title: NB4_CTCF_ChIA-PET

data_processing:
Library strategy: ChIA-PET
Filtering linker sequence in ChIA-PET using in-house script
Mapping ChIA-PET reads to reference genome using BWA MEM (version 0.7.16)
Deduplicating ChIA-PET reads using Picard (MarkDuplicates)
Peak-calling for ChIA-PET using MACS (v.1.4.2)
Producing 2D contact map of ChIA-PET using Juicer tool (version 1.6.1)
Mapping ChIP-Seq reads from ABI SOLiD sequencing platform (csfasta+QV.qual) using SOLiD BioScope (version 1.0.1)
Mapping ChIP-Seq reads from Illumina sequencing platform using BWA-MEM (version 0.7.16), and peak-calling using MACS (version 1.4.2)
Mapping RNA-Seq reads uinsg Bowtie2, and processing using edge R
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt format for peak (bed), loop (bedpe), binary data format for Juicebox (hic)

extract_protocol:
When performing ChIA-PET library, the same precedures were used as those in previous paper. (Li et al., 2012; Tang et al., 2015)
Paired-end sequencing (2 ×150bp) was used for ChIA-PET libraries  with Illumina Hiseq 2500 or Illumina Nextseq 500.

value: ChIA-PET

value: CTCF (Abcam, catalog# ab70303)

value: nuclear chromatin


title: NB4_PML_ChIA-PET

status: Public on Dec 17 2019

type: SRA

city: FARMINGTON

first: Yijun

last: Ruan

state: CT

address: 10 DISCOVERY DR

department: Ruan

country: USA

institute: The Jackson Laboratory

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Both U937-PR9 and NB4 cells were cultured in RPMI 1640 (ThermoFisher, A10491), supplemented with 10% fetal bovine serum (ThermoFisher, 10082147). These cells were cultured at 37 ℃ , 5% CO2, and ambient oxygen levels.

treatment_protocol: The U937-PR9 cells were treated with 100 μM ZnSO4 (Sigma, Z0251) for 4 hours for ChIA-PET and ChIP-Seq experiment. The U937-PR9 cells were treated with 100 μM ZnSO4  and then collected these cells at 4, 6, 12, 24 hours for RNA-Seq experiment. These cells was preincubated with 100 μM ZnSO4 for 4 hours and then treated with ATRA (Sigma, R2625) for 24 and 48 hours used for RNA-Seq experiment. NB4 cells were treated with ATRA for 24 and 48 hours used for RNA-Seq experiment.

tag: cell type

tag: method

tag: factor

value: PML (Santa Cruz, catalog# sc-996X)

tag: molecule subtype


title: patients #3

type: protein

city: Chongqing

first: Jun

last: Rao

address: No 183, Xinqiao street, Shapingba

department: Medical center of hematology

country: China

institute: Xinqiao hospital

description:
Secreted proteins
SAMPLE 3

hyb_protocol: Place each membrane printed side up into a Plastic Incubation Tray. Add 8 ml of Blocking Buffer to each membrane and cover with the lid. Incubate at room temperature with gentle shaking for 1 hour. Aspirate Blocking Buffer from each tray. Add 8 ml of diluted or undiluted sample onto each membrane and cover with the lid. Incubate at room temperature with gentle shaking for 2 hours. Dilute 20X Wash Buffer 1 with deionized or distilled water to prepare the 1X Wash Buffer 1. Aspirate the samples from each tray and then wash by adding 20 ml of 1X Wash Buffer I at room temperature with gentle shaking (5 min per wash). Repeat the wash 2 more times for a total of 3 washes. Aspirate the 1X Wash Buffer 1 from each tray. Dilute 20X Wash Buffer 2 with deionized or distilled water to prepare the 1X Wash Buffer 2. Wash 3 times with 20 ml of 1X Wash Buffer 2 at room temperature with gentle shaking. Aspirate the 1X Wash Buffer 2 from each tray. Dilute the 500X HRP-Conjugated Streptavidin with Blocking Buffer to prepare the 1X HRP-Conjugated Streptavidin. Add 8 ml of 1X HRPConjugated Streptavidin to each membrane. Incubate at room temperature with gentle shaking for 2 hours. Wash as previously directed.

scan_protocol: The signal can be detected directly from the membrane using a chemiluminescence imaging system or by exposing the array to x-ray film (we recommend using Kodak X-Omat™ AR film) with subsequent development. Expose the membranes for 40 seconds. Then re-expose the film according to the intensity of signals. If the signals are too strong (background too high), reduce the exposure time (e.g., 5–30 seconds). If the signals are too weak, increase the exposure time (e.g., 5–20 min or overnight) or re-incubate membranes overnight with 1X HRPConjugated Streptavidin, and repeat detection on the second day.

data_processing: The manufac Individual array spots were background subtracted locally by subtracting the median background across spot replicated in each sample, and then normalized using two positive controls.

label: biotin

molecule: protein

source_name: Bone marrow Serum

label_protocol: Immediately before use, prepare 1X Labeling Reagent by briefly centrifuging down the Labeling Reagent vial and add 100 ul 1X PBS (pH=8.0) into the vial. Pipette up and down or vortex briefly to dissolve the powder. Add an appropriate amount of 1X Labeling Reagent into the tube containing the sample and immediately mix the reaction solution. Incubate the reaction solution at room temperature for 30 minutes with gentle shaking. Gently tap the tube to mix the reaction solution every 5 minutes. Add 5 ul Stop Solution (Item D) into the reaction solution and then use the Spin Column to remove any unbound biotin. a). Twist off the bottom closure of the Spin Column and loosen the cap (but keep the cap on). Place the Spin Column into a 50 ml conical collection tube. b). Centrifuge the Spin Column at 1,000 g for 3 minutes to remove storage solution. c). Add 5 ml 1X PBS (pH=8.0) into the Spin Column and centrifuge at 1,000 x g for 3 minutes to remove the 1X PBS. Repeat an additional 2 times to wash the Spin Column. d). Place the Spin Column in a new 50 ml conical collection tube and slowly load 3.5 ml of sample to the center of the compact resin bed. e). Centrifuge the Spin Column at 1,000 x g for 3 minutes. The sample should filter through the resin and deposit into the 50 ml conical collection tube. Store at -80 oC until needed. Discard the Spin Column after use.

extract_protocol: 5-fold diluted culture supernatant from whole blood

treatment_protocol: Whole blood was collected in vacutainer serum tubes, incubated undisturbed at room temperature for 30 min, then centrifuged at 2000 rpm for 15 min at 4 oC . The supernatant was collected and frozen at -80 oC for storage.

tag: disease state

value: acute myeloid leukemia

tag: tissue

value: Bone marrow serum

tag: gender

value: female

tag: age


title: GmEM_GLYMA.06G314400-B-ChIP_br2

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Peaks were identified for each biological replicates using MACS2, using default parameters and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

organism: Glycine max

source_name: embryos

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3 ug of an antibody raised against the peptide SDTRRPGRKRGTSED corresponding to the amino acids 224-238 of GLYMA.06G314400.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Early maturation stage embryos were dissected from 6 to 7 mm seeds.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

tag: Stage

value: early maturation stage

tag: antibody

value: anti-peptide GLYMA.06G314400


title: patients #2

description:
Secreted proteins
SAMPLE 2


title: GmEM_GLYMA.06G314400-B-ChIP_br1


title: Progeny1-1449 [a550818-4325018-051918-781_A02]

type: genomic

city: Gainesville

first: Jianping

last: Wang

state: Florida

address: 2033 Mowry Road

department: Agronomy

institute: University of Florida

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The Affymetrix bioinformatics team processed the raw intensities in cell intensity files (.CEL) to obtain normalized intensities for each probe set. Further, these normalized intensities were converted to genotype calls with the Axiom Genotyping Algorithm version one
primary data description: Genotype Call (SNP call): AA=0, AB=1, BB=2, NoCall="-"; 'Signal' = Summarized signal

label: Biotin

organism: Saccharum officinarum

source_name: Progeny from cross Green German and IND81-146

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: These plant samples were maintained at the United States Department of Agriculture (USDA), Agricultural Research Service (ARS) Sugarcane Field Station at Canal Point, FL, which were under nature condition.

extract_protocol: Genomic DNA samples were extracted using MagJET Plant Genomic DNA Kit (Thermo Fisher Scientific, MA, USA).

treatment_protocol: Young leaf tissues were collected and stored at -80 °C for DNA extraction.

value: Unknown


title: GmEM--Input_br2 (GLYMA.06G314400 control)


title: CDKN2a-sg2 (Cut&Run ChiP-seq)

city: Memphis

first: Chunliang

last: Li

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

data_processing:
Library strategy: CUT&RUN
Cut&Run ChiP-seq reads from each species were aligned using Bowtie2  2.3.4
bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. DeepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016)) was used to convert apping .bam file to .bw file
Genome_build: hg19
Supplementary_files_format_and_content: .bw

source_name: B cell precursor leukemia

growth_protocol: SEM cells were maintained in RPMI-1640 containing 10% fetal bovine serum (FBS) (HyClone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Invitrogen). All cells were maintained at 37°C in a 5% CO2 atmosphere and 95% humidity.

extract_protocol:
Cut&Run ChiP-seq was performed according the the protocol in, Skene PJ, Henikoff S.  2017.  An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites on Elife. Antibodies against dCas9 for a pulldown assay. DCas9 antibody from Abcam (ab70303) was used for immunoprecipitation.
NEBNext Ultra II DNA Library Prep Kit from New England Biolabs (E7645S)

value: B cell precursor leukemia

tag: cell line

value: SEM

tag: genotype/variation

value: sgRNA2 target CDKN2aINK4A promoter

tag: chip antibody

value: dCas9 (Abcam, ab70303)


title: CDKN2a-sg1 (Cut&Run ChiP-seq)

value: sgRNA1 target CDKN2aINK4A promoter


title: Progeny1-1465 [a550818-4325018-051918-781_A01]


title: NT sgRNA

data_processing:
Library strategy: Capture-C
The paired-end reads were reconstructed into single reads with FLASH1.2.11
Digested in silico with the DpnII2E.pl script
aligned to the human genome using Bowtie 1.0.0 (http://bowtie-bio.sourceforge.net/index.shtml).
Interaction frequencies were determined using CCanalyser2.pl (https://github.com/telenius/captureC/releases).
Genome_build: hg19, mm9

extract_protocol:
Suspension cells (SEM) cells were collected at 1X107 cells per reaction while adherent cells (IMR90, HCT116 and human iPS) were trypsinized before collection. Cells were fixed and lysed in 15 mL conical tubes before storage in -80°C for up to 1 month before library construction. Cells were thawed on ice and spun down for 5 minutes at 4000rpm, 4°C. The remaining lysis buffer was removed and discarded. The pellets were re-suspended in 1 mL of 1x DpnII buffer and transferred to a 2 mL tube for homogenization with a pestle. The homogenized samples were then centrifuged for 14,000 rpm at 5 mins in 4°C. The supernatant was removed and discarded. After decrosslinking, phenol-chloroform-isoamylalcohol DNA extraction, and sodium acetate precipitation, a small portion of DNA was run on a gel to check for digest and ligation efficiency. Once the 3C library was construction was complete, 5-6ug of the 3C DNA in a total volume of 130ug per covaris tube (microTUBE AFA Fiber Crimp-Cap 6X16mm, catalog). Each 2ug of 3C library generated one Capture.NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles.The Nimblegen SeqCap EZ Hybridization and Wash Buffer Kit (Roche) was used for subsequent hybridization and wash steps. Constructed library was sequenced on Miseq for paired-end 150bp.
NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles. Agencourt AMPure XP beads were used at 0.8x for all cleanup steps.

