title: GSCLC4_MS094_121

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description:
Single cell transcriptome of amplified cDNA from GSCLC cell
AcrAct_EGFP reporter

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome mm10 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and mm10 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample ...

source_name: GSCLC

growth_protocol: GSC_2 was derived from independent P7 testes. GSCLC_4 was derived from reconstituted testes cultured under condtion1 (cultured at 34°C for 3 weeks).

extract_protocol:
GSCLCs/GSCs were incubated in 0.05% of Trypsin- 0.53mM EDTA for around 4 min at 37°C, and dispersed into single cells in 1% (vol/vol) KSR/PBS (Thermo Fisher Scientific). The cDNA synthesis was performed according to the SC3-seq method described previously (Nakamura et al., 2015).
The cDNA libraries for Nextseq500 (Illumina) were constructed based on the SC3-seq method with several modifications: Five nanograms of quality-checked cDNAs were added to the pre-amplification buffer [1 × ExTaq buffer [Takara Bio (RR006), Shiga, Japan], 0.2 mM of each dNTP [Takara Bio (RR006)], 0.01 µg/µl of the N-V3 (dT)24 primer (attachment of amine at the 5-prime end), 0.01 µg/µl of the V1(dT)24 primer and 0.025 U/ µl of ExTaqHS [Takara Bio (RR006)]], and were amplified by four cycles of PCR. The surplus primers and PCR byproducts such as primer dimers were removed by three rounds of purification using a 0.6 × volume of AMPureXP beads for each round [Beckman Coulter (A63881), Tokyo, Japan] according to the manufacturer’s instructions. The purified cDNAs were diluted to 50 µl by DDW and fragmented by shearing with Covaris E220 (duty factor: 20%; peak incident power: 175; cycles per burst: 200; duration: 60 s; an intensifier was installed in the case of E220) [Covaris, Woburn, MA, USA] and then end-polished in the End-polish buffer [1×NEBnext EndRepair Reaction buffer [NEB (B6052S), Ipswich, MA, USA], 0.01 U/ µl of T4 DNA polymerase [NEB (M0203)] and 0.033 U/ µl of T4 polynucleotide kinase [NEB (M0201)]] for 30 min at 20°C. After incubation, a 0.7 × volume of the AMPureXP was immediately added, the solution was mixed for more than 20 min and then the supernatant was transferred to a 0.9 × volume of the AMPureXP reagent and the cDNAs were purified. Next, to provide the purified cDNAs with an Rd2SP-adaptor sequence, the cDNAs were incubated in 30 µl of the Rd2SP adaptor extension buffer [1 × ExTaq Buffer, 0.23 mM of each dNTP, 0.67 µM of the Rd2SP-V1(dT)20 primer, 0.033 U/µl of ExTaqHS] using the following thermal cycler program: 95°C for 3 min, 67°C for 2 min, and 72°C for 2 min. The reactions were terminated by chilling in an ice-block, and after the addition of 20 µl of the Rd1SP-adaptor ligation buffer [a mixture of 10 µl of 5 × NEBNext Quick Ligation Reaction Buffer [NEB (B6058S)], 0.6 µl of 5 µM of the Pd1SP-T adaptor and 1 µl of T4 ligase [NEB (M0202M)]], the solution was incubated for 15 min at 20°C and for 20 min at 72°C. After two rounds of cDNA purification by adding a 0.8 × volume of AMPureXP, the cDNAs were added into the final amplification buffer [1 × ExTaq buffer, 0.2 mM of each dNTP, 1 µM of the S5XX index primer, 1 µM of the N7XX index primer (HPLCpurified), 0.025 U/µl of ExTaqHS] and amplified by PCR using the following thermal cycler program: 95°C for 3 min, 55°C for 1 min, and 72°C for 1 min; followed by ten cycles of 95°C for 30 s, 60°C for 1 min and 72°C for 1 min; with a final extension of 72°C for 3 min. Finally, the cDNA libraries were purified two times by using a 0.9 × volume of AMPureXP and dissolved in 30 µl of TE buffer.

treatment_protocol: GSC and GSCLC were cultured in StemPro-34 SFM (Invitrogen) supplemented with StemPro supplement (Invitrogen), 1% FBS, 1×GlutaMAXTM-I(Invitrogen), 1×minimal essential medium (MEM) Vitamin Solution (SIGMA), 5 mg/ml AlbuMAX-II (Invitrogen), 5×10-5 M 2-mercaptoethanol, 1×MEM nonessential amino acid solution (Invitrogen), 30 μg/ml pyruvic acid, 1×ITS-G (Invitrogen), 100 U/ml penicillin, 0.1 mg/ml streptomycin, and growth factors . [recombinant rat GDNF (10 ng/ml) (R&D Systems), human bFGF (10 ng/ml) (Invitrogen), LIF/ESGRO (103 U/ml) (Invitrogen), and mouse EGF (20 ng) (Invitrogen)]

tag: background strain

value: 129/SvJcl x C57BL/6

value: GSC-like cells (GSCLCs)


title: TYP120731-01

status: Public on Dec 06 2016

type: SRA

city: Charleston

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

country: USA

institute: National Ocean Services

library_source: transcriptomic

data_processing:
Illumina BCL output files were converted to FASTQ-sanger file format in Galaxy with FASTQ Groomer. Sequence quality trimming was performed using Trimmomatic  with a minimum quality score of phred >20 over the length of the reads.  The trimmed reads were then quality checked using the FASTQC tool.
Reads were mapped to the Ensembl T. truncatus genome, version turTru1 v76.1, with Bowtie2 v 2.2.4 as the alignment engine within the package RNA-Seq by Expectation Maximization (RSEM), generating mapped read counts as FPKM (fragments per kilobase of transcript per million mapped reads).
A table of summarized FPKMs for all samples was created.

molecule: total RNA

organism: Tursiops truncatus

source_name: skin

extract_protocol:
Qiagen RNeasy Lipid Tissue Mini Kit with on-column DNase digestion.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina, indexed with the NEBNextMulitplex Oligos for Illumina.

tag: tissue

value: skin

tag: Sex

value: male

value: USA:Cooper, Ashley, Wando, and Stono River Basin (CAWS), South Carolina


title: WT_4154_A11

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 platform using the default RTA analysis software.
Reads were trimmed using trim galore v0.4 using default parameters to remove standard illumina adapters. Reads were mapped to the GRCh38 human genome assembly plus the ERCC spike in control sequences using HiSat v2.0.1b guided by splice junctions imported from the gene models in Ensembl v78. Uniquely mapping reads were imported into SeqMonk v0.32.1 for analysis. Quantitation was performed on a gene set of annotated models with a biotype of protein_coding or lincRNA at a gene level counting reads overlapping any valid exon in each gene. Counts were expressed as log2 reads per million reads of library (log2RPM).
Genome_build: GRCh38
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) Chromosome; (2) Start; (3) End; (4) Strand; (5) mRNA Name; (6) mRNA ID (Ensembl) (7) Description (Ensembl); (8-228) log2 RPM value

organism: Homo sapiens

source_name: single cell transcriptome EZH2 +/+ wildtype  human ESC

growth_protocol: Human ESC (WA09; obtained from WiCell) were cultured on CF1 irradiated mouse embryonic fibroblasts (MEF) in Advanced DMEM containing 20% Knockout Serum Replacement (Life Technologies) supplemented with 2mM L-Glutamine (Life Technologies), 0.1mM B-Mercaptoethanol (Sigma-Aldrich), 1x Penicillin/Streptomycin (Life Technologies), 1x Non-Essential Amino Acids (Life Technologies) and 4ng/ml FGF2 (WT-MRC Cambridge Stem Cell Institute). Cells were passaged using 1mg/ml Collagenase IV (Life Technologies).

extract_protocol:
SSEA4-positive live hESC were deposited by FACS directly into 96-well plates. Poly-A cDNA from single cells was obtained as described by Picelli et al.
Illumina Nextera DNA LT library preparation kit was used following the Fluidigm protocol described for cDNA generation using the Fluidigm C1 machine (available online). Spike-ins (ERCC RNA Spike-in Mix, Ambion) were added in a final dilution of 1:10E6.

treatment_protocol: All samples were flow sorted for SSEA4.

tag: cell type

value: H9 embryonic stem cell (ESC)

