title: sarcoma classifier reference case 878

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 878


title: sarcoma classifier reference case 894

status: Public on Mar 01 2020

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 894

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Average Beta

molecule: genomic DNA

organism: Homo sapiens

source_name: sarcoma sample

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: tissue

value: sarcoma

tag: material preparation

value: FFPE


title: sarcoma classifier reference case 900

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 900


title: sarcoma classifier reference case 901

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 901


title: sarcoma classifier reference case 903

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 903


title: sarcoma classifier reference case 880

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 880


title: sarcoma classifier reference case 887

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 887


title: sarcoma classifier reference case 910

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 910


title: Genomic DNA from T-cell lymphoblastic lymphoma 11

status: Public on May 04 2020

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850K Human Methylation BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
DNA methylation data were analyzed using the methylation analysis module within BeadStudio software employing default parameters (Illumina, Inc., San Diego CA, USA).
normalized_data.txt: Tab-delimited text file includes Normalized (Beta-Mixture Quantile dilation method) Average Beta.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from T-LBL samples using Qiagen DNeasy Kit according to standard instructions.

value: T-cell lymphoblastic lymphoma

tag: disease state

value: Relapse T-LBL


title: gDNA from normal human bone marrow RO02776B

status: Public on Jan 01 2020

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

country: USA

institute: University of Arkansas for Medical Sciences

hyb_protocol: Bisulfite-converted genomic DNA was analyzed using the Infinium Human Methylation EPIC Beadchip Kit (Illumina). DNA amplification, fragmentation, array hybridization, extension and staining were performed with reagents provided in the kit according to the manufacturer’s protocol (Illumina Infinium II Methylation Assay). Briefly, 4 µl of bisulfite-converted genomic DNA at a minimum  concentration of 20 ng/µL) was added to 0.8 ml 96-well storage plate (Thermo Fisher Scientific), denatured in 0.014N sodium hydroxide, neutralized and then amplified for 20-24 hours at 37oC. Samples were fragmented at 37oC for 60 minutes and precipitated in isopropanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 15 µl of each sample was loaded onto a 12-sample BeadChip, assembled in the hybridization chamber as instructed by the manufacturer and incubated at 48oC for 16-20 hours.  Following hybridization, the BeadChips were washed and assembled in a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided.

scan_protocol: Polymer-coated BeadChips were scanned in an iScan scanner (Illumina) using Inf Methylation mode.

data_processing:
Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
matrix_processed.csv: normalized (SeSAMe) Average Beta
matrix_signals.csv: Unmethylated and methylated signal intensities, and non-detection p-values

source_name: Bone marrow, normal

label_protocol: Bisulfite conversion of genomic DNA was performed with EZ DNA methylation Kit (Zymo Research, Irvine, CA, #D5002) following the manufacturer’s protocol with modifications for the Infinium Methylation Assay. Briefly, 250ng of genomic DNA was mixed with 5 µl of Dilution Buffer and incubated at 37oC for 15 minutes and then mixed with 100 µl of conversion reagent prepared as instructed in the protocol. Mixtures were incubated in a thermocycler for 16 cycles at 95oC for 30 seconds and 50oC for 60 minutes. Bisulfite-converted DNA samples were loaded onto the provided 96-column plates for desulphonation, washing and elution. The concentration of bisulfite-converted, eluted DNA was measured by UV-absorbance using a NanoDrop-1000 (Thermo Fisher Scientific, Waltham, MA).

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

treatment_protocol: Diagnostic (presentation) bone marrow or peripheral blood specimens were collected from patients prior to induction therapy. Additional genomic data types and clinical covariates are available for these specimens under the TARGET-AML study (phs000465), available through the database of genotypes and phenotypes (dbGaP) and the NCI Genomic Data Commons (GDC).

tag: group

value: normal

tag: age at diagnosis (days)

tag: gender


title: Genomic DNA from T-cell lymphoblastic lymphoma 6


title: gDNA from normal human bone marrow RO02652


title: gDNA from normal human bone marrow RO02619B


title: gDNA from normal human bone marrow RO02609


title: gDNA from normal human bone marrow RO02580A


title: gDNA from normal human bone marrow RO02605A


title: gDNA from normal human bone marrow RO02496


title: gDNA from normal human bone marrow RO02466


title: gDNA from normal human bone marrow RO02462


title: gDNA from normal human bone marrow RO02391A


title: gDNA from normal human bone marrow RO02434B


title: gDNA from normal human bone marrow RO02361B


title: gDNA from normal human bone marrow RO02380


title: gDNA from normal human bone marrow RO02205


title: gDNA from normal human bone marrow RO02379


title: Genomic DNA from T-cell lymphoblastic lymphoma 18


title: gDNA from subject PARJWH

source_name: AML, pre-treatment

value: tumor

value: Male


title: gDNA from subject PARCUK

value: Female


title: gDNA from subject PASPTW


title: gDNA from subject PASAFM


title: gDNA from subject PANTRL


title: gDNA from subject PARTXH


title: gDNA from subject PANGTF


title: gDNA from subject PASYJI


title: gDNA from subject PAPVET


title: gDNA from subject PANCSC


title: gDNA from subject PASPWZ


title: gDNA from subject PASSVI


title: gDNA from subject PARZMZ


title: gDNA from subject PASVWW


title: gDNA from subject PASJRD


title: gDNA from subject PASNKC


title: gDNA from normal human bone marrow RO02209


title: gDNA from subject PARILH


title: gDNA from subject PASANH


title: gDNA from normal human bone marrow RO02224


title: gDNA from subject PATGIG


title: gDNA from normal human bone marrow RO02216


title: Methylation data from TCGA AML tissue 10

status: Public on Jan 15 2020

city: New York City

first: Matija

last: Snuderl

state: NY

address: 240 E 38th St

department: Pathology

institute: New York University Langone Medical Center

description:
AML_10
TCGA-AB-2805
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research. After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification. The amplified DNA is then enzymatically fragmented using end-point fragmentation. The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer. The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization. The DNA hybridizes with the array overnight in an oven at 48⁰C. After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

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

data_processing: The Minfi R package was used to analyze the data. Data was preprocessed, quantile normalized and poor samples and probes were removed based on mean detection Pvalues per sample. 'dmpFinder' was used to identify the differentially methylated probes between MPNSTs and DMs. qvalue < 0.01 are considered significant.

source_name: IDH Mutant AML sample

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit.

value: AML

tag: genotype/variation

value: IDH Mutant

value: AML tissue


title: Methylation data from TCGA AML tissue 13

description:
AML_13
TCGA-AB-2826
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: gDNA from normal human bone marrow RO02240


title: Methylation data from TCGA AML tissue 6

description:
AML_6
TCGA-AB-2807
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from TCGA AML tissue 3

description:
AML_3
TCGA-AB-2866
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: gDNA from subject PANZKA


title: gDNA from subject PAPVDV


title: gDNA from subject PANYNR


title: gDNA from normal human bone marrow RO02249


title: gDNA from subject PARUUB


title: gDNA from subject PASFIT


title: gDNA from normal human bone marrow RO02265


title: gDNA from subject PASFZN


title: gDNA from subject PASBHI


title: gDNA from subject PARZWH


title: gDNA from subject PARMZF


title: gDNA from subject PASPYR


title: gDNA from normal human bone marrow RO02211


title: Methylation data from TCGA AML tissue 7

description:
AML_7
TCGA-AB-2810
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: gDNA from subject PASSSI


title: gDNA from subject PASTPU


title: gDNA from subject PARIFD


title: gDNA from subject PARZHT


title: gDNA from subject PATJIC


title: gDNA from subject PARMMN


title: gDNA from subject PARIYP


title: gDNA from subject PARGYS


title: gDNA from subject PATLHB


title: gDNA from subject PASGZV


title: gDNA from subject PASINA


title: gDNA from subject PARNIL


title: gDNA from subject PATMFM


title: gDNA from subject PAPZZE


title: gDNA from subject PASPTM


title: gDNA from subject PARXNG


title: gDNA from subject PARXBT


title: gDNA from subject PARYFN


title: gDNA from subject PARZUU


title: gDNA from subject PARWDZ


title: gDNA from subject PASARM


title: gDNA from subject PARXNP


title: gDNA from subject PASLPU


title: gDNA from subject PATMIK


title: gDNA from subject PARUAD


title: gDNA from subject PARWWW


title: gDNA from subject PARKCX


title: gDNA from subject PARNPC


title: gDNA from subject PARNJC


title: gDNA from subject PARLMY


title: gDNA from subject PARHYP


title: gDNA from subject PARCVP


title: gDNA from subject PARGMH


title: gDNA from subject PASELF


title: gDNA from subject PASMGW


title: gDNA from subject PARRFC


title: gDNA from subject PASKRJ


title: gDNA from subject PARJRG


title: gDNA from subject PARTST


title: gDNA from subject PAPVKG


title: gDNA from subject PASBBE


title: gDNA from subject PARAEF


title: gDNA from subject PASREH


title: gDNA from subject PASFJB


title: gDNA from subject PARIZR


title: gDNA from subject PARCZL


title: gDNA from subject PATLZB


title: gDNA from subject PATLIG


title: gDNA from subject PATKAH


title: gDNA from subject PASRRL


title: gDNA from subject PASRZX


title: gDNA from subject PATKYC


title: gDNA from subject PATJLP


title: gDNA from subject PATLBC


title: gDNA from subject PATJKC


title: gDNA from subject PARENB


title: gDNA from subject PATJYT


title: gDNA from subject PATIGE


title: gDNA from subject PATILU


title: gDNA from subject PATBIZ


title: gDNA from subject PATGRP


title: gDNA from subject PATGUB


title: gDNA from subject PATJNI


title: gDNA from subject PATGGY


title: gDNA from subject PATEWX


title: gDNA from subject PATENX


title: gDNA from subject PATEMK


title: gDNA from subject PATBYV


title: gDNA from subject PARYTI


title: gDNA from subject PATIVW


title: gDNA from subject PASXAP


title: gDNA from subject PASZEB


title: gDNA from subject PATAVF


title: gDNA from subject PASZYU


title: gDNA from subject PASXYG


title: gDNA from subject PATDNN


title: gDNA from subject PATAEA


title: gDNA from subject PATAWB


title: gDNA from subject PASYRE


title: gDNA from subject PATBVX


title: gDNA from subject PASYRR


title: gDNA from subject PASZBM


title: gDNA from subject PASXSF


title: gDNA from subject PASWGL


title: gDNA from subject PASVVM


title: gDNA from subject PASVYL


title: gDNA from subject PATFRY


title: gDNA from subject PASVMU


title: gDNA from subject PASULX


title: gDNA from subject PASURR


title: gDNA from subject PASUMD


title: gDNA from subject PASUVD


title: gDNA from subject PASUAF


title: gDNA from subject PASSYV


title: gDNA from subject PASTSH


title: gDNA from subject PASXAH


title: gDNA from subject PASSHZ


title: gDNA from subject PASXSS


title: gDNA from subject PASLGD


title: gDNA from subject PASUGU


title: gDNA from subject PASEYM


title: gDNA from subject PASFIE


title: gDNA from subject PASBAX


title: gDNA from subject PASTEI


title: gDNA from subject PARLSW


title: gDNA from subject PARPWL


title: gDNA from subject PASNAL


title: gDNA from subject PASFNP


title: gDNA from subject PASSDX


title: gDNA from subject PASBPW


title: gDNA from subject PASFRD


title: gDNA from subject PARMZC


title: gDNA from subject PASAFH


title: gDNA from subject PARURW


title: gDNA from subject PARKFB


title: gDNA from subject PASNIY


title: gDNA from normal human bone marrow RO02210


title: gDNA from subject PASHYZ


title: gDNA from subject PASKPI


title: gDNA from subject PARTBN


title: gDNA from subject PASPSV


title: gDNA from subject PASSUW


title: gDNA from subject PAREFM


title: gDNA from subject PARBEL


title: gDNA from subject PARCHW


title: gDNA from subject PARUBE


title: gDNA from subject PARASV


title: gDNA from subject PARAHF


title: gDNA from subject PAPVCN


title: gDNA from subject PANIGD


title: gDNA from subject PAPVGE


title: gDNA from subject PAPZXN


title: gDNA from subject PARDMG


title: gDNA from subject PAPUEM


title: gDNA from subject PAPVZK


title: gDNA from subject PAPYUI


title: gDNA from subject PAPWIU


title: gDNA from subject PAPWYK


title: gDNA from subject PAPWHS


title: gDNA from subject PAPXWI


title: GV-12m-5-D

status: Public on Aug 01 2019

type: SRA

first: Thomas

last: Chan

address: Room623, Area 39, CUHK, Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

library_source: genomic

data_processing:
RNA-seq: Raw reads were aligned to reference genome(mm10) using Tophat. Expression levels of transcripts and genes were calculated, and differential expression was compared with Cufflinks.
Bisulfite-seq: Reads with poor quality and adapter contaminations were filtered when Trim Galore. The trimmed reads were mapped to the mouse reference genome (mm10) using Bismark in single-end mode to increase mapping efficiency, and two seperated bams from the same sample were merged. Duplication removal and methylation call extraction were also performed by Bismark.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include FPKM values for each Sample ; Bisulfite-seq: bedgraph files include methylation level of all called cytosine sites.