value: NT sgRNA


title: ARF sgRNA4

value: ARF sgRNA4


title: CDKN2B ARF KRAB block type bait1-2

tag: group

value: CDKN2B promoter probe


title: Progeny2-AF229 [a550818-4325018-051918-780_H11]

description:
processed data file: AxiomGT1.calls.batch2.txt
Hybridized to Axiom Sugarcane100K SNP array

source_name: Progeny from selfing CP80-1827

value: Sugarcane yellow leaf virus free


title: Progeny2-AF220 [a550818-4325018-051918-780_H07]


title: CDKN2B wide type bait1


title: ARF KRAB block type bait1-2

value: ARF promoter probe


title: ARF-sg2 (Cut&Run ChiP-seq)

value: sgRNA2 target ARF


title: Progeny2-AF223 [a550818-4325018-051918-780_H09]


title: ZNF-NT-sgRNA

data_processing:
Library strategy: Cut&Run ChiP-seq
Cut&Run ChiP-seq reads from each species were aligned using Bowtie2  2.3.4
bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. DeepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016)) was used to convert apping .bam file to .bw file
Genome_build: hg19

value: ZNF-NT-sgRNA


title: YY1_ARF-sgRNA-4


title: YY1_NT_sgRNA


title: Progeny2-AF230 [a550818-4325018-051918-780_H12]


title: ZNF-ARF-sgRNA-4


title: Progeny2-AF226 [a550818-4325018-051918-780_H10]


title: Progeny2-AF221 [a550818-4325018-051918-780_H08]


title: Progeny2-AF219 [a550818-4325018-051918-780_H06]

value: Sugarcane yellow leaf virus infected


title: Progeny1-1356 [a550818-4325018-051918-781_A03]


title: ARF wide type bait2


title: ARF wide type bait1


title: Progeny2-AF213 [a550818-4325018-051918-780_H05]


title: CDKN2A wide type bait2

value: CDKN2A promoter probe


title: ARF-sg1 (Cut&Run ChiP-seq)

value: sgRNA1 target ARF


title: CDKN2A wide type bait1


title: Progeny2-AF212 [a550818-4325018-051918-780_H04]


title: Progeny2-AF211 [a550818-4325018-051918-780_H03]


title: Progeny2-AF208 [a550818-4325018-051918-780_H02]


title: Progeny2-AF207 [a550818-4325018-051918-780_H01]


title: Progeny2-AF205 [a550818-4325018-051918-780_G11]


title: Progeny2-AF122 [a550818-4325018-051918-780_G09]


title: CDKN2A ARF KRAB block type bait1-2


title: Progeny2-AF115 [a550818-4325018-051918-780_G07]


title: Progeny2-AF113 [a550818-4325018-051918-780_G06]


title: Progeny2-AF112 [a550818-4325018-051918-780_G05]


title: Tumor specimen 144

type: RNA

city: Detroit

first: Kristen

last: Purrington

state: MI

address: 4100 John R St.

department: Oncology

institute: Wayne State University

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: All statistical analyses were performed in R (https://cran.r-project.org/). Raw probe intensity data were normalized separately by batch as implemented by the “rma” function to perform background subtraction, quantile normalization, summarization of probe sets using median-polish, and log2-transformation. We evaluated batch effects using principal components analysis as implemented by the “princomp function. Batch effects were corrected by standardization of probes (subtracting the mean expression value and dividing by standard deviation) by batch (Batch 1 n=60, Batch 2 n=166). There was no evidence for batch effects after standardization.

molecule: total RNA

source_name: FFPE tumor

label_protocol: Affymetrix

extract_protocol: Qiagen RNeasy FFPE Kit

tag: race

value: Black/African American (AA)

tag: batch

tag: treatment

value: No systemic therapy and/or surgical procedures

tag: vital status

value: Dead


title: Tumor specimen 138

value: Systemic therapy after surgery

value: Alive


title: Tumor specimen 074


title: Tumor specimen 090

value: Systemic therapy before surgery


title: Tumor specimen 222


title: Tumor specimen 164


title: Tumor specimen 076


title: Progeny2-AF107 [a550818-4325018-051918-780_G03]


title: Tumor specimen 083


title: Tumor specimen 112


title: Tumor specimen 182


title: Tumor specimen 124


title: Progeny2-AF108 [a550818-4325018-051918-780_G04]


title: Tumor specimen 099


title: Tumor specimen 223


title: Tumor specimen 150


title: Tumor specimen 087


title: Tumor specimen 205


title: Tumor specimen 149


title: Cbln2-EGFP/Rpl10a (NIDA176) subthalamic nucleus IP [2471]

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Ribosomal-bound RNA
2471_Cbln2_TRAP_NIDA176_subthalamic_nucleus IP_S5

library_source: transcriptomic

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

organism: Mus musculus

source_name: Subthalamic nucleus

growth_protocol: Not applicable

extract_protocol:
The subthalamic nuclei from 7 mice were dissected and homogenized.  Tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: No treatment

tag: strain

tag: animal line

value: Cbln2-TRAP NIDA176

tag: application

value: RNA-seq

tag: sample type

value: Immunopurified (IP)


title: Tumor specimen 219


title: Tumor specimen 105


title: Tumor specimen 166


title: Progeny2-AF105 [a550818-4325018-051918-780_G02]

tag: tissue


title: Tumor specimen 215

tag: age


title: Penk-EGFP/Rpl10a (NIDA186) dentate gyrus IP Rep1 [1663]

description:
Ribosomal-bound RNA
1663_Penk_TRAP_NIDA186_dentate_gyrus_IP_Rep1_S1

source_name: Dentate gyrus

extract_protocol:
The dentate gyrus was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: Penk-TRAP NIDA186


title: Progeny2-af104 [a550818-4325018-051918-780_G01]

value: Sugarcane yellow leaf virus free


title: Tumor specimen 200


title: Tumor specimen 095


title: Tumor specimen 089


title: Progeny2-AF103 [a550818-4325018-051918-780_F12]


title: Drd1-EGFP/Rpl10a (CP73) cocaine self-administration, nonescalating group dorsal striatum input [1621]

description: 1621_Drd1-EGFP/Rpl10a (CP73) cocaine self-administration, nonescalating dorsal striatum input_S8

source_name: Dorsal striatum

extract_protocol:
The dorsal striatum was dissected  and homogenized. Total RNA was purified with the Agilent Nanoprep kit following manufacturer's protocol.
RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: FVB/N-Swiss Webster x 9 generations C57BL/6 minimum

value: Drd1-TRAP CP73

value: Input


title: Penk-EGFP/Rpl10a (NIDA186) dentate gyrus IP Rep2 [1664]

description:
Ribosomal-bound RNA
1664_Penk_TRAP_NIDA186_dentate_gyrus_IP_Rep2_S2


title: Drd1-EGFP/Rpl10a (CP73) cocaine self-administration, escalating group dorsal striatum input [1620]

description: 1620_Drd1-EGFP/Rpl10a (CP73) cocaine self-administration, escalating dorsal striatum input_S7


title: Progeny2-AF101 [a550818-4325018-051918-780_F11]

value: Sugarcane yellow leaf virus infected


title: Tumor specimen 173


title: Progeny2-AF092 [a550818-4325018-051918-780_F09]


title: OG2MEF

city: Guangzhou

first: Zheng

last: Hui

address: Kaiyuan Avenue 190

institute: GIBH

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: Mouse embryonic fibroblast

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

tag: cell type

value: Mouse embryonic fibroblast

tag: passage


title: Vc+10nMRA-2

value: Vc+, 10nMRA


title: Progeny2-AF083 [a550818-4325018-051918-780_F08]


title: Vc+1uMRA-2

value: Vc+, 1uMRA


title: Vc+DMSO-2

value: Vc+, DMSO


title: Tumor specimen 086

value: Black/African American (AA)

value: Dead


title: Tumor specimen 198

value: Systemic therapy after surgery

value: Alive


title: Tumor specimen 068

value: Systemic therapy before surgery


title: Tumor specimen 067

value: No systemic therapy and/or surgical procedures


title: Tumor specimen 114


title: Tumor specimen 187


title: Tumor specimen 207

value: Surgery both before and after systemic therapy


title: Tumor specimen 152


title: Tumor specimen 065


title: Tumor specimen 175


title: Tumor specimen 121


title: Progeny2-AF098 [a550818-4325018-051918-780_F10]


title: Tumor specimen 080


title: Tumor specimen 218


title: Progeny2-AF079 [a550818-4325018-051918-780_F06]


title: Vc-1uMRA-2

value: Vc-, 1uMRA


title: Vc-10nMRA-2

value: Vc-, 10nMRA


title: Tumor specimen 135


title: Progeny2-AF082 [a550818-4325018-051918-780_F07]

value: Sugarcane yellow leaf virus free


title: Penk-EGFP/Rpl10a (NIDA186) dentate gyrus IP Rep3 [1665]

description:
Ribosomal-bound RNA
1665_Penk_TRAP_NIDA186_dentate_gyrus_IP_Rep3_S3

value: Penk-TRAP NIDA186

value: RNA-seq

value: Immunopurified (IP)


title: Progeny2-AF077 [a550818-4325018-051918-780_F05]

value: Sugarcane yellow leaf virus infected


title: Vc-DMSO-2

value: Mouse embryonic fibroblast

value: Vc-, DMSO


title: Tumor specimen 210


title: Progeny2-AF075 [a550818-4325018-051918-780_F04]


title: Progeny2-AF074 [a550818-4325018-051918-780_F03]


title: Vc+1uMRA

value: Vc+, 1uMRA


title: Progeny2-AF073 [a550818-4325018-051918-780_F02]


title: Vc+10nMRA

value: Vc+, 10nMRA


title: Progeny2-AF069 [a550818-4325018-051918-780_F01]


title: Tumor specimen 181

value: Black/African American (AA)


title: Vc+DMSO

value: Vc+, DMSO


title: Tumor specimen 075

value: Alive


title: Tumor specimen 208

value: Dead


title: Tumor specimen 106

value: Systemic therapy after surgery


title: Vc-1uMRA


title: Progeny2-AF066 [a550818-4325018-051918-780_E12]


title: Tumor specimen 147


title: Progeny2-AF064 [a550818-4325018-051918-780_E11]


title: Tumor specimen 073

value: Systemic therapy both before and after surgery


title: Tumor specimen 160


title: Tumor specimen 125


title: Tumor specimen 216

value: No systemic therapy and/or surgical procedures


title: Vc-10nMRA

value: Vc-, 10nMRA


title: Tumor specimen 142

value: Systemic therapy before surgery


title: Progeny2-AF059 [a550818-4325018-051918-780_E10]


