title: GHE1311 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1311

source_name: PROMEGA reference DNA pool (male)


title: GHE1229 [CNV]

status: Public on Oct 24 2019

type: genomic

city: Bron

first: Sylvain

last: Mareschal

address: Centre de Biopathologie Est, 59 boulevard Pinel

department: NGS-HCL platform

country: France

institute: Hospices Civils de Lyon

description:
Characteristics definitions:
ID: sample ID
AGE: age at diagnosis
SEX: male (M) or female (F)
TREATMENT: treatment line used
IPI: calculated IPI
Age_Adjusted_IPI: calculated age-adjusted IPI
PFS_TIME: duration of progression free survival (PFS) in months
CENS_PFS: coded as 0 if PFS event, 1 if not
OS_TIME: duration of overall survival (OS) in months
CENS_OS: coded as 0 if OS event, 1 if not
COO: cell of origin according to Affymetrix GeneChip arrays as described in methods

hyb_protocol: Hybridization was performed according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505C, with FeatureExtraction version 10.5.1.1 (59 arrays), 10.7.1.1 (50 arrays) or 10.7.3.1 (110 arrays, please refer to the provided raw files for details).

data_processing: Agilent FeatureExtraction files were parsed and processed using the standard cghRA 1.6.0 protocol (GRCh37 probe remapping, fresh log2-ratio computation from « processedSignal » columns, flagged probe masking, summarization of replicated probes by their medians and WACA correction of wave artifacts). No normalization nor background-correction was applied to log-ratios provided in the data matrix.

molecule: genomic DNA

organism: Homo sapiens

source_name: DLBCL tumor biopsy, patient GHE-1229

label_protocol: 2µg of Whole-Genome Amplified (WGA) DNA were labeled following Agilent protocol (G4410-90010_CGH_Enzymatic_Protocol_v6.2.1). Yield was assessed with a nanodrop system. Tumor DNA was labeled with cyanine-5 (Cy5), and reference DNA (pooled normal male DNA; Promega, Madison, WI) was labeled with cyanine-3 (Cy3).

extract_protocol: Genomic DNA was extracted from frozen tissues using the QiaAmp DNA MINI kit (Qiagen). Its quality was assessed by spectrometry and agarose gel electrophoresis.

tag: ID

tag: tissue

value: DLBCL tumor biopsy

tag: age

tag: Sex

value: FEMALE

tag: treatment

tag: ipi

tag: coo

value: ABC

value: male


title: GHE1192 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1192

value: R-ACVBP+Conso


title: GHE1413 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1413

value: MALE


title: GHE1035 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1035


title: GHE1099 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1099


title: GHE0997 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0997

value: Other


title: GHE1128 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1128


title: GHE1066 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1066

value: GC


title: GHE1189 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1189


title: GHE1069 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1069


title: GHE1034 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1034


title: GHE1071 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1071


title: GHE1023 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1023


title: GHE1036 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1036


title: GHE1423 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1423


title: GHE1017 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1017


title: GHE1349 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1349

source_name: PROMEGA reference DNA pool (male)


title: GHE1053 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1053


title: GHE0993 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0993


title: GHE1026 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1026


title: GHE1018 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1018


title: GHE1028 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1028


title: GHE1009 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1009


title: GHE1536 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1536


title: GHE0986 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0986


title: GHE0984 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0984


title: GHE0992 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0992


title: GHE1046 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1046


title: GHE0982 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0982


title: GHE0976 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0976

value: ACVBP


title: GHE0955 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0955


title: GHE0923 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0923


title: GHE1104 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1104

value: PMBL


title: GHE0919 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0919

source_name: PROMEGA reference DNA pool (male)


title: GHE0909 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0909


title: GHE0857 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0857


title: GHE0865 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0865


title: GHE0908 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0908


title: GHE0877 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0877


title: GHE0849 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0849


title: GHE0860 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0860


title: GHE0978 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0978


title: GHE0873 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0873


title: GHE0846 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0846


title: GHE0925 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0925


title: GHE0855 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0855


title: GHE0883 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0883


title: GHE0837 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0837


title: GHE0856 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0856


title: GHE0822 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0822


title: GHE0842 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0842

source_name: PROMEGA reference DNA pool (male)


