using MACS with options “-g mm -p 1e-9 --nolambda --nomodel --shiftsize=100” (Zhang et al., Genome Biology, 2008). PETs with two mapped reads that each overlapped a different potential interaction anchor by at least 1 bp were used to identify putative interactions between the overlapped interaction anchors. Each putative interaction was then assigned an observed PET count representing the number of PETs in the dataset that connected the two anchors of the interaction.
From the set of putative interactions, we sought to identify the interactions that represent specific chromatin contacts, defined as chromatin contacts that are detected with greater frequency than expected given the linear genomic distance between the two contacting regions. In contrast, we sought to filter out putative interactions that likely result from PETs arising from non-specific chromatin contacts, defined as contacts resulting from the close linear genomic proximity of the two contacting regions, and from technical artifacts of the ChIA-PET protocol. To this end, we developed and utilized Origami, a statistical method to identify high confidence interactions, representing specific chromatin contacts, among all putative interactions. Conceptually, Origami uses a semi-Bayesian two-component mixture model to estimate the probability that a putative interaction corresponds to one of two groups: specific chromatin contacts or non-specific chromatin contacts and technical artifacts. Origami estimates this probability score for each putative interaction by modeling the relationship between PET count, linear genomic distance between interaction anchors, and read depth at the interaction anchors for each of the two groups. High confidence interactions are then identified as the subset of putative interactions that are highly likely to result from specific chromatin contacts.
Genome_build: mm9
Supplementary_files_format_and_content: CSV files: File contains all putative interactions. Columns 1-3 represent the left end of the putative interaction in 25 kb bins, colums 4-6 are the right end of the putative interaction. Column 7 is the number of PETs supporting that putative interaction. Column 8 is the hypergeometric score (a la ChIA-PET tool). Column 9 is the Origami score

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown on irradiated mouse embryonic fibroblasts (MEFs) in KO DMEM with serum and LIF. For analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates

tag: treatment

tag: time point

value: 24 hours


title: HiChIP_mES_C3_UT_H3K27ac_rep1


title: HiChIP_mES_C3_UT_H3K27ac_rep2


title: YY1_ChIAPET

data_processing:
Library strategy: ChIA-PET
Replicates were merged. Reads were examined for the presence of at least 10 base pairs of linker. Reads that did not contain linker were not processed further. Reads containing linker were trimmed using cutadapt (cutadapt -m 17 -a forward=ACGCGATATCTTATCTGACT -a reverse=AGTCAGATAAGATATCGCGT --overlap 10).
Trimmed mate pairs were mapped independently to mm9 using bowtie (parameters: -n 1 -m 1 -p 6)
After alignment, paired reads were re-linked with an in-house script using read identifiers. To avoid potential artifacts arising from PCR bias, redundant PETs with identical genomic mapping coordinates and strand information were collapsed into a single PET. Potential interaction anchors were determined by identifying regions of local enrichment in the individually mapped reads using MACS with options “-g mm -p 1e-9 --nolambda --nomodel --shiftsize=100” (Zhang et al., Genome Biology, 2008). PETs with two mapped reads that each overlapped a different potential interaction anchor by at least 1 bp were used to identify putative interactions between the overlapped interaction anchors. Each putative interaction was then assigned an observed PET count representing the number of PETs in the dataset that connected the two anchors of the interaction.
From the set of putative interactions, we sought to identify the interactions that represent specific chromatin contacts, defined as chromatin contacts that are detected with greater frequency than expected given the linear genomic distance between the two contacting regions. In contrast, we sought to filter out putative interactions that likely result from PETs arising from non-specific chromatin contacts, defined as contacts resulting from the close linear genomic proximity of the two contacting regions, and from technical artifacts of the ChIA-PET protocol. To this end, we developed and utilized Origami, a statistical method to identify high confidence interactions, representing specific chromatin contacts, among all putative interactions. Conceptually, Origami uses a semi-Bayesian two-component mixture model to estimate the probability that a putative interaction corresponds to one of two groups: specific chromatin contacts or non-specific chromatin contacts and technical artifacts. Origami estimates this probability score for each putative interaction by modeling the relationship between PET count, linear genomic distance between interaction anchors, and read depth at the interaction anchors for each of the two groups. High confidence interactions are then identified as the subset of putative interactions that are highly likely to result from specific chromatin contacts.
Genome_build: mm9
Supplementary_files_format_and_content: CSV files: File contains all putative interactions. Columns 1-3 represent the left end of the putative interaction, colums 4-6 are the right end of the putative interaction. Column 7 is the number of PETs supporting that putative interaction. Column 8 is the hypergeometric score (a la ChIA-PET tool). Column 9 is the Origami score

source_name: mES

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 300-700 bp were immunoprecipitated using YY1 or CTCF antibody. Immunoprecipitated DNA was end-repaired, A-tailed, and proximity ligation was performed in the presence of a bridge-linker (5'-ACGCGATATCTTATCTGACT) with T4 DNA ligase. Unligated DNA was digested with exonuclease treatment followed by RNAse A, and Proteinase K treatment. DNA was then phenol:chloroform:isoamyl alcohol preciptated and subjected to library preperation.
Purified immunoprecipitated DNA were prepared for sequencing according to the Illumina Nextera Tagmentation protocol. Tagmented DNA was subjected to 12 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 300 and 500bp (representing shear fragments between 200 and 400 nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number


title: CTCF_ChIAPET

value: CTCF

value: Millipore 07-729


title: 22 Month SVZ 1

description:
22moSVZ1
svz.22.1

value: wild type


title: HiChIP_K27ac_C3_YY1-degraded_24_rep1


title: HiChIP_K27ac_C3_WT-YY1_24_rep1

value: dTAG-47 @ 0 nM

value: 0 hours


title: mES_WT_0h_r2

data_processing:
Aligned and quantified using kallisto with configuration: quant  -b 100 --single -l 180 -s 20 to the mm9 RefSeq transcriptome (downloaded on 20160201 from UCSC)
Supplementary_files_format_and_content: Reads were quantified with kallisto. Processed data files are the estimated counts for mm9 refseq transcripts. Column 1 is the target ID (refseq ID), column 2 is the length of the transcript, column 3 is the effective length, column 4 is the estimated counts, column 5 is the transcripts per million, column 6 is the refseq gene name

molecule: polyA RNA

extract_protocol:
Library was prepared using TruSeq mRNA kit from Illumina according to the standard protocol.
Total RNA was purified using  Rneasy plus isolation kit (QIAGEN) following the manufacturer instructions.


title: mES_WT_0h_r1


title: mES_YY1_degraded_24h_r1


title: lib5_d72_H10-S94

city: Leuven

first: Sara

last: Aibar

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

data_processing:
Raw Fastq files of the same sample were merged and adapter sequences were removed using fastq-mcf
RNA-seq reads were mapped to the genome (mm10) using STAR (v2.5.1b)
Read counts per gene were obtained from the aligned reads using Subread (v1.4.6)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including gene-sumarized counts for each of the 144 cells that passed the quality control. The counts were size-factor normalized with DESeq2, and the resulting values were log2-transformed (log2(Value+1)).

source_name: d72_melanoma cell

extract_protocol:
SMARTseq2 (Picelli et a. 2014)
Nextera-XT (Illumina)
scRNAseq

treatment_protocol: Topical administration of 4-HT on tail skin of Tyr::CreERT2/+; ROSA26RLSL-tdTomato/+ or Tyr::CreERT2/+; BRafCA/+; Ptenl/l; ROSA26RLSL-tdTomato/+ mice, mechanical separation of epidermis and dermis, preparation of single cell suspensions of tail epidermis (IF melanocytes, d31) or tail skin (d72) via standard enzymatical digestion using collagenase, obtained single cell suspension were subjected to FACS, tdTomato+ cells were sorted into individual wells of a 96 well plate (single cell precision mode).

tag: tissue

value: tumor VGP

value: time after 4HT treatment (72d)