title: Vc-DMSO


title: Tumor specimen 220


title: Tumor specimen 132


title: Tumor specimen 136


title: Tumor specimen 195


title: cont1

city: Boulder

first: Lynn

last: Sanford

state: CO

address: UCB 596

department: Biochemistry

institute: University of Colorado Boulder

data_processing:
Each pair of fastq files was trimmed in a paired-end fashion with trimmomatic (v0.36) using the commands HEADCROP:10 ILLUMINACLIP:/opt/trimmomatic/0.36/adapters/TruSeq2-PE.fa:2:30:10 MINLEN:30
Trimmed fastq files were mapped in a paired-end fashion with HISAT2 (v2.1.0) with the parameters --very-sensitive --max-intronlen 50000 --rna-strandness FR, as well as including the mm10 genes GTF file. Resultant BAM files were indexed with samtools (v1.3.1)
The featureCounts function within the R package Rsubread (v1.24.2, R v3.3.0) was used to generate gene-level read counts, with the following parameters: GTF.featureType=”exon”, GTP.attrType=”gene_id”, useMetaFeatures=TRUE, allowMultiOverlap=FALSE, largestOverlap=FALSE, strandSpecific=2, isPairedEnd=TRUE, requireBothEndsMapped=TRUE, checkFragLength=TRUE, minFragLength=50, maxFragLength=60000, countChimericFragments=FALSE, autosort=TRUE.
Differential expression analysis was performed pairwise between conditions with the R package DESeq2 (v1.14.1). All gene-level counts for all samples were loaded into a dds object, then analyzed. Pairwise comparisons were then extracted.
Genome_build: mm10 (fasta and gtf files were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html) in November 2017)
Supplementary_files_format_and_content: For the following files, column headers or filename abbreviations match sample titles (i.e. cont1 = control treatment, replicate 1; glzn2 = glutamate/ZnCl2 treatment, replicate 2, etc.).     gene_level_counts.txt is a tab-delimited text file of gene-level counts as determined by featureCounts. All samples are included, one sample per column. File was output from an R object, so column headers are offset 1 column in text file, but will read into R correctly.    gene_level_count_annotations.txt is a tab-delimited text file containing the annotation information extracted by featureCounts. This includes a portion of the gene GTF file input, including gene name, chromosomal positions of features (in this case exons), strand, and total gene length (used to calculate TPM).    all_samples_TPM.txt is a tab-delimited text file containing transcripts per million (TPM) values for all genes and all samples, as calculated with the counts and gene length output by featureCounts in the previous two files.    DESeq2 files are tab-delimited text files containing the differential expression output from DESeq2. The sample condition abbreviations in the filenames correspond to "Condition 2 vs. condition 1", hence 'DESeq2_gene_cont_gtpa.txt' contains information for the comparison "Glutamate/TPA treatment" vs. "Control treatment", and any positive fold changes correspond to upregulation in the Glutamate/TPA treatment. Files contain information on base expression as normalized by DESeq2, fold change, and significance of the observed difference.

molecule: polyA RNA

source_name: Normal media_dissociated hippocampal culture

growth_protocol: Cells were extracted from microdissected embryonic (E18) mouse hippocampi, with tissue pooled from 4 embryos prior to dissociation. Cells were grown for 10 days in Neurobasal medium supplemented with 2% B27 supplement and 0.3x GlutaMAX. Cultures were treated with 4 µM cytosine arabinoside from DIV3-6.

extract_protocol:
Cells were lysed and RNA extracted according to the Qiagen RNeasy Miniprep kit using a 25 gauge needle for cell lysis and including on-column DNase digestion.
Libraries were generated from RNA samples according to the TruSeq Stranded mRNA kit protocol using TruSeq RNA CD Indexes

treatment_protocol: Cultures were placed at room temperature. Media was removed and neurons washed in neuron imaging media (NIM: 145 mM NaCl, 3 mM KCl, 1.5 mM CaCl2, 1 mM MgCl2, 10 mM HEPES, 10 mM glucose, pH 7.4). For the TPA condition, media was added 1:1 containing 10 µM final tris(2-pyridylmethyl)amine (TPA) and incubated for one minute. For stimulation, one of four medias was then added 1:1 - NIM (control), 50 µM final glutamate, 50 µM final glutamate with 10 µM final ZnCl2,  or 50 µM final glutamate with 10 µM final TPA (to the neurons previously incubated in TPA). Stimulation was kept on cells for two minutes, then cultures were washed with NIM, placed back in previous culture medium, and incubated for 90 minutes at 37 °C and 5% CO2 before cell lysis and RNA isolation. Each of the four conditions (Control, stimulation, stimulation + ZnCl2, stimulation + TPA) was performed with 5 biological replicates.

value: Embryonic day 18

tag: day in vitro

value: DIV 10

value: Normal media

tag: tissue/cell type

value: dissociated hippocampal culture


title: Progeny2-AF058 [a550818-4325018-051918-780_E09]

value: Sugarcane yellow leaf virus infected


title: Progeny2-AF057 [a550818-4325018-051918-780_E08]


title: CDKN2B wide type bait2

value: B cell precursor leukemia

tag: cell line

value: SEM

value: CDKN2B promoter probe


title: cont3


title: Progeny2-AF053 [a550818-4325018-051918-780_E06]


title: Progeny2-AF055 [a550818-4325018-051918-780_E07]

value: Sugarcane yellow leaf virus free


title: cont4


title: Progeny2-AF051 [a550818-4325018-051918-780_E05]


title: cont5


title: cont2


title: Tumor specimen 130

value: Black/African American (AA)


title: Progeny2-AF045 [a550818-4325018-051918-780_E04]


title: glut1

source_name: 50 uM glutamate_dissociated hippocampal culture

value: 50 uM glutamate


title: Progeny2-AF120 [a550818-4325018-051918-780_G08]


title: Tumor specimen 077

value: Alive


title: Progeny2-AF044 [a550818-4325018-051918-780_E03]


title: glut2


title: Tumor specimen 111

value: Systemic therapy after surgery


title: Tumor specimen 196


title: Tumor specimen 133

value: Dead


title: Tumor specimen 139


title: Tumor specimen 097

value: Systemic therapy both before and after surgery


title: Tumor specimen 069


title: glut3


title: Progeny2-AF043 [a550818-4325018-051918-780_E02]


title: Tumor specimen 151


title: Tumor specimen 064

value: No systemic therapy and/or surgical procedures


title: Tumor specimen 224

value: Systemic therapy before surgery


title: Tumor specimen 174


title: Tumor specimen 154


title: Tumor specimen 100


title: glut4

value: Embryonic day 18


title: Tumor specimen 088


title: Progeny2-AF033 [a550818-4325018-051918-780_E01]


title: Tumor specimen 070


title: Tumor specimen 214


title: glut5

value: DIV 10


title: Progeny2-AF031 [a550818-4325018-051918-780_D12]


title: Progeny2-AF030 [a550818-4325018-051918-780_D11]


title: gtpa1

source_name: 50 uM glutamate/10 uM TPA_dissociated hippocampal culture

value: 50 uM glutamate/10 uM TPA


title: Progeny2-AF027 [a550818-4325018-051918-780_D10]


title: Tumor specimen 119


title: Tumor specimen 209


title: Tumor specimen 078


title: gtpa2

value: dissociated hippocampal culture


title: Tumor specimen 168


title: Progeny2-AF024 [a550818-4325018-051918-780_D09]

value: Sugarcane yellow leaf virus infected


title: Progeny2-AF021 [a550818-4325018-051918-780_D08]


title: gtpa5


title: Tumor specimen 126


title: Progeny2-AF019 [a550818-4325018-051918-780_D07]


title: gtpa4


title: glzn1

source_name: 50 uM glutamate/10 uM ZnCl2_dissociated hippocampal culture

value: 50 uM glutamate/10 uM ZnCl2


title: Tumor specimen 183


title: Progeny2-AF015 [a550818-4325018-051918-780_D06]


title: gtpa3


title: glzn2


title: Tumor specimen 212


title: Tumor specimen 134


title: Progeny2-AF011 [a550818-4325018-051918-780_D04]


title: Tumor specimen 178


title: Tumor specimen 163


title: Tumor specimen 197


title: Tumor specimen 122


title: glzn3


title: Tumor specimen 127


title: Tumor specimen 060


title: Tumor specimen 217


title: Tumor specimen 177


title: Tumor specimen 204


title: Tumor specimen 059


title: Tumor specimen 063


title: Progeny2-AF009 [a550818-4325018-051918-780_D03]


title: glzn4


title: Progeny2-AF005 [a550818-4325018-051918-780_D02]


title: Cultivar-R570 [a550818-4325018-051918-780_C12]

value: Unknown


title: Tumor specimen 199


title: Tumor specimen 058


title: Progeny1-1069 [a550818-4325018-051918-780_C10]


title: Progeny1-1336 [a550818-4325018-051918-780_C11]


title: glzn5


title: chip39

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

data_processing:
Basecalls performed using CASAVA
ChIP-seq and ATAC-seq reads were aligned using bwa v.0.7.15 or bowtie v.0.12.9
ChIP-seq and ATAC-seq peaks were called using MACS v.1.4.2
Genome_build: mm10
Supplementary_files_format_and_content: processed files are tab-delimited txt files representing the position of identified ChIP or ATAC peaks in mm10 coordinates followed by read counts. Also provided are bedgraph files for DMC1 ChIP and HELLS ChIP.

growth_protocol: Isolation of enriched germ cells was conducted from male mice at 12-14 days post-partum. Or whole testis collected from 6 week old male mice.

extract_protocol:
KAPA hyper kit
For ATAC-seq samples and histone ChIP-seq germ cells were enzymatically disaggregated using Liberase enzyme. For testis samples nuclei were first crosslinked in tubules and nuclei extracted using Dounce homogenizer.

value: 12-14 days post-partum

value: testis

tag: chromatin fragmentation

value: Sonication

tag: chip antibody

value: none (input)


title: Tumor specimen 056

tag: race

value: Black/African American (AA)


title: chip40

description:
chip40_GT19-06849_AGGTTATA-CGGAACTG_S7
processed data file:
peakome_k4me3_counts.tsv

source_name: Hells CKO_male germ cells_ChIP-seq

value: Hells CKO

value: male germ cells

value: MNase


title: Progeny1-1245 [a550818-4325018-051918-780_C08]

value: Sugarcane yellow leaf virus free


title: Progeny1-1472 [a550818-4325018-051918-780_C09]


title: chip35

description:
chip35_GT19-06846_GGTCACGA-CATAATAC_S5
processed data file:
hells_chip_ki_merge_peaks.blacklist.tsv

value: IgG (Millipore/Sigma #12-371, lot:2880788)


title: Tumor specimen 096

tag: batch

value: No systemic therapy and/or surgical procedures

value: Dead


title: Tumor specimen 146

tag: treatment


title: Tumor specimen 057

tag: vital status


title: Tumor specimen 192


title: Tumor specimen 052

value: Systemic therapy both before and after surgery


title: chip37

description:
chip37_GT19-06848_TCATCCTT-AGCTCGCT_S6
processed data file:
hells_chip_ki_merge_peaks.blacklist.tsv
hells_ki_merge_treat_afterfiting.bdg.gz

tag: strain

value: HELLS (Millipore/Sigma, ABD41 lot# 3069868)


title: Tumor specimen 171

value: Systemic therapy after surgery

value: Alive


title: Tumor specimen 047


title: Tumor specimen 051

value: Systemic therapy before surgery


title: Tumor specimen 194


title: Tumor specimen 054


title: Tumor specimen 055


title: Tumor specimen 048


title: Tumor specimen 053


title: chip34

description:
chip34_GT19-06845_AACTGTAG-TGCGGCGT_S3
processed data file:
hells_chip_ki_merge_peaks.blacklist.tsv
hells_ki_merge_treat_afterfiting.bdg.gz

value: 12-14 days post-partum


title: chip23

description:
chip23_GT18-18928_TTATAACC-TCGATATC_S4
processed data file:
peakome_k4me3_counts.tsv

source_name: Hells wt_male germ cells_ChIP-seq

value: Hells wt


title: chip21

source_name: Hells CKO_testis_input

value: 6 weeks old

value: testis

value: Sonication


title: Progeny1-1041 [a550818-4325018-051918-780_C07]


title: Progeny1-1226 [a550818-4325018-051918-780_C04]