organism: Mus musculus

source_name: GV oocyte

extract_protocol:
RNA and gDNA were separated from a single oocyte followed by the published protocol with minor modification. Frozen oocytes in PCR tubes were thawed at room temperature for around 5 minutes. The 7µl of soft lysis buffer (500mM KCl, 100 mM Tris-HCl pH=8, 1.35mM MgCl2, 4.5mM DTT, 0.45% Nonidet P-40, 0.18U SUPERase-In and 0.36U RNase-inhibitor) was added into each PCR tube containing a single oocyte, and the lysate was inhibited at 4˚C for 30 min. The tubes were vortexed at room temperature for one minute and then were centrifuged at 1000xg for 5 min. RNA in the cytoplasm was released to the lysate and gDNA storing in the nucleus was at the bottom of the tube. The 6.5µl of lysate supernatant was carefully transferred to another PCR tube for the following RNA-seq. The remaining nucleus with around 2.5µl of lysis buffer was subjected for performing bisulfite sequencing.
RNA-seq: Library preparation for scRNA-seq was according to the modified protocol of Smart-seq2. In brief, the mixture of 2µl of 10mM oligo-dT30VN primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) and 2µl of 10mM dNTP mix was added into the lysate supernatant, and the sample was inhibited at 72˚C for 3 min. Then, the 9.5µl of reverse transcription mixture (200U SuperScript II reverse transcriptase, 20U RNAse inhibitor, 1x Superscript II first-strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1µM TSO (5’-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’) was added into the tube for RNA reverse transcription. The tubes containing total 20µl mixture were put into ProFlex PCR System (Thermo Fisher Scientific) and the reaction condition was as follows: 42˚C for 90min, followed by ten cycles of 50 ˚C for 2 min and 42 ˚C for 2 min. The final enzyme inactivation was performed at 70˚C for 15 min. After finishing the first-strand reaction, the 30µl of PCR preamplification mix (1x KAPA HiFi HotStart ReadyMix, 0.1µM IS PCR primers (5’-AAGCAGTGGTATCAACGCAGAGT-3’)) were added into the tube containing 20µl of the first-strand reaction. PCR preamplification reaction was performed in ProFlex PCR System by using the following program: 98˚C for 3 min, 18 cycles of 98˚C for 20s, 67˚C for 15s and 72˚C for 6min, with the final extension cycle of 72˚C for 5min. Amplified cDNA was purified by using Ampure XP beads (1:1 ratio) according to the manufacturer’s manual and was eluted in 15µl of ddH2O in the end. To check the quality of the cDNA library, 1µl of amplified cDNA was removed to perform additional same PCR amplification reaction as mentioned above and PCR product was run on a 1% agarose gel at 100 Volts for 45min. The yield of amplified cDNA was measure by Qubit3.0 fluorometer. 5ng of amplified cDNA with good quality were used for library construction with TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme) followed by the instruction.
Bisulfite-seq: To construct the scBS-seq libraries, 60fg of unmethylated lambda DNA was added into the retained lysis solution containing a nucleus. Pico Methyl-Seq Library Prep Kit (Zymo) was used for library construction strictly followed by the manufacturer’s manual. The quality of all constructed libraries was assessed by Agilent Bioanalyzer 2100 with High Sensitivity DNA Kit (Agilent Technologies). Qualified libraries were sequenced on Illumina HiSeq4000 to generate 150bp pair-end reads.

treatment_protocol: For collecting oocytes in the stage of metaphase II (MII oocyte), female mice underwent superovulation according to the established protocol. Briefly, mice were injected intraperitoneally with ten units of pregnant mare’s serum gonadotropin (PMSG, Sigma) at 7 pm on the first day. Then, at 7 pm on the third day, they underwent the intraperitoneal injection of 10 units of human chorionic gonadotropin (hCG, Sigma). 14 hours later, mice were anesthetized by intraperitoneal injection of the mixture of ketamine (100mg/kg) and xylazine (15mg/kg), and then their blood was collected through cardiac puncture and executed for the following procedures. Ovary tying with oviduct and part of the uterus were dissected out and put in M2 medium (Sigma). Though chopping the ampulla of oviduct by needle, oocyte-cumulus-complex (COC) were harvested and transferred to a droplet of 100 µl M2 medium containing 1% hyaluronidase (Sigma) to detach cumulus cells from oocytes. After incubation at room temperature for 1-2 minutes, cumulus-free metaphase II (MII) oocytes were successively transferred to two droplets of M2 medium and three droplets of PBS by mouth pipette for washing. Finally, each oocyte within 1-2 µl of PBS was transferred into one PCR tube and was kept in -80˚C freezer for further experiments. For harvesting oocytes in the stage of germline vesicle stage (GV oocytes), female mice were treated with the half-superovulation treatment. Similar to superovulation, mice were also injected intraperitoneally with ten units of PMSG. 2 days later, they were sacrificed to harvest ovaries. These ovaries were put into 35mm dish containing M2 medium and hyaluronidase and were mashed by forceps and needles. Under the dissecting microscope, GV oocytes were found and transferred into a droplet of a 100µl M2 medium by mouth pipette. The following washing and store procedure were the same as MII oocytes collection.

tag: strain

tag: age

value: 12 months

tag: cell type

value: GV oocyte


title: GV-12m-4-D


title: GV-12m-8-D


title: GV-12m-6-D


title: gDNA from subject PANTCT


title: GV-12m-3-D


title: GV-12m-1-D


title: gDNA from subject PAPZFV


title: MII-6w-2-D

source_name: MII oocyte

value: 6 weeks

value: MII oocyte


title: MII-6w-6-D


title: MII-6w-1-D


title: MII-6w-7-D


title: MII-6w-4-D


title: MII-6w-5-D


title: GV-12m-5-R

library_source: transcriptomic

molecule: total RNA


title: GV-6w-7-D


title: GV-12m-6-R


title: GV-12m-4-R


title: GV-6w-4-D


title: GV-12m-3-R


title: GV-6w-1-D


title: GV-6w-8-D


title: MII-6w-6-R


title: MII-6w-4-R


title: GV-6w-3-D


title: GV-12m-1-R


title: MII-6w-7-R


title: MII-6w-2-R


title: MII-6w-1-R


title: GV-6w-2-D


title: GV-12m-8-R


title: GV-6w-8-R


title: MII-6w-5-R


title: GV-6w-3-R


title: GV-6w-4-R


title: GV-6w-2-R


title: Hkan_ENV_F1

status: Public on Jun 05 2019

city: Auzeville Tolosane

first: Sylvain

last: MERLOT

address: 24, chemin de Borde Rouge

department: Biological Sciences

country: France

institute: CNRS

description: Environmental sample

data_processing:
Illumina HiSeq 2000 100bp paired-end mode
Adaptors and low quality pair-end sequences were removed from the raw reads and the ribosomal RNA was filtered using the SortMeRNA algorithm (Kopylova, E., Noé, L. & Touzet, H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012).
To generate transcriptome sequences, paired-end reads originating from one individual plant of Homalium kanaliense (Hkan) or Homalium betulifolium (Hbet) were assembled de novo using CLC Genomic Workbench v9 with Lenght fraction:0.75; Similarity fraction: 0.95; word size: 24 (Hkan), 23 (Hbet). Contig sequences were annotated with Blast2GO using BlastX with E-value≤10-6.
Paired-end reads of all independant samples were mapped to the Hkan_transcriptome_v1 using CLC Genomic Workbench v9 with Lenght fraction 0.5 and Similarity fraction 0.875. Read counts are used for abundance measurements.
Genome_build: Hkan_transcriptome v1.fasta
Supplementary_files_format_and_content: csv file with read count

molecule: polyA RNA

organism: Homalium kanaliense

source_name: Leaf

growth_protocol: Plant samples were collected in their natural environment (Gallery forest and maquis, serpentine soil)

extract_protocol:
Total RNA were extracted from frozen leaves of one individual plant using TRIzol LS Reagent Method (Protocol#10, Johnson et al. 2012, PLoS ONE 7(11): e50226. doi:10.1371), and treated with DNAseI.
Libraries were constructed using 1 µg total RNA with Illumina TruSeq Stranded mRNA kit by the POPS transcriptomic plateform (IPS2, Orsay, France) following Illumina kit recommendations.

treatment_protocol: Samples were stabilized in RNAlater (Sigma). The stabilization solution was removed at the laboratory and samples were stored at -80°C before RNA extraction

tag: phenotype

value: nickel hyperaccumulator

value: Leaf

tag: geographical location

value: Creek pernod, Yate, New Caledonia

tag: gps location

tag: collection date


title: Hkan_ENV_F2

description: Environmental sample


title: Hbet_ENV_F1

description: Environmental sample

organism: Homalium betulifolium

value: non-nickel-accumulator

value: La Tontouta, New Caledonia


title: Hkan_ENV_F3

description: Environmental sample


title: Hbet_ENV_F3

description: Environmental sample


title: Lhav_ENV_F

description: Environmnental sample

data_processing:
Illumina HiSeq 2000 100bp paired-end mode
Adaptors and low quality pair-end sequences were removed from the raw reads and the ribosomal RNA was filtered using the SortMeRNA algorithm (Kopylova, E., Noé, L. & Touzet, H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012).
To generate transcriptome sequences, paired-end reads originating from in vitro sample of L. havanensis (Lhav) or environmental sample of L. microphyllus (Lmic) were assembled de novo using CLC Genomic Workbench 9 with Lenght fraction:0.75; Similarity fraction: 0.95; word size: 40 (Lhav), 30 (Lmic). Contig sequences were annotated using Blast2GO using BlastX with E-value≤10-6.
Paired-end reads of all independant samples were mapped to the Lhav_transcriptome_v1 using CLC Genomic Workbench 9 with Lenght fraction 0.5 and Similarity fraction 0.875. Read counts are used for abundance measurements.
Genome_build: Lhav_transcriptome_v1.fasta
Supplementary_files_format_and_content: cxv file with counts

organism: Leucocroton havanensis

growth_protocol: Plant samples were collected in their natural environment (Serpentine Cuabal and  gallery forest limestone).  L. havanensis was also in vitro cultured on Murashige & Skoog medium with agar containing 500 mg/L NiSO4 as described in Gonzalez, D. & Matrella, S. Nickel hyperaccumulation ‘in vitro’ by Leucocroton havanensis (Euphorbiaceae)

extract_protocol:
Total RNA were extracted using TRIzol LS Reagent Method (Protocol#10, Johnson et al. 2012, PLoS ONE 7(11): e50226. doi:10.1371), and treated with DNAseI.
Libraries were constructed using 1 µg total RNA with Illumina TruSeq Stranded mRNA kit by the POPS transcriptomic plateform (IPS2, Orsay, France) following Illumina kit recommendations.