tag: genotype


title: lib5_d72_H12-S96

value: Tyr::CreERT2/+; BRafCA/+; Ptenl/l; ROSA26RLSL-tdTomato/+


title: lib5_d72_H11-S95


title: HiChIP_K27ac_C3_WT-YY1_24_rep2


title: HiChIP_mES_C3_WO_H3K27ac_rep3


title: lib5_d72_H7-S91


title: scRNAseq_EB_yesDrug


title: lib5_d72_H8-S92


title: lib5_d72_H6-S90


title: HiChIP_K27ac_C3_YY1-degraded_24_rep2


title: HiChIP_K27ac_C3_WT-YY1_24_rep3


title: lib5_d72_H4-S88


title: lib5_d72_H3-S87


title: lib5_d72_G12-S84


title: lib5_d72_G11-S83


title: lib5_d72_H2-S86


title: lib5_d72_G7-S79


title: lib5_d72_G10-S82


title: lib5_d72_G5-S77


title: lib5_d72_G6-S78


title: lib5_d72_G9-S81


title: lib5_d72_H9-S93


title: mES_YY1_degraded_24h_r2


title: lib5_d72_G3-S75


title: lib5_d72_G1-S73


title: lib5_d72_F12-S72


title: lib5_d72_G2-S74


title: lib5_d72_F11-S71


title: lib5_d72_F10-S70


title: lib5_d72_F8-S68


title: lib5_d72_F5-S65


title: lib5_d72_G4-S76


title: lib5_d72_F7-S67


title: lib5_d72_F4-S64


title: lib5_d72_H5-S89


title: lib5_d72_F6-S66


title: lib5_d72_H1-S85


title: lib5_d72_F2-S62


title: lib5_d72_F3-S63


title: lib5_d72_G8-S80


title: lib5_d72_E11-S59


title: lib5_d72_F1-S61


title: lib5_d72_E12-S60


title: lib5_d72_E9-S57


title: lib5_d72_E8-S56


title: lib5_d72_E7-S55


title: lib5_d72_E5-S53


title: lib5_d72_E4-S52


title: lib5_d72_E3-S51


title: lib5_d72_E2-S50


title: lib5_d72_E1-S49


title: lib5_d72_D12-S48


title: lib5_d72_E6-S54


title: lib5_d72_D10-S46


title: lib5_d72_D11-S47


title: lib5_d72_F9-S69


title: lib5_d72_D6-S42


title: lib5_d72_D7-S43


title: lib5_d72_D4-S40


title: lib5_d72_D5-S41


title: lib5_d72_D3-S39


title: lib5_d72_D2-S38


title: lib5_d72_D1-S37


title: lib5_d72_C12-S36


title: lib5_d72_E10-S58


title: lib5_d72_C11-S35


title: lib5_d72_C10-S34


title: lib5_d72_C9-S33


title: lib5_d72_C8-S32


title: lib5_d72_C6-S30


title: lib5_d72_C5-S29


title: lib5_d72_C7-S31


title: lib5_d72_C4-S28


title: lib5_d72_C1-S25


title: lib5_d72_D9-S45


title: lib5_d72_C3-S27


title: lib5_d72_C2-S26


title: lib5_d72_B12-S24


title: lib5_d72_B11-S23


title: lib5_d72_B10-S22


title: lib5_d72_B8-S20


title: lib5_d72_B9-S21


title: lib5_d72_B7-S19


title: lib5_d72_B5-S17


title: lib5_d72_B6-S18


title: lib5_d72_B3-S15


title: lib5_d72_A12-S12


title: lib5_d72_B4-S16


title: lib5_d72_B1-S13


title: lib5_d72_B2-S14


title: lib5_d72_A5-S5


title: lib5_d72_A6-S6


title: lib5_d72_A7-S7


title: lib5_d72_A10-S10


title: lib5_d72_A9-S9


title: lib5_d72_A11-S11


title: lib5_d72_A8-S8


title: lib5_d72_D8-S44


title: lib5_d72_A4-S4


title: lib5_d72_A2-S2


title: lib5_d72_A3-S3


title: lib4_melano_B11-S215

value: epidermis

value: time after 4HT treatment (4d)

value: Tyr::CreERT2/+; ROSA26RLSL-tdTomato/+


title: lib5_d72_A1-S1


title: lib4_melano_B8-S212


title: lib4_melano_B10-S214


title: lib4_melano_B6-S210


title: lib4_melano_B3-S207


title: lib4_melano_B7-S211


title: lib4_melano_B4-S208


title: lib4_melano_B2-S206


title: lib4_melano_B9-S213


title: lib4_melano_A11-S203


title: lib4_melano_A10-S202


title: lib4_melano_A8-S200


title: lib4_melano_A6-S198


title: lib4_melano_B5-S209


title: lib4_melano_A9-S201


title: lib4_melano_A7-S199


title: lib4_melano_A12-S204


title: lib4_melano_A5-S197


title: lib4_melano_A3-S195


title: lib4_melano_A4-S196


title: lib3_d31_H12-S192

source_name: d31_melanoma cell

value: tumor RGP

value: time after 4HT treatment (31d)


title: lib3_d31_H11-S191


title: lib4_melano_A1-S193


title: lib4_melano_A2-S194


title: lib3_d31_H8-S188


title: lib3_d31_H6-S186


title: lib4_melano_B1-S205


title: lib3_d31_H7-S187


title: lib3_d31_H4-S184


title: lib3_d31_H2-S182


title: lib3_d31_H3-S183


title: lib3_d31_H1-S181


title: lib3_d31_G10-S178


title: lib3_d31_G9-S177


title: lib3_d31_H5-S185


title: lib3_d31_G8-S176


title: lib3_d31_G12-S180


title: lib3_d31_G7-S175


title: lib3_d31_G11-S179


title: lib3_d31_G6-S174


title: lib3_d31_G4-S172


title: lib3_d31_G3-S171


title: lib3_d31_G2-S170


title: lib3_d31_G1-S169


title: lib3_d31_F12-S168


title: lib3_d31_H10-S190


title: lib3_d31_F11-S167


title: lib3_d31_F10-S166


title: lib3_d31_F9-S165


title: lib3_d31_F8-S164


title: lib3_d31_F7-S163


title: lib3_d31_F5-S161


title: lib3_d31_F4-S160


title: lib3_d31_F2-S158


title: lib3_d31_F6-S162


title: lib3_d31_F3-S159


title: lib3_d31_F1-S157


title: lib3_d31_E10-S154


title: lib3_d31_E12-S156


title: lib3_d31_E11-S155


title: lib3_d31_E8-S152


title: lib3_d31_E9-S153


title: lib3_d31_G5-S173


title: DB7938357_Etv4_Prom_B3_dCas9-YY1_mES_situ_rep2

data_processing:
library strategy: 4C-seq
Aligned using bowtie with options –k 1 –m 1 against the mm9 genome assembly.  All mapped reads were assigned to their corresponding restriction fragment and non-blind were used for quantile normalization in each sample together. After normalization profiles were smoothened using a 5kb running mean at 50bp steps.
mm9
Supplementary_files_format_and_content: WIG files contain RPM normalized read coverage in variably sized bins

extract_protocol:
Cells were lysed, digested with DpnII, religated, digested for a second time with either CviQI or BafII, and religated again. This template was purified and amplified with specific viewpoint primers to generate the libraries.
Cell lysis and sequential digest followed by ethanol precipitation

tag: restriction enzyme 1

value: DpnII

tag: restriction enzyme 2

value: BfaI

tag: forward primer

value: CAAGGGCAAGTAACCCGATC

tag: reverse primer

value: AATAGATACATCCCCCACCT


title: DB7938357_Etv4_Prom_B3_dCas9_mES_situ_rep3

tag: cell type


title: DB7938357_Etv4_Prom_B3_dCas9-YY1_mES_situ_rep1


title: DB7938357_Etv4_Prom_B3_dCas9-YY1_mES_situ_rep3


title: DB7938357_Etv4_Prom_B3_dCas9_mES_situ_rep2


title: lib3_d31_E6-S150


title: lib3_d31_E5-S149


title: YY1_Input

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
mm9
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Embryonic stem cells

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified."


title: DB7938357_Etv4_Prom_B3_dCas9_mES_situ_rep1


title: DC4688024_WT_mES_situ_rep3

data_processing:
Library strategy: 4C-seq
Aligned using bowtie with options –k 1 –m 1 against the mm9 genome assembly.  All mapped reads were assigned to their corresponding restriction fragment and non-blind were used for quantile normalization in each sample together. After normalization profiles were smoothened using a 5kb running mean at 50bp steps.
mm9
Supplementary_files_format_and_content: WIG files contain quantile normalized read coverage in variably sized bins

value: CviQI

value: CCAGGCTCGAGCGATAGATC

value: CTTCCTCTCCGAAGTTGAC


title: lib3_d31_E4-S148


title: lib3_d31_E3-S147


title: 281X_YY1

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified."

tag: antibody manu.

value: Santa Cruz

tag: antibody catalog


title: DC4688024_WT_mES_situ_rep2


title: lib3_d31_E2-S146


title: lib3_d31_E1-S145


title: lib3_d31_D12-S144


title: lib3_d31_D10-S142


title: DC4688024_Raf1_Prom_G2_mES_situ.rep2


title: DC4688024_Raf1_Prom_G2_mES_situ.rep3


title: lib3_d31_D11-S143


title: DC4688024_Raf1_Prom_G2_mES_situ.rep1


title: lib3_d31_D9-S141


title: lib3_d31_E7-S151


title: lib3_d31_D7-S139


title: lib3_d31_D8-S140


title: lib3_d31_D6-S138


title: lib3_d31_H9-S189


title: DB7938357_Etv4_Prom_B3_mES_situ_rep3


title: DB7938357_WT_mES_situ_rep1


title: lib3_d31_D5-S137


title: DB7938357_Etv4_Prom_B3_mES_situ_rep2


title: lib3_d31_D4-S136


title: lib3_d31_D3-S135


title: lib3_d31_D1-S133


title: DC4688024_WT_mES_situ_rep1


title: lib3_d31_C12-S132


title: lib3_d31_D2-S134


title: XW5

city: Gongzhuling

first: Lichun

last: Zhang

state: Jilin

address: 186 Dongxinhua St

department: Branch of Animal Husbandry

country: China

institute: Jilin Academy of Agricultural Science

data_processing:
Illumina Casava1.4 software used for basecalling.
Sequenced reads were qualified by FastQC, and mapping to Ovis aries reference genome version 4.0 by CLC genomic workbench 9.0
The differential expression gene were identified by Advantage RNA-seq plugin in CLC genomic workbench 9.0
Genome_build: Ovis aries (assembly Oar_v4.0)
Supplementary_files_format_and_content: tab-delimited text files include total counts, RPKM, TPM and CPM values for each Sample …