title: GHE0885 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0885


title: GHE1344 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1344

value: not collected


title: GHE0853 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0853


title: GHE0844 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0844


title: GHE0831 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0831


title: GHE0834 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0834


title: GHE0852 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0852


title: GHE0809 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0809


title: GHE0776 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0776


title: GHE0807 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0807


title: GHE0771 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0771


title: GHE0745 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0745


title: GHE0743 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0743


title: GHE0808 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0808


title: GHE0708 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0708


title: GHE0777 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0777


title: GHE0717 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0717

value: R-ACVBP+ASCT

source_name: PROMEGA reference DNA pool (male)


title: GHE0705 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0705


title: GHE0690 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0690


title: GHE0721 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0721


title: GHE0714 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0714


title: GHE0810 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0810


title: GHE0733 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0733


title: GHE0811 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0811


title: GHE0701 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0701


title: GHE0622 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0622


title: GHE0988 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0988


title: GHE0693 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0693


title: GHE0635 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0635


title: GHE0632 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0632


title: GHE0645 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0645


title: GHE0659 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0659


title: GHE0624 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0624


title: GHE0623 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0623

source_name: PROMEGA reference DNA pool (male)


title: GHE0614 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0614


title: GHE0629 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0629


title: GHE0605 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0605


title: GHE0609 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0609


title: GHE0562 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0562


title: GHE0615 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0615


title: GHE0604 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0604


title: GHE0601 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0601


title: GHE0535 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0535


title: GHE0602 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0602


title: GHE0519 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0519


title: GHE0547 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0547


title: GHE0515 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0515


title: GHE0522 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0522


title: GHE0536 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0536


title: GHE0534 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0534


title: GHE0563 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0563

source_name: PROMEGA reference DNA pool (male)


title: GHE0501 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0501


title: GHE0523 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0523


title: GHE0470 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0470


title: GHE0495 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0495


title: GHE0491 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0491


title: GHE0512 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0512


title: GHE0507 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0507


title: GHE0469 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0469


title: GHE0454 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0454


title: GHE0459 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0459


title: GHE0446 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0446


title: GHE0689 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0689


title: GHE0440 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0440


title: GHE0436 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0436


title: GHE0426 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0426


title: GHE0429 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0429


title: GHE0430 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0430

source_name: PROMEGA reference DNA pool (male)


title: GHE0427 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0427


title: GHE0423 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0423


title: GHE0685 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0685


title: GHE0393 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0393


title: GHE0400 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0400


title: GHE0415 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0415


title: GHE0397 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0397


title: GHE0371 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0371


title: GHE0395 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0395


title: GHE0368 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0368


title: GHE0275 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0275


title: GHE0262 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0262


title: GHE0300 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0300


title: GHE0292 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0292


title: GHE0293 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0293


title: GHE0294 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0294


title: GHE0358 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0358

source_name: PROMEGA reference DNA pool (male)


title: GHE0356 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0356


title: GHE0319 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0319


title: GHE0241 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0241


title: GHE0236 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0236


title: GHE0242 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0242


title: GHE0506 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0506


title: GHE0375 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0375


title: GHE0258 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0258


title: GHE0218 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0218


title: GHE0206 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0206


title: GHE0197 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0197


title: GHE0134 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0134


title: GHE0176 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0176


title: GHE0114 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0114


title: GHE0229 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0229


title: GHE0194 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0194


title: GHE0202 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0202

source_name: PROMEGA reference DNA pool (male)


title: GHE0028 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0028


title: GHE0057 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0057


title: GHE0061 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0061


title: PMD Patient  BAB8971

status: Public on Oct 09 2019

city: Houston

first: Vahid

last: Bahrambeigi

state: Texas

address: 1 Baylor Plaza

department: Human Molecular Genetics

country: USA

institute: Baylor College Of Medicine

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization.