treatment_protocol: Field samples were stabilized in RNAlater (Invitrogen). The stabilization solution was removed at the laboratory and samples were stored at -80°C before RNA extraction

value: La Coca, La Habana del Este, Cuba


title: Lmic_ENV_F

description: Environmnental sample

organism: Lasiocroton microphyllus

value: Cojimar, La Havana del Este, Cuba


title: Lhav_Ni_F

description: in vitro cultured sample


title: Donor 1 intermediate cell phenotype (D2)

status: Public on Mar 18 2019

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

description: RiboZero depleted RNAseq

data_processing:
Raw reads were aligned to the genome using Tophat2.1
BAM files were used to construct BigWig files for visualization

source_name: intermediate differentiation AEC cells

growth_protocol: PurifiedAT2 cells were harvested from a human lung donor without prior history of lung disease and differentiated in vitro for 6 days

extract_protocol:
RNA was isolated using whole-cell extract by performing RNA purification using the Illustra TriplePrep kit.
Library construction was performed at the USC Epigenome center.
Barcodes were attached; D0= ATGTCA, D2=CCGTCC, D4=GTCCGC, D6=GTGAAA. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Paired End 50 cycling. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1.

tag: individual

value: donor 1


title: Donor 1 AT1-like cells (D6)

description: RiboZero depleted RNAseq

source_name: AT1-like cells


title: Donor 1 purified AT2 cells (D0)

description: RiboZero depleted RNAseq

source_name: Purified primary AT2 cells


title: Hbet_ENV_F2

description: Environmental sample


title: GV-6w-7-R


title: Donor 1 AT1-like cells (D4)

description: RiboZero depleted RNAseq


title: tumor biopsy PCNSL_26

status: Public on Oct 01 2019

city: Ulm

first: Julia

last: Vogt

address: Albert-Einstein Allee 11

department: Institute of Human Genetics

institute: Ulm University

description: tumor sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software v2011.1; methylation module 1.9.0
160919_allCpG_detpval0.01

source_name: FFPE tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor FFPE-biopsies using Promega Maxwell 16 FFPE Plus LEV DNA Purification kit/QIAamp DNA FFPE Tissue Kit (Qiagen) and tumor from cryo-preserved biopsies using Genomic-tip 100/G (Qiagen)

value: tumor

value: PCNSL


title: GV-6w-1-R


title: tumor biopsy PCNSL_25

description: tumor sample


title: tumor biopsy PCNSL_16

description: tumor sample


title: tumor biopsy PCNSL_4

description: tumor sample

value: Male


title: tumor biopsy PCNSL_13

description: tumor sample

value: Female


title: tumor biopsy PCNSL_6

description: tumor sample


title: Transitional AT2->1 cells  - H3K27Ac ChIP

description: Histone ChIP

data_processing:
fastx_toolkit_0.0.13 was used to filter low quality reads: average quality score < 30 and length < 20
bwa-0.7.7was used to perform alignment using hg19 genome, with 2 mismatches allowed, and only reads with mapping quality (MAPQ) ≥ 30 are retained using samtools-0.1.19
Duplicates were removed with picard-tools-1.107
SICERv1.1 was used to perform peak calls. Settings used were FAIRE: window size 50, gap size 50, H3K27ac: window size 100, gap size 200,and H3K4me1: window size 200, gap size 20. Fragment size set as 150 for all samples.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called via SICER (.bed files)

source_name: Alveolar epithelial cells

growth_protocol: PurifiedAT2 cells were harvested from a human lung donor without prior history of lung disease.

extract_protocol:
Chomatin of freshly isolated AT2 cells was prepared as previously described (Marconett et al., PLoS Genetics, 2013). INPUT DNA was collected after sonication and supernatant collection but before IP stage. FAIRE was performed on supernanant removed after ChIP immunoprecipiation.
ChIPseq libraries were made by the USC Epigenome Center. The NEB Ultra Kit was used for library construction according to manufacturer's reccomendations. Adapter sequences were obtained from BioScientific. Barcodes were attached. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Single End 50 cycling.  Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Single End 50 cycling.

value: lung

value: Alveolar epithelial cells


title: Differentiated AT1-like cells - FAIREseq

description: FAIRE


title: ChIP input transitional AT2->AT1 cells

description: INPUT DNA


title: ChIP Input AT2 cells

description: INPUT DNA


title: tumor biopsy PCNSL_23

description: tumor sample


title: Differentiated AT1-like cells -H3K27Ac ChIP

description: Histone ChIP


title: Purified AT2 cells- FAIREseq

description: FAIRE


title: tumor biopsy PCNSL_21

description: tumor sample


title: Transitional AT2->1 cells  - FAIREseq

description: FAIRE


title: H522 control sample 3

status: Public on Mar 01 2019

description:
H522-CMV-NEO-3
RiboZero-depleted RNA

data_processing:
FASTQ reads were trimmed to remove bases 1-12 due to lack of sequence complexity.
Reads were filtered to remove those with quality scores of less than 30 for 90% of the read.
Reads were aligned to the hg38 genome and assembled into transcripts based on Gencode annotation. BigWig files provided for visualization are hg38-based.
Transcripts with less than 10 reads across the dataset were removed due to low expression levels.
EdgeR was used for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig visualization files

source_name: stably transfected H522 lung adenocarcinoma cells

growth_protocol: Human H522 LUAD cell lines were grown in RPMI with 10% FBS and 1:1000 Penicillin/Streptomycin.

extract_protocol:
RNA was isolated using the BioRad Arum RNA purification kit.
RNA library preparation was performed at the USC Epigenome Center using the RiboZero depletion protocol.

treatment_protocol: Cells were transfected with CMV-LINC00261 and selected using Puromycin. Stables were derived from monoclonal outgrowths, and verified using qRT-PCR prior to sequencing.

tag: cell line

value: LUAD

tag: transfection

value: CMV-NEO


title: Transitional AT2->1 cells  -H3K4me1 ChIP

description: Histone ChIP

tag: tissue


title: H522 control sample 2

description:
H522-CMV-NEO-2
RiboZero-depleted RNA


title: H522 with CMV-LINC00261 sample 1

description:
H522-CMV-LINC00261-1
RiboZero-depleted RNA


title: Purified AT2 cells- H3K27Ac ChIP

description: Histone ChIP


title: tumor biopsy PCNSL_11

description: tumor sample


title: tumor biopsy PCNSL_12

description: tumor sample


title: Purified AT2 cells- H3K4me1 ChIP

description: Histone ChIP


title: H522 with CMV-LINC00261 sample 3

description:
H522-CMV-LINC00261-3
RiboZero-depleted RNA


title: H1944

description: Ribo-depleted RNA

data_processing:
FASTQ reads were trimmed to remove bases 1-12 due to lack of sequence complexity
Reads were filtered to remove those with quality scores of less than 30 for 90% of the read
Reads were aligned to the lncipedia2.1 transcriptome for differential analysis. BigWig files provided for visualization are hg19-based
Table of counts were assembled for all transcripts for all samples
Transcripts with less than 10 reads across the dataset were removed due to low expression levels
Genome_build: hg19
Supplementary_files_format_and_content: Counts per transcript for lncRNA transcriptome

source_name: human lung adenocarcinoma cell lines

growth_protocol: Primary AEC were isolated and cultured as described previously (Marconett et al., PLoS genetics 2013). Human LUAD cell lines were grown in RPMI with 10% FBS and 1:1000 Penicylin/Streptomycin.

extract_protocol:
RNA was isolated using the Illustra GE Triple Prep kit.
RNA library preparation was performed at the USC Epigenome Center using the RiboZero depletion protocol
Paired end 50bp reads were multiplexed on the Illumina HiSeq2000

treatment_protocol: No Treatment

value: human lung adenocarcinoma (LUAD) cell lines

value: LUAD cell line H1944


title: H1975

description: Ribo-depleted RNA

value: LUAD cell line H1975


title: H2347

description: Ribo-depleted RNA

value: LUAD cell line H2347


title: H292

description: Ribo-depleted RNA

value: LUAD cell line H292


title: PC3

description: Ribo-depleted RNA

value: LUAD cell line PC3


title: ChIP Input AT1-like cells

description: INPUT DNA


title: H2228

description: Ribo-depleted RNA

value: LUAD cell line H2228


title: Differentiated AT1-like cells - H3K4me1 ChIP

description: Histone ChIP


title: H1792

description: Ribo-depleted RNA

value: LUAD cell line H1792


title: H1648

description: Ribo-depleted RNA

value: LUAD cell line H1648


title: HCC827

description: Ribo-depleted RNA

value: LUAD cell line HCC827


title: H3122

description: Ribo-depleted RNA

value: LUAD cell line H3122


title: H522

description: Ribo-depleted RNA

value: LUAD cell line H522


title: H1395

description: Ribo-depleted RNA

value: LUAD cell line H1395


title: H23

description: Ribo-depleted RNA

value: LUAD cell line H23


title: H1650

description: Ribo-depleted RNA

value: LUAD cell line H1650


title: H358

description: Ribo-depleted RNA

value: LUAD cell line H358


title: Patient T39 Pan immune

status: Public on Jun 01 2018

city: Stanford

first: Andrew

last: Gentles

address: 1201 Welch Road

institute: Stanford University

data_processing:
Expression levels of genes were quantified using Salmon 0.4.2 (Patro et al., 2014), with Gencode v23 reference transcriptome , and hg38 as the reference human genome
TPMs were summed for gene-level quantification. TPM values were transformed using a moderated log function: log2(1+TPM)
Genome_build: hg38
Supplementary_files_format_and_content: log2 (1+TPM)

source_name: Non small cell lung cancer

extract_protocol:
Fresh human lung tumor samples were obtained from Stanford Tissue Bank. Tissues were cut into small pieces and dissociated into single cell suspensions by 45 minutes of collagenase I (STEMCELL Technologies) digestion. Dissociated single cells were suspended at 107 per mL in staining buffer (HBSS with 2% heat-inactivated calf serum). After blocking with 10 μg/mL rat IgG, cells were stained with the antibodies listed below. Stained cells were washed and re-suspended in staining buffer with 1 μg/mL DAPI, analyzed, and sorted with a FACS Aria II cell sorter (BD Biosciences). Antibodies used for experiments included CD45-A700 (pan-immune cell marker), CD31-PE (endothelial cell marker), EpCAM-APC (epithelial cell marker), CD10-PE-Cy7 (fibroblast marker). All antibodies were obtained from BioLegend.
Total RNA was extracted from sorted cell populations (range: 500 to 25,000 cells). A median of ~30 ng total RNA was amplified using the Ovation RNA-Seq System V2 (Nugen). 1 mg of resulting cDNA was sheared by sonication (Covaris S2 System) to an average size of 150-200 bp and used to construct DNA libraries for sequencing using NEBNext DNA Library Prep Master Mix (New England Biolabs).  Finally, DNA libraries were sequenced in the Stanford Stem Cell Institute Genome Center on an Illumina HiSeq 2000.