organism: Ovis aries

source_name: Skin

extract_protocol:
wool was shaved behind shoulder blade and skin was cut, immersed into RNAlater reagent were removed, flash frozen by liquid nitrogen and stored in -85°C. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit ) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small Tail Han sheep(STH)

value: Skin

value: 9 months


title: XW8


title: 30126

value: Super Merino sheep(SM)


title: XW3


title: lib3_d31_C11-S131

value: Tyr::CreERT2/+; BRafCA/+; Ptenl/l; ROSA26RLSL-tdTomato/+


title: 30034


title: lib3_d31_C8-S128


title: 128


title: lib3_d31_C9-S129


title: lib3_d31_C10-S130


title: DB7938357_WT_mES_situ_rep3


title: DB7938357_WT_mES_situ_rep2


title: lib3_d31_C6-S126


title: lib3_d31_C4-S124


title: lib3_d31_C3-S123


title: lib3_d31_C5-S125


title: lib3_d31_B12-S120


title: lib3_d31_C2-S122


title: lib3_d31_B10-S118


title: DB7938357_Etv4_Prom_B3_mES_situ_rep1


title: lib3_d31_B11-S119


title: lib3_d31_B9-S117


title: lib3_d31_C1-S121


title: pf2004-TP4_Fresh_Media

city: Tampa

first: Rays HY

last: Jiang

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Department of Global Health

institute: University of South Florida

description: test condition: -SerM medium containing 10 % human serum

data_processing:
RNAseq reads from each sample were aligned to the Plasmodium flaciparum reference genome (PlasmoDB version 28) using Tophat2, allowing a maximum of one mismatch per read.
The mapped reads were used to assemble known transcripts from the reference and their abundances were estimated using Cufflinks 2.2.1. The expression level of each gene was normalized as FPKM (fragments per kilobase of exon per million mapped reads).
Genome_build: PlasmoDB-28_Pfalciparum3D7_Genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Plasmodium falciparum

extract_protocol:
RNA was isolated from 500 μL Trizol solution by three extraction steps (1x using 500 μL phenol:chloroform:isoamyl alcohol (25:24:1); 2x using 100 μL chloroform). After vigorous shaking for 30 seconds, phases were separated by centrifugation (12000g, 10min, 4 °C). RNA was purified from 200 μL of the aqueous phase using an RNeasy micro kit (Qiagen) and corresponding protocol. RNA was eluted in 32 μL DEPC-treated water, quantified by Qubit (Life Technologies) and stored at -80 °C.
0.5 μg - 1.0 μg total RNA of each sample was used for library preparation. Libraries were prepared by using TruSeq Stranded mRNA kit (Illumina). Library quantification was conducted by qPCR and TapeStation (Agilent Technologies) measurements. Libraries were subsequently pooled and sequenced using 300 cycle V2 MiSeq reagent kit (Illumina)

tag: Stage

value: intraerythrocytic developmental cycle (IDC)

tag: hours post infection (hpi)

tag: culture condition

value: -SerM/Serum


title: lib3_d31_B6-S114

value: tumor RGP

tag: age


title: lib3_d31_B8-S116

value: time after 4HT treatment (31d)


title: lib3_d31_B7-S115


title: lib3_d31_B5-S113


title: lib3_d31_B4-S112


title: pf2004-TP4_Induced

description: test condition: -SerM medium

tag: strain

value: -SerM


title: lib3_d31_B3-S111


title: pf2004-TP4_Non-Induced

description: test condition: -SerM medium containing 20 μM LysoPC 16:0

value: -SerM/LysoPC


title: lib3_d31_B1-S109


title: lib3_d31_B2-S110


title: lib3_d31_A12-S108


title: lib3_d31_A10-S106


title: lib3_d31_C7-S127


title: pf2004-TP3_Fresh_Media


title: lib3_d31_A11-S107


title: pf2004-TP3_Non-Induced


title: lib3_d31_A8-S104


title: pf2004-TP3_Induced

description: test condition: -SerM medium


title: lib3_d31_A9-S105


title: CNBP RIP RNA (IP5)

city: Hefei

first: Pengfei

address: 443 Huang-Shan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) software was used to process image and identificate base.
Cutadapt software was used to clip linker sequences.
FastQC was used to conduct quality assessment of reads.
Hisat2 was used to map reads onto the reference genome.
StringTie was used as a assembler of RNA-Seq alignments into potential transcripts.
Ballgown was used to calculate the FPKM and expression levels of genes and transcripts.
Genome_build: HG19
Supplementary_files_format_and_content: Excel file with FPKM values

organism: Homo sapiens

growth_protocol: HCT116 cells were cultured in DMEM (Dulbecco's modified Eagle's medium) medium containing 10% fetal bovine serum.

extract_protocol:
To isolate protein-associated RNAs from the eluted immunocomplexes, samples were treated with proteinase K, and RNAs were extracted by phenol/chloroform.
Libraries were prepared according to Illumina's instructions accompanying the KAPA Stranded RNA-Seq Library Prep Kit (Illumina).

treatment_protocol: Two 10 cm2 dishes of HCT116 cells were washed three times with cold PBS and irradiated at 200 mJ/cm2 at 254 nm in HL-2000 HybriLinkerTM UV Crosslinker. Cells were collected and resuspended in 1 ml RIP buffer. Cells were then homogenized and followed by 3 rounds of sonication on ice. Cell lysates were precleared with protein A/G beads (Pierce) before they were incubated with protein A/G beads coated with the indicated antibodies (CNBP antibody (H-7) (sc-515387. Lot#C2416) ordered from Santa Cruz Biotechnology) at 4°C for 3 hr. After extensive washing, the bead-bound immunocomplexes were eluted using elution buffer (50 mM Tris [pH 8.0], 1% SDS, and 10 mM EDTA) at 65°C for 10 min.

tag: cell line


title: pf2004-TP2_Fresh_Media


title: lib3_d31_A6-S102


title: pf2004-TP2_Induced

description: test condition: -SerM medium


title: lib3_d31_A5-S101


title: pf2004-TP2_Non-Induced


title: Expressing control shRNA (PL-1)

extract_protocol:
Ninety-six hours after infection, total RNA from HCT116 cells expressing either control shRNA or LAST shRNA was extracted by phenol/chloroform.
Libraries were prepared according to Illumina's instructions accompanying the KAPA Stranded RNA-Seq Library Prep Kit (Illumina).

treatment_protocol: HCT116 cells were seeded into 6-wells plate. Twelve hours later, cells were injected with lentiviruses expressing control shRNA or LAST shRNA.

tag: shRNA

value: control


title: Expressing LAST shRNA (Sh-1)

value: lncLAST


title: input RNA (Put5)


title: lib3_d31_A4-S100


title: pf2004-TP1_Non-Induced


title: pf2004-TP1_Induced

description: test condition: -SerM medium


title: lib3_d31_A3-S99


title: lib3_d31_A2-S98


title: lib3_d31_A1-S97


title: NF54-TP4_Non-Induced


title: NRAS metastatic melanoma ChIP-FOSL2 JQ1 (-) [SKmel147]

city: New York

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description: ChIP-FOSL2 JQ1 (-)

data_processing:
Native ChIP-seq: Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 0.12.7) with parameters –l 40-65 –n 2 –S –best –k 1 –m 20. BAM files were generated using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10
XL ChIP-seq: Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 0.12.7) with parameters -k 1 -m 1 --best -S -n 2 -l 65 -q. BAM files were generated using SAMtools. duplicated reads were removed using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters -f BAM -g 2.7e9 -s 100 --bw 200 —slocal 1000 -q 0.01.
ATAC-seq: Reads were trimmed from Illumina adapters using in-house script. Reads (40bp Paired-end) were aligned using Bowtie2 (version  2.1.0) with parameters -q -X 2000. BAM files were generated using SAMtools. Reads that align to mtDNA, with quality value Q<30, as well as duplicated reads, were discarded using in-house scripts and Samtools.. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters –nomodel –nolambada –keepdup all –slocal 10000
RNA-seq: Reads (50bp, Paired-end) were aligned using TopHat (version 2.1.0). Transcriptome assemblies in FPKM, and differential expression ratios were computed with Cufflinks (version 2.1.1). In all samples, genes were called ‘expressed’ if normalized FPKM≥1.5. Genes were called downregulated upon JQ1 treatment if nFPKM≥1.5; log2FoldChange≤-0.625; and Padj<0.05. Genes were called overexpressed over NHM if nFPKM≥1.5 (in the melanoma sample); log2FoldChange≥2; and Padj<0.05. Genes were called downregulated upon AMIGO2 depletion if nFPKM≥1.5 (prior to depletion); log2FoldChange≤-1.2; and Padj<0.05. log2FoldChange≥1.2 for upregulated genes.
SEs calling: Enhancers (TEs) and super enhancers (SEs) were called based on ChIP-seq BRD4 enrichment in SKmel147 using the ROSE (Rank Ordering of Super-Enhancers) algorithm (stitching distance 12.5Kb and TSS exclusion zone size 2.5Kb. BRD4 levels were normalized to Input control; ChIP-Input)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: fastq - raw illumina reads. bigwig - aligned reads pileup. diff - gene expression in normalized FPKM

source_name: Cell culture

growth_protocol: grown in DMEM supplemented with 10% FBS, penicillin and streptomycin.