tag: genotype


title: TYP120724-04

value: USA:Ashepoo, Combahee, Edisto River Basin, South Carolina


title: WT_4154_A8


title: TYP131122-02


title: TYP120731-03


title: TYP120731-05


title: GSCLC4_MS094_119

organism: Mus musculus


title: GSCLC4_MS094_118


title: WT_4063_H9


title: WT_4154_A1


title: TYP120724-01


title: TYP120718-03


title: GSCLC4_MS094_122


title: TYP120718-04


title: TYP120629-01


title: WT_4063_H8


title: TYP120620-04


title: TYP120628-04


title: TYP120620-01


title: GSCLC4_MS094_115


title: TYP120620-02


title: GSCLC4_MS094_116


title: GSCLC4_MS094_117


title: WT_4063_H5


title: TYP120619-01


title: TYP120628-03


title: TYP120517-04


title: GSCLC4_MS094_114


title: WT_4063_H3


title: TYP120502-03


title: WT_4063_H4


title: GSCLC4_MS094_113


title: TYP120517-01


title: GSCLC4_MS094_111


title: TYP120502-02


title: WT_4063_H2


title: TYP110111-02

value: female

value: USA:Barataria Bay, Louisiana


title: WT_4063_H6


title: TYP120502-01


title: WT_4063_H7


title: WT_4063_H1


title: TYP120620-03


title: TYP100918-01

value: USA:Chandeleur Sound, Louisiana


title: GSCLC4_MS094_108


title: TYP100917-02


title: TYP100917-04


title: WT_4063_H11


title: TYP100916-02

value: USA:Mississippi Sound, Mississippi


title: TYP100915-03


title: GSCLC4_MS094_107


title: GSCLC4_MS094_106


title: TYP100915-02


title: TYP100818-01


title: GSCLC4_MS094_105


title: GSCLC4_MS094_101


title: WT_4063_G9


title: TYP100831-01


title: GSCLC4_MS094_109


title: WT_4063_G7


title: TYP100817-02


title: WT_4063_G8


title: TYP100814-06


title: TYP100816-01


title: GSCLC4_MS094_099


title: TYP052710-01


title: WT_4063_G6


title: GSCLC4_MS094_098


title: TE120220-03


title: TE100909-03


title: WT_4063_G5


title: WT_4063_G4


title: GSCLC4_MS094_097


title: WT_4063_H12


title: R3111216-02


title: R3111220-01


title: TYP100828-01


title: GSCLC4_MS094_095


title: TYP052810-02


title: GSCLC4_MS094_093


title: R3111209-01


title: R3111212-02


title: GSCLC4_MS094_100


title: WT_4063_G1


title: WT_4063_G3


title: R3111208-02


title: R3111205-01


title: R3111208-01


title: WT_4063_F9


title: R3110829-01


title: R3111202-01


title: GSCLC4_MS094_091


title: TYP100915-01


title: R3110828-02


title: WT_4063_F8


title: R3110828-01


title: GSCLC1_MS094_185


title: WT_4063_F6


title: R3110823-03


title: WT_4063_F5


title: GSCLC1_MS094_184


title: R3110821-02


title: GSCLC1_MS094_183


title: WT_4063_F4


title: R3110823-02


title: WT_4063_H10


title: R3110817-05


title: WT_4063_F3


title: GSCLC1_MS094_182


title: GSCLC1_MS094_186


title: GSCLC4_MS094_092


title: GSCLC1_MS094_181


title: R3110817-01


title: R3110208-01


title: R3110816-03


title: R3100517-03


title: R3111216-01


title: GSCLC1_MS094_180


title: R3110828-03


title: R3100517-02


title: WT_4063_F1


title: R3110820-03


title: GSCLC1_MS094_177


title: R3100512-04


title: WT_4063_F2


title: GSCLC1_MS094_176


title: R3100512-03


title: WT_4063_F11


title: R3100515-01


title: R3100512-02


title: GSCLC1_MS094_175


title: WT_4063_E9


title: WT_4063_F12


title: R3100513-02


title: R3100511-01


title: R3100510-04


title: GSCLC1_MS094_173


title: R3100510-03


title: GSCLC1_MS094_172


title: GSCLC1_MS094_171


title: R3100510-02


title: WT_4063_E7


title: R3100508-02


title: R2110829-02


title: GSCLC1_MS094_170


title: R2110828-01


title: WT_4063_G11


title: R2110824-01


title: WT_4063_E5


title: R2110823-03


title: GSCLC1_MS094_169


title: R2110823-01


title: GSCLC1_MS094_168


title: WT_4063_E3


title: R2110815-01


title: WT_4063_E11


title: WT_4063_E8


title: BW120223-05


title: BW120223-02


title: WT_4063_E10


title: BW120223-01


title: WT_4063_E6


title: BW120221-05


title: GSCLC1_MS094_166


title: WT_4063_D7


title: R3100511-04


title: BW120220-01


title: GSCLC1_MS094_165


title: GSCLC1_MS094_164


title: WT_4063_D5


title: WT_4063_D6


title: WT_4063_D12


title: GSCLC1_MS094_162


title: GSCLC1_MS094_163


title: WT_4063_D11


title: GSCLC1_MS094_161


title: GSCLC1_MS094_159


title: WT_4063_C8


title: WT_4063_D10


title: BW120225-03


title: bulk RNA-seq MRD199_Ctrl_M85_H6

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

description:
ALL-199
processed data file: MRD199bulk.counts.txt

data_processing:
Sequencing reads were demultiplexed from the Nextera (i5 and i7) indices using deML (Renaud 2014, Bioinformatics)
Demultiplexed reads were aligned to the human genome (hg19) and ERCC reference usingSTAR (Dobin et al., 2014)
Count data was generated from mapped readson ENSEMBL gene models (GRCh38.74) considering UMI information using the Drop-seq pipeline (Macosko et al., 2015)
Genome_build: hg19
Supplementary_files_format_and_content: processed data files are text files with count data, where columns equal to samples and rows equal to genes

source_name: ALL-199_bulk M85 untreated PDX

extract_protocol: cDNA synthesis protocol: 1000 cells were sorted into TCL lysis buffer (Qiagen). mRNA was cleaned up from the crude lysate using AMPure XP RNA beads. cDNA was synthesised and pooled according to the SCRB-seq protocol (Soumillon et al., 2014). 0.8ng of cDNA pool was used for library construction using the Nextera XT protocol (Illumina).

tag: patient

value: BCP-ALL pediatric

tag: mouse id

value: NOD scid gamma

value: PDX cell

tag: treatment


title: bulk RNA-seq MRD199_VCRCyclo_M11_H3

source_name: ALL-199_bulk M11 treated PDX

value: VCR & Cyclo treatment


title: bulk RNA-seq MRD199_Ctrl_M86_G6

source_name: ALL-199_bulk M86 untreated PDX


title: GSCLC1_MS094_157


title: bulk RNA-seq MRD199_VCRCyclo_M302327_H5

source_name: ALL-199_bulk M302328 treated PDX


title: bulk RNA-seq MRD199_Ctrl_M7_G2

source_name: ALL-199_bulk M7 untreated PDX


title: WT_4063_C7


title: WT_4063_C6


title: WT_4063_C5


title: BW120221-02


title: GSCLC1_MS094_158


title: bulk RNA-seq MRD199_VCRCyclo_M17_G1

source_name: ALL-199_bulk M17 treated PDX


title: WT_4063_C3


title: bulk RNA-seq MRD199_Ctrl_M85_F6


title: WT_4063_C1


title: GSCLC1_MS094_153


title: bulk RNA-seq MRD199_Ctrl_M94_E6

source_name: ALL-199_bulk M94 untreated PDX


title: bulk RNA-seq MRD199_VCRCyclo_M19_E1

source_name: ALL-199_bulk M19 treated PDX


title: GSCLC1_MS094_151


title: WT_4063_C12


title: bulk RNA-seq MRD199_Ctrl_M94_D6


title: GSCLC1_MS094_167


title: bulk RNA-seq MRD199_VCRCyclo_M11_D5


title: GSC2_MS094_062

description:
Single cell transcriptome of amplified cDNA from GS cell
AcrAct_EGFP reporter

source_name: GSC

value: germline stem cells (GSCs)


title: bulk RNA-seq MRD199_VCRCyclo_M20_D4

source_name: ALL-199_bulk M20 treated PDX


title: WT_4063_C11


title: GSC2_MS094_061


title: GSCLC1_MS094_156


title: bulk RNA-seq MRD199_VCRCyclo_M18_C3

source_name: ALL-199_bulk M18 treated PDX


title: GSCLC1_MS094_155


title: bulk RNA-seq MRD199_Ctrl_M86_B6


title: WT_4063_C10


title: bulk RNA-seq MRD199_VCRCyclo_M9_C2

source_name: ALL-199_bulk M9 treated PDX


title: GSC2_MS094_060


title: WT_4063_B9


title: WT_4063_B8


title: bulk RNA-seq MRD199_VCRCyclo_M19_B1


title: bulk RNA-seq MRD199_VCRCyclo_M302223_A6

source_name: ALL-199_bulk M302223 treated PDX


title: GSC2_MS094_055


title: bulk RNA-seq MRD199_VCRCyclo_M17_A2


title: GSC2_MS094_052


title: WT_4063_B7


title: WT_4063_B6


title: bulk RNA-seq MRD199_VCRCyclo_M18_A1


title: bulk RNA-seq MRD4-D30

description:
MRD Patient 4
processed data file: PatientMRD.counts.txt

source_name: MRD Patient 4_bulk MRD 4 d30

value: primary cell


title: bulk RNA-seq MRD199_Ctrl_M13_A5

source_name: ALL-199_bulk M13 untreated PDX


title: GSC2_MS094_048

value: 129/SvJcl x C57BL/6


title: WT_4063_B5


title: WT_4063_B3


title: bulk RNA-seq MRD3-D30

description:
MRD Patient 3
processed data file: PatientMRD.counts.txt

source_name: MRD Patient 3_bulk MRD 3 d30


title: bulk RNA-seq MRD3-D0

source_name: MRD Patient 3_bulk MRD 3 diagnosis


title: bulk RNA-seq MRD2-D0

description:
MRD Patient 2
processed data file: PatientMRD.counts.txt

source_name: MRD Patient 2_bulk MRD 2 diagnosis


title: GSC2_MS094_044


title: GSC2_MS094_059


title: bulk RNA-seq MRD6-D30

description:
MRD Patient 6
processed data file: PatientMRD.counts.txt

source_name: MRD Patient 6_bulk MRD 6 d30


title: bulk RNA-seq MRD1-D0

description:
MRD Patient 1
processed data file: PatientMRD.counts.txt

source_name: MRD Patient 1_bulk MRD 1 diagnosis


title: GSC2_MS094_045


title: GSC2_MS094_043


title: WT_4063_B12

source_name: single cell transcriptome EZH2 +/+ wildtype  human ESC


title: bulk RNA-seq P-nLRC-3

description:
StemB Patient 3
processed data file: StemBbulkLRC.counts.txt

source_name: StemB Patient 3_bulk StemB non-LRC 3

value: BCR-ABL adult


title: bulk RNA-seq P-nLRC-2

description:
StemB Patient 2
processed data file: StemBbulkLRC.counts.txt

source_name: StemB Patient 2_bulk StemB non-LRC 2


title: WT_4063_A9


title: single-cell RNA-seq LRCpt1_13

description:
StemB Patient 1
processed data file: LRCptsc.counts.txt

source_name: StemB Patient 1_single-cell StemB LRC 13

extract_protocol: cDNA synthesis protocol: single-cells were sorted into 5 µl lysis buffer (Phusion HF, NEB). cDNA was synthesised and pooled from the cell lysate using the SCRB-seq protocol (Soumillon et al., 2014). 0.8ng of cDNA pool was used for library construction using the Nextera XT protocol (Illumina).

value: GMALL 0703


title: WT_4063_A8


title: bulk RNA-seq MRD4-D0

source_name: MRD Patient 4_bulk MRD 4 diagnosis


title: bulk RNA-seq MRD199_VCRCyclo_M302119_C6

source_name: ALL-199_bulk M302119 treated PDX


title: GSC2_MS094_041

source_name: GSC


title: single-cell RNA-seq LRCpt1_11

source_name: StemB Patient 1_single-cell StemB LRC 11


title: WT_4063_A7


title: GSC2_MS094_042


title: single-cell RNA-seq LRCpt1_10

source_name: StemB Patient 1_single-cell StemB LRC 10


title: single-cell RNA-seq LRCpt1_12

source_name: StemB Patient 1_single-cell StemB LRC 12


title: GSC2_MS094_039


title: GSC2_MS094_037


title: single-cell RNA-seq LRCpt1_9

source_name: StemB Patient 1_single-cell StemB LRC 9


title: single-cell RNA-seq LRCpt1_8

source_name: StemB Patient 1_single-cell StemB LRC 8


title: single-cell RNA-seq LRCpt1_7

source_name: StemB Patient 1_single-cell StemB LRC 7


title: WT_4063_A4


title: GSC2_MS094_036


title: WT_4063_B10


title: single-cell RNA-seq LRCpt1_6

source_name: StemB Patient 1_single-cell StemB LRC 6


title: GSC2_MS094_033


title: bulk RNA-seq P-nLRC-1

description:
StemB Patient 1
processed data file: StemBbulkLRC.counts.txt

source_name: StemB Patient 1_bulk StemB non-LRC 1


title: single-cell RNA-seq LRCpt1_5

source_name: StemB Patient 1_single-cell StemB LRC 5


title: single-cell RNA-seq LRCpt1_4

source_name: StemB Patient 1_single-cell StemB LRC 4


title: bulk RNA-seq P-LRC-3

source_name: StemB Patient 3_bulk StemB LRC 3


title: GSC2_MS094_032


title: WT_4063_A3

source_name: single cell transcriptome EZH2 +/+ wildtype  human ESC


title: single-cell RNA-seq LRCpt1_3

source_name: StemB Patient 1_single-cell StemB LRC 3


title: WT_4063_A1


title: single-cell RNA-seq LRCpt1_2

source_name: StemB Patient 1_single-cell StemB LRC 2


title: single-cell RNA-seq LRCpt1_1

source_name: StemB Patient 1_single-cell StemB LRC 1


title: WT_4063_A12


title: GSC2_MS094_031


title: GSC2_MS094_029


title: single-cell RNA-seq M3022-23 treated mrd99

description:
mrd99
processed data file: ALL199_MRD_counts.txt

data_processing:
Sequencing reads were demultiplexed from the Nextera (i5 and i7) indices using deML (Renaud 2014, Bioinformatics)
Demultiplexed reads were aligned to the human genome (hg19) and ERCC reference using NextGenMap (Sedlazeck et al., 2013)
Count data was generated from mapped reads using featureCounts (Liao et al., 2014) on ENSEMBL gene models (GRCh38.74)
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] processed data files are text files with count data, where columns equal to samples and rows equal to genes

source_name: PDX Sample ALL-199

growth_protocol: human patient cells are grown as patient-derived xenograft cells in immunodeficient NOD scid gamma mice and re-isolated from bone marrow

extract_protocol:
cDNA synthesis protocol: cells were loaded on the 10-17 μm mRNA-seq IFC (Fluidigm) with ERCC spike-in controls. Cell lysis, reverse transcription and pre-amplification of cDNA was done on-chip using the SMARTer Ultra Low RNA Kit for C1 (Clontech).
0.2-1 ng of pre-amplified cDNA was used as input for tagmentation by the Nextera XT Sample Preparation Kit (Illumina), where amplification was performed for 12-14 PCR cycles.
Cells were isolated from the murine bone marrow, enriched by a MACS step and sorted for the population of interest. All steps were performed at 4°C.