tag: patient id

value: Non small cell lung cancer

tag: population

value: Pan immune

tag: histology

value: Squamous cell carcinoma

tag: sorting strategy

value: CD45+ EPCAM-


title: Patient T40 Bulk

value: Bulk

value: Unsorted


title: Patient T40 Malignant

value: Malignant

value: EPCAM+ CD45-


title: Patient T39 Malignant


title: Patient T40 Pan immune


title: Patient T40 Fibroblast

value: Fibroblast

value: CD10+ EPCAM- CD45- CD31-


title: AEC Donor 1

description: Ribo-depleted RNA

source_name: purified primary human alveolar epithelial cells

value: primary human alveolar epithelial cells


title: Patient T40 Endothelial

value: Endothelial

value: CD31+ EPCAM- CD45-


title: Patient T39 Endothelial


title: Patient T39 Fibroblast


title: Patient T38 Malignant

value: Adenocarcinoma


title: Patient T39 Bulk


title: Patient T38 Endothelial


title: PC9

description: Ribo-depleted RNA

value: human lung adenocarcinoma (LUAD) cell lines

value: LUAD cell line PC9


title: Patient T38 Pan immune


title: Patient T38 Fibroblast


title: Patient T38 Bulk


title: Patient T37 Pan immune

value: Mixed adenocarcinoma


title: Patient T37 Endothelial

value: Non small cell lung cancer


title: Patient T36 Endothelial


title: AEC Donor 2

description: Ribo-depleted RNA

value: purified primary human alveolar epithelial cells


title: Patient T37 Fibroblast


title: Patient T37 Malignant


title: Patient T35 Pan immune

value: Pan immune


title: Patient T35 Fibroblast


title: Patient T35 Endothelial


title: Patient T34 Pan immune

value: Squamous cell carcinoma

value: CD45+ EPCAM-


title: Patient T34 Malignant


title: Patient T35 Malignant


title: Patient T35 Bulk

value: Bulk

value: Unsorted


title: Patient T33 Pan immune


title: Patient T34 Bulk


title: Patient T33 Fibroblast


title: Patient T34 Endothelial


title: Patient T34 Fibroblast


title: Patient T33 Endothelial


title: Patient T32 Endothelial


title: Patient T32 Pan immune


title: Patient T31 Pan immune


title: Patient T32 Malignant

value: Malignant

value: EPCAM+ CD45-


title: Patient T31 Endothelial


title: Patient T36 Malignant


title: Patient T36 Pan immune


title: Patient T36 Fibroblast

value: Fibroblast

value: CD10+ EPCAM- CD45- CD31-


title: Patient T30 Bulk


title: Patient T30 Pan immune


title: Patient T30 Fibroblast rerun


title: Patient T30 Fibroblast


title: Patient T31 Malignant


title: Patient T36 Bulk


title: Patient T37 Bulk


title: Patient T30 Endothelial

value: Endothelial


title: AEC Donor 3

description: Ribo-depleted RNA

value: primary human alveolar epithelial cells


title: Patient T29 Bulk

value: Adenocarcinoma


title: Patient T29 Pan immune


title: Patient T29 Pan immune rerun


title: Patient T29 Endothelial

value: CD31+ EPCAM- CD45-


title: Patient T28 Bulk


title: Patient T30 Malignant rerun


title: Patient T29 Endothelial rerun


title: Patient T28 Pan immune


title: Patient T28 Endothelial


title: Patient T28 Fibroblast


title: Patient T27 Bulk


title: Patient T27 Pan immune


title: Patient T27 Endothelial


title: Patient T28 Fibroblast rerun


title: Patient T27 Fibroblast


title: Patient T26 Pan immune


title: Patient T26 Endothelial


title: Patient T26 Bulk


title: Patient T26 Fibroblast


title: Patient T25 Pan immune rerun


title: Patient T26 Malignant


title: Patient T25 Pan immune


title: Patient T30 Malignant


title: Patient T27 Malignant


title: Patient T25 Malignant


title: Patient T23 Bulk

value: Fetal adenocarcinoma


title: Patient T25 Fibroblast


title: Patient T23 Fibroblast


title: Patient T22 Fibroblast


title: Patient T23 Endothelial


title: Patient T22 Endothelial


title: Patient T20 Pan immune


title: Patient T20 Endothelial


title: Patient T22 Pan immune


title: Patient T20 Bulk


title: Patient T23 Malignant


title: Patient T18 Pan immune


title: Patient T20 Malignant


title: Patient T20 Fibroblast


title: Patient T18 Bulk


title: Patient T18 Fibroblast


title: Patient T18 Endothelial


title: Patient T17 Bulk


title: Patient T25 Endothelial


title: Patient T18 Malignant rerun


title: Patient T17 Pan immune


title: Patient T18 Malignant


title: Patient T17 Fibroblast


title: Patient T17 Malignant


title: Patient T28 Malignant


title: Patient T16 Endothelial


title: Patient T16 Pan immune


title: Patient T16 Fibroblast


title: Patient T15 Bulk


title: Patient T22 Malignant


title: Patient T15 Pan immune


title: Patient T16 Malignant


title: Patient T15 Endothelial


title: Patient T14 Pan immune rerun


title: Patient T15 Malignant


title: Patient T14 Bulk


title: Patient T14 Pan immune


title: Patient T15 Fibroblast


title: Patient T14 Endothelial


title: Patient T14 Malignant


title: Patient T12 Bulk


title: Patient T12 Pan immune


title: Patient T12 Fibroblast


title: Patient T12 Malignant


title: Patient T12 Endothelial


title: Patient T11 Bulk


title: Patient T17 Endothelial


title: Patient T11 Pan immune


title: Patient T11 Malignant


title: Patient T10 Bulk


title: Patient T11 Endothelial


title: Patient T10 Pan immune


title: Patient T10 Endothelial


title: Patient T10 Pan immune rerun


title: Patient T10 Malignant rerun


title: Patient T9 Endothelial

value: Adenosquamous


title: Patient T10 Fibroblast

value: Non small cell lung cancer


title: Patient T9 Bulk


title: Patient T9 Pan immune


title: Patient T8 Bulk


title: Patient T9 Fibroblast


title: Patient T8 Pan immune rerun


title: Patient T8 Fibroblast


title: Patient T7 Bulk


title: Patient T7 Endothelial


title: Patient T7 Pan immune


title: Patient T7 Fibroblast


title: Patient T7 Malignant


title: Patient T11 Fibroblast


title: Patient T14 Endothelial rerun


title: Patient T6 Pan immune


title: Patient T6 Endothelial


title: Patient T5 Bulk


title: Patient T6 Malignant


title: Patient T5 Pan immune


title: Patient T6 Fibroblast


title: Patient T10 Malignant


title: Patient T9 Malignant


title: Patient T8 Endothelial


title: Patient T4 Bulk


title: Patient T4 Pan immune


title: Patient T5 Malignant


title: Patient T5 Fibroblast


title: Patient T8 Pan immune


title: Patient T5 Endothelial


title: Patient T4 Endothelial


title: Patient T3 Bulk


title: Patient T4 Fibroblast


title: Patient T3 Pan immune


title: Patient T8 Malignant


title: Patient T3 Endothelial


title: Patient T3 Fibroblast


title: Patient T3 Malignant


title: Patient T6 Bulk


title: Patient T2 Endothelial

value: NOS


title: Patient T2 Pan immune

value: Pan immune


title: Patient T2 Malignant


title: Patient T2 Fibroblast


title: Patient T1 Pan immune


title: Patient T1 Bulk


title: Patient T1 Fibroblast


title: Patient T1 Malignant rerun


title: Patient T1 Malignant


title: Stratagene reference replicate 6

source_name: Stratagene human reference RNA

value: Stratagene human reference RNA

value: Reference RNA


title: Patient T1 Endothelial


title: Stratagene reference replicate 5


title: Patient T4 Malignant

value: Squamous cell carcinoma


title: Stratagene reference replicate 3


title: Stratagene reference replicate 2


title: Stratagene reference replicate 1


title: Donor 1- Input DNA that underwent reverse crosslinking from purified primary AT2 cells

status: Public on Feb 07 2018

description: sonicated DNA

data_processing:
AT2 Sequencing data collection: Sequencing data for this study included that which our group generated for primary AT2 alveolar epithelial cells from Donor 1 and Donor2, described below, as well as publicly available pre-processed A549 lung adenocarcinoma ChIP-Seq data from the UCSC Genome Browser website (https://genome.ucsc.edu).  Data we generated in-house from highly pure populations of primary AT2 cells included ChIP-seq and whole-genome bisulfite sequencing (WGBS). Libraries and FASTQ files were generated at the USC Epigenome Center.
AT2 Sequencing data filtering and alignment: For single-end ChIP-seq sequencing data: we started from raw FASTQ files and used cutadapt-1.5(Martin 2011) to filter reads with a quality score below 20. Remaining high-quality reads were aligned to the reference human genome, hg19 assembly, using bowtie2 (Langmead 2012). For paired-end WGB sequencing data (WGBS), we first used cutadapt-1.5 to trim low-quality sequencing reads. Remaining reads were aligned to hg19 using bwa-0.7.7 mem (Li and Durbin 2010) with default parameters. WGBS data were aligned with BSMAP V 2.5(Xi and Li 2009).
AT2 ChIP-seq Peak calling: SICER (Zang et al. 2009) was applied with default parameters to call peaks for histone H3K27Ac & H3K4me1 ChIP-Seq. Window size and gap size for H3K27ac and H3K4me1 ChIP-seq were set to 200bp (FDR cutoff = 1 x 10-3).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contain the read density over the entire hg19-genome. Files have been binned into 30bp windows. BED files contain H3k4me1 and H3K27ac Peaks called in SICER (Zang et al. 2009).

source_name: donor lung

growth_protocol: Human AT1 and AT2 cells were isolated from two de-identified non-smoker remnant transplant lung as previously described and were used to obtain WGBS & histone mark ChIP data.