title: Progeny1-1373 [a550818-4325018-051918-780_C06]


title: Progeny1-1277 [a550818-4325018-051918-780_C05]


title: chip20

description:
chip20_GT18-12503_AGTTCC_S1
processed data file:
dmc1_hells_mut_peaks.merge.bed

source_name: Hells CKO_testis_ChIP-seq

value: Hells CKO

value: DMC1 (Santa Cruz sc-8973, lot:K2614)


title: chip22

description:
chip22_GT18-18927_CCGCGGTT-CTAGCGCT_S6
processed data file:
peakome_k4me3_counts.tsv

value: male germ cells

value: MNase


title: Progeny1-1176 [a550818-4325018-051918-780_C03]

value: Sugarcane yellow leaf virus free


title: Progeny1-1086 [a550818-4325018-051918-780_C02]

value: Sugarcane yellow leaf virus infected


title: Tumor specimen 050

value: Black/African American (AA)

value: Dead


title: chip18

source_name: Hells het_testis_input

value: Hells het

value: none (input)


title: Progeny1-1262 [a550818-4325018-051918-780_C01]

source_name: Progeny from cross Green German and IND81-146


title: chip19

description:
chip19_GT18-12502_CTTGTA_S4
processed data file:
dmc1_hells_mut_peaks.merge.bed


title: chip17

description:
chip17_GT18-12500_GCCAAT_S6
processed data file:
dmc1_hells_wt_peaks.merge.bed

source_name: Hells het_testis_ChIP-seq


title: Tumor specimen 046

value: Systemic therapy after surgery

value: Alive


title: Tumor specimen 062

value: Systemic therapy before surgery


title: Tumor specimen 093

value: No systemic therapy and/or surgical procedures


title: chip16

description:
chip16_GT18-12499_ACAGTG_S5
processed data file:
dmc1_hells_wt_peaks.merge.bed

value: 6 weeks old


title: Tumor specimen 045


title: Tumor specimen 109


title: Tumor specimen 049


title: Tumor specimen 117


title: Progeny1-1027 [a550818-4325018-051918-780_B12]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array


title: Tumor specimen 043


title: Tumor specimen 185


title: Tumor specimen 162


title: Tumor specimen 184


title: Tumor specimen 044


title: chip15

description:
chip15_GT18-10848_ATATCTCG-ACTAAGAT_S1
processed data file:
peakome_k4me3_counts.tsv

value: 12-14 days post-partum


title: Tumor specimen 128


title: Tumor specimen 042


title: chip11

description:
chip11_GT18-10765_GGTGAACC-TCCAACGC_S3
processed data file:
peakome_k9ac.counts.tsv

source_name: Spo11/Spo11_male germ cells_ChIP-seq


title: Progeny1-1146 [a550818-4325018-051918-780_B09]


title: Progeny1-1326 [a550818-4325018-051918-780_B10]

value: Unknown


title: Tumor specimen 085

source_name: FFPE tumor


title: Progeny1-1202 [a550818-4325018-051918-780_B08]


title: chip9

source_name: Hells CKO_male germ cells_input

value: Hells CKO


title: chip10

description:
chip10_GT18-10764_AACAGGTT-CTTGGTAT_S4
processed data file:
peakome_k4me3_counts.tsv


title: Progeny1-1054 [a550818-4325018-051918-780_B06]


title: Progeny1-1070 [a550818-4325018-051918-780_B07]


title: Tumor specimen 040


title: Tumor specimen 037


title: Progeny1-1282 [a550818-4325018-051918-780_B05]


title: chip2-input

source_name: Spo11/+_male germ cells_input


title: chip2

description:
chip2_GT17-11182_ACAGTG-_S3
processed data file:
peakome_k4me3_counts.tsv

source_name: Spo11/+_male germ cells_ChIP-seq


title: chip1-input

source_name: Spo11/Spo11_male germ cells_input


title: Progeny1-1364 [a550818-4325018-051918-780_B04]


title: Tumor specimen 039


title: Progeny1-1337 [a550818-4325018-051918-780_B03]


title: Tumor specimen 113


title: Tumor specimen 201


title: Normal Appearing MS Grey Matter_Follicle Positive_MS176

city: Roma

first: Eleonora

last: Arico'

state: RM

address: viale Regina Elena 299

country: Italy

institute: ISS

description:
NAGM_Fpos_MS176
4311471225_G

hyb_protocol: The samples were applied to the arrays and assembled into the BeadChip Hybr Chamber and hybridization was carried out using the Illumina whole genome gene expression direct assay system at 58°C overnight. After washes, the signal was developed with Streptavidin-Cy3 and the BeadChips were scanned using the Illumina BeadArray Reader

data_processing:
The data from the Illumina BeadArray Reader were extracted using the BeadStudio 3.2 software package (Illumina). The lists of data obtained using BeadStudio 3.2 were converted for data normalization using the Rosetta Resolver ® system software (Rosetta Biosoftware).
BeadStudio 3.2 signal intensity data, converted for normalization using the Rosetta Biosoftware and log2 transformed

label_protocol: Biotin-labelled cRNA was synthesized from dsDNA and then was captured using RNA binding beads

growth_protocol: Precentral gyrus (motor cortex) from Healthy subjects or Multiple Sclerosis patients were Snap frozen and stored at UK MS Tissue Bank

extract_protocol: RNA extractions were performed using the RNeasy Lipid Tissue Midi Kit (Qiagen)

treatment_protocol: Frozen tissues were dissected with the scalpel. Approximately 50-150 mg of tissue was collected for each area. 50 mg of tissue yielded approximately 25µg of total RNA

tag: disease state

value: Multiple Sclerosis

tag: presence of follicles

value: Follicle Positive

tag: normal appearing or ms lesion

value: Normal Appearing

value: motor cortex


title: ATAC86

source_name: Hells CKO_male germ cells_ATAC-seq

extract_protocol:
TDE1 Tagment DNA Enzyme
For ATAC-seq samples and histone ChIP-seq germ cells were enzymatically disaggregated using Liberase enzyme. For testis samples nuclei were first crosslinked in tubules and nuclei extracted using Dounce homogenizer.

value: male germ cells


title: Normal Appearing MS Grey Matter_Follicle Positive_MS234

description:
NAGM_Fpos_MS234
4311471224_D

scan_protocol: BeadChips were scanned using the Illumina BeadArray Reader

tag: tissue


title: Normal Appearing MS Grey Matter_Follicle Positive_MS160

description:
NAGM_Fpos_MS160
4311471277_F


title: Tumor specimen 221

value: Black/African American (AA)

tag: age


title: Tumor specimen 036


title: Progeny1-1419 [a550818-4325018-051918-780_B02]

value: Sugarcane yellow leaf virus free


title: Tumor specimen 035


title: Progeny1-1254 [a550818-4325018-051918-780_B11]


title: ATAC85

source_name: Hells wt_male germ cells_ATAC-seq

value: Hells wt


title: Progeny1-1299 [a550818-4325018-051918-780_B01]


title: Tumor specimen 038


title: Normal Appearing MS Grey Matter_Follicle Positive_MS154

description:
NAGM_Fpos_MS154
4311471277_C


title: ATAC84


title: chip1

description:
chip1_GT17-11181_TGACCA-_S1
processed data file:
peakome_k4me3_counts.tsv

value: MNase


title: Tumor specimen 041

value: Dead


title: Tumor specimen 176

value: Systemic therapy after surgery

value: Alive


title: ATAC62


title: Progeny1-1188 [a550818-4325018-051918-780_A12]


title: Progeny1-1264 [a550818-4325018-051918-780_A11]


title: ATAC61


title: Progeny1-1231 [a550818-4325018-051918-780_A10]


title: ATAC58

source_name: Spo11/Spo11_male germ cells_ATAC-seq


title: Normal Appearing MS Grey Matter_Follicle Positive_MS153

description:
NAGM_Fpos_MS153
4311471247_G


title: ATAC57


title: Progeny1-1460 [a550818-4325018-051918-780_A09]


title: Normal Appearing MS Grey Matter_Follicle Positive_MS180

description:
NAGM_Fpos_MS180
4311471224_A


title: Progeny1-1412 [a550818-4325018-051918-780_A08]


title: ATAC56

source_name: Spo11/+_male germ cells_ATAC-seq


title: Progeny1-1468 [a550818-4325018-051918-780_A07]


title: Tumor specimen 172

value: No systemic therapy and/or surgical procedures


title: Tumor specimen 034

value: Systemic therapy before surgery


title: NB4_RNA-Seq_ATRA treatment_48h

description: NB4_RNA-Seq_ATRA treatment_48h

data_processing:
Filtering linker sequence in ChIA-PET using in-house script
Mapping ChIA-PET reads to reference genome using BWA MEM (version 0.7.16)
Deduplicating ChIA-PET reads using Picard (MarkDuplicates)
Peak-calling for ChIA-PET using MACS (v.1.4.2)
Producing 2D contact map of ChIA-PET using Juicer tool (version 1.6.1)
Mapping ChIP-Seq reads from ABI SOLiD sequencing platform (csfasta+QV.qual) using SOLiD BioScope (version 1.0.1)
Mapping ChIP-Seq reads from Illumina sequencing platform using BWA-MEM (version 0.7.16), and peak-calling using MACS (version 1.4.2)
Mapping RNA-Seq reads uinsg Bowtie2, and processing using edge R
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt format for peak (bed), loop (bedpe), binary data format for Juicebox (hic)

extract_protocol:
When performing ChIA-PET library, the same precedures were used as those in previous paper. (Li et al., 2012; Tang et al., 2015)
Paired-end sequencing (2 × 34bp) was used for RNA-seq libraries  with Illumina Nextseq 500.

tag: cell type

tag: method

value: RNA-Seq

tag: factor

value: total RNA

tag: molecule subtype


title: Normal Appearing MS Grey Matter_Follicle Positive_MS121

description:
NAGM_Fpos_MS121
4311471227_H


title: Tumor specimen 115


title: Tumor specimen 033

value: Systemic therapy both before and after surgery


title: Normal Appearing MS Grey Matter_Follicle Positive_MS136

description:
NAGM_Fpos_MS136
4311471226_D

value: Multiple Sclerosis


title: Progeny1-1353 [a550818-4325018-051918-780_A06]


title: NB4_RNA-Seq_ATRA treatment_24h

description: NB4_RNA-Seq_ATRA treatment_24h


title: Normal Appearing MS Grey Matter_Follicle Negative_MS200

description:
NAGM_Fneg_MS200
4311471224_F

value: Follicle Negative


title: Tumor specimen 032


title: NB4_RNA-Seq_Control


title: Normal Appearing MS Grey Matter_Follicle Positive_MS079

description:
NAGM_Fpos_MS079
4311471228_G

value: Follicle Positive

value: Normal Appearing


title: Tumor specimen 203


title: Progeny1-1238 [a550818-4325018-051918-780_A04]


title: Tumor specimen 141


title: Normal Appearing MS Grey Matter_Follicle Negative_MS114

description:
NAGM_Fneg_MS114
4311471277_H

value: motor cortex


title: Tumor specimen 031

value: Black/African American (AA)


title: Progeny1-1046 [a550818-4325018-051918-780_A05]

value: Sugarcane yellow leaf virus free


title: Normal Appearing MS Grey Matter_Follicle Negative_MS163

description:
NAGM_Fneg_MS163
4311471224_C


title: Tumor specimen 161


title: PR9_RNA-Seq_ZnSO4 Treatment_4h_ATRA treatment_48h


title: PR9_RNA-Seq_ZnSO4 Treatment_4h_ATRA treatment_24h


title: Progeny1-1127 [a550818-4325018-051918-780_A03]