title: single-cell RNA-seq M3022-23 treated mrd96

description:
mrd96
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd97

description:
mrd97
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd95

description:
mrd95
processed data file: ALL199_MRD_counts.txt


title: WT_4063_A6


title: single-cell RNA-seq M3022-23 treated mrd90

description:
mrd90
processed data file: ALL199_MRD_counts.txt


title: GSC2_MS094_027

source_name: GSC


title: WT_4063_A11


title: GSC2_MS094_024


title: 16-_4067_H8

source_name: single cell transcriptome EZH2 -/- null human ESC

value: EZH2 -/- (Null)


title: single-cell RNA-seq M3022-23 treated mrd89

description:
mrd89
processed data file: ALL199_MRD_counts.txt


title: GSC2_MS094_023


title: single-cell RNA-seq M3022-23 treated mrd87

description:
mrd87
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_H4


title: single-cell RNA-seq M3022-23 treated mrd86

description:
mrd86
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_H3


title: single-cell RNA-seq M3022-23 treated mrd83

description:
mrd83
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd84

description:
mrd84
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd85

description:
mrd85
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_150

description:
Single cell transcriptome of amplified cDNA from GS cell
AcrAct_EGFP reporter


title: WT_4063_A10


title: single-cell RNA-seq M3022-23 treated mrd77

description:
mrd77
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd78

description:
mrd78
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_147


title: single-cell RNA-seq M3022-23 treated mrd72

description:
mrd72
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd88

description:
mrd88
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_H10


title: 16-_4067_G7


title: 16-_4067_G6


title: 16-_4067_G5


title: single-cell RNA-seq M3022-23 treated mrd7

description:
mrd7
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_149


title: single-cell RNA-seq M3022-23 treated mrd76

description:
mrd76
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd74

description:
mrd74
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_G3


title: GSC1_MS094_145


title: GSC2_MS094_022


title: single-cell RNA-seq M3022-23 treated mrd67

description:
mrd67
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd65

description:
mrd65
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_144


title: GSC2_MS094_021


title: single-cell RNA-seq M3022-23 treated mrd66

description:
mrd66
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd8

description:
mrd8
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_146


title: single-cell RNA-seq M3022-23 treated mrd73

description:
mrd73
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_G12


title: 16-_4067_G2


title: 16-_4067_G9


title: GSC1_MS094_143


title: GSC1_MS094_142


title: 16-_4067_G1


title: single-cell RNA-seq M3022-23 treated mrd6

description:
mrd6
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_G10


title: single-cell RNA-seq M3022-23 treated mrd55

description:
mrd55
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd62

description:
mrd62
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd54

description:
mrd54
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd61

description:
mrd61
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd63

description:
mrd63
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd56

description:
mrd56
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd53

description:
mrd53
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_140

description:
Single cell transcriptome of amplified cDNA from GS cell
AcrAct_EGFP reporter


title: 16-_4067_F7


title: single-cell RNA-seq M3022-23 treated mrd50

description:
mrd50
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd44

description:
mrd44
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_137


title: single-cell RNA-seq M3022-23 treated mrd49

description:
mrd49
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_F9


title: single-cell RNA-seq M3022-23 treated mrd51

description:
mrd51
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_138


title: 16-_4067_F6


title: single-cell RNA-seq M3022-23 treated mrd42

description:
mrd42
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_136


title: GSC1_MS094_133


title: GSC1_MS094_141


title: 16-_4067_F5


title: single-cell RNA-seq M3022-23 treated mrd41

description:
mrd41
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd52

description:
mrd52
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd40

description:
mrd40
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_F3


title: 16-_4067_F1


title: single-cell RNA-seq M3022-23 treated mrd5

description:
mrd5
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_F2


title: single-cell RNA-seq M3022-23 treated mrd4

description:
mrd4
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd37

description:
mrd37
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd39

description:
mrd39
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd38

description:
mrd38
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd32

description:
mrd32
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_129


title: GSC1_MS094_132


title: GSC1_MS094_080


title: 16-_4067_E9


title: single-cell RNA-seq M3022-23 treated mrd3

description:
mrd3
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd43

description:
mrd43
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd31

description:
mrd31
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd29

description:
mrd29
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_079

description:
Single cell transcriptome of amplified cDNA from GS cell
AcrAct_EGFP reporter


title: single-cell RNA-seq M3022-23 treated mrd30

description:
mrd30
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_F11


title: GSC1_MS094_077


title: 16-_4067_E8


title: single-cell RNA-seq M3022-23 treated mrd28

description:
mrd28
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd27

description:
mrd27
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd26

description:
mrd26
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_E6


title: GSC1_MS094_131


title: GSC1_MS094_076


title: single-cell RNA-seq M3022-23 treated mrd25

description:
mrd25
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_075


title: single-cell RNA-seq M3022-23 treated mrd20

description:
mrd20
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_E5


title: single-cell RNA-seq M3022-23 treated mrd2

description:
mrd2
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_E11


title: single-cell RNA-seq M3022-23 treated mrd19

description:
mrd19
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_073


title: 16-_4067_E10


title: 16-_4067_D8


title: GSC1_MS094_072


title: 16-_4067_D7


title: GSC1_MS094_071


title: GSC1_MS094_070


title: single-cell RNA-seq M3022-23 treated mrd15

description:
mrd15
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd16

description:
mrd16
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd14

description:
mrd14
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd137

description:
mrd137
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd136

description:
mrd136
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_D6


title: single-cell RNA-seq M3022-23 treated mrd132

description:
mrd132
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd135

description:
mrd135
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd133

description:
mrd133
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd131

description:
mrd131
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd18

description:
mrd18
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd13

description:
mrd13
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd130

description:
mrd130
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_069

description:
Single cell transcriptome of amplified cDNA from GS cell
AcrAct_EGFP reporter


title: 16-_4067_D4


title: single-cell RNA-seq M3022-23 treated mrd17

description:
mrd17
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_068


title: GSC1_MS094_067


title: 16-_4067_D11


title: 16-_4067_D1


title: single-cell RNA-seq M3022-23 treated mrd124

description:
mrd124
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd122

description:
mrd122
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd123

description:
mrd123
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd121

description:
mrd121
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_D10


title: single-cell RNA-seq M3022-23 treated mrd120

description:
mrd120
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_C5


title: H3K27me3-HL-E115-Wt-Mm-Rep2-L6988

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description: The merged .bw file for this sample is available on GSM2251496

library_source: genomic

data_processing:
Single-end reads from ChIP-seq experiments were mapped with Bowtie-2.2.6 to reference genome mm9. Mapped reads were filtered for mapping quality ≥10, and duplicates were removed.
Reads were extended to a length of 300bp and a scaled (one million / total of unique reads) coverage was computed using genomeCoverageBed from bedtools. We then produced the bigwig files using bedGraphToBigWig tool from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: Embryonic Limb Bud

growth_protocol: Limb bud and midbrain were micro-dissected from mouse embryos

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate chromatin modification ChIP and 30μg for CTCF and RAD21 ChIP. ChIP for H3K4me1 (Abcam: 8898), H3K4me3 (Milipore: 07-473), H3K27Ac (Diagenode: C1540174), H3K27me3 (Milipore: 07-449), CTCF (Active motif: 613111) and RAD21 (Abcam: ab992) was then performed as in Lee et al., 2006. Libraries were prepared using the Nextera adaptors and sequenced.

treatment_protocol: For chromatin modifications, chromatin was prepared from the different tissues with a 1% FA crosslinking for 15 minutes and resuspended in buffer 3 for sonication (Lee et al.,). For CTCF and RAD21 ChIP-seq we prepared chromatin as follow: tissues were disrupted in 0.1% collagenase at 37°C and homogenized using a needle. Cell were then centrifuged and resuspended in (10%FCS, 0.2%Cs, 1% L-Glu, 0.5% Pen-Strep in DMEM:HAM’s F-12 1:1)) and fixed in 1% FA for 10’ on ice. Cell were then lysed in buffer 1 and 2 and resuspended in buffer 3 for sonication (Lee et al. 2006).

value: hindlimb

tag: developmental stages

tag: strain

tag: chip antibody


title: single-cell RNA-seq M3022-23 treated mrd118

description:
mrd118
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd113

description:
mrd113
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd125

description:
mrd125
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd119

description:
mrd119
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd112

description:
mrd112
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_C3

value: H9 embryonic stem cell (ESC)


title: H3K27Ac-HL-E135-Wt-Mm-Rep1-L6984

value: H3K27Ac (Diagenode:C1540174)


title: 16-_4067_C1


title: H3K27Ac-FL-E115-Wt-Mm-Rep2-L6983

description: The merged .bw file for this sample is available on GSM2251476

value: forelimb


title: single-cell RNA-seq M3022-23 treated mrd111

description:
mrd111
processed data file: ALL199_MRD_counts.txt


title: GSC1_MS094_065


title: single-cell RNA-seq M3022-23 treated mrd110

description:
mrd110
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd109

description:
mrd109
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_B9


title: single-cell RNA-seq M3022-23 treated mrd108

description:
mrd108
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_B6


title: H3K4me3-HL-E115-Wt-Mm-Rep2-L6989

description: The merged .bw file for this sample is available on GSM2251468

value: H3K4me3 (Milipore:07-473)


title: H3K4me1-MB-E105-Wt-Mm-Rep1-L6986

source_name: Embryonic Midbrain

value: midbrain


title: 16-_4067_B5


title: single-cell RNA-seq M3022-23 treated mrd106

description:
mrd106
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd107

description:
mrd107
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd101

description:
mrd101
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_B4


title: H3K4me1-HL-E135-Wt-Mm-Rep1-L6985


title: H3K4me3-MB-E105-Wt-Mm-Rep1-L6990


title: RNA-MB-E105-Wt-Mm-Rep2-L6126

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm9) using the STAR mapper (Dobin et al., 2013) (splice junctions based on RefSeq ;options: ‐‐alignIntronMin 20 ‐‐alignIntronMax 500000 --outFilterMultimapNmax 5 ‐‐outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.1).
To create bigwig files coverage profiles were generated by creating a bedgraph file using bedtools genomecov (-ibam —bg split -scale (normalized per million reads)) (bedtools v2.17.0) and then transformed to bigwig files using the bedgraphtobigwig tool from UCSC (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v287/bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for normalized RNA-seq profiles