source_name: DNA extracted from whole blood

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,  PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: gender

tag: disease state

value: Pelizaeus-Merzbacher disease

value: peripheral blood

source_name: Reference sample NA10851

tag: cell line

value: Lymphoblastoid cell line NA10851

tag: cell type

value: EBV-immortalized B-Lymphocyte


title: GHE0228 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0228


title: GHE0047 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0047


title: GHE0092 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0092


title: GHE0219 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0219


title: GHE0002 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0002


title: GHE0024 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0024


title: GHE0052 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0052


title: PMD Patient  BAB8970


title: GHE0050 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0050


title: PMD Patient  BAB8967


title: GHE0016 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0016


title: GHE0006 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0006


title: GHE0049 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0049


title: PMD Patient  BAB8969


title: GHE0025 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0025

source_name: PROMEGA reference DNA pool (male)


title: GHE0150 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0150


title: PMD Patient  BAB8968


title: GHE0001 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0001


title: PMD Patient  BAB8963

source_name: DNA extracted from whole blood


title: PMD Patient  BAB8965

source_name: Reference sample NA10851


title: PMD Patient  BAB8964


title: PMD Patient  BAB8966


title: PMD Patient  BAB8961


title: PMD Patient  BAB8960


title: PMD Patient  BAB8962


title: PMD Patient  BAB8959


title: PMD Patient  BAB8958


title: PMD Patient  BAB8955


title: PMD Patient  BAB8954


title: PMD Patient  BAB8950


title: PMD Patient  BAB8939


title: PMD Patient  BAB8953


title: PMD Patient  BAB8940


title: PMD Patient  BAB8951


title: PMD Patient  BAB8947


title: PMD Patient  BAB8949


title: PMD Patient  BAB8944


title: PMD Patient  BAB8942


title: PMD Patient  BAB8943


title: PMD Patient  BAB8946


title: PMD Patient  BAB8957


title: PMD Patient  BAB8956


title: PMD Patient  BAB8945


title: GHE0015 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0015


title: PMD Patient  BAB8952


title: GHE0169 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0169


title: PMD Patient  BAB8948


title: PMD Patient  BAB8936


title: PMD Patient  BAB8934


title: PMD Patient  BAB8938


title: PMD Patient  BAB8935


title: PMD Patient  BAB8937


title: PMD Patient  BAB8931


title: PMD Patient  BAB8932


title: PMD Patient  BAB8930


title: PMD Patient  BAB8933


title: PMD Patient  BAB8929


title: HG00732 Rep2

status: Public on Oct 02 2019

type: SRA

city: La Jolla

first: Yunjiang

last: Qiu

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

description: HiSeq 2500

library_source: genomic

data_processing:
Library strategy: Hi-C
Read ends were aligned to the hg19 reference genome using BWA MEM 0.7.8-r455 as single-end reads using a modified WASP pipeline (PMID: 26366987) to control for potential allelic mapping biases. Briefly, aligned reads were further processed to keep only the five prime alignment, and reads with low mapping quality (<10) were filtered out. Read ends were then paired together manually. PCR duplicates were removed using Picard tool.
Intra-chromosomal read pairs that are at least 20Kb away were further divided into 40Kb bin pairs based on five prime positions. Number of read pairs in each 40Kb bin pairs were aggregated to the contact matrices per chromosome. Raw counts in the contact matrices were then normalized using HiCNorm (PMID: 23023982) to remove potential biases.
Normalized matrices were further quantile normalized across replicates and samples to remove possible batch effects.
PC1 scores were computed using methods defined previously (Lieberman-Aiden et al., 2009; PMID: 19815776).
Directional Index (DI) was computed as previously described (Dixon et al. 2012; PMID: 22495300).
Insulation scores were computed by adapting previous methods (Crane et al., 2015; PMID: 26030525).
FIRE scores were computed using HiCNormCis as described in Schmitt et al. 2016. (PMID: 27851967)
Phasing of variants was performed based on Haploseq pipeline. (PMID: 24185094 )
Genome_build: hg19
Supplementary_files_format_and_content: Contact matrices are NxN matrices in compressed text format. PC1, DI, IS, and FIRE scores are in bigwig format. Phased SNPs are in VCF format.