extract_protocol:
ChIP-seq on AT2 cells was performed as previously described(Marconett et al. 2013).
ChIP-Seq of AT2 cells from Donor 1 and Donor 2 in this Study. ChIP-seq of human AT2 cells from Donor1 and Donor2 in this study: Human AT2 cells underwent ChIP-seq using a modified version of the Sigma ChIP-it kit (Sigma). Specifically, 2 million human AT2 were used per ChIPseq of H3K27Ac (Cat # 39135, ActiveMotif), H3K4me1 (Cat # 39297, ActiveMotif). All cells were crosslinked with 3.75% formaldehyde at 25C for 5 minutes with gentle nutation. Fixation was quenched with 2.5mM glycine, then cells frozen at -80C until differentiation of all time points was complete. Each sample underwent nuclei fractionation using cell lysis buffer prepared per manufacturer’s recommendations. Upon nuclei isolation, cells were sonicated into fragments (average size 300bp) using a Bioruptor2000 (Diagenode) with 30-second pulses for a total of 30 minutes of sonication (15 on, 15 off). StaphSeq (Cat # S6576, Sigma) was used for antibody binding. All ChIPs were verified for enrichment by site-specific PCR prior to sequencing using the active region of PGDH for enhancer marks. All ChIP-seq samples underwent library preparation and sequencing at the USC Epigenomic Core. Samples were multiplexed using adapter barcoding and underwent single-end 50bp sequencing using the IlluminaHiSeq2000.
Whole genome bisulfite sequencing (WGBS) of AT2 cells from Donor 1 and Donor 2 in this Study. Total DNA from 8x10^6 Donor 1 and Donor 2 AT2 cells in this study was isolated using the Illustra Triple Prep kit (GE LifeSciences, Piscataway NJ). Four μg of sample genomic DNA was sonicated using a Covaris S2 to an average molecular weight of 150 bp.   Achievement of the desired size range was verified by Bioanalyzer (Agilent) analysis. Fragmented DNA was repaired to generate blunt ends using the END-It kit (Epicentre Biotechnologies, Madison, WI) according to manufacturer’s instructions.  Following incubation, the treated DNA was purified using AmpureX beads from Agencourt.  In general, magnetic beads were employed for all nucleic acid purifications in the following protocol.  Following end repair, A-tailing was performed using the NEB dA-tailing module according to manufacturer’s instructions (New England Biolabs, Ipswich, MA). Adapters with a 3’ ‘T’ overhang were then ligated to the end-modified DNA.  For whole genome bisulfite sequencing, modified Illumina paired-end (PE) adapters were used in which cytosine bases in the adapter are replaced with 5-methylcytosine bases. Ligation was carried out using ultrapure, rapid T4 ligase (Enzymatics, Beverly, MA) according to manufacturer’s instructions.  The final product was then purified with magnetic beads to yield an adapter-ligation mix. Prior to bisulfite conversion, bacteriophage lambda DNA that had been through the same library preparation protocol described above to generate adapter-ligation mixes was combined with the genomic sample adapter ligation mix at 0.5% w/w.  Adapter-ligation mixes were then bisulfite converted using the Zymo DNA Methylation Gold kit (Zymo Research, Orange, CA) according to the manufacturer’s recommendations. Final modified product was purified by magnetic beads and eluted in a final volume of 20 ul. Amplification of one-half the adapter-ligated library was performed using Kapa HiFi-U Ready Mix for the following protocol: 98° 2’, Then six cycles of: 98° 30”, 65° 15”, 72° 60”, with a final 72° 10’ extension, in a 50 ul total volume reaction. Final library product was examined on the Agilent Bioanalyzer, then quantified using the Kapa Biosystems Library Quantification kit according to manufacturer’s instructions.   Optimal concentrations to get the right cluster density were determined empirically but tended to be higher than for non-bisulfite libraries.  Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Donor 1 samples underwent Paired End 100 cycling; Donor 2 and 3 samples underwent Paired End 75 cycling. Image analysis and basecalling were carried out using RTA 1.13.48.0, deconvolution and fastq file generation were carried out using CASAVA_v1.7.1a5. Alignment to the genome was carried out using bsmap V 2.5.
Libraries were prepared at the USC Epigenome Core as previously  described (Marconett, 2013).

value: purified primary alveolar epithelial type 2 cells


title: Donor 2- ChIPseq of H3K27Ac in purified primary AT2 cells

description: sonicated and immunoprecipitated DNA


title: Donor 2- Input DNA that underwent reverse crosslinking from purified primary AT2 cells

description: sonicated DNA


title: Donor 1- ChIPseq of H3K4me1 in purified primary AT2 cells

description: sonicated and immunoprecipitated DNA


title: Donor 2- ChIPseq of H3K4me1 in purified primary AT2 cells

description: sonicated and immunoprecipitated DNA


title: Stratagene reference replicate 4


title: Donor 1- ChIPseq of H3K27Ac in purified primary AT2 cells

description: sonicated and immunoprecipitated DNA


title: Donor2-WGBS library from purified primary AT2 cells

description: Bisulfite-converted DNA


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 2 weeks Replicate 2

data_processing:
Image analysis and basecalling were carried out using RTA 1.13.48.0, deconvolution and fastq file generation were carried out using CASAVA_v1.7.1a5.
RNAseq fastq files were aligned to the hg19  genome using tophat2-2.0.9.
Genome_build: hg19
Supplementary_files_format_and_content: Tophat FPKM values

extract_protocol:
RNA was isolated from treated A549 cells using the Illustra TriplePrep Kit from GE.
RNA was isolated from treated A549 cells grown on 15cm plates using the GE TriplePrep kit (Cat# 28-9425-44, Pittsburgh PA). 2ug of RNA was made into libraries using the Illumina (Madison WI) Ribo-Zero™ Gold Magnetic Kit (MRZG 12324) and sequenced using the Illumina HiSeq2000 at the University of Southern California Epigenome Center Core. Basecalls were converted into FASTQ files and aligned to the hg19 genome using tophat2-2.0.9 through Illumina Basespace.
2ug of RNA was made into libraries using the Illumina (Madison WI) Ribo-Zero™ Gold Magnetic Kit (MRZG 12324)

value: A549 Lung Adenocarcinoma cells

tag: stress

value: Cigarette smoke condensate (CSC)

tag: time

value: 2 weeks


title: A549 RNAseq: DMSO vehicle treated for 48 Hours Replicate 2

source_name: DMSO vehicle treated for 48 Hours

value: DMSO

value: 48 hours


title: PLASMA, sample 2251 [reference set]

status: Public on Jan 14 2018

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

description: Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'
Average beta

label: biotin/DNP

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: methylation class

value: PLASMA

tag: material

value: FFPE


title: PLASMA, sample 2237 [reference set]


title: A549 RNAseq: DMSO vehicle treated for 48 Hours Replicate 3


title: A549 RNAseq: DMSO vehicle treated for 2 weeks Replicate 2

source_name: DMSO vehicle treated for 2 weeks


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 48 Hours Replicate 1


title: PLASMA, sample 2257 [reference set]


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 2 weeks Replicate 1


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 48 Hours Replicate 3


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 2 weeks Replicate 3


title: LYMPHO, sample 961 [validation set]

status: Public on Jan 18 2018

description:
SAMPLE 961
Methylation data from brain tumor sample.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'.

value: brain tumor

value: LYMPHO


title: A549 RNAseq: DMSO vehicle treated for 2 weeks Replicate 1


title: A549 RNAseq: 20uM Cigarette smoke condensate (CSC) treated for 48 Hours Replicate 2


title: A549 RNAseq: DMSO vehicle treated for 2 weeks Replicate 3


title: Donor1-WGBS library from purified primary AT2 cells

description: Bisulfite-converted DNA

tag: cell type


title: PLASMA, sample 1796 [reference set]


title: LYMPHO, sample 2350 [reference set]


title: PLASMA, sample 2328 [reference set]


title: LYMPHO, sample 792 [reference set]


title: LYMPHO, sample 854 [reference set]


title: PLASMA, sample 1602 [reference set]


title: LYMPHO, sample 791 [reference set]


title: LYMPHO, sample 1351 [reference set]


title: PLASMA, sample 2300 [reference set]


title: LYMPHO, sample 2771 [reference set]


title: HD3_C-TALE rep2

status: Public on Jul 12 2017

city: Cambridge

first: Aleksandra

last: Galitsyna

state: Massachusetts

address: 77 Massachusetts Avenue

department: IMES

institute: Massachusetts Institute of Technology

description:
C-TALE DNA library
HD3.raw_heatmap.txt
HD3.heatmap.txt

data_processing:
Library strategy: C-TALE
[C-TALE] Illumina HiSeq 2500 bcl2fastq v1.8.4 Conversion Software was used for base-calling
[C-TALE] Reads were aligned independently with hiclib iterative mapping procedure (minimal mapping length 25, iteration step 5) and Bowtie 2 version 2.2.1 to the region 11700000-12450000 of chromosome 14
[C-TALE] The reads mapped in close proximity to DpnII restriction sites (5 bp) and possible PCR duplicates were eliminated. Reads mapped to extremely short (<100 bp) and long (>100 Kb) fragments were filtered out.
[C-TALE] Read pairs that were both uniquely mapped and passed filtering procedure were retained. Resulting pairs were binned into 5 Kb genomic windows of the region of interest. The maps were iteratively corrected.
Genome_build: galgal4
Supplementary_files_format_and_content: [C-TALE] Processed data files are maps of raw and iteratively corrected interactions of 5 Kb genome region bins in tab-delimited text format.

organism: Gallus gallus

source_name: cultured erythroid cells

growth_protocol: The avian erythroblastosis virus-transformed chicken (Gallus gallus) erythroblast cell line HD3 (clone A6 of line LSCC and the DT40 lymphoid cell line (CRL-2111, ATCC) were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 2% chicken serum (CS) and 8% fetal bovine serum (FBS) at 37 °C with 5% CO2