molecule: polyA RNA

extract_protocol:
RNA was extracted from the different tissues using a RNeasy kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type


title: single-cell RNA-seq M3022-23 treated mrd1

description:
mrd1
processed data file: ALL199_MRD_counts.txt

value: BCP-ALL pediatric


title: 16-_4067_B1


title: single-cell RNA-seq M3000-94 non-treated ctrl93

description:
ctrl93
processed data file: ALL199_MRD_counts.txt

value: NOD scid gamma

value: non-treated


title: single-cell RNA-seq M3022-23 treated mrd100

description:
mrd100
processed data file: ALL199_MRD_counts.txt

value: PDX cell

value: VCR & Cyclo treatment


title: RNA-HL-E135-Wt-Mm-Rep2-L6128

value: Hindlimb


title: RNA-MB-E105-Wt-Mm-Rep1-L6122


title: single-cell RNA-seq M3000-94 non-treated ctrl92

description:
ctrl92
processed data file: ALL199_MRD_counts.txt


title: H3K27me3-FL-E115-Wt-Mm-Rep2-L6987

description: The merged .bw file for this sample is available on GSM2251490


title: 16-_4067_B12


title: single-cell RNA-seq M3000-94 non-treated ctrl91

description:
ctrl91
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl81

description:
ctrl81
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_A7


title: single-cell RNA-seq M3000-94 non-treated ctrl80

description:
ctrl80
processed data file: ALL199_MRD_counts.txt


title: RNA-HL-E135-Wt-Mm-Rep1-L6124


title: single-cell RNA-seq M3000-94 non-treated ctrl70

description:
ctrl70
processed data file: ALL199_MRD_counts.txt


title: RNA-HL-E115-Wt-Mm-Rep2-L6537


title: 16-_4067_A6


title: single-cell RNA-seq M3000-94 non-treated ctrl79

description:
ctrl79
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3022-23 treated mrd102

description:
mrd102
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl69

description:
ctrl69
processed data file: ALL199_MRD_counts.txt


title: RNA-HL-E115-Wt-Mm-Rep1-L6499


title: 16-_4067_A5


title: single-cell RNA-seq M3000-94 non-treated ctrl59

description:
ctrl59
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl68

description:
ctrl68
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl58

description:
ctrl58
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl57

description:
ctrl57
processed data file: ALL199_MRD_counts.txt


title: RNA-FL-E135-Wt-Mm-Rep1-L6123


title: 16-_4067_A1


title: RNA-HL-E105-Wt-Mm-Rep2-L6535


title: single-cell RNA-seq M3000-94 non-treated ctrl45

description:
ctrl45
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl47

description:
ctrl47
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl33

description:
ctrl33
processed data file: ALL199_MRD_counts.txt


title: RNA-HL-E105-Wt-Mm-Rep1-L6497


title: 16-_4066_H4


title: 16-_4066_H5


title: RNA-FL-E135-Wt-Mm-Rep2-L6127


title: 16-_4066_H6


title: single-cell RNA-seq M3000-94 non-treated ctrl48

description:
ctrl48
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl36

description:
ctrl36
processed data file: ALL199_MRD_counts.txt


title: RNA-FL-E115-Wt-Mm-Rep1-L6536


title: single-cell RNA-seq M3000-94 non-treated ctrl140

description:
ctrl140
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl35

description:
ctrl35
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl34

description:
ctrl34
processed data file: ALL199_MRD_counts.txt


title: 16-_4067_A4


title: RNA-FL-E115-Wt-Mm-Rep2-L6498


title: single-cell RNA-seq M3000-94 non-treated ctrl138

description:
ctrl138
processed data file: ALL199_MRD_counts.txt


title: 16-_4066_H1


title: 16-_4066_H11


title: single-cell RNA-seq M3000-94 non-treated ctrl24

description:
ctrl24
processed data file: ALL199_MRD_counts.txt


title: RNA-FL-E105-Wt-Mm-Rep2-L6534

value: Forelimb


title: single-cell RNA-seq M3000-94 non-treated ctrl126

description:
ctrl126
processed data file: ALL199_MRD_counts.txt


title: RNA-FL-E105-Wt-Mm-Rep1-L6496


title: single-cell RNA-seq M3000-94 non-treated ctrl12

description:
ctrl12
processed data file: ALL199_MRD_counts.txt


title: 16-_4066_G7


title: single-cell RNA-seq M3000-94 non-treated ctrl127

description:
ctrl127
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl114

description:
ctrl114
processed data file: ALL199_MRD_counts.txt


title: 16-_4066_G12


title: 16-_4066_G2


title: RAD21-MB-E105-Wt-Mm-Rep2-L8220-1

description: The merge-qfrags.bw file for this sample is available on GSM2251514

value: RAD21 (Abcam:ab992)


title: single-cell RNA-seq M3000-94 non-treated ctrl23

description:
ctrl23
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl116

description:
ctrl116
processed data file: ALL199_MRD_counts.txt


title: single-cell RNA-seq M3000-94 non-treated ctrl21

description:
ctrl21
processed data file: ALL199_MRD_counts.txt


title: RAD21-MB-E105-Wt-Mm-Rep1-L8217-1


title: RAD21-HL-E135-Wt-Mm-Rep1-L8190-1


title: single-cell RNA-seq M3000-94 non-treated ctrl10

description:
ctrl10
processed data file: ALL199_MRD_counts.txt


title: 16-_4066_G11


title: single-cell RNA-seq M1288 LRC_19

description:
LRC_19
processed data file: single_cell_countdata_LRC_validcells.txt

source_name: PDX Sample ALL-265

tag: cell status

value: LRC


title: single-cell RNA-seq M1288 LRC_18

description:
LRC_18
processed data file: single_cell_countdata_LRC_validcells.txt


title: 16-_4066_F8

value: EZH2 -/- (Null)


title: single-cell RNA-seq M3000-94 non-treated ctrl105

description:
ctrl105
processed data file: ALL199_MRD_counts.txt


title: RAD21-HL-E135-Wt-Mm-Rep2-L8191-1

description: The merge-qfrags.bw file for this sample is available on GSM2251512

value: hindlimb


title: single-cell RNA-seq M1288 LRC_14

description:
LRC_14
processed data file: single_cell_countdata_LRC_validcells.txt


title: RAD21-HL-E115-Wt-Mm-Rep2-L8226-1

description: The merge-qfrags.bw file for this sample is available on GSM2251510


title: single-cell RNA-seq M3000-94 non-treated ctrl11

description:
ctrl11
processed data file: ALL199_MRD_counts.txt


title: 16-_4066_G10

value: H9 embryonic stem cell (ESC)


title: 16-_4066_F4


title: single-cell RNA-seq M1288 LRC_13

description:
LRC_13
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1288 LRC_7

description:
LRC_7
processed data file: single_cell_countdata_LRC_validcells.txt


title: RAD21-HL-E115-Wt-Mm-Rep1-L8224-1


title: 16-_4066_F3


title: 16-_4067_D2


title: single-cell RNA-seq M1288 LRC_22

description:
LRC_22
processed data file: single_cell_countdata_LRC_validcells.txt


title: bulk RNA-seq MRD199_VCRCyclo_M9_B4

description:
ALL-199
processed data file: MRD199bulk.counts.txt

source_name: ALL-199_bulk M9 treated PDX


title: 16-_4066_F2


title: single-cell RNA-seq M1288 LRC_6

description:
LRC_6
processed data file: single_cell_countdata_LRC_validcells.txt


title: 16-_4066_F1


title: single-cell RNA-seq M1288 LRC_5

description:
LRC_5
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1288 LRC_4

description:
LRC_4
processed data file: single_cell_countdata_LRC_validcells.txt


title: RAD21-HL-E105-Wt-Mm-Rep2-L8219-1

description: The merge-qfrags.bw file for this sample is available on GSM2251508


title: single-cell RNA-seq M1288 LRC_2

description:
LRC_2
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1288 LRC_1

description:
LRC_1
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1288 LRC_3

description:
LRC_3
processed data file: single_cell_countdata_LRC_validcells.txt


title: RAD21-FL-E135-Wt-Mm-Rep2-L8260-1

description: The merge-qfrags.bw file for this sample is available on GSM2251506


title: RAD21-FL-E135-Wt-Mm-Rep1-L8189-1


title: 16-_4066_F11


title: single-cell RNA-seq M1288 LRC_11

description:
LRC_11
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1288 LRC_12

description:
LRC_12
processed data file: single_cell_countdata_LRC_validcells.txt


title: RAD21-FL-E115-Wt-Mm-Rep2-L8225-1

description: The merge-qfrags.bw file for this sample is available on GSM2251504


title: single-cell RNA-seq M1288 LRC_9

description:
LRC_9
processed data file: single_cell_countdata_LRC_validcells.txt


title: RAD21-HL-E105-Wt-Mm-Rep1-L8216-1


title: 16-_4066_E9


title: single-cell RNA-seq M1289 non-LRC_37

description:
non-LRC_37
processed data file: single_cell_countdata_LRC_validcells.txt

value: non-LRC


title: single-cell RNA-seq M1289 non-LRC_32

description:
non-LRC_32
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_31

description:
non-LRC_31
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_30

description:
non-LRC_30
processed data file: single_cell_countdata_LRC_validcells.txt


title: 16-_4066_E7


title: single-cell RNA-seq M1289 non-LRC_28

description:
non-LRC_28
processed data file: single_cell_countdata_LRC_validcells.txt


title: RAD21-FL-E105-Wt-Mm-Rep2-L8218-1

description: The merge-qfrags.bw file for this sample is available on GSM2251502

value: forelimb


title: single-cell RNA-seq M1289 non-LRC_29

description:
non-LRC_29
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_27

description:
non-LRC_27
processed data file: single_cell_countdata_LRC_validcells.txt


title: RAD21-FL-E105-Wt-Mm-Rep1-L8215-1


title: single-cell RNA-seq M1289 non-LRC_26

description:
non-LRC_26
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_36

description:
non-LRC_36
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27me3-MB-E105-Wt-Mm-Rep2-L7123

description: The merged .bw file for this sample is available on GSM2251500


title: 16-_4066_E11


title: 16-_4066_F10


title: single-cell RNA-seq M1289 non-LRC_35

description:
non-LRC_35
processed data file: single_cell_countdata_LRC_validcells.txt


title: 16-_4066_E2


title: H3K27me3-MB-E105-Wt-Mm-Rep1-L7122


title: single-cell RNA-seq M1289 non-LRC_25

description:
non-LRC_25
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_34

description:
non-LRC_34
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27me3-HL-E135-Wt-Mm-Rep2-L7119

description: The merged .bw file for this sample is available on GSM2251498


title: 16-_4066_D6


title: 16-_4066_E8


title: RAD21-FL-E115-Wt-Mm-Rep1-L8223-1


title: single-cell RNA-seq M1289 non-LRC_21

description:
non-LRC_21
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_20

description:
non-LRC_20
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27me3-HL-E135-Wt-Mm-Rep1-L7118


title: single-cell RNA-seq M1289 non-LRC_18

description:
non-LRC_18
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27me3-HL-E115-Wt-Mm-Rep1-2061


title: H3K27me3-HL-E105-Wt-Mm-Rep2-L4883

description: The merged .bw file for this sample is available on GSM2251494


title: single-cell RNA-seq M1289 non-LRC_17

description:
non-LRC_17
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_16

description:
non-LRC_16
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_19

description:
non-LRC_19
processed data file: single_cell_countdata_LRC_validcells.txt