extract_protocol:
For FOSL2 and TEAD4, 10x10^6 cells, were crosslinked with 0.25M DSG for 45min, followed by 1% PFA crosslinking for 10 min at RT. ChIP was performed essentially as previously described (Tian et al., Two-step Crosslinking for Analysis of Protein-chroamtin Interactions. Methods Mol Biol, 2012. 809:105-120. Roe, J.S., et al., BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Mol Cell, 2015. 58(6): p. 1028-39).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).

treatment_protocol: untreated

tag: passage

tag: antibodies

value: FOSL2 (Santa Cruz SC-604)


title: NF54-TP4_Fresh_Media


title: HiChIP_HCT116_YY1

extract_protocol:
Cells were fixed with formaldehyde and then the genome was digested with restriction enzyme. Proximity ligation was carried out, followed by sonication and immunoprecipitation with an antibody (abcam #ab109237) directed towards YY1.
Library was prepared by Tn5 transposition per nextera instructions

value: Colorectal Cancer


title: lib3_d31_A7-S103

tag: tissue

tag: genotype


title: NF54-TP3_Induced

description: test condition: -SerM medium


title: HiChIP_K562_YY1

value: Chronic Myeloid Leukemia


title: ChIP_Jurkat_Input

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: T-ALL

extract_protocol: Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Jurkat

tag: chip antibody


title: HiChIP_Jurkat_YY1

value: T-cell Acute Lymphoblastic Leukemia


title: Normal Human Melanocytes Input-XL [NHM1]

description: Input-XL

source_name: Foreskin

growth_protocol: cultured in Melanocyte Growth Media 254 supplemented with Human Melanocyte Growth Supplement (Life Technologies), CaCl2 (0.2uM, Life Technologies: 50-9702) and PMA (10 ng/ml, Sigma: P8139).

value: foreskin, NHM1


title: NF54-TP3_Fresh_Media


title: pf2004-TP1_Fresh_Media


title: ChIP_Jurkat_YY1

value: Abcam


title: Normal Human Melanocytes ChIP-BRD4 (JQ1-) [NHM1]

description: ChIP-BRD4 (JQ1-)

extract_protocol:
For BRD2, BRD4 and MED1, 72x10^6 cells, were crosslinked with 1% PFA for 10 min at RT. ChIP was performed essentially as previously described (Roe, J.S., et al., BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Mol Cell, 2015. 58(6): p. 1028-39).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).

value: BRD4 (Bethyl Laboratories, A301-985A)


title: NF54-TP2_Fresh_Media


title: NF54-TP3_Non-Induced


title: NRAS metastatic melanoma Input-Native [SKmel2]

description: Input-Native

extract_protocol:
Native ChIP was done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).


title: NF54-TP2_Induced

description: test condition: -SerM medium


title: pf2004-TP0_TP_of_induction

description: This culture was split at the indicated time point and henceforth cultured under different test conditions.

value: time point of induction


title: NF54-TP2_Non-Induced

value: intraerythrocytic developmental cycle (IDC)


title: 96_15_YK-4-279

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LuCaP 96: treated with YK-4-279, sample: 15

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.64.0 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg19 human and mm9 mouse genomes using TopHat v2.0.12. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.)
Mean and standard deviation of fragment size were calculated with picard-tools v2.1.0.
Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are tab delimited text files. Each file contains 7 columns: Entrez gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped)

growth_protocol: CB-17 SCID mice (Charles River) were implanted subcutaneously with either LuCaP 23.1, 86.2, 35, or 96 tumor tissue.  Animals underwent rolling enrollment once tumors reached 100 mm3 and were randomized into one of two groups (Control vs. Treatment).

extract_protocol:
Flash frozen LuCaP PCa xenograft tissue samples were histologically evaluated for regions of viable tumor.  RNA was isolated from 16 animals (2 control, 2 treated from each line) with 10-micron sections from xenografts with ≥80% tumor content taken.  For xenografts with <80% tumor, stroma and necrotic tissue were removed prior to sectioning.  RNA was extracted using the Qiagen RNeasy Kit, (Qiagen Inc.), according to the manufacturer's protocol.  On-column DNase digestion was performed.  RNA concentration, purity, and integrity was assessed by NanoDrop (Thermo Fisher Scientific Inc) and Agilent Bioanalyzer.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

treatment_protocol: Group 1 (Control) received vehicle (37.5 L DMSO/ 12.5 L PBS) via intraperitoneal injection while Group 2 (Treatment) received YK-4-279 (150 mg/kg) in 37.5 L DMSO/ 12.5 L PBS.  All animals were dosed thrice weekly with dosing continued until tumors reached 1000 mm3.  Tumor volumes (TV) and body weights (BW) were measured twice weekly.  Serum PSA was measured weekly until euthanasia (Architect, Total PSA assay, Abbot Laboratories).  Animals were euthanized after up to 10 weeks of follow up, when tumors exceeded 1,000 mm3, or when animals became otherwise compromised.  The tumors were then divided equally into paraffin blocks with the remainder flash frozen for subsequent sequencing analysis.

tag: gender

value: male

tag: tumor type

value: LuCaP 96 PDX tumor

tag: treatment group


title: 96_17_YK-4-279

description: LuCaP 96: treated with YK-4-279, sample: 17


title: 96_34_Ctrl

description: LuCaP 96: control, sample: 34

source_name: LuCaP 96: control, sample: 34


title: BRAF metastatic melanoma Input-Native [SKmel239]

description: Input-Native


title: Normal Human Melanocytes Input-Native [NHM1]

description: Input-Native

tag: cell type


title: NF54-TP1_Fresh_Media

value: -SerM/Serum


title: NRAS metastatic melanoma ChIP-CTCF JQ1 (-) [SKmel147]

description: ChIP-CTCF JQ1 (-)

extract_protocol:
For CTCF, 72x10^6 cells, were crosslinked with 1% PFA for 10 min at RT. ChIP was performed essentially as previously described (Roe, J.S., et al., BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Mol Cell, 2015. 58(6): p. 1028-39).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).

value: CTCF (Millipore 07-729)


title: NF54-TP4_Induced

description: test condition: -SerM medium

value: -SerM


title: NF54-TP1_Induced

description: test condition: -SerM medium


title: NRAS metastatic melanoma Input-XL [SKmel147]

description: Input-XL


title: 96_18_Ctrl

description: LuCaP 96: control, sample: 18

source_name: LuCaP 96: control, sample: 18

value: control


title: NRAS metastatic melanoma ChIP-MED1 [SKmel147]

value: MED1 (Bethyl Laboratories, A300-793A)


title: NF54-TP1_Non-Induced

value: -SerM/LysoPC


title: 86.2_29_YK-4-279

description: LuCaP 86.2: treated with YK-4-279, sample: 29

value: LuCaP 86.2 PDX tumor


title: 86.2_23_YK-4-279

description: LuCaP 86.2: treated with YK-4-279, sample: 23


title: 86.2_28_Ctrl

description: LuCaP 86.2: control, sample: 28

source_name: LuCaP 86.2: control, sample: 28


title: Normal Human Melanocytes ChIP-BRD2 (JQ1-) [NHM1]

description: ChIP-BRD2 (JQ1-)

value: BRD2 (Bethyl Laboratories, A302-583A)


title: 86.2_15_Ctrl

description: LuCaP 86.2: control, sample: 15

source_name: LuCaP 86.2: control, sample: 15


title: SD40-3

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

data_processing:
The original image data was transferred into sequence data by base calling (using CASAVA version 1.5+), (defined as ‘raw reads’) and saved as fastq files that include the detailed reads sequences and the reads quality information.
To obtain clean reads, it is necessary to remove the dirty raw reads prior to data analysis. This process encompasses the following procedures: (1) remove reads with adaptors; (2) remove reads in which unknown bases are greater than 10%; (3) remove low-quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read)
A comparison of “clean reads” by SOAPaligner/soap2(parameters:-m 0 -x 1000 -s 28 -l 32 -v 2 -r 2) was carried out using the reference databases from large-scale transcriptome profiling
Genome_build: MRZV00000000; PRJNA354676, FASTA file of transcript IDs is available on the series record.
Supplementary_files_format_and_content: text file expected count and FPKM.

organism: Apostichopus japonicus

source_name: Apostihopus japonicus intestine

extract_protocol:
According to the instructions provided by the manufacturer of the RNase-free DNase (Qiagen Inc., Hilden, Germany), an RNeasy mini kit including DNase treatment was used to isolate total RNA from nine samples.
The RNA samples from three individuals per replicate were pooled in equal amounts for library construction. Libraries were prepared from the nine RNA pools by Beijing Genomics Institute, Shenzhen, China (BGI-Shenzhen). Strict quality control (QC) was applied in each experimental step to obtain highly reliable sequencing data. Magnetic beads with poly-T-oligos attached were used to isolate poly(A) mRNA. The target RNA was then purified. The target RNA was fragmented into short sequences, reverse-transcribed into single-strand cDNA using the N6 random primer (Promega, Madison, WI, USA), and synthesized into double-stranded cDNA (dscDNA) with DNA polymerase I and RNase H (Promega, Madison, WI, USA). Next, the end of the dscDNA was repaired and ligated with a sequencing adapter. The ligation product was amplified using specific primers. The PCR product was denatured by heating and the single strand DNA was cyclized using splint oligo and DNA ligase. Finally, high throughput sequencing was performed with the prepared cDNA libraries using the BGISEQ-500 RS platform at BGI-Shenzhen.