title: Normal Appearing MS Grey Matter_Follicle Negative_MS104

description:
NAGM_Fneg_MS104
4311471277_E


title: PR9_RNA-Seq_ZnSO4 Treatment_24h

description: PR9_RNA-Seq_ZnSO4 Treatment_24h


title: Normal Appearing MS Grey Matter_Follicle Negative_MS100

description:
NAGM_Fneg_MS100
4311471247_B


title: Tumor specimen 129


title: Normal Appearing MS Grey Matter_Follicle Negative_MS056

description:
NAGM_Fneg_MS056
4311471226_A


title: Normal Appearing MS Grey Matter_Follicle Negative_MS074

description:
NAGM_Fneg_MS074
4311471226_F


title: Normal Appearing MS Grey Matter_Follicle Negative_MS127

description:
NAGM_Fneg_MS127
4311471225_B


title: Progeny1-1357 [a550818-4325018-051918-780_A01]


title: Tumor specimen 169


title: Tumor specimen 108


title: Tumor specimen 158


title: Normal Appearing MS Grey Matter_Follicle Positive_MS092

description:
NAGM_Fpos_MS092
4311471227_C


title: Male-parent-IND81-146-1 [a550818-4325018-051918-779_H12]

value: Sugarcane yellow leaf virus resistant


title: Tumor specimen 030


title: Female-parent -Green German1 [a550818-4325018-051918-779_H11]

source_name: Female-parent -Green German

value: Sugarcane yellow leaf virus susceptible


title: PR9_RNA-Seq_ZnSO4 Treatment_12h

description: PR9_RNA-Seq_ZnSO4 Treatment_12h


title: PR9_RNA-Seq_ZnSO4 Treatment_6h

description: PR9_RNA-Seq_ZnSO4 Treatment_6h


title: PR9_RNA-Seq_ZnSO4 Treatment_4h

description: PR9_RNA-Seq_ZnSO4 Treatment_4h


title: Normal Appearing MS Grey Matter_Follicle Negative_MS003

description:
NAGM_Fneg_MS003
4311471228_B


title: Progeny2-AF403 [a550818-4325018-051918-779_H10]

description:
processed data file: AxiomGT1.calls.batch2.txt
Hybridized to Axiom Sugarcane100K SNP array

source_name: Progeny from selfing CP80-1827


title: Progeny1-1436 [a550818-4325018-051918-780_A02]


title: PR9_RNA-Seq_Control


title: Progeny2-AF274 [a550818-4325018-051918-779_H07]


title: Progeny2-AF248 [a550818-4325018-051918-779_H06]


title: IRF1_ChIP-Seq_ZnSO4 Treatment

description: IRF1_ChIP-Seq_ZnSO4 Treatment

extract_protocol:
When performing ChIA-PET library, the same precedures were used as those in previous paper. (Li et al., 2012; Tang et al., 2015)
Paired-end sequencing (2 ×150bp) was used for ChIP-Seq libraries  with  Illumina Nextseq 500.

value: ChIP-Seq

value: IRF1 (Santa Cruz, catalog# sc-497)

value: nuclear chromatin


title: Progeny2-AF227 [a550818-4325018-051918-779_H05]


title: GreyMatterLesion_FolliclePositive_MS180

description:
GML_Fpos_MS180
4311471225_F

source_name: Grey Matter MS Lesion_ Follicle Positive

value: MS Lesion


title: Tumor specimen 028

value: Systemic therapy after surgery

value: Alive


title: GreyMatterLesion_FolliclePositive_MS176

description:
GML_Fpos_MS176
4311471225_C


title: IRF1_ChIP-Seq_Control


title: Tumor specimen 029

value: Dead


title: GreyMatterLesion_FolliclePositive_MS234

description:
GML_Fpos_MS234
4311471224_G


title: Tumor specimen 225


title: Tumor specimen 190


title: Tumor specimen 116

value: No systemic therapy and/or surgical procedures


title: Progeny2-AF224 [a550818-4325018-051918-779_H04]


title: CEBPB_ChIP-Seq_Control

value: CEBPB (Santa Cruz, catalog# sc-150X)


title: GreyMatterLesion_FolliclePositive_MS160

description:
GML_Fpos_MS160
4311471277_B

value: Multiple Sclerosis


title: Progeny2-AF026 [a550818-4325018-051918-779_H02]


title: PU.1_ChIP-Seq_Control

value: PU.1 (Santa Cruz, catalog# sc-352X)


title: Selfing-parent-CP1827 [a550818-4325018-051918-779_H01]

value: Sugarcane yellow leaf virus infected


title: CEBPB_ChIP-Seq_ZnSO4 Treatment

description: CEBPB_ChIP-Seq_ZnSO4 Treatment


title: Progeny2-AF063 [a550818-4325018-051918-779_H03]


title: GreyMatterLesion_FolliclePositive_MS153

description:
GML_Fpos_MS153
4311471247_C

value: Follicle Positive

value: motor cortex


title: Progeny2-AF409 [a550818-4325018-051918-779_G11]

value: Sugarcane yellow leaf virus free


title: Tumor specimen 027

value: Black/African American (AA)


title: GreyMatterLesion_FolliclePositive_MS092

description:
GML_Fpos_MS092
4311471228_H


title: GreyMatterLesion_FolliclePositive_MS136

description:
GML_Fpos_MS136
4311471226_G


title: Tumor specimen 026


title: Progeny2-AF405 [a550818-4325018-051918-779_G10]


title: Tumor specimen 104


title: Tumor specimen 123


title: GreyMatterLesion_FolliclePositive_MS121

description:
GML_Fpos_MS121
4311471227_D


title: JUN-HA-28z-2

city: Stanford

first: David

middle: G

last: Gennert

address: 269 Campus Drive

department: Genetics

institute: Stanford University School of Medicine

data_processing:
Adapter sequences were trimmed by a custom Python script.
Reads were aligned to the hg19 genome by Bowtie2.
Duplicate reads were filtered by Picard, mitochondrial reads were removed, and reads were filtered for MAPQ quality scores ≥10.
Peaks were called with MACS2 using an FDR cutoff of 0.01.
Sequencing tracks were generated with the Washington University Epigenome Browser using read_number normalized BigWig files.
Differential peak analysis was carried out using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: ENCODE narrowPeak files were generated for each ATAC_seq sample.

source_name: CAR T cells

growth_protocol: Primary human T cells were isolated from healthy donors using the RosetteSep Human T cell Enrichment kit (Stem Cell Technologies). Buffy coats were purchased from Stanford Blood Center and processed according to the manufacturer’s protocol using Lymphoprep density gradient medium and SepMate_50 tubes. Isolated T cells were cryopreserved at 2x107 T cells per vial in CryoStor CS10 cryopreservation medium (Stem Cell Technologies).  Cryopreserved T cells were thawed and activated same day with Human T_Expander CD3/CD28 Dynabeads (Gibco) at 3:1 beads:cell ratio in T cell media (AIMV supplemented with 5% FBS, 10mM HEPES, 2mM GlutaMAX, 100 U/mL penicillin, and 100ug/mL streptomycin (Gibco)). Recombinant human IL_2 (Peprotech) was provided at 100 U/mL.  T cells were transduced with retroviral vector on days 2 and 3 post activation and maintained at 0.5_1 x106 cells per mL in T cell media with IL_2. Non_tissue culture treated 12_well plates were coated overnight at 4C with 1mL Retronectin (Takara) at 25ug/mL in PBS. Plates were washed with PBS and blocked with 2% BSA for 15min. Thawed retroviral supernatant was added at ~1mL per well and centrifuged for 2 hours at 32C at 3200 RPM before the addition of cells. CAR T cells were used for in vitro assays on day 10_11 post activation.

extract_protocol:
100,000 cells from each sample were sorted by FACS into culture media, centrifuged at 500g at 4°C, then resuspended in ATAC_seq Resuspension Buffer (RSB) (10 mM Tris_HCl, 10 mM NaCl, 3mM MgCl2) supplemented with 0.1% NP_40,0.1% Tween_20, and 0.01% Digitonin.  Samples were split into two replicates each prior to all subsequent steps.  Samples were incubated on ice for 3 minutes, then washed out with 1 mL RSB supplemented with 0.1% Tween_20.  Nuclei were pelleted at 500g for 10 minutes at 4°C.
The nuclei pellet was resuspended in 50 μL transposition mix (25 μl 2x TD buffer, 2.5 μl transposase (Illumina), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween_20, 5 μl H2O) and incubated at 37°C for 30 minutes in a thermomixer with 1000 RPM shaking.  The reaction was cleaned up using the Qiagen MinElute PCR Purification Kit. Libraries were PCR_amplified using the NEBNext Hi_Fidelity PCR Master Mix and custom primers (IDT) as described previously20. Libraries were sufficiently amplified following 5 cycles of PCR, as indicated by qPCR fluorescence curves20.  Libraries were purified with the Qiagen MinElute PCR Purification Kit and quantified with the KAPA Library Quantification Kit. Libraries were sequenced on the Illumina NextSeq at the Stanford Functional Genomics Facility with paired_end 75bp reads.

value: CAR T cell

tag: car target


title: PU.1_ChIP-Seq_ZnSO4 Treatment

description: PU.1_ChIP-Seq_ZnSO4 Treatment

value: ChIP-Seq


title: HA-28z-2


title: JUN-HA-28z-1


title: Progeny2-AF402 [a550818-4325018-051918-779_G09]


title: Tumor specimen 110


title: HA-28z-1


title: Tumor specimen 206

value: Systemic therapy before surgery


title: GreyMatterLesion_FolliclePositive_MS079

description:
GML_Fpos_MS079
4311471228_C


title: Normal Appearing MS Grey Matter_Follicle Negative_MS042

description:
NAGM_Fneg_MS042
4311471227_E

value: Follicle Negative

value: Normal Appearing


title: GreyMatterLesion_FollicleNegative_MS200

description:
GML_Fneg_MS200
4311471224_B

source_name: Grey Matter MS Lesion_Follicle Negative

value: MS Lesion


title: Tumor specimen 025

value: Systemic therapy both before and after surgery


title: Tumor specimen 103

value: Alive


title: GreyMatterLesion_FollicleNegative_MS163

description:
GML_Fneg_MS163
4311471225_H


title: Tumor specimen 157

value: Systemic therapy after surgery


title: Progeny2-AF401 [a550818-4325018-051918-779_G08]


title: Tumor specimen 024

value: Dead


title: Progeny2-AF397 [a550818-4325018-051918-779_G07]


title: Progeny2-AF396 [a550818-4325018-051918-779_G06]


title: LnCAP-GLYATL1-sh1

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

data_processing:
The raw sequence reads obtained as FASTQ files were trimmed using Trim Galore (v0.4.1) [http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] to remove adapter sequences and low quality reads.
After performing the quality control analysis using FastQC (v0.11.5) [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/], the trimmed reads were mapped to human genome (GRCh38/hg38) using TopHat v2.1.0.
The aligned reads were sorted via samtools (Version: 1.3.1). HTSeq-count (version 0.6.0) was used to obtain raw read counts for each annotated human gene. Differential expression analysis between GLYATL1 shRNA and non-targeting shRNA treated samples was carried out using DESeq19 considering “blind” method for estimating dispersion and “fit-only” sharing mode.  Genes with absolute fold change of 1.5 or more and p-value <0.05 were considered as differentially expressed.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file include normalized read counts for each sample from DESeq.