title: 16-_4066_D2


title: 16-_4066_D10


title: 16-_4066_C8


title: single-cell RNA-seq M1289 non-LRC_15

description:
non-LRC_15
processed data file: single_cell_countdata_LRC_validcells.txt


title: 16-_4066_D7


title: 16-_4066_C6


title: single-cell RNA-seq M1289 non-LRC_23

description:
non-LRC_23
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_22

description:
non-LRC_22
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27me3-HL-E105-Wt-Mm-Rep1-L4292


title: single-cell RNA-seq M1289 non-LRC_14

description:
non-LRC_14
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_24

description:
non-LRC_24
processed data file: single_cell_countdata_LRC_validcells.txt


title: 16-_4066_C3


title: single-cell RNA-seq M1289 non-LRC_13

description:
non-LRC_13
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27me3-FL-E135-Wt-Mm-Rep1-L7116


title: 16-_4066_C1


title: single-cell RNA-seq M1289 non-LRC_9

description:
non-LRC_9
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_8

description:
non-LRC_8
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27me3-FL-E105-Wt-Mm-Rep2-L4878

description: The merged .bw file for this sample is available on GSM2251488


title: single-cell RNA-seq M1289 non-LRC_7

description:
non-LRC_7
processed data file: single_cell_countdata_LRC_validcells.txt


title: 16-_4066_C11


title: H3K27me3-FL-E115-Wt-Mm-Rep1-2069


title: single-cell RNA-seq M1289 non-LRC_6

description:
non-LRC_6
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_5

description:
non-LRC_5
processed data file: single_cell_countdata_LRC_validcells.txt


title: single-cell RNA-seq M1289 non-LRC_4

description:
non-LRC_4
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27Ac-MB-E105-Wt-Mm-Rep2-L7323

description: The merged .bw file for this sample is available on GSM2251486

value: H3K27Ac (Diagenode:C1540174)


title: single-cell RNA-seq M1289 non-LRC_2

description:
non-LRC_2
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27me3-FL-E135-Wt-Mm-Rep2-L7117

description: The merged .bw file for this sample is available on GSM2251492


title: 16-_4066_B8


title: 16-_4066_B7


title: H3K27Ac-MB-E105-Wt-Mm-Rep1-L7114

value: midbrain


title: 16-_4066_B4


title: H3K27Ac-HL-E135-Wt-Mm-Rep2-L7111

description: The merged .bw file for this sample is available on GSM2251484


title: single-cell RNA-seq M1289 non-LRC_10

description:
non-LRC_10
processed data file: single_cell_countdata_LRC_validcells.txt


title: 16-_4066_B12


title: 16-_4066_B2


title: H3K27Ac-HL-E115-Wt-Mm-Rep2-2481

description: The merged .bw file for this sample is available on GSM2251482


title: H3K27Ac-HL-E115-Wt-Mm-Rep1-2062


title: 16-_4066_C10


title: 16-_4066_A9


title: 16-_4066_B11


title: H3K27Ac-HL-E105-Wt-Mm-Rep2-L4871

description: The merged .bw file for this sample is available on GSM2251480


title: H3K27Ac-HL-E105-Wt-Mm-Rep1-L4289


title: bulk RNA-seq M1289nonLRC

extract_protocol:
cDNA synthesis protocol: Cells were sorted into lysis buffer composed of 0.2 % Triton X-100 (Sigma) and 2 U/μl of RNAse Inhibitor (Life Technologies). ERCC spike-in controls (Life Technologies) were added to the cell lysis mix at 1:5,000 dilution. RNA was cleaned-up from the crude lysate with Agencourt RNAclean XP SPRI beads (Beckman-Coulter). cDNA was synthesized and pre-amplified from 5 μl of lysate according to the Smart-seq2 protocol (Picelli et al., 2013)
0.2-1 ng of pre-amplified cDNA was used as input for tagmentation by the Nextera XT Sample Preparation Kit (Illumina), where amplification was performed for 12-14 PCR cycles.
Cells were isolated from the murine bone marrow, enriched by a MACS step and sorted for the population of interest. All steps were performed at 4°C.


title: bulk RNA-seq M772LRC


title: 16-_4066_A7


title: H3K27me3-FL-E105-Wt-Mm-Rep1-L4291


title: single-cell RNA-seq M1289 non-LRC_12

description:
non-LRC_12
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27Ac-FL-E135-Wt-Mm-Rep2-L7110

description: The merged .bw file for this sample is available on GSM2251478


title: F. proliferatum NRRL 62905, 20 days on maize roots

city: Freising

first: Ulrich

last: Guldener

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

data_processing:
RNA-seq reads were mapped on the reference genome using tophat2 (v2.0.8).
The interval for allowed intron lengths were set to min 20 nt and max 1 kb (Kim, 2013, Trapnell et al., 2009).
Cufflinks was used  to determine the abundance of transcripts in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) and calculated differentially expressed genes using cuffdiff (Trapnell et al., ,2012, Trapnell et al., 2010).
The gene models were included as raw junctions. Genes with a minimum of fourfold increase or decrease in expression (|log2 of the FPKM values +1| ≥ 2) between the two experimental conditions were considered as regulated.
Genome_build: Zea mays: http://www.plantgdb.org/ZmGDB/ version B73_RefGen_v2, working gene set 5a.59; F. mangiferae: http://www.ebi.ac.uk/ena/data/view/PRJEB9887; F. proliferatum ET1: http://www.ebi.ac.uk/ena/data/view/PRJEB9885; F. proliferatum 62905: http://www.ebi.ac.uk/ena/data/view/PRJEB9886
Supplementary_files_format_and_content: tab-delimited text files holding FPKM values for each sample

organism: Fusarium proliferatum

source_name: Maize root samples

growth_protocol: RNA was isolated from lyophilized mycelia grown before on CM agar plates for 5 days or from lyophilized infected maize roots after 4, 10 or 20 days post infection.

extract_protocol:
Total RNA was extracted using Trizol and DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).
Illumina TruSeq RNA Library
Total RNA was sequenced using Illumina HiSeq 2000 technology by BGI Tech Solutions (Hong Kong) Co., Limited.

value: wild type

tag: dpi


title: F. proliferatum NRRL 62905, 4 days on maize roots


title: F. proliferatum NRRL 62905, 10 days on maize roots


title: single-cell RNA-seq M1289 non-LRC_11

description:
non-LRC_11
processed data file: single_cell_countdata_LRC_validcells.txt

value: BCP-ALL pediatric


title: bulk RNA-seq M1287nonLRC

value: NOD scid gamma


title: 16-_4066_A5


title: bulk RNA-seq M1289LRC


title: single-cell RNA-seq M1289 non-LRC_1

description:
non-LRC_1
processed data file: single_cell_countdata_LRC_validcells.txt


title: H3K27Ac-FL-E115-Wt-Mm-Rep1-2070


title: H3K27Ac-FL-E135-Wt-Mm-Rep1-L7109


title: bulk RNA-seq M1287LRC


title: 16-_4066_A6


title: 16-_4066_A4


title: bulk RNA-seq M772nonLRC


title: F. proliferatum ET1, 20 days on maize roots

organism: Fusarium proliferatum ET1


title: 16-_4066_A3


title: bulk RNA-seq M1284nonLRC


title: H3K4me3-MB-E105-Wt-Mm-Rep2-L7136

description: The merged .bw file for this sample is available on GSM2251472

value: H3K4me3 (Milipore:07-473)


title: F. proliferatum ET1, 10 days on maize roots


title: H3K27Ac-FL-E105-Wt-Mm-Rep1-L4288


title: H3K27Ac-FL-E105-Wt-Mm-Rep2-L4877

description: The merged .bw file for this sample is available on GSM2251474


title: 16-_4066_A1


title: F. proliferatum ET1, 4 days on maize roots


title: H3K4me3-HL-E135-Wt-Mm-Rep2-L7133

description: The merged .bw file for this sample is available on GSM2251470


title: F. proliferatum NRRL 62905, CM

source_name: liquid culture, complete media


title: 16-_4066_A12


title: bulk RNA-seq M1283nonLRC

value: PDX cell


title: H3K4me3-HL-E135-Wt-Mm-Rep1-L7132


title: RAD51 ChIP-seq CX-5461, rep3

city: Vancouver

first: Steven

last: McKinney

state: BC

address: 675 West 10th Ave

department: Molecular Oncology

country: Canada

institute: British Columbia Cancer Agency

data_processing:
Adaptor trimmer, trim_galore, v0.4.1, default settings.
Alignment, bowtie2, v2.2.7, -I 100 -X 500 -p 8.
Quality filter, samtools, 1.3.1, view -f 2 -hb -q 30.
Sorting, samtools, v1.3.1, sort -@ 4.
Peak-calling, macs2, callpeak --gsize 'hs' --format 'AUTO' --qvalue '0.25'.
10 BAM input files were split into two groups, 2 background + 8 conditions of interests, and then each condition of interest was evaluated against both background, yielding 16 result files.
Genome_build: hg19_rDNA, standard hg19 with rDNA sequences appended to start of chr13
Supplementary_files_format_and_content: MACS2 called ChIP-seq narrowPeak text files.

source_name: U2OS cells, CX-5461, RAD51 ChIP

growth_protocol: U2OS cells cultured with McCoy's 5A Medium with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and RAD51-DNA complexes were isolated with antibody.
NEBNext Ultra Library Prep Kit for Illumina.

treatment_protocol: Incubate with CX-5461 10-7M for 24 hours or vehicle (NaH2PO4 50mM).

tag: cell line

value: sarcoma-derived cells

value: anti-RAD51 (Santa Cruz, SC-8349, lot:G2314)


title: F. proliferatum ET1, CM


title: bulk RNA-seq M1283LRC


title: F. mangiferae MRC7560, 20 days on maize roots

organism: Fusarium mangiferae


title: RAD51 ChIP-seq CX-5461, rep2


title: Null+EZH2_RNA_Rep3

data_processing:
RNA-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the human GRCh38 genome assembly using Tophat 2.0.12 guided by the gene models from the Ensembl v70 release. BAM files were imported into Seqmonk v32.1 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline on the Ensembl v70 gene set using non-directional counts.
Processed data files format and content: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) mRNA ID (Ensembl) (7) Description (Ensembl); (8-19) log2 RPM value
Libraries were sequenced on the Illumina HiSeq1000/2500 platforms using the default RTA analysis software.
Genome_build: GRCh38

extract_protocol:
Human ESC were isolated by FACS straight into TRIzol LS (Life Technologies). Total RNA was purified and then cleaned up using an RNeasy kit (Qiagen).
Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina).