extract_protocol:
Hi-C libraries suitable for the downstream application in the C-TALE protocol were prepared as described previously (Belton et al. 2012), with the minor modifications described below. A total of 3-5 million cells were fixed with 1% formaldehyde (Sigma) in DMEM geowth medium for 10 min at room temperature. The reaction was stopped by adding 2 M glycine to a final concentration of 125 mM. The cell suspension was incubated on ice for 5 min, and the cells were pelleted (10 min at 1000 x g in a pre-chilled (4oC) centrifuge). The supernatant was removed, and the cell pellet was washed with 500 μl of 1× PBS, frozen and, if necessary, stored in a liquid nitrogen. After thawing, the cells were lysed for 15 min in 1.5 ml of ice-cold lysis buffer (50 mM Tris-HCl (pH8.0), 150 mM NaCl, 0.5% (v/v) NP-40, 1% (v/v) Triton-X100, 1× Protease Inhibitor Cocktail (CALBIOCHEM #539137 of Thermo Scientific #78430)). The nuclei were harvested at 5000 x g for 7 min in a pre-chilled centrifuge, washed twice with 100 μl of 1.2× DpnII reaction buffer  (NEB) and resuspended in 200 μl of 1.2× DpnII reaction buffer. Then, 20% SDS was added to a final concentration of 0.3%, and the nuclei were incubated at 37oC for 1 h with constant shaking. After incubation, 330 μl of 1.2× DpnII reaction buffer was added, 20% Triton X-100 was added to a final concentration of 1.8%, and the samples were incubated for 1 h under the same conditions. DNA was digested overnight with 600-800 U of 50 U/μl DpnII restriction endonuclease (NEB) at 37oC with shaking. The next morning, 200 U of DpnII was added, and the samples were incubated for 2 h under the same conditions. The nuclei were harvested for 10 min at 5000 x g and 25oC and resuspended in 50 μl of 1× NEBuffer 2. Cohesive DNA ends were biotinylated by adding 7.6 μl of the biotin fill-in mixture prepared in 1× NEBuffer 2 (0.025 mM dATP (Thermo Scientific), 0.025 mM dGTP (Thermo Scientific), 0.025 mM dTTP (Thermo Scientific), 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/μl Klenow enzyme (NEB)). The samples were incubated at 37oC for 75 min with slow shaking, and 20% SDS was added to a final concentration of 1.8%; the samples were heated at 65oC for 20 min to inactivate the Klenow enzyme and residual DpnII. The samples were transferred into 10-ml tubes with 3 ml of 1× T4 DNA ligase reaction buffer (Thermo Scientific) supplied with 1.8% Triton X-100, incubated at 37oC for 1 h and then cooled on ice. Next, 100 U of T4 DNA ligase (Thermo Scientific) was added, and the DNA was ligated for 6 h at 22oC with slow agitation. The cross-links were reversed by overnight incubation at 65oC in the presence of proteinase K (100 μg/ml). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction followed by ethanol precipitation (tRNA (Sigma) at a concentration of 7.5 μg/ml and glycogen (Thermo Scientific) at a concentration of 20 μg/ml were used as co-precipitators due to the low amount of DNA in the samples). After precipitation, the pellets were dissolved in 500 μl 10 mM Tris-HCl pH 8.0. To remove residual salts and DTT, the DNA was additionally purified using AMICON Ultra Centrifugal Filter Units (0.5 ml, 30 K, Millipore #UFC5030BK) by washing with 10 mM Tris-HCl pH 8.0 (after two washing steps, the final volume of the DNA solution was 40-50 μl). Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries in the presence of 1.5 U of T4 DNA polymerase (NEB) in NEBuffer 2 supplied with 0.025 mM dATP and 0.025 mM dTTP at 20oC for 4 h. Next, the DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA pellets were dissolved in 500 μl of sonication buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 0.1% SDS) and treated with 50 μg of RNase A (Thermo Scientific) for 45 min at 37oC; the DNA was then sheared to a size of approximately 100-1000 bp using a VirSonic 100 (VerTis). The samples were concentrated (and simultaneously purified) using AMICON Ultra Centrifugal Filter Units. The fraction of 100-500-bp DNA fragments was captured using Agencourt AMPure XP beads (Beckman Coulter), and the fragments were eluted with 50 μl of 10 mM Tris-HCl (pH 8.0). The DNA ends were repaired by adding 62.5 μl MQ water, 14 μl of 10× T4 DNA ligase reaction buffer, 3.5 μl of 10 mM dNTP mix, 5 μl of 3 U/μl T4 DNA polymerase (NEB), 5 μl of 10 U/μl T4 polynucleotide kinase (NEB), and 1 μl of 5 U/μl Klenow DNA polymerase (NEB) and incubating at 20oC for 30 min. The DNA was purified with Agencourt AMPure XP beads and eluted with 50 μl of 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, the DNA samples were supplemented with 6 μl 10× NEBuffer 2, 1.2 μl of 10 mM dATP, 1 μl of MQ water and 3.6 μl of 5 U/μl Klenow (exo-) (NEB). The reactions were carried out for 30 min at 37oC in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65oC for 20 min. The DNA was purified using Agencourt AMPure XP beads and eluted with 100 μl of 10 mM Tris-HCl (pH 8.0). Biotin pull-down of the ligation junctions was performed as described previously, with minor modifications. Briefly, 4 μl of MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads with captured ligation junctions were resuspended in 50 μl of adapter ligation mixture composed of 41.5 μl MQ water, 5 μl 10× T4 DNA ligase reaction buffer (Thermo Scientific), 2.5 μl of Illumina TruSeq adapters and 1 μl of 5 U/μl T4 DNA ligase (Thermo Scientific). Adapter ligation was performed at 22oC for 2.5 h, and the beads were sequentially washed twice with 100 μl of TWB (5 mM Tris-HCl (pH8.0), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), once with 100 μl of 1× binding buffer (10 mM Tris-HCl (pH8.0), 1 mM EDTA, 2 M NaCl) and once with 100 μl of CWB (10 mM Tris-HCl (pH 8.0) and 50 mM NaCl) and then resuspended in 20 μl of MQ water. Test PCR reactions containing 4 μl of the streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles needed to generate enough PCR products for downstream applications. The PCR reactions (volume of each reaction is 25 μl) were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98oC, followed by 6, 9, 12, 15 and 18 cycles of 20 s at 98oC, 15 s at 65oC, and 20 s at 72oC. The PCR reactions were separated on a 2% agarose gel supplied with ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 12-15 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined, and the products were purified with QIAGEN PCR Purification Kit. The DNA was eluted with 50 μl of 10 mM Tris-HCl (pH 8.0) and separated on a 1.8% agarose gel supplied with ethidium bromide; 200-600-bp fragments were excised from the gel, purified using QIAGEN Gel Extraction Kit
C-TALE libraries were prepared in two independent biological replicates. At the first step, in situ DpnII-Hi-C libraries suitable for sequencing on Illumina HiSeq platform were prepared from each cell type according to previously published protocol [4]. Next, we produced hybridization baits using BACs CH261-93N17, CH261-75C12 and CH261-85E12 (CHORI BACPAC) covering the genomic region chr14:11721574-12436767. BACs purified from overnight shaker-cultures were mixed in an equimolar ratio (totally 5 μg) in 500 μl of sonication buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.1% SDS), incubated on ice for 20 min, and the DNA was then sheared to a size of approximately 200-600 bp using a VirSonic 100 (VerTis). The sample was centrifuged at 13400 g for 5 min and concentrated on AMICON Ultra Centrifugal Filter Units (30K). The DNA was purified using Agencourt AMPu

treatment_protocol: To induce terminal erythroid differentiation, HD3 cells at a density of 8 × 10^5 cells/ml were incubated in the growth medium containing 10 mM HEPES (pH 8.0) and 20 μM iso-H-7 (1-(5-Isoquinolinylsulfonyl)-3-methylpiperazine dihydrochloride, Fluka, Seelze, Germany) at 42°C in 100% air atmosphere for 14 hours

tag: developmental stage

value: adult

value: Avian erythroblastosis virus-transformed erythroblast cell line (clone A6 of line LSCC)


title: HD3_C-TALE rep1


title: HD3ind_C-TALE rep2

description:
C-TALE DNA library
HD3ind.raw_heatmap.txt
HD3ind.heatmap.txt

source_name: terminally differentiated HD3 cells

value: Terminally differentiated (producing hemoglobin) HD3 cells


title: HD3ind_5C_rep2

description: 5C DNA library

data_processing:
Library strategy: 5C (carbon-copy 3C)
[5C] Illumina HiSeq 2500 bcl2fastq v1.8.4 Conversion Software was used for base-calling
[5C] Reads were divided in two parts and checked for the presence of HindIII restriction site, then two parts were aligned independently with Bowtie 2 version 2.2.1
[5C] Primers were checked to have non-zero interactions in all experiments.
[RNA-Seq] Illumina Casava 1.8.2 was used for base-calling
[RNA-seq] Reads were mapped to the G. gallus reference genome (version galGal4) and ENSEMBL gene annotation using TopHat v2.0.12 with options --no-novel-juncs.
[RNA-seq] Htseq-counts v0.6.0 was used to calculate per gene counts.
[RNA-seq]BedTools v2.16.2 was used to calculate to calculate read coverage.
Genome_build: galgal4
Supplementary_files_format_and_content: [5C] Processed data files are maps of primers interactions in tab-delimited text format.
Supplementary_files_format_and_content: [RNA-seq] Processed data files are tab-delimited text files reporting raw read counts. Each file with raw read counts for genes has two columns: (1) gene ENSEMBL ID and (2) read count. Each file with genome coverage has 4 columns: (1) chromosome, (2) left coordinate of genome fragment, (3) right coordinate of genome fragment, (4) read count for this fragment

extract_protocol:
Libraries of proximity ligation products were prepared as described previously (Hagege et al. 2007). Briefly, a total of 10 millions cells were pelleted and resuspended in 10 ml of DMEM supplemented with 8% of FBS and 2% of CS and fixed with 1% formaldehyde (Sigma) for 10 min at room temperature. The reaction was stopped by adding 2 M glycine to a final concentration of 125 mM. The cell suspension was incubated on ice for 5 min, and the cells were pelleted (10 min at 1000 x g in a pre-chilled (4oC) centrifuge). The supernatant was removed, and the cell pellet was washed with 1 ml of ice-cold 1× PBS. The cells were lysed for 15 min in 10 ml of ice-cold lysis buffer (50 mM Tris-HCl (pH8.0), 150 mM NaCl, 0.5% (v/v) NP-40, 1% (v/v) Triton-X100, 1× Protease Inhibitor Cocktail (Thermo Scientific #78430)). The nuclei were harvested at 1000 x g for 7 min in a pre-chilled centrifuge, washed twice with 100 μl of 1.2× restriction NEBuffer 2 (NEB) and resuspended in 200 μl of 1.2× NEBuffer 2. Then, 20% SDS was added to a final concentration of 0.3%, and the nuclei were incubated at 37oC for 1 h with constant shaking. After incubation, 330 μl of 1.2× NEBuffer 2 was added, 20% Triton X-100 was added to a final concentration of 1.8%, and the samples were incubated for 1 h under the same conditions. DNA was digested overnight with 600-800 U of 100 U/μl HindIII-HF restriction endonuclease (NEB) at 37oC with shaking. The next morning, 200 U of HindIII-HF was added, and the samples were incubated for 2 h under the same conditions. 20% SDS was added to a final concentration of 1.8% and the samples were heated at 65oC for 20 min to inactivate the restriction enzyme. The samples were transferred into 50-ml tubes with 6.5 ml of 1.07× T4 DNA ligase reaction buffer (Thermo Scientific) supplied with 1.8% Triton X-100, incubated at 37oC for 1 h and then cooled on ice. Next, 100 U of T4 DNA ligase (Thermo Scientific) was added, and the DNA was ligated for 6 h at 16oC with slow agitation. The cross-links were reversed by overnight incubation at 65oC in the presence of proteinase K (100 μg/ml). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction followed by ethanol precipitation (glycogen (Thermo Scientific) at a concentration of 20 μg/ml was used as co-precipitator). After precipitation, the pellets were dissolved in 500 μl 10 mM Tris-HCl pH 8.0. To remove residual salts and DTT, the DNA was additionally purified using AMICON Ultra Centrifugal Filter Units (0.5 ml, 30 K, Millipore #UFC5030BK) by washing with 10 mM Tris-HCl pH 8.0 (after two washing steps, the final volume of the DNA solution was 40-50 μl). DNA concentration was measured on Qubit fluorometer (Invitrogen).
5C libraries were prepared in two biological replicates as described previously (Dostie and Dekker, 2007) with minor modifications. Briefly, 5C primer stocks (17 mM) were mixed and diluted in water to a final concentration of 1.7 nM of each primer. 5C primers were mixed with 3C libraries in 10 μl of annealing mixtures of the following composition: 1 μl of annealing buffer (10× NEBuffer 4 (NEB)), 1.7 μl of 5C primer mix, 600 ng of 3C library, 900 ng of salmon testis DNA and MQ water. Samples were denatured for 5 min at 95°C and annealed for 16 h at 57°C. Ligation with 10 U of Taq DNA ligase was performed for 1 h at 57°C. 2 μl of each 5C library was then PCR-amplified individually with primers to T7- and T3-tails using KAPA High Fidelity DNA Polymerase (KAPA). The temperature profile was 5 min at 98oC, followed by 22, 24, 26, 28 and 30 cycles of 20 s at 98oC, 15 s at 65oC, and 20 s at 72oC. The PCR reactions were separated on a 2% agarose gel supplied with ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 28-30 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined, and the products were purified with QIAGEN PCR Purification Kit. The DNA was eluted with 50 μl of 10 mM Tris-HCl (pH 8.0) and separated on a 1.8% agarose gel supplied with ethidium bromide; 100-bp fragments were excised from the gel, purified using QIAGEN Gel Extraction Kit and sequenced with an Illumina HiSeq 2000 by single-end 101-nt reads.