source_name: LnCAP Cells

extract_protocol:
RNA from culture cells were extracted with Direct-zol RNA miniprep kit (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stable knockdowns were created using shRNA purchased from SBI (System Biosciences, Mountain View, CA). Lentiviruses for creating these stable knockdowns were created by the University of Alabama at Birmingham Vector Core. After infection of prostate cells with lentiviruses expressing GLYATL1 shRNA or nontargeting shRNA, stable knockdown cell lines were generated by selection with 1µg/ml puromycin (Life Technologies).

tag: cell line

value: LnCAP

value: GLYATL1 shRNA


title: GreyMatterLesion_FollicleNegative_MS127

description:
GML_Fneg_MS127
4311471225_E

value: Multiple Sclerosis


title: LnCAP-Scr

value: Non targeting shRNA


title: Progeny2-AF393 [a550818-4325018-051918-779_G04]

value: Sugarcane yellow leaf virus infected


title: 22Rv1-GLYATL-sh1

source_name: 22RV1 Cells


title: Progeny2-AF395 [a550818-4325018-051918-779_G05]

value: Sugarcane yellow leaf virus free


title: 22Rv1-Scr


title: Progeny2-AF391 [a550818-4325018-051918-779_G03]


title: Progeny2-AF389 [a550818-4325018-051918-779_G02]


title: ade_glc__2

city: San Diego

first: Anand

last: Sastry

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample

organism: Escherichia coli

source_name: E. coli K12 MG1655

growth_protocol: glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate.

extract_protocol:
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: media

value: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine


title: Progeny2-AF387 [a550818-4325018-051918-779_G01]

extract_protocol: Genomic DNA samples were extracted using MagJET Plant Genomic DNA Kit (Thermo Fisher Scientific, MA, USA).


title: bw_delpurR_cytd__2

source_name: E. coli BW25113

value: M9 minimal media w/ 2g/L glucose and 1 mM cytidine


title: bw_delpurR_cytd__1


title: GreyMatterLesion_FollicleNegative_MS114

description:
GML_Fneg_MS114
4311471277_D

value: motor cortex


title: GreyMatterLesion_FolliclePositive_MS154

description:
GML_Fpos_MS154
4311471247_H

value: Follicle Positive


title: GreyMatterLesion_FollicleNegative_MS074

description:
GML_Fneg_MS074
4311471226_B

value: Follicle Negative


title: Tumor specimen 021

source_name: FFPE tumor

tag: race

value: Black/African American (AA)


title: Tumor specimen 022

tag: batch


title: Progeny2-AF386 [a550818-4325018-051918-779_F12]


title: ade_glc__1


title: GreyMatterLesion_FollicleNegative_MS056

description:
GML_Fneg_MS056
4311471227_F

value: MS Lesion


title: GreyMatterLesion_FollicleNegative_MS104

description:
GML_Fneg_MS104
4311471277_A


title: GreyMatterLesion_FollicleNegative_MS003

description:
GML_Fneg_MS003
4311471228_E


title: Tumor specimen 193

tag: treatment

value: Systemic therapy before surgery


title: Tumor specimen 213

value: No systemic therapy and/or surgical procedures

tag: vital status

value: Alive


title: GreyMatterLesion_FollicleNegative_MS042

description:
GML_Fneg_MS042
4311471227_A


title: Progeny2-AF385 [a550818-4325018-051918-779_F11]


title: wt_glc_6__1

tag: strain

value: M9 minimal media w/ 2g/L glucose


title: Tumor specimen 023

value: Systemic therapy after surgery

value: Dead


title: wt_glc_5__1


title: GreyMatterLesion_FollicleNegative_MS100

description:
GML_Fneg_MS100
4311471247_E

tag: disease state

value: Multiple Sclerosis


title: Tumor specimen 202


title: Progeny2-AF383 [a550818-4325018-051918-779_F10]


title: Progeny2-AF379 [a550818-4325018-051918-779_F09]


title: Control_Grey_Matter_Tissue_C41

description:
Control_C41
4311471226_H

source_name: Control Grey Matter

value: Healthy Control

tag: presence of follicles


title: Control_Grey_Matter_Tissue_C14

description:
Control_C14
4311471228_D

tag: normal appearing or ms lesion


title: Control_Grey_Matter_Tissue_C28

description:
Control_C28
4311471226_C

tag: tissue


title: Tumor specimen 143

tag: age


title: Tumor specimen 019


title: tyr_glcn__2

value: M9 minimal media w/ 4g/L D-gluconate

tag: supplement


title: Progeny2-AF378 [a550818-4325018-051918-779_F08]

value: Sugarcane yellow leaf virus free


title: Progeny2-AF371 [a550818-4325018-051918-779_F06]


title: ura_pyr__1

value: M9 minimal media w/ 3.3g/L pyruvate

value: Uracil (1 mM)


title: tyr_glcn__1


title: Tumor specimen 165


title: ura_pyr__2


title: thm_gal__1

value: M9 minimal media w/ 4g/L galactose


title: thm_gal__2


title: Tumor specimen 020


title: Control_Grey_Matter_Tissue_A05-149

description:
Control_A05-149
4311471277_G

value: motor cortex


title: Control_Grey_Matter_Tissue_A06-189

description:
Control_A06-189
4311471225_D


title: Control_Grey_Matter_Tissue_A05-58

description:
Control_A05-58
4311471247_D


title: Control_Grey_Matter_Tissue_CMS-RZ84

description:
Control_CMS-RZ84
4311471247_A


title: Tumor specimen 018


title: Tumor specimen 101


title: Tumor specimen 131


title: Progeny2-AF365 [a550818-4325018-051918-779_F03]


title: 10 µM DD, 6 h, rep 2

city: Austin

first: Dennis

middle: Cates

last: Wylie

state: Texas

address: 102 East 24th Street

department: Center for Biomedical Research Support

institute: University of Texas at Austin

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were aligned to Phaeodactylum_tricornutum.ASM15095v2.29.dna_sm.toplevel.fa (from Ensembl) using TopHat in single-end mode using default settings
Reads aligning to genes annotated in Phaeodactylum_tricornutum.ASM15095v2.29.gff3 (from Ensembl) using HTSeq (htseq-count -m intersection-nonempty -s reverse -i Parent -t exon)
Genome_build: Phaeodactylum_tricornutum.ASM15095v2.29.dna_sm.toplevel.fa
Supplementary_files_format_and_content: processed

organism: Phaeodactylum tricornutum

source_name: Axenic culture

growth_protocol: Cultures were grown in autoclaved f/2 media made with filtered seawater from the Gulf of Mexico in flasks under cool white fluorescent light (90 - 100 µmol m−2s−1) at 20˚C in a 12 h light: 12 h dark cycle.

extract_protocol:
Cultures were harvested by vacuum filtration (Whatman GF/FNuclepore 0.4 µM filters). Cells on filters were frozen by liquid nitrogen and stored in - 80˚C. Cells were resuspended in PureLinkTM Plant RNA Reagent (12322012 Thermo Fisher) according to the manufacturer’s protocol. Samples were mechanically disrupted in QIAGEN Tissue LyserLT (2 X 2 min, 1 X 1 min, 30 sec pauses, 50 oscillations/sec) with Zirconia-silica beads (0.5 mm, Biospec). Total RNA was purified according to the PureLinkTM Plant RNA Reagent protocol.
Poly (A) enrichment using Poly (A) Purist Magnetic Kit (Thermo Fisher) and stranded RNA-Seq library was prepared using NEBNext reagents (New England Biolabs)

treatment_protocol: Trans, trans-2, 4-decadienal (DD, W313505) stock was freshly prepared in anhydrous DMSO solvent (276855) (Millipore Sigma). Each biological replicate was treated with 10 µM DD or 0.1 % DMSO solvent control for 3 or 6 h.  Treatments initiated at 3 h after the onset of the light cycle.

tag: cell density


title: Progeny2-AF370 [a550818-4325018-051918-779_F05]


title: 10 µM DD, 6 h, rep 1


title: Progeny2-AF376 [a550818-4325018-051918-779_F07]


title: Progeny2-AF362 [a550818-4325018-051918-779_F01]

value: Sugarcane yellow leaf virus infected


title: phe_acgam__2

value: M9 minimal media w/ 4g/L N-acetylglucosamine


title: Progeny2-AF363 [a550818-4325018-051918-779_F02]


title: Progeny2-AF358 [a550818-4325018-051918-779_E12]


title: Progeny2-AF356 [a550818-4325018-051918-779_E11]


title: 0.1% DMSO, 6 h, rep 2


title: phe_acgam__1


title: no3_anaero__2

value: anaerobic M9 minimal media w/ 2g/L glucose

value: KNO3 (20mM)


title: met_glc__2


title: no3_anaero__1


title: 0.1% DMSO, 6 h, rep 1


title: 10 µM DD, 3 h, rep 2


title: 0.1% DMSO, 3 h, rep 2


title: Progeny2-AF353 [a550818-4325018-051918-779_E09]


title: 10 µM DD, 3 h, rep 1


title: 0.1% DMSO, 3 h, rep 1


title: Control_Grey_Matter_Tissue_CMS-RZ77

description:
Control_CMS-RZ77
4311471228_F


title: met_glc__1


title: leu_glcr__1

value: M9 minimal media w/ 4g/L glucarate

value: leucine (10mM)


title: leu_glcr__2


title: gth__2

value: M9 minimal media w/ 2g/L glucose

value: glutathione


title: gth__1


title: Progeny2-AF351 [a550818-4325018-051918-779_E08]


title: Control_Grey_Matter_Tissue_A06-65

description:
Control_A06-65
4311471225_A


title: cytd_rib__2

value: M9 minimal media w/ 4g/L D-ribose

value: Cytidine (1 mM)


title: Progeny2-AF355 [a550818-4325018-051918-779_E10]


title: Tumor specimen 015

value: Black/African American (AA)

value: No systemic therapy and/or surgical procedures

value: Dead


title: Progeny2-AF344 [a550818-4325018-051918-779_E06]

value: Sugarcane yellow leaf virus free


title: Tumor specimen 156

value: Systemic therapy after surgery

value: Alive


title: Tumor specimen 016

value: Systemic therapy before surgery


title: Tumor specimen 145


title: Control_Grey_Matter_Tissue_CMS-RZ90

description:
Control_CMS-RZ90
4311471247_F

value: Healthy Control

value: motor cortex


title: Progeny2-AF347 [a550818-4325018-051918-779_E07]


title: Tumor specimen 102


title: Tumor specimen 071


title: Tumor specimen 014


title: Tumor specimen 189


title: Tumor specimen 013


title: Progeny2-AF342 [a550818-4325018-051918-779_E05]


title: Tumor specimen 188


title: Tumor specimen 118


title: Tumor specimen 017


title: arg_sbt__2

value: M9 minimal media w/ 4g/L D-sorbitol

value: L-arginine (5.75mM)


title: Progeny2-AF339 [a550818-4325018-051918-779_E03]


title: Progeny2-AF336 [a550818-4325018-051918-779_E02]


title: Progeny2-AF334 [a550818-4325018-051918-779_E01]

value: Sugarcane yellow leaf virus infected


title: cytd_rib__1


title: Progeny2-AF330 [a550818-4325018-051918-779_D12]


title: Progeny2-AF340 [a550818-4325018-051918-779_E04]


title: Progeny2-AF325 [a550818-4325018-051918-779_D11]


title: wt_glc__1


title: wt_glc__3


title: arg_sbt__1


title: Progeny2-AF322 [a550818-4325018-051918-779_D09]


title: swi6-1

city: Daejeon

first: Sang-Cheol

last: Jun

address: 62 Daehak-ro, Dong-gu

country: South Korea

institute: Daejeon University

description: swi6 deletion mutant

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to fungi(Aspergillus_fumigatus_Af293) whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: Aspergillus_fumigatus_Af293
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Aspergillus fumigatus

source_name: 24 hour cultured hyphae

growth_protocol: 10x5 conidia were spread on MMY agar plate and incubated at 37°C for 24 hours.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.