value: embryonic stem cell (ESC)

tag: genotype/variation

value: EZH2 -/- +EZH2 (Null + EZH2)


title: Null+EZH2_RNA_Rep2


title: Null+EZH2_RNA_Rep1


title: H3K4me3-HL-E115-Wt-Mm-Rep1-2060


title: F. mangiferae MRC7560, 4 days on maize roots


title: RAD51 ChIP-seq CX-5461, rep1


title: H3K4me3-HL-E105-Wt-Mm-Rep1-L4870


title: F. mangiferae MRC7560, CM


title: bulk RNA-seq M1284LRC

value: LRC


title: H3K4me3-HL-E105-Wt-Mm-Rep2-L4881

description: The merged .bw file for this sample is available on GSM2251466


title: Null_RNA_Rep2

value: EZH2 -/- (Null)


title: RAD51 ChIP-seq vehicle, rep2

source_name: U2OS cells, vehicle, RAD51 ChIP

value: vehicle


title: H3K4me3-FL-E135-Wt-Mm-Rep2-L7131

description: The merged .bw file for this sample is available on GSM2251464


title: RAD51 ChIP-seq vehicle, rep1


title: F. fujikuroi IMI58289, 10 days on maize roots

organism: Fusarium fujikuroi IMI 58289


title: Null_RNA_Rep1


title: H3K4me3-FL-E135-Wt-Mm-Rep1-L7130


title: F. fujikuroi IMI58289, 20 days on maize roots


title: H3K4me3-FL-E115-Wt-Mm-Rep2-2068

description: The merged .bw file for this sample is available on GSM2251462


title: IgG ChIP-seq CX-5461, rep2

source_name: U2OS cells, CX-5461, IgG ChIP

value: anti-IgG (Santa Cruz, SC-2027, lot:F2413)


title: F. mangiferae MRC7560, 10 days on maize roots


title: IgG ChIP-seq CX-5461, rep3


title: Het_RNA_Rep3

value: EZH2 -/+ (Het)


title: Het_RNA_Rep2


title: F. fujikuroi IMI58289, 4 days on maize roots


title: F. fujikuroi IMI58289, CM


title: Null_RNA_Rep3


title: H3K4me3-FL-E115-Wt-Mm-Rep1-1776

value: forelimb


title: IgG ChIP-seq vehicle, rep2

source_name: U2OS cells, vehicle, IgG ChIP


title: WT_RNA_Rep3


title: Het_RNA_Rep1


title: GSCLC_4_rep1

description:
SC3-seq amplified from 1 ng total RNA extracted from GSC-like cells derived under condition1.
Processed data file: expression_RPM.txt

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome mm10 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the "—no-coverage-search" option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the "—compatible-hits-norm", "—no-length-correction" and "—library-type fr-secondstrand" options and mm10 reference gene annotations with extended TTSs. We also set the cufflinks option "—max-mle-iterations" to 50,000, because default iterations (5,000) resulted in "FAILED" when estimating the expression levels of some genes. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: expression_RPM.txt: Tab-delimited text file includes RPM values for each Sample.

source_name: GSCLC, condition1

growth_protocol:
GSC_1 and GSC_2 are derived from independent P7 testes. GSCLCs are derived from reconstituted testes cultured under condition1 (cultured at 34°C for 3 weeks; GSCLC_1 and GSCLC_4) or condition2 (cultured at 37°C for 2 weeks, then 34°C for 1 week; GSCLC_2 and GSCLC_3).
GSC and GSCLC were cultured in StemPro-34 SFM (Invitrogen) supplemented with StemPro supplement (Invitrogen), 1% FBS, 1x GlutaMAXTM-I (Invitrogen), 1x minimal essential medium (MEM) Vitamin Solution (SIGMA), 5 mg/ml AlbuMAX-II (Invitrogen), 5x10-5 M 2-mercaptoethanol, 1x MEM nonessential amino acid solution (Invitrogen), 30 μg/ml pyruvic acid, 1x ITS-G (Invitrogen), 100 U/ml penicillin, 0.1 mg/ml streptomycin, and growth factors [recombinant rat GDNF (10 ng/ml) (R&D Systems), human bFGF (10 ng/ml) (Invitrogen), LIF/ESGRO (103 U/ml) (Invitrogen), and mouse EGF (20 ng) (Invitrogen)]. Rep1 and rep2 are biological replicates for GSCs and GSCLCs culture.

extract_protocol:
Total RNA was extracted from GSCs and GSCLCs by using an RNeasy Micro Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions. Synthesis and amplification of cDNAs using 1 ng of purified total RNA, and construction of cDNA libraries for RNA sequencing (ABI SOLiD 5500XL system; Life Technologies), were performed as described in Nakamura et al., 2015.
cDNA synthesis and amplification from isolated RNAs/single cells were performed essentially as reported in Kurimoto, K.et al., Nucleic Acids Research, 34(5), e42. Library constructions for SOLiD System were performed as reported in Nakamura et al., Nucleic Acids Res. (2015).

tag: strain/background

value: C57BL/6 x 129/SvJcl

value: AcrAct_EGFP reporter

value: germline stem cell-like cells (GSCLC)

tag: condition

value: 34C for 3 wks


title: GSCLC_4_rep2


title: H3K4me3-FL-E105-Wt-Mm-Rep1-L4294


title: Zea mays, grown for 20 days in sterile vermiculite

organism: Zea mays

value: White sweet maize variety Silver Queen

value: wild type


title: WT_RNA_Rep1


title: GSCLC_3_rep1

description:
SC3-seq amplified from 1 ng total RNA extracted from GSC-like cells derived under condition2.
Processed data file: expression_RPM.txt

source_name: GSCLC, condition2

value: 37C for 2 wks, then 34C for 1 wk


title: H3K4me1-MB-E105-Wt-Mm-Rep2-L7129

description: The merged .bw file for this sample is available on GSM2251458

value: midbrain


title: WT_RNA_Rep2


title: H3K4me1-HL-E135-Wt-Mm-Rep2-L7126

description: The merged .bw file for this sample is available on GSM2251456

value: hindlimb


title: GSCLC_3_rep2


title: H3K4me1-HL-E115-Wt-Mm-Rep2-2479

description: The merged .bw file for this sample is available on GSM2251454


title: Null+EZH2_Input

description:
Null+EZH2_Input_Rep1
Null+EZH2_Input_Rep2
ChIP-Seq_RPM.txt

data_processing:
ChIP-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the human GRCh38 genome assembly using Bowtie 2 v2.2.5 using default parameters. BAM files were imported to Seqmonk and reads were extended by 200bp at their 5’ end to approximate the true insert size.
Processed data files format and content: Quantitated ChIP-Seq data file is tab delimited and shows log2 RPM data for -/+2.5kb surrounding each TSS: (1) mRNA transcript associated with TSS (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Associated gene name (Ensembl) (7) mRNA ID (Ensembl); (8) Description (Ensembl); (9-29) log2 RPM value
Libraries were sequenced on the Illumina HiSeq1000/2500 platforms using the default RTA analysis software.
Genome_build: GRCh38

extract_protocol:
Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100μl RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Life Technologies) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. Crosslinked ChIP for profiling EZH2 occupancy was performed using iDeal ChIP-Seq kit for Transcription Factors (Diagenode).
Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB).

value: embryonic stem cell (ESC)


title: input DNA

city: Wageningen

first: Luca

last: Santuari

address: Droevendaalsesteeg 1

department: Plant Sciences Group

country: Netherlands

institute: Wageningen University

data_processing:
CSFASTQ files were extracted from the XSQ file using the XSQConverter tool developed by Wim Spee in the Cuppen group
Quality checking and filtering was performed with the script SOLiD_preprocess_filter_v2.pl written by Ariella Sasson, Rutgers University (https://github.com/fls-bioinformatics-core/HTS_SOLiD_Preprocessing) with the following parameters: SOLiD_preprocess_filter_v2.pl -f IP1.csfasta -g IP1_F3_QV.qual -p 3 -q 22 -e 10 -d 9 -n on -t on -u 25 -a on -v on -o IP1
CSFASTA and QUAL files were converted back to CSFASTQ files using the script qualfa2fq.pl of bwa version 0.5.9
CSFASTQ files were converted to encoded FASTQ files with the script solid2fastq_v2.pl
reads were mapped on the Arabidopsis thaliana TAIR10 genome release with the command bwa samse version 0.5.9 and default parameter settings
the SAM file was converted into a BAM file with SAMtools version 0.1.19-44428cd
only uniquely mapped reads were retained and BAM files were converted into CSAR input file format as follows: samtools view -b -F 1548 -q 30 IP1.bam | bamToBed -i stdin | awk '{print 1 "\t" $3-$2 "\t" $6 "\t" $1 "\t" $2+1}' | gzip -c > IP1.csar.gz
bamToBed is from BEDtools version 2.17.0
To maximize the IP signal, reads from the two IP samples, IP1 and IP2, were pooled as follows. Only one read per position was considered: gzcat PLT2_IP1_IP2.pooled.rmdup.csar.gz | sort -k4,5 -n -r | uniq | gzip -c > PLT2_IP1_IP2.rmdup.csar.gz
The fragment length estimated by the R package spp 18 for the pooled IP1 and IP2 samples was 130 bp
Peaks were called using CSAR version 1.10.0. The fragment length was provided as estimated, using the parameter w in the function mappedReads2Nhits. Ten iterations of the function permutatedWinScores were used to estimate the False Discovery Rate. To account for the pooling of the two replicate IPs, a stringent FDR threshold of 0.01 was used to retain significant peaks. The other parameter settings were maintained as default.
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig file was generated using CSAR; Scores represent CSAR scores.

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: Five ml of dry Arabidopsis seeds (PTL2::PLT2-YFP) were sterilized with chlorine gas for 8h and stratified in 10ml sterile MQ water for 48h. Seeds were transferred to 0.5x GM agar plates topped with a nylon mesh (Sefar Nitex 03-100/44) and grown for 4-5 days (~120 plates/ChIP). Root tips (~5mm) were cut and transferred to PBS-S (PBS + 0.4M Sucrose).

extract_protocol:
Two replicate ChIP samples and one input sample were sequenced. Sequencing library preparation and subsequent Solid Sequencing were performed as described in Mokry, M. et al. Efficient Double Fragmentation ChIP-seq Provides Nucleotide Resolution Protein-DNA Binding Profiles. PloS one 5, e15092.
According to Mokry, M. et al. Efficient Double Fragmentation ChIP-seq Provides Nucleotide Resolution Protein-DNA Binding Profiles. PloS one 5, e15092

treatment_protocol: PBS-S medium was complemented with 1% (V/V) formaldehyde (16% methanol-free formaldehyde, Polysciences). A vacuum pump was used to reduce the pressure to ~0.2 atm for 3 times within 5 min. Root tips were left to cross link protein-DNA complexes for an additional 2x 5min. Cross linking was stopped by the addition of 2M glycine to a final concentration of 0.125M followed by an incubation for 10 min. Root material was washed 3 times in PBS-S and stored at -80°C. ChIP was performed as described by Song, J., Rutjens, B. & Dean, C. in Plant Epigenetics and Epigenomics Vol. 1112 Methods in Molecular Biology (eds Charles Spillane & Peter C. McKeown) Ch. 11, 165-175 (Humana Press, 2014), with the following modifications: Ground samples were thawed in extraction buffer 1 and passed through a double layer of Miracloth and pelleted. The nuclei-enriched pellet was treated twice with extraction buffer 2. After the second spin the pellet was resuspended in 200 μl NLB and sonicated in a Bioruptor (Diagenode) for 2x 5min on low and 1x 5min on medium energy. In between sonication sessions the water was cooled with ice. 5 μl anti-GFP antibody (AB290, Abcam) was used to coat 15 μl Protein-A Dynabeads (Invitrogen) in CDB for 2h at room temperature. Diluted ChIP samples and antibody coated Dynabeads were incubated O/N at 4°C on a rotator. Beads were washed 2x with LSB, 1x HSB and 2x TE. Beads were incubated with 100 µl TE+1%SDS at 65°C on an Eppendorf Thermomix (800 rpm) for 15 min upon which the isolated DNA was purified using Zymo Research ChIP DNA clean-up (according to the manufacturer’s instructions).