source_name: Lymphoblastoid Cell Lines

growth_protocol: Lymphoblastoid lines were grown according to guidelines from Coriell: https://www.coriell.org/0/PDF/Lymphoblast_Culture_FAQ.pdf. Cells for Hi-C replicates were grown independently for at least 2 passages.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10 min, quenched with 2.5M Glycine for 5 min, collected by centrifugation, and snap frozen in liquid nitrogen. These cell pellets were used as input for Hi-C library construction.
HindIII Hi-C performed as previously reported in Lieberman-Aiden et al., 2009. (PMID: 19815776)

tag: restriction enzyme

value: HindIII


title: HG00733 Rep2

description: HiSeq 2500


title: HG00732 Rep1

description: HiSeq 2000 and HiSeq 2500


title: HG00733 Rep1

description: HiSeq 2000 and HiSeq 2500


title: HG00731 Rep2

description: HiSeq 2500


title: HG00731 Rep1

description: HiSeq 2000 and HiSeq 2500


title: HG00513 Rep2

description: HiSeq 2500


title: HG00514 Rep2

description: HiSeq 2500


title: HG00514 Rep1

description: HiSeq 2000 and HiSeq 2500


title: PMD Patient  BAB8924


title: PMD Patient  BAB8921


title: PMD Patient  BAB8920


title: PMD Patient  BAB8928


title: PMD Patient  BAB8926


title: PMD Patient  BAB8925


title: PMD Patient  BAB8923


title: PMD Patient  BAB8922


title: GHE0004 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-0004

value: DLBCL tumor biopsy


title: GM19240 Rep1

description: HiSeq 4000 and HiSeq 2500


title: HG00512 Rep1

description: HiSeq 2000 and HiSeq 2500


title: HG00512 Rep2

description: HiSeq 2500


title: GM19240 Rep2

description: HiSeq 4000 and HiSeq 2500


title: HG00513 Rep1

description: HiSeq 2000 and HiSeq 2500


title: GM19238 Rep1

description: HiSeq 2000 and HiSeq 2500


title: GM19204 Rep1

description: HiSeq 2000 and HiSeq 2500


title: GM19204 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM19099 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM19141 Rep1

description: HiSeq 2000 and HiSeq 2500


title: GM18522 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM18516 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM19193 Rep1

description: HiSeq 2000 and HiSeq 2500


title: GM19239 Rep1

description: HiSeq 2500


title: GM19141 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM18508 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM19099 Rep1

description: HiSeq 2000 and HiSeq 2500


title: GM19193 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM18508 Rep1

description: HiSeq 2000 and HiSeq 2500


title: GM19239 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM19238 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM18507 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM18505 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM18486 Rep1

description: HiSeq 2000 and HiSeq 2500


title: XAV939 rep1

status: Public on Sep 24 2019

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

library_source: transcriptomic

data_processing:
Sequence reads were trimmed with Trimmomatic 0.32 and mapped against the mouse reference genome (mm10) using TopHat 2.0.13. Read counts per gene were calculated using HTSeq 0.6.1p1.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample. Gene ID = NCBI Gene ID.

molecule: total RNA

organism: Mus musculus

source_name: Articular chondrocytes

growth_protocol: Primary cultured mouse articular chondrocytes were maintained in DMEM supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Total RNAs were extracted using TRI reagent (Molecular Research Center, Inc.).
RNA-Seq libraries were prepared with TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: Cells were treated with DMSO or 10 μM of XAV939 or IWR-1 for 108 h or transfected with control siRNA or Tnks and Tnks2 siRNAs using METAFECTENE PRO (Biontex).