tag: salinity level

value: intestine


title: NRAS metastatic melanoma ChIP-BRD4 JQ1 (+) [SKmel147]

description: ChIP-BRD4 JQ1 (+)

treatment_protocol: treated with 10nM JQ1 (JQ1(+)) for 6 hours


title: NRAS metastatic melanoma ChIP-BRD2 JQ1 (+) [SKmel147]

description: ChIP-BRD2 JQ1 (+)


title: SD40-2


title: 35_29_YK-4-279

description: LuCaP 35: treated with YK-4-279, sample: 29

value: LuCaP 35 PDX tumor


title: 35_04_YK-4-279

description: LuCaP 35: treated with YK-4-279, sample: 04


title: SD40-1


title: SD30-3


title: 35_30_Ctrl

description: LuCaP 35: control, sample: 30

source_name: LuCaP 35: control, sample: 30


title: 35_11_Ctrl

description: LuCaP 35: control, sample: 11

source_name: LuCaP 35: control, sample: 11


title: SD30-2


title: 23.1_22_YK-4-279

description: LuCaP 23.1: treated with YK-4-279, sample: 22

value: LuCaP 23.1 PDX tumor


title: Normal Human Melanocytes ChIP-H3K27ac [NHM1]

value: foreskin, NHM1


title: NF54-TP0_TP_of_induction

tag: Stage


title: SD30-1


title: SD20-3


title: 23.1_16_YK-4-279

description: LuCaP 23.1: treated with YK-4-279, sample: 16


title: 23.1_14_Ctrl

description: LuCaP 23.1: control, sample: 14

source_name: LuCaP 23.1: control, sample: 14


title: NRAS metastatic melanoma ChIP-H3K4me1 [SKmel2]

value: H3K4me1 (Abcam, ab8895)


title: NRAS metastatic melanoma ChIP-BRD4 JQ1 (-) [SKmel147]

description: ChIP-BRD4 JQ1 (-)

value: BRD4 (Bethyl Laboratories, A301-985A)


title: Normal Human Melanocytes ChIP-H3K4me1 [NHM1]


title: SD20-2


title: NRAS metastatic melanoma ChIP-TEAD4 JQ1 (-) [SKmel147]

description: ChIP-TEAD4 JQ1 (-)

value: TEAD4 (Santa Cruz SC-101184)


title: h1ddm1.rep3.mnase_seq

status: Public on Nov 15 2017

city: Norwich

first: David

middle: B.

last: Lyons

state: Norfolk

address: Colney Lane

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

data_processing:
For all sequencing experiments, Illumina Hi-seq basecalls were converted to fastq with Illumina software 'bcl2fq' at the sequencing core facility
For bisulfite-seq, we used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 100 base reads were divided into the first 50 and the last 50 bases, 100 base reads were divided in half and 50 base reads were processed as single reads. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
For MNase-seq, paired-end reads were aligned using default bowtie2 settings and nucleosomes were identified with iNPS (Chen et al. 2014).   Group_1 is the best-positioned; Group_4 is the worst.
For RNA-seq, reads were mapped with Tophat and PCR duplicates were removed with samtools prior to identification of transcripts with cufflinks.  Transcript abundance estimates were made with kallisto/sleuth in the provided table, requires unaligned reads, which is why fastq and bam are both provided here.
Genome_build: TAIR10
Supplementary_files_format_and_content: bisulfite-seq single-c GFF files contain the per-base calculated methylated cytosine level; mnase-seq bigwig files are iNPS-smoothed read depth normalized to the library size (RPM) across the TAIR10 genome; bed files from MNase-seq are the nucleosome coordinates as called by iNPS (only 'MainPeaks') across the TAIR10 genome.

organism: Arabidopsis thaliana

source_name: 1-month-old leaf

growth_protocol: ddm1-10 (Zhang et al., 2016), h1.1 (Zemach et al., 2013) and h1.2 (Zemach et al., 2013) Arabidopsis thaliana (Columbia ecotype) were crossed to generate h1ddm1 and siblings for this study. ddm1 was not homozygous at any point prior to the F2 reported herein.  For MNase-seq, RNA-seq, and bisulfite-seq samples, plants were germinated on agarose plates supplemented with Gamborg’s B-5 growth media (GBP07, Caisson Labs). Following germination, they were transferred to soil and grown on a 16hr-light/8hr-dark long-day schedule.

extract_protocol:
Approximately 1 g of pulverized flash frozen rosette leaf tissue from F4 generation plants was resuspended on ice in nuclei isolation buffer (0.25 M sucrose, 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 0.9% Triton X-100, 1 mM PMSF, 1X protease inhibitor cocktail) and allowed to thaw for 15 minutes. The suspension was then strained once through Miracloth (EMD-Millipore, cat. no. 475855) and the nuclear pellet was centrifuged in a swinging-bucket rotor at 2000g in pre-chilled 5 ml conical tubes. Buffer was carefully aspirated from the loose pellet, which was subsequently resuspended in TM2 (10 mM Tris–HCl, pH 8, 2 mM MgCl2) and washed twice in TM2. The pellet was then resuspended in pre-warmed MNase digestion buffer (50 mM Tris-HCl, pH 8, 5 mM CaCl2) and 25 units of MNase were added per 0.1 g initial starting material and incubated for 10 minutes at 37°C with periodic agitation; reactions were stopped with EGTA (20mM final concentration). This was followed by the addition of SDS to a final concentration of 0.625%, increasing the temperature to 75°C, addition of RNase A for 10 minutes, and the addition of proteinase-K for an additional 15 minutes. DNA was then extracted with phenol/chloroform, pelleted in 70% EtOH, then resuspended in TE pH 8.0.
Verification of MNase digestion was carried out by fractionating one-tenth of the total reaction on a standard TAE gel and checking for a majority mononucleosomal fraction. Following removal of short DNA with beads, libraries were synthesized using total DNA (without PCR amplification) using the Nugen Ovation kit (Cat. no. 0319) following the manufacturer’s protocol.

value: rosette leaf

tag: genotype/variation


title: SD20-1


title: NRAS metastatic melanoma ChIP-BRD2 JQ1(-) [SKmel147]

description: ChIP-BRD2 JQ1(-)


title: h1ddm1.rep2.mnase_seq


title: 23.1_02_Ctrl

description: LuCaP 23.1: control, sample: 02

source_name: LuCaP 23.1: control, sample: 02

value: male


title: ddm1.rep2.mnase_seq


title: BRAF metastatic melanoma ChIP-H3K27ac [SKmel239]


title: h1ddm1.rep1.mnase_seq


title: NRAS metastatic melanoma ChIP-H3K27ac [SKmel2]


title: ddm1.rep1.mnase_seq


title: wt.rep2.mnase_seq

value: wt


title: h1.rep1.mnase_seq


title: wt.rep1.mnase_seq


title: dex2

city: Heidelberg

first: Jan

last: Lohmann

address: Im Neuenheimer Feld, 230

department: Stem Cell Biology

country: Germany

institute: Centre for Organismal Studies

data_processing:
Quality control: FastQC
Read alignment: TOPHAT2
BAM SAM conversion: samtools
Read table reconstruction: HT-seq
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with normalized read count table

source_name: inflorescence

growth_protocol: 23°C; 65% humidity;  16h light/8h dark; LED lights 200µE

extract_protocol:
RNAeasy plant mini kit according to manufacturer instructions (Qiagen, Hilden, Germany)
The RNA were poly A selected using the NEB Poly (A) Magnetic isolation module (7490), then the NEBnext Ultra Direction RNA Prep Kit (E7420) for Illumina with the NEBnext Multiplex Oligo's for Illumina (E7335). For RNA 1 µg inout was used.

treatment_protocol: 0.01% ethanol,0.015% Silwet, with or without 10µM dexamethasone,

tag: ecotype

value: inflorescence

value: 30 days after germination

tag: developmental stage

value: until flower stage 3-4


title: BRAF metastatic melanoma ChIP-H3K4me1 [SKmel239]


title: mock3

tag: age


title: dex1


title: mock2


title: mock1


title: WT2

data_processing:
Quality control: FastQC
Read alignment: BOWTIE2
Peak calling: MACS2
Peak annotation: HOMER
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with table HEC1-bound genes

source_name: seedling

growth_protocol: 23°C; 65% humidity;  16h light/8h dark; LED lights 200µE on 0.5xMS, 0.8% agarose plates

extract_protocol:
ChIP performed as described in (Schuster & al 2015)
ChIP libraries were generated with the Rubicon Thru-Plex DNA-seq kit

value: seedling

value: 12 days after germination

tag: tissue type

value: aboveground tissues


title: WT1


title: 35S-HEC1-1


title: RNA_NHBEC_CalPolyIC

first: Ting

last: Wang

address: 1100 Fairview Ave. N.