value: plt1plt2 double mutant

tag: tissue type

value: roots


title: IgG ChIP-seq CX-5461, rep1

value: sarcoma-derived cells


title: H3K4me1-HL-E115-Wt-Mm-Rep1-2058

tag: tissue


title: GSCLC_2_rep2


title: GSCLC_2_rep1


title: PLT2_IP1


title: Null+EZH2_H3K4me1

description:
Null+EZH2_H3K4me1_Rep1
Null+EZH2_H3K4me1_Rep2
ChIP-Seq_RPM.txt

value: EZH2 -/- +EZH2 (Null + EZH2)

value: H3K4me1 (Abcam, ab8895)


title: H3K4me1-HL-E105-Wt-Mm-Rep2-L4879

description: The merged .bw file for this sample is available on GSM2251452


title: Null+EZH2_H3K4me3

description:
Null+EZH2_H3K4me3_Rep1
Null+EZH2_H3K4me3_Rep2
ChIP-Seq_RPM.txt

value: H3K4me3 (Abcam, ab8580)


title: H3K4me3-FL-E105-Wt-Mm-Rep2-L4876

description: The merged .bw file for this sample is available on GSM2251460

value: forelimb

value: H3K4me3 (Milipore:07-473)


title: GSCLC_1_rep1

value: C57BL/6 x 129/SvJcl

value: AcrAct_EGFP reporter


title: Null+EZH2_H3K27ac

description:
Null+EZH2_H3K27ac_Rep1
Null+EZH2_H3K27ac_Rep2
ChIP-Seq_RPM.txt

value: H3K27ac (Abcam, ab4729)


title: GSCLC_1_rep2

value: germline stem cell-like cells (GSCLC)

value: 34C for 3 wks


title: H3K4me1-HL-E105-Wt-Mm-Rep1-L4298


title: H3K4me1-FL-E135-Wt-Mm-Rep2-L7125

description: The merged .bw file for this sample is available on GSM2251450


title: GSC_2_rep1

description:
SC3-seq amplified from 1 ng total RNA extracted from GS cells.
Processed data file: expression_RPM.txt

value: germline stem cells (GSCs)


title: GSC_2_rep2


title: Null_Input

description:
Null_Input_Rep1
Null_Input_Rep2
ChIP-Seq_RPM.txt

value: EZH2 -/- (Null)


title: IgG ChIP-seq vehicle, rep1

value: vehicle

value: anti-IgG (Santa Cruz, SC-2027, lot:F2413)


title: H3K4me1-FL-E135-Wt-Mm-Rep1-L7124


title: PLT2_IP2

value: plt1plt2 double mutant


title: GSC_1_rep2


title: H3K4me1-FL-E115-Wt-Mm-Rep2-2066

description: The merged .bw file for this sample is available on GSM2251448


title: Null+EZH2_H3K27me3

description:
Null+EZH2_H3K27me3_Rep1
Null+EZH2_H3K27me3_Rep2
ChIP-Seq_RPM.txt

value: embryonic stem cell (ESC)

value: H3K27me3 (Millipore, 07-449)


title: H3K4me1-FL-E115-Wt-Mm-Rep1-1774


title: Null_H3K27ac

description:
Null_H3K27ac_Rep1
Null_H3K27ac_Rep2
ChIP-Seq_RPM.txt


title: Null_H3K4me3

description:
Null_H3K4me3_Rep1
Null_H3K4me3_Rep2
ChIP-Seq_RPM.txt


title: GSC_1_rep1


title: H3K4me1-FL-E105-Wt-Mm-Rep2-L4862

description: The merged .bw file for this sample is available on GSM2251446


title: Null_H3K27me3

description:
Null_H3K27me3_Rep1
Null_H3K27me3_Rep2
ChIP-Seq_RPM.txt


title: Het_Input

description:
Het_Input_Rep1
Het_Input_Rep2
ChIP-Seq_RPM.txt

value: EZH2 -/+ (Het)


title: Het_H3K4me1

description:
Het_H3K4me1_Rep1
Het_H3K4me1_Rep2
ChIP-Seq_RPM.txt

value: H3K4me1 (Abcam, ab8895)


title: Het_H3K27ac

description:
Het_H3K27ac_Rep1
Het_H3K27ac_Rep2
ChIP-Seq_RPM.txt


title: CTCF-MB-E105-Wt-Mm-Rep1-L8221-1

value: midbrain

value: CTCF (Active motif:613111)


title: H3K4me1-FL-E105-Wt-Mm-Rep1-L4297

value: forelimb


title: Het_H3K4me3

description:
Het_H3K4me3_Rep1
Het_H3K4me3_Rep2
ChIP-Seq_RPM.txt

value: H3K4me3 (Abcam, ab8580)


title: CTCF-HL-E135-Wt-Mm-Rep2-L8185-1

description: The merged .bw file for this sample is available on GSM2251442

value: hindlimb


title: CTCF-MB-E105-Wt-Mm-Rep2-L8222-1

description: The merged .bw file for this sample is available on GSM2251444


title: CTCF-HL-E135-Wt-Mm-Rep1-L8184-1


title: WT_Input

description:
WT_Input_Rep1
WT_Input_Rep2
ChIP-Seq_RPM.txt


title: CTCF-HL-E115-Wt-Mm-Rep2-L8230-1

description: The merged .bw file for this sample is available on GSM2251440


title: CTCF-HL-E115-Wt-Mm-Rep1-L8228-1


title: WT_H3K4me1

description:
WT_H3K4me1_Rep1
WT_H3K4me1_Rep2
ChIP-Seq_RPM.txt


title: WT_H3K27ac

description:
WT_H3K27ac_Rep1
WT_H3K27ac_Rep2
ChIP-Seq_RPM.txt

value: H3K27ac (Abcam, ab4729)


title: CTCF-HL-E105-Wt-Mm-Rep2-L7327-1

description: The merged .bw file for this sample is available on GSM2251438


title: Null_H3K4me1

description:
Null_H3K4me1_Rep1
Null_H3K4me1_Rep2
ChIP-Seq_RPM.txt


title: CTCF-HL-E105-Wt-Mm-Rep1-L7326-1


title: CTCF-FL-E135-Wt-Mm-Rep2-L8183-1

description: The merged .bw file for this sample is available on GSM2251436


title: CTCF-FL-E135-Wt-Mm-Rep1-L8182-1


title: WT_H3K4me3

description:
WT_H3K4me3_Rep1
WT_H3K4me3_Rep2
ChIP-Seq_RPM.txt


title: CTCF-FL-E115-Wt-Mm-Rep2-L8229-1

description: The merged .bw file for this sample is available on GSM2251434


title: Vitamin D, KD, rep2

city: Los Angeles

first: Yi

last: Xing

state: CA

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA

description:
D.KD-2
yes vitamin D treatment, yes HNRNPC knockdown

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 72) then hg19 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-unstranded --initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cufflinks v2.0.2 with uniquely and properly mapped pairs.
Genome_build: hg19
Supplementary_files_format_and_content: The .txt file reports FPKMs for all samples.

source_name: Human MG63 osteosarcoma cells

extract_protocol:
Human MG63 osteosarcoma cells (American Type Culture Collection, CRL-1427) were cultured in Dulbecco’s modified Eagle medium (DMEM, high glucose, Gibco, 11995-065) supplemented with 10% Fetal Bovine Serum (FBS) cultured at 37oC with 5% CO2. Crystalline 1,25-dihydroxyvitamin D3 (1,25(OH)2D3, Enzo Life Sciences, BML-DM200-0050) was reconstituted in ethanol. Ethanol (0.1%) was used as vehicle treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone

tag: age

value: 14 years old

value: MG63 osteosarcoma cells

value: HNRNPC KD

tag: agent


title: Vitamin D, KD, rep3

description:
D.KD-3
yes vitamin D treatment, yes HNRNPC knockdown


title: Vitamin D, CTRL, rep3

description:
D.CTRL-3
yes vitamin D treatment, no HNRNPC knockdown

value: Control


title: WT_H3K27me3

description:
WT_H3K27me3_Rep1
WT_H3K27me3_Rep2
ChIP-Seq_RPM.txt

tag: cell type


title: Vitamin D, KD, rep1

description:
D.KD-1
yes vitamin D treatment, yes HNRNPC knockdown


title: CTCF-FL-E115-Wt-Mm-Rep1-L8227-1


title: CTCF-FL-E105-Wt-Mm-Rep1-L7324-1


title: Vitamin D, CTRL, rep1

description:
D.CTRL-1
yes vitamin D treatment, no HNRNPC knockdown


title: Het_H3K27me3

description:
Het_H3K27me3_Rep1
Het_H3K27me3_Rep2
ChIP-Seq_RPM.txt


title: Vitamin D, CTRL, rep2

description:
D.CTRL-2
yes vitamin D treatment, no HNRNPC knockdown


title: Vehicle, KD, rep2

description:
V.KD-2
no vitamin D treatment, yes HNRNPC knockdown

value: Vehicle


title: Vehicle, KD, rep1

description:
V.KD-1
no vitamin D treatment, yes HNRNPC knockdown


title: Vehicle, KD, rep3

description:
V.KD-3
no vitamin D treatment, yes HNRNPC knockdown


title: CC-HL-E135-Wt-Mm-Rep2

description:
Captured genomic DNA from 3C library
Processed data file for smoothed signal, peaks, and enhancer data are located on GSM2251430

data_processing:
Library strategy: Capture-C
Frag profiles: Paired-end sequencing data from Capture-C experiments was mapped and cleaned from invalid di-tags and duplicates using the HiCUP pipeline v0.5.8 (Wingett et al. 2015) and Bowtie 2.2.6 (Langmead and Salzberg 2012). All sequencing data was mapped to mouse reference genome mm9. Viewpoint-specific contact profiles were generated from BAM files with custom Java code using htsjdk 1.139 (https://samtools.github.io/htsjdk/) for the processing of BAM files. A di-tag was considered only if one mate was located in an enriched viewpoint region while the other mapped to the non-enriched part of the genome. Contact profiles were generated for each viewpoint by counting the number reads per restriction fragment. Count data was binned into a regular grid of 1 kb intervals centered around the middle of the corresponding viewpoint region. The count value of each restriction fragment was assigned to the bin, which contains the fragment center.
Smoothed profiles: count data per fragments was combined from both replicates, binned, smoothed with a running window of 3 and 5 bins. To make contact profiles with different read densities comparable, each profile was scaled by the total contact count on the chromosome of the viewpoint (Sum of cis contacts/1000).
Peak calling: Scaled contact profiles were pooled across all samples and viewpoints to generate a simple, empirical background model, which incorporates the distance dependent decay of the contact frequency. The positioning of the grid around viewpoint center allows an overlay of all profiles by aligning their centers. Now, each 1 kb bin can be described by its offset relative to the viewpoint center and has the contact information from 6244 profiles (7 tissues/stages × 446 viewpoints × 2 replicates). The 99th and 95th percentile of the empirical distribution were used to derive an individual threshold for each bin. A spline function was used to smooth the resulting threshold line. To avoid the calling of spurious interactions due to a lower profile density at locations distant from the viewpoint, the threshold was set constant for all regions more than 0.5 Mb away from the viewpoint. A bin was selected as candidate region, when the contact value exceeds the threshold in both replicates. Within the candidate region the maximum value from the merged profile was used to determine the peak center. A region +-10 kb around the selected peak was excluded from the candidate region to suppress peaks nearby. The selection of maxima and exclusion of sub-peaks was repeated until no further candidates were left.
Enhancer calling: Putative enhancers were called based on the combination of three thresholds: the 95th percentile of the empirical background for the interaction strength, the 99th percentile for H3K27Ac and 95th percentile for H3K4me1. Percentiles of the histone modifications were computed based on genome wide distribution of mapped reads within 5 kb windows.
Genome_build: mm9
Supplementary_files_format_and_content: Bed and bedgraph files were generated in each sample for 446 different viewpoints and packed for each analysis into one archive. Smoothed profiles, peak files and enhancer files contain data summarized across the two replicates. The files are located on the 'Rep1' sample.