tag: strain

value: ICR

value: Articular chondrocytes

tag: passages

tag: treated with


title: siCtrl rep3

value: siCtrl


title: siCtrl rep1


title: siTnks/2 rep2


title: siCtrl rep2


title: XAV939 rep2


title: siTnks/2 rep1


title: GM18505 Rep1

description: HiSeq 2000 and HiSeq 2500


title: XAV939 rep3


title: siTnks/2 rep3


title: IWR-1 rep3


title: IWR-1 rep1


title: GM18522 Rep1

description: HiSeq 2000 and HiSeq 2500


title: DMSO rep3

value: DMSO


title: DMSO rep2


title: DMSO rep1


title: GM18486 Rep2

description: HiSeq 2000 and HiSeq 2500


title: GM18516 Rep1

description: HiSeq 2000 and HiSeq 2500


title: IWR-1 rep2


title: H0038467

status: Public on Sep 13 2019

type: RNA

city: South San Francisco

first: David

middle: Fong

last: Choy

address: 1 DNA Way

institute: Genentech, Inc.

description: PAXgene whole blood mRNA

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA/Bioconductor

label: biotin

source_name: PAXgene whole blood mRNA

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol RNA extraction

tag: disease

value: Asthma at baseline


title: H0038462

description: PAXgene whole blood mRNA


title: H0038466

description: PAXgene whole blood mRNA


title: H0038463

description: PAXgene whole blood mRNA


title: H0038457

description: PAXgene whole blood mRNA


title: GM18507 Rep1

description: HiSeq 2000 and HiSeq 2500


title: H0038464

description: PAXgene whole blood mRNA


title: H0038427

description: PAXgene whole blood mRNA


title: H0038420

description: PAXgene whole blood mRNA


title: H0038429

description: PAXgene whole blood mRNA


title: H0038458

description: PAXgene whole blood mRNA


title: H0038443

description: PAXgene whole blood mRNA


title: H0038435

description: PAXgene whole blood mRNA


title: H0038452

description: PAXgene whole blood mRNA


title: H0038421

description: PAXgene whole blood mRNA


title: H0038465

description: PAXgene whole blood mRNA


title: H0038447

description: PAXgene whole blood mRNA


title: H0038417

description: PAXgene whole blood mRNA


title: H0038454

description: PAXgene whole blood mRNA


title: H0038448

description: PAXgene whole blood mRNA


title: H0038456

description: PAXgene whole blood mRNA


title: H0038426

description: PAXgene whole blood mRNA


title: H0038419

description: PAXgene whole blood mRNA


title: H0038416

description: PAXgene whole blood mRNA


title: H0038423

description: PAXgene whole blood mRNA


title: H0038424

description: PAXgene whole blood mRNA


title: H0038415

description: PAXgene whole blood mRNA


title: H0038436

description: PAXgene whole blood mRNA


title: H0038414

description: PAXgene whole blood mRNA


title: H0038409

description: PAXgene whole blood mRNA


title: H0038407

description: PAXgene whole blood mRNA


title: H0038390

description: PAXgene whole blood mRNA


title: H0038389

description: PAXgene whole blood mRNA


title: H0038382

description: PAXgene whole blood mRNA


title: H0038388

description: PAXgene whole blood mRNA


title: H0038378

description: PAXgene whole blood mRNA


title: H0038461

description: PAXgene whole blood mRNA


title: H0038383

description: PAXgene whole blood mRNA


title: H0038405

description: PAXgene whole blood mRNA


title: H0038384

description: PAXgene whole blood mRNA


title: H0038372

description: PAXgene whole blood mRNA


title: H0038377

description: PAXgene whole blood mRNA


title: H0038401

description: PAXgene whole blood mRNA


title: H0038373

description: PAXgene whole blood mRNA


title: H0038365

description: PAXgene whole blood mRNA


title: H0038379

description: PAXgene whole blood mRNA


title: H0038376

description: PAXgene whole blood mRNA


title: H0038374

description: PAXgene whole blood mRNA


title: H0038397

description: PAXgene whole blood mRNA


title: H0038358

description: PAXgene whole blood mRNA