title: DT40_C-TALE rep1

description:
C-TALE DNA library
DT40.raw_heatmap.txt
DT40.heatmap.txt

source_name: cultured lymphoid cells

value: Avian leukosis virus (ALV) induced bursal lymphoma cell line derived from a Hyline SC chicken


title: DT40_C-TALE rep2


title: DT40_5C_rep2

description: 5C DNA library


title: DT40_5C_rep1

description: 5C DNA library


title: HD3ind_RNA-Seq_rep2

description: Total ribosomal RNA-depleted cellular RNA

data_processing:
[5C] Illumina HiSeq 2500 bcl2fastq v1.8.4 Conversion Software was used for base-calling
[5C] Reads were divided in two parts and checked for the presence of HindIII restriction site, then two parts were aligned independently with Bowtie 2 version 2.2.1
[5C] Primers were checked to have non-zero interactions in all experiments.
[RNA-Seq] Illumina Casava 1.8.2 was used for base-calling
[RNA-seq] Reads were mapped to the G. gallus reference genome (version galGal4) and ENSEMBL gene annotation using TopHat v2.0.12 with options --no-novel-juncs.
[RNA-seq] Htseq-counts v0.6.0 was used to calculate per gene counts.
[RNA-seq]BedTools v2.16.2 was used to calculate to calculate read coverage.
Genome_build: galgal4
Supplementary_files_format_and_content: [5C] Processed data files are maps of primers interactions in tab-delimited text format.
Supplementary_files_format_and_content: [RNA-seq] Processed data files are tab-delimited text files reporting raw read counts. Each file with raw read counts for genes has two columns: (1) gene ENSEMBL ID and (2) read count. Each file with genome coverage has 4 columns: (1) chromosome, (2) left coordinate of genome fragment, (3) right coordinate of genome fragment, (4) read count for this fragment

extract_protocol:
Total RNA was extracted from the cells using TRIzol Reagent (Thermo Scientific #15596-026) according to manufacturer`s protocol
Total RNA was depleted with ribosomal RNA using RiboZero Human/Mouse Kit (Illumina). For library preparation,TruSeq Stranded RNA Sample Prep kit (Illumina, USA) was used following manufacturer's instructions. After preparation, the quality of the libraries were checked using quantitative PCR and Bioanalyser


title: HD3_5C_rep1

description: 5C DNA library


title: HD3ind_RNA-Seq_rep1


title: HD3ind_C-TALE rep1


title: DT40_RNA-Seq_rep2


title: HD3_5C_rep2

description: 5C DNA library


title: HD3ind_5C_rep1

description: 5C DNA library


title: adult_rep1

description: 5С DNA library

data_processing:
[5C] Illumina HiSeq 2000 bcl2fastq v1.8.4 Conversion Software was used for base-calling
[5C] Reads were divided in two parts and checked for the presence of MboI restriction site, then two parts were aligned independently with Bowtie 2 version 2.2.2
[5C] Primers were checked to have non-zero interactions in all experiments.
Genome_build: danrer7
Supplementary_files_format_and_content: [5C] Processed data files are maps of primers interactions in tab-delimited text format.

organism: Danio rerio

source_name: adult

growth_protocol: Blood was extracted from 18 dpf zebrafishes or adult fishes. Fishes were euthanized by an overdose of tricaine (ethyl 3-aminobenzoate methanesulfonate, 100 mg/L)

extract_protocol:
For the 3C library preparation, blood was extracted from 18 dpf zebrafishes or adult fishes. Fishes were euthanized by an overdose of tricaine (ethyl 3-aminobenzoate methanesulfonate, 100 mg/L). For each 3C experiment, a minimum of 107 cells was used. The blood was collected into red cell isolation buffer (0.14 M NaCl, 20 mM HEPES pH 8.0, 5% fetal bovine serum, and 100 U heparin/mL) and fixed with 2% formaldehyde (Sigma) for 10 min at room temperature. The reaction was stopped by adding glycine to a final concentration of 125 mM. All downstream manipulations were performed essentially as described previously (Gavrilov et al. 2008).
5C libraries were prepared in two biological replicates as described previously {Dostie, 2007 #2674}. 5C primer stocks were mixed and diluted to a final concentration of 1.7 nM of each primer. Ten microliters of annealing mixture included the following components: 1 μl of 10×NEBuffer 4 (NEB); 1.7 μl of 5C primer mix; 350 ng of 3C library; 1150 ng of salmon testis DNA (Sigma); and mQ water. Samples were denatured for 5 min at 95°C and annealed for 16 h at 46°C and then ligation in 1×Taq DNA ligase buffer with 10 U of Taq DNA ligase (NEB) was performed for 1 h at 46°C. A total of 2 μl of each 5C library was then PCR-amplified individually with primers to the T7- and T3-tails using KAPA High Fidelity DNA Polymerase (KAPA); 28 PCR cycles were necessary to obtain a sufficient amount of DNA. The PCR mixtures were combined, and the products were purified with a QIAGEN PCR Purification Kit. The DNA was eluted with 50 μl of 10 mM Tris-HCl (pH 8.0) and separated on a 1.8% agarose gel supplied with ethidium bromide; 100 bp fragments were excised from the gel, purified using a QIAGEN Gel Extraction Kit and sequenced on Illumina HiSeq 2000 using single-end 101 bp reads.

value: adult danio

value: blood cells

tag: library strategy

value: 5C (carbon-copy 3C)


title: larvae_rep2

description: 5С DNA library

source_name: larvae

value: larvae danio


title: larvae_rep1

description: 5С DNA library


title: AT2 WGBS Donor 1

status: Public on Nov 06 2016

description: Bisulfite-treated DNA

data_processing:
Image analysis and basecalling were carried out using RTA 1.13.48.0, deconvolution and fastq file generation were carried out using CASAVA_v1.7.1a5.
WGBS fastq files were aligned to the hg19 BS genome using BSmap2.0. ChIPseq Fastq files were aligned to the genome using BWA0.6.2.
ChIPseq data underwent .bam to .bed format conversion and peaks were called using the SICER peakcalling program.
Genome_build: hg19
Supplementary_files_format_and_content: .fastq files are raw sequence, .bw files are wiggle tracks designed to display the enrichment of ChIPseq regions, .txt peak calling files are the locations of called peaks.

source_name: Whole genome bisulfite sequencing

extract_protocol:
DNA was isolated from freshly isolated primary AT2 cells using the Illustra TriplePrep Kit.
WGBS libraries were made by the USC Epigenome Center. 4 μg of sample genomic DNA was sonicated using a Covaris S2 to an average molecular weight of 150 bp.   Achievement of the desired size range was verified by Bioanalyzer (Agilent) analysis. Fragmented DNA was repaired to generate blunt ends using the END-It kit (Epicentre Biotechnologies, Madison, WI) according to manufacturer’s instructions.  Following incubation, the treated DNA was purified using AmpureX beads from Agencourt.  In general, magnetic beads were employed for all nucleic acid purifications in the following protocol.  Following end repair, A-tailing was performed using the NEB dA-tailing module according to manufacturer’s instructions (New England Biolabs, Ipswich, MA). Adapters with a 3’ ‘T’ overhang were then ligated to the end-modified DNA.  For whole genome bisulfite sequencing, modified Illumina paired-end (PE) adapters were used in which cytosine bases in the adapter are replaced with 5-methylcytosine bases. Ligation was carried out using ultrapure, rapid T4 ligase (Enzymatics, Beverly, MA) according to manufacturer’s instructions.  The final product was then purified with magnetic beads to yield an adapter-ligation mix. Prior to bisulfite conversion, bacteriophage lambda DNA that had been through the same library preparation protocol described above to generate adapter-ligation mixes was combined with the genomic sample adapter ligation mix at 0.5% w/w.  Adapter-ligation mixes were then bisulfite converted using the Zymo DNA Methylation Gold kit (Zymo Research, Orange, CA) according to the manufacturer’s recommendations. Final modified product was purified by magnetic beads and eluted in a final volume of 20 ul. Amplification of one-half the adapter-ligated library was performed using Kapa HiFi-U Ready Mix for the following protocol: 98° 2’, Then six cycles of: 98° 30”, 65° 15”, 72° 60”, with a final 72° 10’ extension, in a 50 ul total volume reaction. Final library product was examined on the Agilent Bioanalyzer, then quantified using the Kapa Biosystems Library Quantification kit according to manufacturer’s instructions.   Optimal concentrations to get the right cluster density were determined empirically but tended to be higher than for non-bisulfite libraries.  Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Rep 1 underwent Paired End 100 cycling; rep 2 underwent Paired End 75 cycling.

value: purified AT2 cells

value: Donor 1


title: adult_rep2

description: 5С DNA library


title: AT2 WGBS Donor 2 -Run2

description: Bisulfite-treated DNA

value: Donor 2


title: AT2 WGBS Donor 2 -Run1

description: Bisulfite-treated DNA


title: RNAseq_Donor2_AT2_cells

status: Public on Nov 03 2016

data_processing:
Image analysis and basecalling were carried out using RTA 1.13.48.0, deconvolution and fastq file generation were carried out using CASAVA_v1.7.1a5.
RNAseq fastq files were aligned to the hg19 genome using tophat2-2.0.8b. ChIPseq Fastq files were aligned to the genome using BWA0.6.2.
Genome_build: hg19
Supplementary_files_format_and_content: .fastq files are raw sequence. BigWig (bw) files are wiggle tracks designed to display the enrichment of ChIPseq regions.

source_name: Purified AT2 cells Donor 2

extract_protocol:
RNA was isolated from freshly isolated primary AT2 cells using the Illustra TriplePrep Kit.
RNA was isolated from 1million human AT2 or in vitro differentiated AT1-like cells using the GE TriplePrep kit (Cat# 28-9425-44, Pittsburgh PA). 2ug of RNA was made into libraries using the Illumina (Madison WI) Ribo-Zero™ Gold Magnetic Kit (MRZG 12324) and sequenced using the Illumina HiSeq2000 at the University of Southern California Epigenome Center Core. Basecalls were converted into FASTQ files and aligned to the hg19 genome using tophat2-2.0.8b.

value: alveolar epithelial type 2


title: LYMPHO, sample 794 [reference set]


title: RNAseq_Donor1_AT1-like_cells

source_name: Purified AT1-like cells Donor 1

extract_protocol:
RNA was isolated from in vitro differentiated AT1-like cells using the Illustra TriplePrep Kit.
RNA was isolated from 1million human AT2 or in vitro differentiated AT1-like cells using the GE TriplePrep kit (Cat# 28-9425-44, Pittsburgh PA). 2ug of RNA was made into libraries using the Illumina (Madison WI) Ribo-Zero™ Gold Magnetic Kit (MRZG 12324) and sequenced using the Illumina HiSeq2000 at the University of Southern California Epigenome Center Core. Basecalls were converted into FASTQ files and aligned to the hg19 genome using tophat2-2.0.8b.

value: alveolar epithelial type 1


title: RNAseq_Donor2_AT1-like_cells

source_name: Purified AT1-like cells Donor 2


title: HD3_RNA-Seq_rep2


title: HD3_RNA-Seq_rep1


title: DT40_RNA-Seq_rep1


title: PLASMA, sample 2329 [reference set]

value: PLASMA


title: RNAseq_Donor1_AT2_cells

source_name: Purified AT2 cells Donor 1


title: Lavage [5700760021_K]

type: RNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadStudio was used to convert images to raw signal data.

data_processing: Using R (version 2.11.1), quality was accessed using the LUMI package PMID: 18467348). Analysis included the 21 samples listed here and GEO dataset GSE38570, which were analyzed together. Of the 36 measured samples, 4 were of a poor technical quality and removed from downstream normalization and analysis. The poor data quality samples were: 5700760018_C (Pancreas),5700760021_H (Fibroblasts), 5700760018_G (Buffy Coat), and 5700760021_J (AEC pure AT1).  Normalization was performed with VSN using LUMI  to allow for a large number of significantly differentially expressed genes. Statistical analyses were performed using LIMMA (PMID: 15297296). An unpaired T-test with Benjamini-Hochberg (BH) correction (Benjamini & Hochberg, 1995) was used to control for FDR.

label: biotin

organism: Rattus norvegicus

source_name: Whole Tissue RNA

label_protocol: IlluminaTotalPrep RNA kit

growth_protocol: RNA was harvested from primary rat tissue and purified AT1 cells.

extract_protocol: pure rat AT1 cells were isolated as previously described (PMC2793185). Tissues were isolated as previously described (PMID: 2440339).

treatment_protocol: Differentiating in culture over time, no extra treatments added.