title: swi6-2

description: swi6 deletion mutant


title: A185: control serum,biological replicate 4

city: Kalyani

first: Bishnupriya

last: Chhatriya

state: West Bengal

address: PO NSS

country: India

institute: National Institute of Biomedical Genomics

description: miRNa expression data from healthy individual.

hyb_protocol: Biotinylated RNA were hybridized on Affymetrix GeneChip® miRNA 4.0 Arrays at 48 °C and 60 rpm for 16 h . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Data were processed using R bioconductor Packages.

source_name: Serum

label_protocol: RNA were biotinylated using the FlashTag Biotin HSR RNA Labelling kit (Affymetrix) according to manufacturer’s instructions.

extract_protocol: miRNA was isolated using miRNeasy kit from QIAGEN with glycogen method.

value: Healthy

value: Serum

value: 68 years

tag: gender

value: Male


title: A109: control serum,biological replicate 1

value: 53 years


title: A162: control serum,biological replicate 3

value: 71 years


title: Progeny2-AF320 [a550818-4325018-051918-779_D08]

data_processing:
The Affymetrix bioinformatics team processed the raw intensities in cell intensity files (.CEL) to obtain normalized intensities for each probe set. Further, these normalized intensities were converted to genotype calls with the Axiom Genotyping Algorithm version one
primary data description: Genotype Call (SNP call): AA=0, AB=1, BB=2, NoCall="-"; 'Signal' = Summarized signal


title: Tumor specimen 012

extract_protocol: Qiagen RNeasy FFPE Kit

value: Black/African American (AA)

value: No systemic therapy and/or surgical procedures


title: Tumor specimen 148


title: wt_glc__2

value: M9 minimal media w/ 2g/L glucose


title: swi4-2

description: swi4 deletion mutant


title: Progeny2-AF324 [a550818-4325018-051918-779_D10]

value: Sugarcane yellow leaf virus free


title: A160: control serum,biological replicate 2

value: 57 years


title: Tumor specimen 084

value: Alive


title: S021: patient serum,biological replicate 2

description: miRNa expression data from  serum of Pancreatic Ductal Adenocarcinoma patient.

value: Pancreatic Ductal Adenocarcinoma

value: 35 years


title: wt_glc__4


title: Tumor specimen 011

value: Systemic therapy after surgery


title: Tumor specimen 010


title: Progeny2-AF319 [a550818-4325018-051918-779_D07]


title: Tumor specimen 180

value: Systemic therapy before surgery


title: Tumor specimen 120


title: S003: patient serum,biological replicate 1

description: miRNA expression data from serum of Pancreatic Ductal Adenocarcinoma patient.

value: 48 years


title: Tumor specimen 098

value: Dead


title: Tumor specimen 211


title: Tumor specimen 008


title: Tumor specimen 009

value: Systemic therapy both before and after surgery


title: swi4-1

description: swi4 deletion mutant


title: Progeny2-AF318 [a550818-4325018-051918-779_D06]

value: Sugarcane yellow leaf virus infected


title: Tumor specimen 226


title: nopA-2

description: nopA deletion mutant

value: [delta]nopA


title: Progeny2-AF317 [a550818-4325018-051918-779_D05]


title: Progeny2-AF316 [a550818-4325018-051918-779_D04]


title: rgsA-2

description: rgsA deletion mutant

value: [delta]rgsA


title: Progeny2-AF315 [a550818-4325018-051918-779_D03]


title: Control_d for 11PP17 Plants

city: MALAGA

first: FERNANDO

last: DE LA TORRE

state: MALAGA

address: CAMPUS DE TEATINOS SN

department: BIOLOGIA MOLECULAR Y BIOQUIMICA

country: Spain

institute: UNIVERSIDAD MALAGA

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the microarrays. They were incubated in SureHyb microarray hybridization chambers with gasket slides (Agilent Technologies) at 65ºC for 17 h in an rotary oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 s with acetonitrile and 30 s in Agilent's stabilization and drying solution, then air dried.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: Limma package for R.

organism: Pinus pinaster

source_name: Control plants

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by NucleoSpin® Gel and PCR Clean-up column purification (Macherey-Nagel, Düren, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Transgenic and control plants were cultivated in a greenhouse under controlled conditions (24 C 16 hours light/8 hours dark). Stem samples were collected after 16 months

extract_protocol: Total RNA was isolated following the method of Chang S et al. Plant Mol Biol Rep 1993, 11:113–116

treatment_protocol: Standard growth conditions without treatment

tag: line

value: control

tag: developmental stage

value: Plantlet (16 month old)

tag: genotype

value: Stem


title: nopA-1

description: nopA deletion mutant


title: rgsA-1

description: rgsA deletion mutant


title: Progeny2-AF314 [a550818-4325018-051918-779_D02]


title: WT-2

description: Wild-type


title: WT-1

description: Wild-type


title: Progeny2-AF312 [a550818-4325018-051918-779_C12]


title: Tumor specimen 107

value: Black/African American (AA)


title: Progeny2-AF313 [a550818-4325018-051918-779_D01]

value: Sugarcane yellow leaf virus free


title: D39_CEP_RR07_D

city: Odense

first: Mikkel

middle: Girke

last: Jørgensen

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Sourthern Denmark

data_processing:
Reads mapped using Bowtie2 (Langmead and Salzberg, 2012)
Converted to BAM files and sorted via Samtools (Li et al, 2009)
Loaded into SeqMonk  No removal of duplicate reads  Treated as RNA-Seq data  Min mapping quality 20  Primary alignments only
All datasets quantificated via RNA-Seq quantification pipeline in seqmonk  Feature: Gene  Raw counts used
Feature report for all datasets via seqmonk  Annotated to Gene  with exactly overlapping probes   No merging of isoforms  Included all features
Differential Expression calcualted in R via EdgeR  Raw reads for all features in datasets used.  Variation for each gene in dataset replicates calculated and used to it a negative binomial generalized log-linear model to the read counts for each gene.   Genewise statistical test and, calculated fold change
Genome_build: GCA_000014365.2
Supplementary_files_format_and_content: Tab-deliminated file includes, fold-changes, FDR and raw read counts

organism: Streptococcus pneumoniae D39

source_name: D39 overexpressing the response regulator of Two-Component System 7 (SPD_0158)

growth_protocol: Grown in C+Y to OD600 = 0.5

extract_protocol:
Total RNA was extracted with an hot phenol-chloroform protocol, pelleted in ethanol and resuspended in H2O.
Ribosomal RNA was removed with the Ribo-Zero rRNA Removal Kit for Gram-Positive Bacteria (Illumina) according to manufacturers guidelines. Subsequent library preparation was performed using the NEBNext RNA library prep kit for Illumina. Library quality was assessed using the Fragment Analyzer followed by library qPCR quantification (Kapa library quantification kit).

tag: serotype

tag: genotype/variation


title: Tumor specimen 140

tag: race

tag: batch


title: Control_b for 11PP17 Plants


title: D39_D

source_name: D39 wildtype

value: wild type


title: Progeny2-AF309 [a550818-4325018-051918-779_C10]


title: 11PP17_c Plants downregulated for PpMYB8

source_name: 11PP17c Plants downregulated for PpMYB8

value: downregulated for PpMYB8


title: D39_CEP_RR07_C

value: overexpressing the response regulator of Two-Component System 7 (SPD_0158)


title: 11PP17_b Plants downregulated for PpMYB8

source_name: 11PP17b Plants downregulated for PpMYB8


title: Tumor specimen 186

tag: treatment

tag: vital status

value: Alive


title: Control_c for 11PP17 Plants


title: Control_a for 11PP17 Plants


title: Progeny2-AF305 [a550818-4325018-051918-779_C09]

source_name: Progeny from selfing CP80-1827


title: Progeny2-AF366 [a550818-4325018-051918-779_F04]


title: Progeny2-AF303 [a550818-4325018-051918-779_C08]


title: Progeny2-AF310 [a550818-4325018-051918-779_C11]


title: 11PP17_d Plants downregulated for PpMYB8

source_name: 11PP17d Plants downregulated for PpMYB8


title: GmEM-Input_br2 (GLYMA.13G317000 control)

city: Davis

first: John

last: Harada

address: One Shields Avenue

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Peaks were identified for each biological replicates using MACS2, using default parameters and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

source_name: embryos

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 2 ug of an antibody raised against the peptide TENLRAMRRPLSASW corresponding to the amino acids 322-336 of GLYMA.13G317000 .  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

tag: cultivar

value: Williams 82

tag: Stage

value: early maturation stage

tag: antibody


title: GmEM-Input_br1 (GLYMA.13G317000 control)


title: Progeny2-AF301 [a550818-4325018-051918-779_C07]

city: Gainesville

first: Jianping

last: Wang

address: 2033 Mowry Road

tag: tissue


title: Tumor specimen 167

data_processing: All statistical analyses were performed in R (https://cran.r-project.org/). Raw probe intensity data were normalized separately by batch as implemented by the “rma” function to perform background subtraction, quantile normalization, summarization of probe sets using median-polish, and log2-transformation. We evaluated batch effects using principal components analysis as implemented by the “princomp function. Batch effects were corrected by standardization of probes (subtracting the mean expression value and dividing by standard deviation) by batch (Batch 1 n=60, Batch 2 n=166). There was no evidence for batch effects after standardization.

value: Systemic therapy after surgery

tag: age


title: Progeny2-AF297 [a550818-4325018-051918-779_C06]


title: Control_d for 11PP16 Plants


title: Progeny2-AF296 [a550818-4325018-051918-779_C05]


title: Control_c for 11PP16 Plants


title: GmEM_GLYMA.13G317000-B-ChIP_br2

value: anti-peptide GLYMA.13G317000


title: D39_C

tag: strain


title: Tumor specimen 170


title: GmEM_GLYMA.13G317000-B-ChIP_br1


title: Tumor specimen 066

value: Systemic therapy before surgery

value: Dead


title: Tumor specimen 094


title: Progeny2-AF293 [a550818-4325018-051918-779_C04]


title: 11PP17_a Plants downregulated for PpMYB8

source_name: 11PP17a Plants downregulated for PpMYB8


title: Control_b for 11PP16 Plants


title: Tumor specimen 007

value: No systemic therapy and/or surgical procedures


title: Tumor specimen 006


title: 11PP16_d Plants downregulated for PpMYB8m

source_name: 11PP16d Plants downregulated for PpMYB8


title: Progeny2-AF292 [a550818-4325018-051918-779_C03]


title: Control

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W Walnut Street

department: Nephrology and Hypertension

institute: Indiana University School of Medicine

data_processing:
The CellRanger (10x Genomics) pipeline was utilized to align data from sequencing to mm10 genome. CellRanger .mtx and .tsv files were
Genome_build: mm10
Supplementary_files_format_and_content: .mtx, .tsv

source_name: Kidney

extract_protocol: The sample was targeted to 10,000 cell recovery and applied to a single cell master mix with lysis buffer and reverse transcription reagents, following the Chromium Single Cell 3’ Reagent Kits V3 User Guide, CG000183 Rev A (10X Genomics, Inc.). This was followed by cDNA synthesis and library preparation.The resulting library was sequenced in a custom program for 28b plus 91b paired-end sequencing on Illumina NovaSeq 6000. 50K reads per cell were generated and 91% of the sequencing reads reached Q30 (99.9% base call accuracy).