title: H0038370

description: PAXgene whole blood mRNA


title: H0038360

description: PAXgene whole blood mRNA


title: H0038355

description: PAXgene whole blood mRNA


title: H0038392

description: PAXgene whole blood mRNA


title: H0038371

description: PAXgene whole blood mRNA


title: H0038368

description: PAXgene whole blood mRNA


title: H0038354

description: PAXgene whole blood mRNA


title: H0038357

description: PAXgene whole blood mRNA


title: H0038356

description: PAXgene whole blood mRNA


title: H0038352

description: PAXgene whole blood mRNA


title: H0038363

description: PAXgene whole blood mRNA


title: H0038350

description: PAXgene whole blood mRNA


title: H0038351

description: PAXgene whole blood mRNA


title: H0038346

description: PAXgene whole blood mRNA


title: H0038331

description: PAXgene whole blood mRNA


title: H0038343

description: PAXgene whole blood mRNA


title: H0038322

description: PAXgene whole blood mRNA


title: H0038338

description: PAXgene whole blood mRNA


title: H0038327

description: PAXgene whole blood mRNA


title: H0038299

description: PAXgene whole blood mRNA


title: H0038348

description: PAXgene whole blood mRNA


title: H0038308

description: PAXgene whole blood mRNA


title: H0038318

description: PAXgene whole blood mRNA


title: H0038305

description: PAXgene whole blood mRNA


title: H0038300

description: PAXgene whole blood mRNA


title: H0038347

description: PAXgene whole blood mRNA


title: H0038307

description: PAXgene whole blood mRNA


title: H0038287

description: PAXgene whole blood mRNA


title: H0038298

description: PAXgene whole blood mRNA


title: H0038293

description: PAXgene whole blood mRNA


title: H0038337

description: PAXgene whole blood mRNA


title: H0038315

description: PAXgene whole blood mRNA


title: H0038290

description: PAXgene whole blood mRNA


title: H0038281

description: PAXgene whole blood mRNA


title: H0038295

description: PAXgene whole blood mRNA


title: H0038296

description: PAXgene whole blood mRNA


title: H0038288

description: PAXgene whole blood mRNA


title: H0038276

description: PAXgene whole blood mRNA


title: H0038314

description: PAXgene whole blood mRNA


title: H0038336

description: PAXgene whole blood mRNA


title: H0038274

description: PAXgene whole blood mRNA


title: H0038278

description: PAXgene whole blood mRNA


title: H0038267

description: PAXgene whole blood mRNA


title: H0038271

description: PAXgene whole blood mRNA


title: H0038272

description: PAXgene whole blood mRNA


title: H0038262

description: PAXgene whole blood mRNA


title: H0038280

description: PAXgene whole blood mRNA


title: H0038275

description: PAXgene whole blood mRNA


title: H0038259

description: PAXgene whole blood mRNA


title: H0038260

description: PAXgene whole blood mRNA


title: H0038251

description: PAXgene whole blood mRNA


title: H0038257

description: PAXgene whole blood mRNA


title: H0038245

description: PAXgene whole blood mRNA


title: H0038242

description: PAXgene whole blood mRNA


title: H0038246

description: PAXgene whole blood mRNA


title: H0038247

description: PAXgene whole blood mRNA


title: H0038244

description: PAXgene whole blood mRNA


title: H0038263

description: PAXgene whole blood mRNA


title: H0038223

description: PAXgene whole blood mRNA


title: H0038230

description: PAXgene whole blood mRNA


title: H0038231

description: PAXgene whole blood mRNA


title: H0038225

description: PAXgene whole blood mRNA


title: H0038236

description: PAXgene whole blood mRNA


title: H0038243

description: PAXgene whole blood mRNA


title: H0038261

description: PAXgene whole blood mRNA


title: H0038250

description: PAXgene whole blood mRNA


title: H0038222

description: PAXgene whole blood mRNA


title: H0038233

description: PAXgene whole blood mRNA


title: H0038232