tag: strain background

value: Sprague-Dawley

tag: gender

value: male

tag: tissue/cell type

value: Lavage


title: Skeletal Muscle [5700760018_J]

value: Skeletal Muscle


title: Testis [5700760021_E]

value: Testis


title: Kidney [5700760018_D]

value: Kidney


title: AEC pure AT1 [5665175063_L]

source_name: Alveolar Epithelial Cells

value: Alveolar Epithelial Cells


title: Spleen [5700760018_K]

value: Spleen


title: Colon [5700760018_L]

value: Colon


title: Illium [5700760021_C]

value: Illium


title: Skin [5700760018_E]

value: Skin


title: Heart [5700760021_L]

value: Heart


title: Trachea [5700760021_B]

value: Trachea


title: Salivary glands [5700760018_H]

value: Salivary glands


title: Liver [5700760018_B]

value: Liver


title: Duodenum [5700760018_I]

value: Duodenum


title: KO5

status: Public on Jan 15 2016

hyb_protocol: Standard Illumina hybridization protocol.

data_processing: Data were imported into BeadStudio and raw signal data exported for analysis. Using the software R, probes were filtered using reannotation data from reMOAT, specifically filtering out probes matching to the wrong sequence, non-matching probes, and those with SNPs. Preprocessing of raw data revealed that one knockout lung sample was a technical failure, which was not used in subsequent analysis. Background correction using variance stabilizing transformation (VST) and quantile normalization were performed using the LUMI package in R. Heatmaps were generated in R by selecting the top 5% of variant probes and clustering samples, and probes with average linkage. A strict 2-fold cut-off was enforced to delineate genes with altered expression in the knockout. Pathway analysis was performed using Ingenuity Pathway Analysis (IPA) software (Ingenuity, Redwood City, CA), and pathways were ranked based on Benjamini-Hochberg (BH) corrected p-value of enrichment.

label: Biotin

source_name: Whole lung extract, cGrp78f/f

label_protocol: Total RNA was converted into cRNA and used for Illumina MouseRef-8 v2 whole genome expression analysis (Illumina, San Diego, CA).

growth_protocol: Whole lungs were homogenized in Trizol with a Polytron.

extract_protocol: One microgram of RNA from four Grp78f/f and three cGrp78f/f whole lungs was extracted using TriZol.

tag: mixed strain background

value: C57BL/6 (major); 129S6/SvEvTac (minor); ICR (minor)

tag: age

value: lung


title: KO4

tag: tissue


title: FF7-1

source_name: Whole lung extract, Grp78f/f


title: FF7-2


title: KO6


title: Brain [5700760021_G]

value: Sprague-Dawley

value: male

value: Brain


title: Stomach [5700760021_F]

value: Stomach


title: AEC pure AT1 [5665175063_F]


title: FF12


title: WildType_1

status: Public on Apr 06 2014

description: 5388884001_E_Replicate 1

data_processing: Background correction using variance stabilizing transformation (VST) and quantile normalization were performed using the LUMI package (v.1.14.0) in R v.2.11.1 (2010-05-31).

extract_protocol: 1μg of RNA from four replicates each from wildtype and claudin-18 knockout whole lung was converted into cRNA and was used for Illumina mouseRef-8 v2 whole genome expression analysis. Expression arrays were carried out at the Southern California Genotyping Consortium (SCGC) at the University of California, Los Angeles.

treatment_protocol: No treatment

value: mixed 129S6/SvEvTac, C57BL/6J, Balb/c

tag: genotype/variation

value: WildType

value: 3-4 months

value: Male

value: whole lung tissue


title: WildType_3

description: 5388884001_G_Replicate 3


title: CLDN18_KnockOut_2

description: 5388884001_B_Replicate 2


title: WildType_4

description: 5388884001_H_Replicate 4


title: FF2

value: C57BL/6 (major); 129S6/SvEvTac (minor); ICR (minor).


title: CLDN18_KnockOut_1

description: 5388884001_A_Replicate 1


title: AT cell D8 (AT1-like) X5626686013_L

status: Public on Apr 15 2013

description: AT cell D8 (AT1-like)

data_processing: Using R (version 2.11.1), normalization was performed with VSN using LUMI (Du et al., 2008) to allow for a large number of significantly differentially expressed genes. Statistical analyses were performed using LIMMA (Smyth, 2004). The most variant probes were selected and a linear regression model was fitted over the time-course of differentiation. Technical replicates were removed, and T-tests were performed between Day 0 samples and Day 8 samples. P-values were controlled for false-discovery using the Benjamini-Hochberg (BH) correction (Benjamini & Hochberg, 1995).

source_name: Alveolar Epithelial type 2 (AT2 cell)

growth_protocol: Remnant human transplant lungs were obtained in compliance with Institutional Review Board-approved protocols for the use of human source material in research (HS-07-00660) and processed within 3 days of death. Lung tissue was processed as previously described (Ballard et al., 2010) with inclusion of anti-EpCAM conjugated beads to select for epithelial cells.  Cells were plated in 50:50 [DMEM High glucose media (GIBCO 21063): DMEM-F12 (Sigma D6421)]. Differentiation into AT1-like cells was verified by measuring SFTPC and AQP5 expression.

extract_protocol: RNA was extracted with the Illustra TriplePrep Kit (GE LifeSciences, Piscataway, NJ).

value: AT cell (AT1-like)

tag: Sex

value: female

tag: age (y)

tag: smoker

value: non-smoker

tag: cod

value: CVA-Stroke


title: AT cell D4 X5626686013_J

description: AT cell D4

tag: time

value: AT cell


title: AT cell D0 (AT2) X5626686013_K

description: AT cell D0 (AT2)

value: AT cell (AT2)

value: ICH-Stroke


title: WildType_2

description: 5388884001_F_Replicate 2


title: AT cell D4 X5626686013_C

description: AT cell D4


title: CLDN18_KnockOut_3

description: 5388884001_D_Replicate 3


title: AT cell D0 (AT2) X5626686013_G

description: AT cell D0 (AT2)


title: AT cell D2 X5626686013_F

description: AT cell D2


title: AT cell D8 (AT1-like) X5626686013_I

description: AT cell D8 (AT1-like)


title: AT cell D2 X5626686013_H

description: AT cell D2


title: AT cell D6 X5626686013_E

description: AT cell D6


title: AT cell D0 (AT2) 5626686013_A

description: AT cell D0 (AT2)


title: AT cell D6 X5626686013_B

description: AT cell D6


title: AT cell D4 X5626686013_D

description: AT cell D4


title: AT cell D2 5626686051_H

description: AT cell D2

value: Anoxia


title: AT cell D8 (AT1-like) 5626686051_L

description: AT cell D8 (AT1-like)


title: genomic DNA from CD34+38+ of AML patient SU306

status: Public on Oct 01 2015

city: Baltimore

last: Feinberg

state: MD

address: 855 N. Wolfe St., Rangos 570

department: Medicine

institute: Johns Hopkins University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Minfi v1.8.9; beta values not normalized

source_name: CD34+38+ of AML patient

extract_protocol: Genomic DNA was extracted and purified from AML and normal bone marrow samples using Epicentre Kit according to standard instructions

tag: subject id

tag: subject status

value: AML

value: male

tag: phenotype

value: BLAST (blast cells)


title: AT cell D4 5626686051_C

description: AT cell D4

tag: cell type


title: genomic DNA from CD34- of AML patient SU014

source_name: CD34- of AML patient


title: genomic DNA from CD34- of AML patient SU266


title: AT cell D8 (AT1-like) 5665175063_J

description: AT cell D8 (AT1-like)

growth_protocol: Rat AT2 cells were isolated as previously described (Zhou et al., 2008; Borok et al., 1998).


title: AT cell D0 (AT2) 5700760021_A

description: AT cell D0 (AT2)


title: genomic DNA from CD34- of AML patient SU306


title: AT cell D8 (AT1-like) 5665175063_G

description: AT cell D8 (AT1-like)


title: AT cell D2 5700760018_A

description: AT cell D2


title: genomic DNA from CD34+38- of AML patient SU036

source_name: CD34+38- of AML patient


title: AT cell D0 (AT2) 5665175063_H

description: AT cell D0 (AT2)


title: AT cell D8 (AT1-like) 5700760021_I

description: AT cell D8 (AT1-like)


title: AT cell D0 (AT2) 5626686051_F

description: AT cell D0 (AT2)


title: AT cell D6 5700760021_D

description: AT cell D6


title: AT cell D4 5700760018_F

description: AT cell D4


title: AT cell D2 5665175063_D

description: AT cell D2


title: AT cell D4 5665175063_E

description: AT cell D4


title: AT cell D4 5665175063_K

description: AT cell D4


title: genomic DNA from CD34+38+ of AML patient SU014


title: AT cell D0 (AT2) 5665175063_I

description: AT cell D0 (AT2)


title: AT cell D6 5626686051_A

description: AT cell D6


title: AT cell D2 5665175063_C

description: AT cell D2


title: AT cell D6 5665175063_B

description: AT cell D6


title: genomic DNA from CD34+38- of AML patient SU032


title: genomic DNA from CD34- of AML patient SU006


title: genomic DNA from CD34- of AML patient SU032


title: Day 0 input DNA

description: Day 0 (D0)

data_processing:
ChIP products underwent Illumina GAII single-end sequencing
reads were aligned to the hg18 human genome build using the MAQ 0.7.1 aligner, performed by the USC Epigenome Center.
SICER (Zhang et al., 2009) peak calling was performed using a window size of 600 bp (H3K9/14Ac and H3K27me3) and gap size of 600 bp.  Input DNA was used for background normalization.
Differential peak occupancy was determined using the UCSC table browser.
Genome_build: hg18
Supplementary_files_format_and_content: peak calls in .bed format contain coordinates for peak occupancy

extract_protocol: ChIPseq libraries were constructed using the standard protocol from the New England Biolabs library prep kit (NEB Cat#E6200, Ipswich, MA).

treatment_protocol: Differentiating in culture over time, no extra treatments added. Chromatin immunoprecipitations for H3K9/14Ac (Millipore, #06-599) and H3K27me3 (Millipore, #07-449) were performed as previously described (Jia et al., 2003).

value: anoxia

value: Primary isolated AT2 cells

tag: chip antibody


title: Day 8 input DNA

description: Day 8 (D8)

value: in vitro diffrentiated AT1 cells


title: Day 8 H3K27me3 ChIPSeq

description: Day 8 (D8)

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: Day 8 H3K9/14Ac ChIPSeq

description: Day 8 (D8)


title: Day 0 H3K27me3 ChIPSeq

description: Day 0 (D0)


title: Day 0 H3K9/14Ac ChIPSeq

description: Day 0 (D0)


title: BM_Mac_DNaselHS

status: Public on Feb 21 2011

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: double strands

data_processing: Peaks: Peak finding analysis was performed using FindPeaks4, Vancouver Short Read Analysis Package, (http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=Main_Page#FindPeaks_4.0) using mm9 as a reference genome.

source_name: BM derived Mac DNasel

growth_protocol: Bone marrow was isolated from C57/Bl6 mice and subjected to red cell lysis. Remaining cells were cultured for 8 days in IMDM, with 10% FCS, 10% L-cell conditioned medium as a source for CSF-1, and 5% IL-3 conditioned medium (X63 Ag8–653 myeloma cells carrying an expression vector for IL-3). Adherent cells were assayed.

extract_protocol: DNA from in vivo DNase1 treated cells was run on an agarose gel and fragments in the range of 100-600 bp were excised and isolated. This DNA was used to prepare the libraries, according to Illumina's sample preparation protocol

value: Bone marrow derived-macrophages

tag: target

value: DNase1 DHS