department: Clinical Research

institute: Fred Hutchinson Cancer Research Center

data_processing:
Quality control for raw fastq files were performed with FastQC
Low quality reads and 3’ adapters were trimmed with Trim Galore! and Cutadapt.
The trimmed ATAC-seq reads were aligned to hg19 with Bowtie2, and the trimmed RNA-seq were aligned to hg19 with STAR v2.5.2a
ATAC-seq peaks were called using MACS2, read counts within peaks were counted using BEDTools multicov, RNA expressions were quantified using RSEM
Read coverage bigWig file for each sample was generated with bedGraphToBigWig or bam2wig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format, signal means normalized read coverage

source_name: Normal human bronchial epithelium

growth_protocol: BEAS-2B, NHBEC, and AAEC were cultured according to ATCC (American Type Culture Collection)-recommended protocols. After flask treatment with coating mixture (0.01 mg/mL fibronectin, 0.03 mg/mL bovine collagen type I and 0.01 mg/mL bovine serum albumin [BSA] dissolved in Bronchial Epithelial Growth Medium [BEGM™]), cells were inoculated at 3000 cells per cm2 with BEGM without antibiotics, and incubated at 37o C with 5% carbon dioxide. Cells were inspected daily and culture media was changed every 2-3 days. Once the cells reached 80% confluence, four treatments were performed on cells in 4 different wells:1) BEGM complete media at time 0 and 20 min (“Sham”); 2) 100 nM of calcitriol at time 0 and 20 min (“Calcitriol”); 3) BEGM complete media at time 0 then 10 µg/ml poly I:C at 20 min (“Poly I:C”); and 4) 10 µg/ml poly I:C at time 0 followed by 10 µg/ml poly I:C and 100nM Calcitriol at 20 min (“Calcitriol/Poly I:C”).

extract_protocol:
ATAC-Seq was performed using a protocol modified from Buenrostro et al. Briefly, cells (50,000) were spun down at 500×g for 5 min at 4°C, washed with 50 µl cold 1x PBS buffer, and spun again. Cells were re-suspended in 50 μl cold lysis buffer and spun immediately at 500×g for 10 min at 4°C. Transposition reaction (25 μl TD, 2.5 μl TDE1, 22.5 μl Nuclease Free H2O) was performed immediately and incubated at 37°C for 30 min. Transposed DNA was purified using the MinElute PCR Purification Kit (Qiagen, Germantown, MD) prior to PCR amplification for 6 cycles (1 cycle: 5 min 72°C, 30 sec 98°C; then 5 cycles: 10 sec 98°C, 30 sec 63°C, 1min 72°C). To reduce PCR GC and size bias, the appropriate number of additional PCR cycles was determined using qPCR; this method has the additional benefit of serving as an estimate of library complexity. Total RNA was immediately extracted from the head of the pancreas using TRIzol (Ambion). RNA was treated with DNase I (Zymo Research) at room temperature for 20 minutes. The concentration of DNase I-treated RNA was measured using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific) and the integrity of the DNase I-treated RNA was analyzed on the Agilent TapeStation. All DNase I-treated RNA samples used for RNA library construction had RNA Integrity Numbers (RINs) above 6.4.
Amplified DNA fragments were purified using the Qiagen MinElute PCR Purification Kit, and purified DNA library quality assessment was performed using a high-sensitivity DNA chip on Bio-Analyzer (Agilent technologies, Santa Clara, CA). As large fragments (>1kb) are relatively hard to quantify and may result in reduced clustering efficiency during sequencing, we carried out size selection prior to sequencing, in order to eliminate the potentially confounding long fragments and maintain high library complexity. We excised fragments in window of 140-650 bp using pippin prep (Sage Science, Beverly, MA). The size-selected library was checked on the Bio-Analyzer and library quantitation was performed using the KAPA Library Quant Kit for Illumina Sequencing Platforms (KAPA Biosystems, Wilmington, MA). RNA libraries were prepared for sequencing using Illumina TruSeq Total Stranded RNA sample preparation kit with ribosomal depletion.
Libraries were submitted for 75bp paired-end sequencing on the Illumina NextSeq 500 sequencer.

value: Normal human bronchial epithelium

tag: treatment

value: Calcitriol + Poly I:C


title: RNA_NHBEC_PolyIC

treatment_protocol: Once the cells reached 80% confluence, four treatments were performed on cells in 4 different wells:1) BEGM complete media at time 0 and 20 min (“Sham”); 2) 100 nM of calcitriol at time 0 and 20 min (“Calcitriol”); 3) BEGM complete media at time 0 then 10 µg/ml poly I:C at 20 min (“Poly I:C”); and 4) 10 µg/ml poly I:C at time 0 followed by 10 µg/ml poly I:C and 100nM Calcitriol at 20 min (“Calcitriol/Poly I:C”).

value: Poly I:C


title: h1.rep2.mnase_seq


title: RNA_NHBEC_Cal

value: Calcitriol


title: RNA_AAEC_Sham

source_name: Asthma human bronchial epithelium

value: Asthma human bronchial epithelium

value: Sham (culture media)


title: RNA_BEAS2B_Cal

value: BEAS-2B immortalized human bronchial epithelium


title: RNA_BEAS2B_Sham


title: RNA_AAEC_PolyIC


title: RNA_BEAS2B_PolyIC


title: RNA_NHBEC_Sham


title: h1ddm1_bsseq

extract_protocol: Genomic DNA (gDNA) was extracted from 1-month-old Arabidopsis thaliana rosette leaves with the DNeasy plant mini kit (Qiagen, cat. no. 69104) per the manufacturers’ instructions. Libraries were prepared from roughly 500ng of purified gDNA that was sheared to approximately 400bp on a Misonix water bath sonicator, then purified using 1.2X volume of Agencourt Ampure beads (referred to as “beads” henceforth, cat. no. A63881). Following ligation of methylated Truseq sequencing adapters (Illumina), bisulfite conversion of DNA was carried out according to manufacturer’s protocol (Qiagen Epitect Kit, cat. no. 59104) except without using carrier RNA. DNA was purified twice with 1.2X beads and converted a second time to ensure complete bisulfite conversion of unmethylated cytosine. NEB next indexing primers (cat. no. E7335S) were used for generating multiplexed libraries during PCR amplification of libraries.


title: RNA_BEAS2B_CalPolyIC


title: dex3


title: RNA_AAEC_CalPolyIC


title: ATAC_NHBEC_Sham


title: RNA_AAEC_Cal


title: Rao-2017-RAD21-mAC-4-T-S

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Library strategy: PRO-Seq
For analysis of PRO-Seq data, we aligned 30-bp paired-end reads to the hg19 reference (bowtie2 v2.1.0, (Langmead and Salzberg, 2012)), removed duplicate reads (Picard http://picard.sourceforge.net), and discarded reads with MAPQ < 30.
We counted reads overlapping RefSeq genes (collapsed by gene symbol to the longest isoform) — this quantification procedure includes signal both at the paused position (near the TSS) as well as in the gene body.
We identified genes showing significant differences in transcription with DESeq2 (Love et al., 2014), excluding genes with zero coverage in all samples and calling significance at Benjamini-Hochberg corrected p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: counts files, DESeq2 results, tdf files

source_name: Colorectal carcinoma

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
To measure changes in transcription resulting from cohesin loss, we performed precision run-on sequencing (PRO-Seq) (Jonkers and Lis, 2015), a variant of global run-on sequencing (GRO-Seq), using a single biotinylated nucleotide (biotin-11-CTP) as previously described (Engreitz et al., 2016). We made one modification to the protocol: at the end of each biotin enrichment, we eluted biotinylated RNAs from the streptavidin-coated magnetic beads by heating beads in 25 μl of 20 mM Tris-HCl pH 7.5, 10 mM EDTA, 2% N-lauroylsarcosine at 95°C for 5 minutes, followed by a magnetic-bead nucleic acid purification with 20 μl of MyONE SILANE beads. During the nuclei preparation step, we processed pairs of RAD21-mAC cells with and without auxin treatment in parallel. In addition, we performed PRO-Seq on HCT-116 CMV-OsTIR1 cells, the parental cell line of RAD21-mAC containing the OsTIR1 gene integrated at the AAVS1 locus and no mAID tags integrated on any protein.
standard Illumina library construction protocol, The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols

treatment_protocol: Cells were treated with 500uM auxin as described in the characteristics above

tag: cell line

value: 500uM auxin (360 min)


title: ATAC_NHBEC_CalPolyIC


title: ATAC_NHBEC_PolyIC


title: 35S-HEC1-2


title: Rao-2017-RAD21-mAC-3-T-S


title: ATAC_BEAS2B_Sham


title: Rao-2017-RAD21-mAC-3-NT-S


title: Rao-2017-RAD21-mAC-2-T-S


title: ATAC_BEAS2B_PolyIC


title: ATAC_BEAS2B_CalPolyIC


title: Rao-2017-RAD21-mAC-2-NT-S


title: Rao-2017-RAD21-mAC-1-T-NS


title: ATAC_BEAS2B_Cal


title: ATAC_AAEC_Sham


title: Rao-2017-RAD21-mAC-1-NT-NS


title: Rao-2017-CMV-OsTIR1-4-T-S


title: ATAC_AAEC_CalPolyIC


title: Rao-2017-CMV-OsTIR1-4-NT-S


title: ATAC_AAEC_PolyIC


title: ATAC_AAEC_Cal


title: Rao-2017-CMV-OsTIR1-3-T-S


title: Input

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

data_processing:
The data was processed as described in the following paper https://doi.org/10.1038/ng.3662. Details about the analysis can also be found at https://github.com/sblab-bioinformatics/dna-secondary-struct-chrom-lands/blob/master/Methods.md.
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at https://github.com/taoliu/MACS/.