description: PAXgene whole blood mRNA


title: H0038212

description: PAXgene whole blood mRNA


title: H0038221

description: PAXgene whole blood mRNA


title: H0038206

description: PAXgene whole blood mRNA


title: H0038204

description: PAXgene whole blood mRNA


title: H0038208

description: PAXgene whole blood mRNA


title: H0038213

description: PAXgene whole blood mRNA


title: H0038199

description: PAXgene whole blood mRNA


title: H0038241

description: PAXgene whole blood mRNA


title: H0038193

description: PAXgene whole blood mRNA


title: H0038201

description: PAXgene whole blood mRNA


title: H0038220

description: PAXgene whole blood mRNA


title: H0038187

description: PAXgene whole blood mRNA


title: H0038188

description: PAXgene whole blood mRNA


title: H0038175

description: PAXgene whole blood mRNA


title: H0038200

description: PAXgene whole blood mRNA


title: H0038195

description: PAXgene whole blood mRNA


title: H0038182

description: PAXgene whole blood mRNA


title: H0038169

description: PAXgene whole blood mRNA


title: H0038198

description: PAXgene whole blood mRNA


title: H0038174

description: PAXgene whole blood mRNA


title: H0038164

description: PAXgene whole blood mRNA


title: H0038203

description: PAXgene whole blood mRNA


title: H0038155

description: PAXgene whole blood mRNA


title: H0038159

description: PAXgene whole blood mRNA


title: H0038176

description: PAXgene whole blood mRNA


title: H0038170

description: PAXgene whole blood mRNA


title: H0038207

description: PAXgene whole blood mRNA


title: H0038166

description: PAXgene whole blood mRNA


title: H0038162

description: PAXgene whole blood mRNA


title: H0038151

description: PAXgene whole blood mRNA


title: H0038147

description: PAXgene whole blood mRNA


title: H0038143

description: PAXgene whole blood mRNA


title: H0038186

description: PAXgene whole blood mRNA


title: H0038173

description: PAXgene whole blood mRNA


title: H0038144

description: PAXgene whole blood mRNA


title: H0038136

description: PAXgene whole blood mRNA


title: H0038142

description: PAXgene whole blood mRNA


title: H0038141

description: PAXgene whole blood mRNA


title: H0038154

description: PAXgene whole blood mRNA


title: H0038133

description: PAXgene whole blood mRNA


title: H0038139

description: PAXgene whole blood mRNA


title: H0038146

description: PAXgene whole blood mRNA


title: H0038119

description: PAXgene whole blood mRNA


title: H0038115

description: PAXgene whole blood mRNA


title: H0038122

description: PAXgene whole blood mRNA


title: H0038116

description: PAXgene whole blood mRNA


title: H0038123

description: PAXgene whole blood mRNA


title: H0038113

description: PAXgene whole blood mRNA


title: H0038108

description: PAXgene whole blood mRNA


title: H0038110

description: PAXgene whole blood mRNA


title: H0038102

description: PAXgene whole blood mRNA


title: H0038120

description: PAXgene whole blood mRNA


title: H0038135

description: PAXgene whole blood mRNA


title: H0038099

description: PAXgene whole blood mRNA


title: H0038098

description: PAXgene whole blood mRNA


title: H0038091

description: PAXgene whole blood mRNA


title: H0038104

description: PAXgene whole blood mRNA


title: H0038114

description: PAXgene whole blood mRNA


title: H0038118

description: PAXgene whole blood mRNA


title: H0038093

description: PAXgene whole blood mRNA


title: H0038087

description: PAXgene whole blood mRNA


title: H0038100

description: PAXgene whole blood mRNA


title: H0038084

description: PAXgene whole blood mRNA


title: H0038081

description: PAXgene whole blood mRNA


title: H0038111

description: PAXgene whole blood mRNA


title: H0038090

description: PAXgene whole blood mRNA


title: H0038126

description: PAXgene whole blood mRNA


title: H0038080

description: PAXgene whole blood mRNA