growth_protocol: Limb buds and midbrain were micro-dissected from mouse embryos

extract_protocol:
The 3C library was prepared according to (Hagege et al. 2007), i.e. crosslinking, cell lysis, DpnII digestion, ligation and de-crosslinking. Re-ligated products were then sheared using a covaris sonicator (Duty cycle: 10%, Intensity:5, Cycles per Burst: 200, Time: 6 cycles of 60 sec each, Set Mode: Frequency sweeping, Temperature: 4° to 7°C).
Adaptors were added to the sheared DNA and amplified. The adapted-ligated library was then hybridized to the custom-designed sure-select beads indexed for sequencing using an indexing PCR following Agilent instructions.

value: Hindlimb

tag: developmental stage

tag: genotype

value: wild type


title: CC-HL-E115-Wt-Mm-Rep2

description:
Captured genomic DNA from 3C library
Processed data file for smoothed signal, peaks, and enhancer data are located on GSM2251426


title: CC-FL-E135-Wt-Mm-Rep1

description: Captured genomic DNA from 3C library

value: Forelimb


title: CC-HL-E135-Wt-Mm-Rep1

description: Captured genomic DNA from 3C library


title: Vehicle, CTRL, rep3

description:
V.CTRL-3
no vitamin D treatment, no HNRNPC knockdown


title: CC-FL-E135-Wt-Mm-Rep2

description:
Captured genomic DNA from 3C library
Processed data file for smoothed signal, peaks, and enhancer data are located on GSM2251428


title: Vehicle, CTRL, rep2

description:
V.CTRL-2
no vitamin D treatment, no HNRNPC knockdown


title: CC-FL-E115-Wt-Mm-Rep2

description:
Captured genomic DNA from 3C library
Processed data file for smoothed signal, peaks, and enhancer data are located on GSM2251424


title: Vehicle, CTRL, rep1

description:
V.CTRL-1
no vitamin D treatment, no HNRNPC knockdown


title: CC-FL-E115-Wt-Mm-Rep1

description: Captured genomic DNA from 3C library


title: CC-HL-E115-Wt-Mm-Rep1

description: Captured genomic DNA from 3C library


title: CTCF-FL-E105-Wt-Mm-Rep2-L7325-1

description: The merged .bw file for this sample is available on GSM2251432


title: CC-MB-E105-Wt-Mm-Rep1

description: Captured genomic DNA from 3C library

value: Midbrain


title: CC-HL-E105-Wt-Mm-Rep2

description:
Captured genomic DNA from 3C library
Processed data file for smoothed signal, peaks, and enhancer data are located on GSM2251420


title: CC-FL-E105-Wt-Mm-Rep2

description:
Captured genomic DNA from 3C library
Processed data file for smoothed signal, peaks, and enhancer data are located on GSM2251418


title: HL60-3

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

institute: University of North Texas

data_processing:
Used Tophat and Bowtie for read alignment onto Arabidopsis reference genome and Cufflinks for obtaining the FPKMs and assessment of significance of fold change
Genome_build: TAIR9
Supplementary_files_format_and_content: Excel file; FPKMs for Control, 20 second light stress, and 60 second light stress

source_name: Shoot

growth_protocol: Plants were grown for 21 days in 9x9x6-cm3 pots covered with a fiberglass screen net at 23oC under constant low light (50 µmol m-2s-1).

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) and cleaned on RNeasy Mini columns (Qiagen).
RNA-Seq

treatment_protocol: Plants were exposed to a light intensity of 1000 µmol m-2s-1 at 21oC for periods of 0, 20 and 60 sec in a growth chamber (E-30-HB, Percival Scientific). Samples were collected by immediately dipping the pots in liquid nitrogen.

tag: Stage

tag: treatment

value: Exposed to 60sec high light

value: shoot


title: HL60-2

tag: strain


title: jc969 MCF7 P6 input

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

data_processing:
Reads were mapped to hg19 genome using Gsnap version 2015-09-29 (Wu TD1, Nacu S., 2010).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.0.10.20131216 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
For the ChIP samples of Histones with mono and tri-methyl modifications the broad peaks were called. The peaks yielded with MACS2 q value <= 1e-5 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh37
Supplementary_files_format_and_content: bed/text

source_name: MCF7 breast cancer cell line

growth_protocol: MCF-7 cells were obtained from ATCC. MCF-7 were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated foetal bovine serum (FBS), 2 mM L-glutamine, 50U/ml penicillin and 50μg/ml. All cell lines were regularly genotyped using STR profilling (Promega GenePrint 10 system). Cell lines were regularly tested for mycoplasma infection.

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275951
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.

treatment_protocol: Cells were treated either with control, MLL3 or FOXA1 siRNA prio to extraction of genomic DNA for Chip-seq analysis.

tag: chip antibody

value: Input

value: asynchonous cells

value: No treatment


title: HL60-1


title: jc1864 siCt input rep2

value: Input siCt

value: Nonspecific siRNA


title: jc1866 siCt input rep3


title: HL20-3

value: Exposed to 20sec high light


title: jc2023 MCF7 MLL3 custom rep3

description: mll3_untreated-sict_input_peaks.narrowPeak

value: custom anti-MLL3 antibody was provided by Prof. Ali Shilatifard (Stowers Institute, Kansas City, USA and Northwestern University Feinberg School of Medicine, Chicago, USA)


title: jc2022 MCF7 MLL3 custom rep2


title: HL20-1


title: jc2021 MCF7 MLL3 custom rep1


title: Contr-3


title: Contr-2


title: jc1791 MLL3 new


title: Contr-1


title: Input DNA control in staged YA

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description:
a fraction of the input total chromatin that was used for LET-607:GFP ChIP
ENCFF152APScontrol
processed data file: ENCFF405WPOcontrolnormsignal.bigWig

data_processing:
FASTQ files were processed and mapped using BWA (Li et al., 2009), retaining only high quality alignments (Q ≥ 30).
Transcription factor binding sites were determined and scored using SPP peak caller (Kharchenko et al. 2008).
High confidence binding events were identified using IDR (Irreproducible Discovery Rate)
A cross-replicate threshold was obtained using a 5% IDR score threshold.  Additionally, a rescue threshold method was also determined using IDR scoring.  A final rank threshold for each data set was calculated by combining the cross-replicate and rescue threshold scores.  Finally, reads from all replicates were pooled and the SPP and IDR framework was applied again to rank peaks by signal-score. The final rank threshold score determined from the individual replicates was used as a significance threshold for the ranked pooled-data peaks.
Genome_build: WS220
Supplementary_files_format_and_content: WIG files were generated as an output of the SPP program

organism: Caenorhabditis elegans

source_name: staged young adult (YA) from YL529 (LET-607-GFP transgenic strain)

growth_protocol: Gravid adults were bleached and synchronized by L1 starvation.  Starved L1s were plated on peptone-enriched NGM plates seeded with OP50, and grown until the desired developmental stage(young adult) at 20˚C. Worms were harvested and washed free of bacteria in M9.

extract_protocol:
For all ChIP-seq samples, worms  were crosslinked in 2% formaldehyde in M9 buffer for 30 minutes rotating at room temperature.  Crosslinking was quenched with 1M Tris pH 7.5, followed by two washes with M9, and one wash with FA buffer containing protease inhibitors.  Final Triton X-100 concentration in all FA buffers used was  1%.  Worm pellets were flash-frozen in liquid nitrogen and stored at -80˚C.  Using the Fisher Scientific Sonic Dismembrator 550 (Pittsburgh, PA), samples were sonicated with a microtip on ice for sixteen cycles of 10 sec on, and 60 sec off on the “microtip” setting to fragment the majority of DNA within 200-800bp range.  Sonicated extract containing 2mg of protein was immunoprecipitated as previously described (Zhong et al., 2010) with 7.5µg of anti-GFP antibody (gift from Kevin White).
ChIP-seq library preparation for enriched DNA and the genomic DNA input control for at least two biological replicates was performed as described in (Zhong et al. 2010), except Qiagen MinElute PCR purification and gel extraction kits were used after the Klenow step.  Libraries were multiplexed as described in Lefrancois et al. (2009) in order to sequence four samples in a single flow cell using the Illumina Genome Analyzer II platform.

value: YA

value: whole animal

tag: chipped factor

value: none - input


title: jc2066 MCF7 MLL3 siFoxA1 Rep3

description: mll3_sifoxa1-sict_input_peaks.narrowPeak

value: FOXA1 siRNA


title: jc2064 MCF7 MLL3 siFoxA1 Rep2


title: jc2062 MCF7 MLL3 siFoxA1 Rep1


title: LET-607 ChIP in staged YA rep 2

description:
ChIP was performed with anti-GFP of GFP-tagged LET-607
ENCFF281XQFrep2
processed data file: ENCFF489OCJread-depthnormsignal.bigWig

value: anti-GFP (gift from Kevin White)


title: LET-607 ChIP in staged YA rep 1

description:
ChIP was performed with anti-GFP of GFP-tagged LET-607
ENCFF731HDArep1
processed data file: ENCFF489OCJread-depthnormsignal.bigWig


title: jc2063 MCF7 MLL3 siCt Rep2


title: CC-MB-E105-Wt-Mm-Rep2

description:
Captured genomic DNA from 3C library
Processed data file for smoothed signal, peaks, and enhancer data are located on GSM2251422

value: wild type


title: jc2065 MCF7 MLL3 siCt Rep3


title: Early maturation-stage seed coat biological replicate 2

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
EM-SC BR2
Seed coats from seeds 6.0 - 7.0 mm in length were collected.

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls)).
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine

organism: Glycine max

source_name: Soybean early maturation-stage seed coat

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).  Whole seeds containing early-maturation (EM) stage embryos were collected. The embryo was dissected out of the seed coat and the axis was manually separated from the cotyledons of the EM-stage embryo.

extract_protocol: Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA  was isolated from the powder using the DNEASY Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.Approximately one microgram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications. We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion. Two libraries were constructed from genomic DNA isolated from seed coat. One library was spiked in ~ three nanogram of unmethylated lambda DNA as all other libraries; the other library was spiked in ~ three nanogram of methylated lambda DNA to serve as a control for over conversion (i.e. conversion of methylated cytosine to uracil) during the bisulfite conversion step. The methylated lambda DNA was generated by treating unmethylated lambda DNA with CpG Methyltransferase (New England BioLabs). Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

value: early maturation stage

value: seed coat


title: jc2663 H3K4me3 siMLL3 rep4

description: h3k4me3_simll3-sict_input_peaks.broadPeak

tag: cell line

value: anti-H3K4me3 (05-1339) Millipore

value: MLL3 siRNA


title: Early maturation-stage seed coat biological replicate 1

description:
EM-SC BR1
Seed coats from seeds 6.0 - 7.0 mm in length were collected.


title: jc2061 MCF7 MLL3 siCt Rep1

value: asynchonous cells