source_name: HaCaT cell line

growth_protocol: HaCaT cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% FBS.

extract_protocol:
Chromatin was isolated from HaCaT cells that were cross-linked using 1% formaldehyde for 10 min at RT and prepared using a ChIP-qPCR Kit (Chromatrap, cat. no. 500117). Chromatin was sonicated using a Bioruptor Plus (Diagenode) to give a fragment distribution of 100-500 bp. For further details see methods section in the associated manuscript.
G4 ChIPed DNA was subjected to Nextera library preparation (Illumina, cat. no. FC-121-1030). For further details see methods section in the associated manuscript.

value: HaCaT


title: BG4-ChIP-rep2


title: BG4-ChIP-rep3


title: Rao-2017-CMV-OsTIR1-2-T-S


title: Rao-2017-CMV-OsTIR1-2-NT-S


title: Rao-2017-RAD21-mAC-4-NT-S


title: Rao-2017-CMV-OsTIR1-3-NT-S


title: ATAC_NHBEC_Cal


title: Rao-2017-CMV-OsTIR1-1-NT-NS


title: BG4-ChIP-rep1


title: TEAD4 KD RNASeq 2

first: Gonzalo

last: Lopez

address: 1399 Park avenue

department: Genetics and Genomic Sciences

data_processing:
The RNA-Seq libraries were aligned to hg19 human genome using TopHat
Raw counts of each gene were generated using GenomicFeatures R-system package (Bioconductor)
The data was then normalized using voom implemented in edgeR R Bioconductor package
The ChIP-Seq libraries were aligned to hg19 human genome using bowtie 1.1.1 with parameters -k 2 -m 2 --best --sam and -l 40
Peaks were called using MACS2 with corresponding input or IgG control, -p 1e-9 and --keep-dup=auto
Genome_build: hg19
Supplementary_files_format_and_content: txt and bed files were generated containing gene level normalized values and peak calling respectively

source_name: bone marrow metastatic neuroblastoma

growth_protocol: BE2 cell lines were maintained in DMEM or RPMI-1640 supplemented with 10% FBS, 20 mM L-glutamine and antibiotics

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep kit (Zymo Research)
RNA-Seq libraries were made with Illumina TruSeq RNA Sample Prep protocol by Columbia Genome Center and sequenced on Illumina NextSeq 500

treatment_protocol: Lentiviral particles encoding  2 hairpins against MYCN using pLKO.1-puro lentiviral constructs (Sigma)

value: neuroblastoma cell line


title: TEAD4 KD RNASeq 3


title: TEAD4 KD RNASeq 1


title: Control RNASeq 5

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3)
The data was then normalized using voom implemented in edgeR R Bioconductor package
Genome_build: hg19
Supplementary_files_format_and_content: txt  files were generated containing gene level normalized expression values

growth_protocol: BE2 cell lines were maintained at 80 – 90% confluence in DMEM/F-12 supplemented with 10% FBS and antibiotics

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep kit (Zymo Research) according to manufacturer’s indications
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq. Libraries are then sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.

treatment_protocol: a 1:1 mix of lentiviral particles carrying empty TRC1 and TRC2 Plko.1-puro vectors was used as a negative control

value: control


title: WWTR1 KD RNASeq 2

treatment_protocol: Two short hairpin RNA constructs against WWTR1 were purchased from Sigma (TRCN0000019469, TRCN0000370007), packaged in HEK293T cells, and used in a 1:1 ratio for lentiviral-mediated cell transduction

value: shMYCN


title: MYCN KD RNASeq 3

treatment_protocol: Lentiviral particles encoding 2 hairpins against TEAD4 using pLKO.1-puro lentiviral constructs (Sigma)


title: MYCN KD RNASeq 2


title: WWTR1 KD RNASeq 1


title: Control RNASeq 4


title: MYCN KD RNASeq 1


title: Control RNASeq 3

treatment_protocol: Lentiviral particles encoding control shRNA (SHC002, SHC202)


title: Control RNASeq 2


title: Control RNASeq 1


title: Pooled_ETV6_IP

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

description: Negative IP/background

data_processing:
Raw reads were aligned using bowtie v2.2.3 and filtered using a mapping quality threshold of 20. Reads were merged for both ETV6 and ETV6-HA populations (n=3) and peaks were called in the ETV6-HA condition over the background obtained in the ETV6 condition (negative IP control) using MACS v2.1.1.20160309 with a q-value threshold of 0.1
Genome_build: hg19

source_name: pre-B leukemia cell line, Negative IP/background

growth_protocol: Reh (ATCC ® CRL-8286™), a t(12;21)-positive pre-B ALL cell line, was maintained in RPMI 1640 (Wisent) 10% Fetal Bovine Serum (FBS; Wisent) in a 5% CO2 incubator at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and ETV6-HA/DNA complexes were isolated with Anti-HA magnetic beads. Protein/DNA complexes were eluted from the beads by competition with HA peptides prior to reverse-crosslinking and standard purification using phenol/chloroform/isoamyl alcohol
The purified ChIP DNA was processed through TruSeq ChIP Sample Preparation Kit (Illumina) according to the manufacturer protocol

treatment_protocol: 200ng of concentrated virus (pCCL ETV6-HA or ETV6) were added to cells with polybrene (Sigma) to a final concentration of 8μg/mL. 24h post-infection, medium was changed with fresh RPMI 1640 10% FBS. These cells were maintained 2 weeks in culture before carrying out further experiments.

value: Reh (ATCC CRL-8286)

tag: transduction

value: pCCL ETV6

value: Anti-HA magnetic beads (Thermo Fisher Scientific)


title: Control RNASeq 3


title: Pooled_ETV6_HA_IP

description: Positive IP/test condition

source_name: pre-B leukemia cell line, Positive IP/test condition

value: pCCL ETV6-HA


title: APS_42

city: Ann Arbor

first: Amr

last: Sawalha

state: MI

address: 1150 W. Medical Center Drive

institute: University of Michigan

data_processing:
Data formatting and demultiplexing of reads in FASTQ format was performed using bcltofastq-1.8.4
Read cleaning was performed using Trimmomatic-0.32 with parameters "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:25" and PhiX screening with Bowtie-2.2.1 using parameters "-N 1"
Read mapping was performed using SHRiMP 2.2.3 with parameters "--qv-offset 33 --all-contigs" and aligned reference genome build hg19
Raw gene-level counts for each sample were calculated using edgeR 3.8.5
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files contain raw count values at the gene level for each sample

source_name: Neutrophil

extract_protocol:
Citrated blood was fractionated by density gradient centrifugation using Ficoll-Paque Plus (GE Healthcare).  Neutrophils were then further purified by dextran sedimentation of the red blood cell layer, before lysing residual red blood cells with 0.2% sodium chloride.  Neutrophil preparations were at least 95% pure as confirmed by both flow cytometry and nuclear morphology. Purified neutrophils were resuspended in TriPure Isolation Reagent (Roche) and stored at -80 degrees.  RNA was later prepared by the Direct-zol RNA MiniPrep kit (Zymo Research) according to manufacturer’s instructions.  RNA Integrity Number (RIN) was >7 for all included samples.
Sequencing libraries were created using the TruSeq Stranded mRNA library kit (Illumina) and 100bp single-end mRNA reads were generated on an Illumina HiSeq 2500 instrument.

value: Neutrophil

tag: disease

value: primary antiphospholipid syndrome

tag: Sex

value: M

tag: ethnicity

value: White


title: APS_50


title: APS_39

value: F


title: Rao-2017-CMV-OsTIR1-1-T-NS


title: APS_51


title: APS_47

value: Black


title: P12_m6A_Null_IP rep 2

city: Bethesda

first: Pedro

middle: J

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Libraries were separated by barcode, matching reads were collapsed and barcodes removed. Single-end RNA-Seq reads were mapped to the mouse genome (mm9 assembly) using STAR.
Reads for each transcript were extracted using HTSeq. Differential gene expression was calculated with DESeq2. To determine sites of m6A modification RPKM and winscore of each 100bp sliding window along the transcriptome is calculated using in house generated script.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include fold change and p-value calculated by DESeq2 (DGE_P12 and DGE_P14). tab-delimited text file (m6A_peaks_winscore.txt) include windscore for 100bp windows enriched after m6A immuprecipitation.

source_name: testes

extract_protocol:
Total RNA was isolated using TriZol.
Total RNA was subjected to two rounds of poly(A) RNA selection, using the MicroPoly(A) Purist kit, (Life Technologies) according to the manufacturer's protocol. RNA was fragmented by incubating for 45 second with pre-warmed Zinc chloride buffer (10 mM ZnCl2, 10mM Tris-HCl, ph 7.0), to fragment the RNA to ~100 nucleotide long fragments. The reaction was stopped with 0.2M EDTA and immediately placed on ice. A fraction of teh RNA was subjected to immunoprecipitation with a anti-m6A antibody. A strand specific protocol was used to generate cDNA from input and anti-m6A immunoprecipitated samples.