value: C57BL WT

value: male

value: WT


title: Tumor specimen 092

city: Detroit

first: Kristen

last: Purrington

address: 4100 John R St.


title: Progeny2-AF289 [a550818-4325018-051918-779_B12]


title: miRNA extracted from advanced- HCV patients 4

city: Riyadh

first: Saira

last: Khalid

address: Amr Ibn Alaas street

country: Saudi Arabia

institute: King Saud University

description:
Test:liver biopsy sample from chronic hepatitis C patients with fibrosis stage
SAMPLE 8

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package:https://dataanalysis.qiagen.com/mirna/arrayanalysis.php
For the normalization the average of two housekeeping genes: SNORD61, SNORD68 was choosen.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (fibrosis stage2or3or4/fibrosis stage1) ratios.

label: SYBR Green

source_name: HCV-fibrosis stage 4

label_protocol: miRNAs were reverse transcribed into first strand cDNA using a miRNA first strand kit(Qiagen). PCR assays were performed using the Human miFinder  miRNA PCR array from Qiagen miscript SYBR Green PCR kit (Qiagen) following the Manufacturer’s instructions. Quantitative real-time PCR were performed (7500 Real Time cycler, Applied Biosystems) with 40 cycles at 95ºC for 15 s; 60°C for 30–40 s; and finally a step at 72ºC for 30 s.

growth_protocol: liver biopsy samples were taken from HCV positive patients

extract_protocol: The miRNAs were purified from paraffin embedded liver biopsy samples of HCV and HCC patients, using an miRNeasy mini kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: samples were taken for the diagnosis of disease stage, prior the start of treatment

tag: Sex

value: Male

value: Fibrosis stage 4


title: Tumor specimen 005

source_name: FFPE tumor

value: Black/African American (AA)


title: miRNA extracted from advanced- HCV patients 5

description:
Test:liver biopsy sample from chronic hepatitis C patients with fibrosis stage
SAMPLE 9

value: Female


title: Tumor specimen 004


title: H1t_Input1

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

data_processing:
Data Quality Check: First all 4 samples ( the raw illumina sequenced files in fastq) were quality checked with  FastQC (version 0.11.5)
Alignment to Mouse Genome: Each sample ( two Input controls and two H1t) were then aligned to mouse genome version (GRCm38.p5) using bowtie2 with alignment parameters: -D 15 -R 2 -N 1 -i S,1,0.75 --local and only concordantly aligned reads were taken for further processing
Peak Calling: The aligned samples ( sam files) were used to find the peaks with MAC2 version 2.1.2, with parameters: # effective genome size = 1.87e+09, #band width = 300 # model fold = [5, 50] # pvalue cutoff for narrow/strong regions = 5.00e-02# pvalue cutoff for broad/weak regions = 5.00e-02# Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is on# Paired-End mode is on
Then various in house perl scripts were used to do the rest of the analysis like (1) comparisions with various other data sets, (2) RPBase repeat Analysis,(3) rDNA analysis,(4) Comparision with other data sets methylation analysis/comparisions(used Bismark)
Genome_build: MM10 : Reference Consortium Mouse Build 38 patch release 5 (GRCm38.p5)
Supplementary_files_format_and_content: .bam  files of bowtie2 aligned samples, AND MAC2 peak enrichment file converted to .xls file

source_name: Testicular cells

extract_protocol:
Chromatin Immunprecipitation were carried using the published protocol (Tardar et al., 2010). Briefly, chromatin were extracted from P20 mouse testicular cells, sonicated for 40 cycles, set for overnight antibody binding at 4 degrees. The dynabeads were added the next day and washes were given with multiple wash buffers. DNA were extracted from the elute fractions using the phenol-choloroform method.
The input and ChIP DNA libraries were prepared using the NEBNext Ultra II DNA library preparation kit.

tag: cell type

value: Pachytene cells

value: post natal day 20

tag: chip antibody


title: H1t_Input2


title: Progeny2-AF288 [a550818-4325018-051918-779_B11]

institute: University of Florida

value: Sugarcane yellow leaf virus free


title: miRNA extracted from advanced- HCV patients 3

description:
Test:liver biopsy sample from chronic hepatitis C patients with fibrosis stage
SAMPLE 7

source_name: HCV-fibrosis stage 3

value: Fibrosis stage 3


title: miRNA extracted from advanced- HCV patients 2

description:
Test:liver biopsy sample from chronic hepatitis C patients with fibrosis stage
SAMPLE 6


title: H1t_ChIPseq_P20_2


title: Tumor specimen 079

institute: Wayne State University


title: Tumor specimen 137


title: miRNA extracted from advanced- HCV patients 1

description:
Test :liver biopsy sample from chronic hepatitis C patients with fibrosis stage
SAMPLE 5


title: H1t_ChIPseq_P20_1


title: Progeny2-AF291 [a550818-4325018-051918-779_C02]


title: 11PP16_b Plants downregulated for PpMYB8m

source_name: 11PP16b Plants downregulated for PpMYB8

tag: line

tag: developmental stage

value: Plantlet (16 month old)

value: downregulated for PpMYB8

value: Stem


title: miRNA extracted from early- HCV patients 4

description:
Test:liver biopsy sample from chronic hepatitis C patients with fibrosis stage
SAMPLE 4

source_name: HCV-fibrosis stage 2

value: Fibrosis stage 2


title: CUTRUN Eed CKO FGO H3K27me3 rep2

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

description: CUTRUN Eed CKO FGO H3K27me3 rep2

data_processing:
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Cmpartment analysis are done as previously described (Lieberman et al., 2009)
TAD calling is done with insulation score as previously described ( Crane et al., 2015)
CUT&RUN reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together. And the mouse profiles were normalized to the yeast reads.
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: CUTRUN Eed CKO FGO H3K27me3

extract_protocol:
To isolate PGCs, germinal ridges were isolated from E11.5 and E13.5 embryos. To obtain the single cell su¬spension, the germinal ridges were digested with 0.25% trypsin-EDTA at 37°C for 10min. For E13.5 embryos, the germinal ridges were digested separately based on the gender. GFP-positive PGCs were sorted and collected by FACS.WT oocytes were collected from wild-type C57BL/6N females. Briefly, growing oocytes were isolated by mechanical dissection using a 26 gauge needle in M2 medium. Growing oocytes I were isolated from 7 or 10d old mice and growing oocytes II were from 14d old mice. Full-grown oocytes were isolated from superovulated 8-week-old mice 46 h after PMSG injection. The whole ovaries were clipped mechanically with a razor blade. To remove the granulosa cells, the dissociated oocyte-granulosa cell complexes were transferred into M2 medium containing 0.1% hyaluronidase and digested for 5 min. Oocytes were then crosslinked with 1% formaldehyde after removing the zona pellucida by acidic Tyrode’s solution treatment. Eedfl/wt and EedmNull late 2-cell embryos were harvested by mating Eedfl/fl  or Eedfl/fl;Gdf9-Cre females with PWK/PhJ males.
sisHi-C libraries were produced as described (Du et al., 2017). Briefly, PGCs, oocytes or embryos were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Then formaldehyde was quenched with glycine for 10 min at RT. After being washed with 1 × PBS, the samples were incubated in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min and the chromatin was solubilized with 0.5% SDS. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP, the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, Cat # 65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Extaq (Takara), and the products were purified and size-selected with AMPure XP beads （Beckman Coulter, Cat # A63881）  RNA-seq libraries of Ring1-/-Rnf2fl/fl and Ring1/Rnf2 dKO oocytes were prepared as follows. Cumulus oocyte complexes were isolated from ovaries of approx. 3 months old females. Granulosa cells were removed by repeated pipeting using a fine-pulled capilary glass needle in M2 medium. Oocytes were washed twice in M2 medium and subsequently washed twice in DNA suspension Buffer (TEKnova, Cat # PNT0221). For RNA isolation, 15 GV oocytes from one mouse were pooled and RNA was extracted using the RNAEasy Micro Kit (Qiagen,Cat # 74004) according to the manufacturer’s instructions. RNA was amplified and converted to cDNA using the Ovation v2 Kit (NuGen, Cat # 7102). Sequencing libraries were prepared with the Truseq DNA LT kit (Illumina, Cat # FC-121-2001).  CUT&RUN libraries of Eedfl/fl and Eed-/- oocytes were conducted as previously described (Skene and Henikoff, 2017). A low constant amount of yeast DNA was added to each reaction as spike-in DNA.

treatment_protocol: To collect oocytes undergoing germinal vesicle break down (GVBD), the full-grown oocytes with granulosa cells removed were firstly cultured in M2 medium supplemented with 5μM milrinone. Then half of the FGOs were washed out of milrinone and cultured at 37℃ to allow synchronized resumption of meiosis. After 2-4hours of incubation, oocytes that exit meiosis arrest and lose the GV were collected. The other half of the FGOs cultured with milrinone were collected at the same time as control.

value: Full-grown oocytes


title: Progeny2-AF285 [a550818-4325018-051918-779_B09]


title: Progeny2-AF284 [a550818-4325018-051918-779_B08]


title: Progeny2-AF287 [a550818-4325018-051918-779_B10]

value: Sugarcane yellow leaf virus infected


title: Progeny2-AF282 [a550818-4325018-051918-779_B07]


title: CUTRUN Eed flfl FGO H3K27me3 rep2

description: CUTRUN Eed flfl FGO H3K27me3 rep2

source_name: CUTRUN Eed flfl FGO H3K27me3


title: CUTRUN Eed CKO FGO H3K27me3 rep1

description: CUTRUN Eed CKO FGO H3K27me3 rep1


title: CUTRUN Eed flfl FGO H3K27me3 rep1

description: CUTRUN Eed flfl FGO H3K27me3 rep1


title: miRNA extracted from early- HCV patients 2

description:
Control:liver biopsy sample from chronic hepatitis C patients with fibrosis stage
SAMPLE 2

source_name: HCV-fibrosis stage 1

value: Fibrosis stage 1


title: miRNA extracted from early- HCV patients 3

description:
Test:liver biopsy sample from chronic hepatitis C patients with fibrosis stage
SAMPLE 3


title: 11PP16_c Plants downregulated for PpMYB8m

source_name: 11PP16c Plants downregulated for PpMYB8

tag: genotype


title: Tumor specimen 081

value: Systemic therapy after surgery

value: Alive


title: miRNA extracted from early- HCV patients 1

description:
Control:liver biopsy sample from chronic hepatitis C patients with fibrosis stage
SAMPLE 1


title: Progeny2-AF279 [a550818-4325018-051918-779_B05]


title: Tumor specimen 002

value: Systemic therapy before surgery

value: Dead


title: CUTRUN Eed CKO GOII H3K27me3 rep1

description: CUTRUN Eed CKO GOII H3K27me3 rep1

source_name: CUTRUN Eed CKO GOII H3K27me3

value: Growing oocytes II


title: Progeny2-AF276 [a550818-4325018-051918-779_B04]

source_name: Progeny from selfing CP80-1827


title: Progeny2-AF280 [a550818-4325018-051918-779_B06]


title: Tumor specimen 001

value: Black/African American (AA)


title: Hi-C Ring1 Rnf2 dKO FGO rep2

description:
Hi-C Ring1 Rnf2 dKO FGO rep2
processed data file:
Ring1_Rnf2_dKO_FGO_rep123_allValidPairs.txt.gz

source_name: Hi-C Ring1 Rnf2 dKO FGO