tag: strain

tag: genotype

value: YTHDC2/BGCN Null

tag: fraction

value: RNA fraction of m6A IP


title: P14_m6A_WT rep 2

value: Wild Type

value: Total RNA


title: P14_m6A_WT rep 1


title: P14_m6A_Null rep 2


title: P14_m6A_Null rep 1


title: P12_m6A_Null_IP rep 1


title: APS_37

tag: cell type


title: APS_38


title: P12_m6A_WT_IP rep 1


title: CON_69

value: healthy


title: P12_m6A_Null rep 1


title: P12_m6A_Null rep 2


title: P12_m6A_WT_IP rep 2


title: APS_6


title: P12_m6A_WT rep 2


title: CON_65


title: CON_67


title: CON_64


title: APS_12


title: fRIP_WT-IP rep 2

data_processing:
For fRIP libraries, pair-end RNA-Seq reads were first mapped to mouse ribosomal RNA. Reads aligning to the rRNA were discarded, and remaining reads mapped to the mouse genome (mm9 assembly) using STAR.
Reads for each transcript were extracted using HTSeq. Enrichment was calculated with multifactor analysis using DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include fold change and p-value calculated by DESeq2.

extract_protocol:
P12 testes were cross-linked in 0.1% formaldehyde at room temperature for 10 minutes. Crosslinking reaction was quenched by adding glycine to a final concentration of 125mM and incubating for 5 minutes at room temperature. Cross-linked testes were washed 2x in 4C PBS, flash frozen and stored at -80ºC. Frozen testes were resuspended in RIPA lysis buffer (50mM Tris-HCl pH8.0, 150mM KCl, 0.1% SDS, 1% Triton-X-100, 5mM EDTA, 0.5% sodium deoxycholate, 0.5mM DTT, 1x Complete protease inhibitor, and 100U/mL RNasOUT). Testes were mechanically disrupted in lysis buffer and incubated for 15 minutes at 4C then sonicated using a Bioruptor (1 cycle, 30 sec on/off, medium setting at 4C). After lysis, lysates were centrifuged for 10 minutes at max speed at 4C. The supernatant was collected and diluted with an equal volume of binding/wash buffer (25mM Tris-HCl pH7.5, 150mM KCl, 5mM EDTA, 0.5% NP-40, 0.5mM DTT, 1x Complete protease inhibitor, and 100U/mL RNasOUT). Lysates were precleared by incubation with uncoupled Protein A Dynabeads (Invitrogen) for 1 hour at 4C. Following preclearing, 10% of the lysate was saved for input and stored at 4C, and the remaining lysate was added to Protein A Dynabeads chemically crosslinked to rabbit anti-YTHDC2 (Bethyl laboratories) with dimethylprimelimidate (DMP, Sigma) (5.4 mg DMP per mL 0.2M triethanolamine) per manufacture’s instructions, and incubated for 4 hours at 4C. After incubation, samples were washed 4x with binding/wash buffer for 10 minutes at 4C. Beads and Input samples for 2 biological replicates of both wild type and Ythdc2-/- were suspended in PK buffer (10mM Tris pH 7.0, 100mM NaCl, 1mM EDTA, 0.5% SDS), 5uL Proteinase K and 1uL RNasOUT (100uL total volume). Samples were incubated for 1 hour at 42C and then 1 hour at 55C. RNA was isolated using TRIzol (Life Technologies), according to manufacturer’s instructions.
Ribosomal RNA was removed from the Input and fRIP samples using the RiboMinus Eukaryote System v2 Kit (Ambion) following manufacture’s instructions. Library preparation for high-throughput sequencing was performed using a TruSeq RNA Sample preparation Kit (Illumina) per manufacture’s instruction, except RNA was not fragmented with FPF solution.

value: RNA fraction of YTHDC2/BGCN IP


title: CON_63


title: CON_62


title: fRIP_WT-IP rep 1


title: fRIP_WT-input rep 1


title: fRIP_WT-input rep 2


title: CON_60


title: fRIP_Null-IP rep 2


title: fRIP_Null-input rep 1


title: CON_61


title: fRIP_Null-input rep 2


title: fRIP_Null-IP rep 1


title: Sample 16_noninfected-Experiment-2-RIG-I-input

city: Chicago

first: Michaela

middle: U

last: Gack

state: IL

address: 920 E 58th St

department: Microbiology

institute: The University of Chicago

data_processing:
Raw read quality trimming with TRIM Galore
Tophat2 alignment to hg38 or HSV-1 F strain
htseq-count  and subsequent TC normalisation in R
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includes transcript abundance and gene name

growth_protocol: HEK 293T cells were routinely grown in DMEM supplemented with 10% FCS and Penicillin/Streptomycin

extract_protocol: Samples 1-8 or 11-18 labeled "PD" were subjected to an FLAG pulldown to purify overexpressed FLAG-GFP or FLAG-RIG-I. After digestion of the protein, RNA was isolated by phenol-chloroform extraction. For samples 1-8 or 11-18 labeled "input" and samples 9-10, total RNA was purified from whole cell lysates by phenol-chloroform extraction.

treatment_protocol: For samples 1-8 and 11-18, HEK 293T cells were transfected with FLAG-RIG-I or FLAG-GFP using polyethylenimine. 24 h later, cells were infected with either HSV-1mut (MOI 300) (Sample 1-8) or left uninfected (Sample 11-18). For samples 9-11, HEK 293T cells were infected with wild-type HSV-1 or HSV-1mut (both MOI 1)

value: HEK 293T

value: human embryonic kidney cells

tag: passage

tag: infected with

value: none (non-infected)

tag: method

value: total


title: Sample 17_noninfected-Experiment-2-GFP-PD

value: pulldown


title: Sample 18_noninfected-Experiment-2-GFP-input


title: CON_57

value: Neutrophil


title: ILCp.5

first: Margaret

middle: C

last: Cam

institute: NIH

data_processing:
Basecalling by RTA 1.18.64, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 1.8.4, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq fastq reads were aligned to mouse genome (mm10) using STAR (v. 2.4.0h) on 2-pass mode with mouse gencode (release 4) gtf
Genes were subsequently counted using Rsubread and further normalized using TMM (edgeR) and analyzed for gene expression changes using limma-voom with quantile normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Genes were subsequently counted using Rsubread and further normalized using TMM (edgeR) and analyzed for gene expression changes using limma-voom with quantile normalization. The gene and sample-specific normalization factors were then used to correct counts to generate bedgraph files used for further visualization.

source_name: ILCp

growth_protocol: samples were isolated by cell sorting from bone marrow and thymus single cell suspensions

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen)
mRNA sequencing libraries were prepared using the SMARTer Ultra Low Input RNA Kit v3 (Clontech) and Nextera XT DNA library preparation kit (Illumina)

value: Plzf-cre-GFP/+

tag: tissue

value: bone marrow

tag: sorting profile

value: linlow Ly-6Dlow CD122low Kitpos GFPhigh Thy-1.2pos IL-7Rahigh a4b7pos

tag: batch


title: ILCp.4


title: Sample 14_noninfected-Experiment-1-GFP-input


title: Sample 15_noninfected-Experiment-2-RIG-I-PD


title: Sample 13_noninfected-Experiment-1-GFP-PD


title: ILCp.2


title: Sample 12_noninfected-Experiment-1-RIG-I-input


title: P12_m6A_WT rep 1

tag: developmental stage


title: EILP.7

source_name: EILP

value: linlow Ly-6Dlow CD122low Kitpos GFPhigh Thy-1.2low IL-7Ra int/low


title: ILCp.1


title: Sample 11_noninfected-Experiment-1-RIG-I-PD


title: Sample 10_HSV-1 WT

source_name: HEK293T-HSV-1 WT

value: wildtype HSV-1


title: Sample 8_Experiment-2-GFP-input

tag: transfected with

value: FLAG-GFP

value: HSV1 K220A mutated


title: Sample 9_mock infected cells

source_name: HEK293T-mock infected cells

tag: cell line

value: none (mock-infected)


title: EILP.6


title: EILP.5


title: EILP.4


title: Sample 7_Experiment-2-GFP-PD


title: EILP.3


title: Sample 6_Experiment-2-RIG-I-input

value: FLAG-RIG-I


title: EILP.2


title: EILP.1


title: Sample 4_Experiment-1-GFP-input


title: ALP.6

source_name: ALP

value: linlow Ly-6Dlow Kitpos IL-7Rapos Flt3high


title: ALP.7


title: Sample 2_Experiment-1-RIG-I-input


title: ALP.5


title: ALP.4


title: Sample 1_Experiment-1-RIG-I-PD


title: Sample 5_Experiment-2-RIG-I-PD


title: Sample 3_Experiment-1-GFP-PD


title: ILCp.3


title: ALP.1


title: TEAD4 ChIPSeq

growth_protocol: neuroblastoma cell lines were sourced from the American Type Tissue Culture Collection, and kept in growth medium of RPMI+10% heat-inactivated FCS with 1% penicillin–streptomycin

extract_protocol: Cells were lysed for protein, with subsequent protein quantified by spectrophotometry. Protein was resolved on 8–14% Tris-Bis gels, transferred to PVDF membranes, blocked and subjected to primary and secondary antibodies

treatment_protocol: primary antibody was ab58310; abcam

value: neuroblastoma cell line

tag: chip antibody

value: anti-TEAD4 (ab58310; abcam)


title: ALP.3


title: Input ChIPSeq

treatment_protocol: input antibody

value: input