title: H0038078

description: PAXgene whole blood mRNA


title: H0038076

description: PAXgene whole blood mRNA


title: H0038067

description: PAXgene whole blood mRNA


title: H0038077

description: PAXgene whole blood mRNA


title: H0038065

description: PAXgene whole blood mRNA


title: H0038069

description: PAXgene whole blood mRNA


title: H0038057

description: PAXgene whole blood mRNA


title: H0038059

description: PAXgene whole blood mRNA


title: H0038066

description: PAXgene whole blood mRNA


title: H0038054

description: PAXgene whole blood mRNA


title: H0038045

description: PAXgene whole blood mRNA


title: H0038042

description: PAXgene whole blood mRNA


title: H0038070

description: PAXgene whole blood mRNA


title: H0038060

description: PAXgene whole blood mRNA


title: H0038038

description: PAXgene whole blood mRNA


title: H0038046

description: PAXgene whole blood mRNA


title: H0038050

description: PAXgene whole blood mRNA


title: H0038056

description: PAXgene whole blood mRNA


title: H0038051

description: PAXgene whole blood mRNA


title: H0038047

description: PAXgene whole blood mRNA


title: H0038032

description: PAXgene whole blood mRNA


title: H0038029

description: PAXgene whole blood mRNA


title: H0038039

description: PAXgene whole blood mRNA


title: H0038025

description: PAXgene whole blood mRNA


title: H0038030

description: PAXgene whole blood mRNA


title: H0038033

description: PAXgene whole blood mRNA


title: H0038021

description: PAXgene whole blood mRNA


title: H0038152

description: PAXgene whole blood mRNA


title: H0038035

description: PAXgene whole blood mRNA


title: H0037968

description: PAXgene whole blood mRNA


title: H0038014

description: PAXgene whole blood mRNA


title: H0037977

description: PAXgene whole blood mRNA


title: H0037969

description: PAXgene whole blood mRNA


title: H0037984

description: PAXgene whole blood mRNA


title: H0038028

description: PAXgene whole blood mRNA


title: H0037982

description: PAXgene whole blood mRNA


title: H0037993

description: PAXgene whole blood mRNA


title: H0038012

description: PAXgene whole blood mRNA


title: H0037981

description: PAXgene whole blood mRNA


title: H0037976

description: PAXgene whole blood mRNA


title: H0038022

description: PAXgene whole blood mRNA


title: H0037973

description: PAXgene whole blood mRNA


title: H0037989

description: PAXgene whole blood mRNA


title: H0037985

description: PAXgene whole blood mRNA


title: H0038034

description: PAXgene whole blood mRNA


title: H0037986

description: PAXgene whole blood mRNA


title: H0038000

description: PAXgene whole blood mRNA


title: H0038011

description: PAXgene whole blood mRNA


title: H0037978

description: PAXgene whole blood mRNA


title: H0037970

description: PAXgene whole blood mRNA


title: H0037988

description: PAXgene whole blood mRNA


title: H0038006

description: PAXgene whole blood mRNA


title: H0038020

description: PAXgene whole blood mRNA


title: H0038010

description: PAXgene whole blood mRNA


title: H0037955

description: PAXgene whole blood mRNA


title: H0037922

description: PAXgene whole blood mRNA


title: H0037961

description: PAXgene whole blood mRNA


title: H0037928

description: PAXgene whole blood mRNA


title: H0037929

description: PAXgene whole blood mRNA


title: H0037949

description: PAXgene whole blood mRNA


title: H0037938

description: PAXgene whole blood mRNA


title: H0037951

description: PAXgene whole blood mRNA


title: H0037939

description: PAXgene whole blood mRNA


title: H0037948

description: PAXgene whole blood mRNA


title: H0037957

description: PAXgene whole blood mRNA


title: H0037952

description: PAXgene whole blood mRNA


title: H0037931

description: PAXgene whole blood mRNA


title: H0037916

description: PAXgene whole blood mRNA


title: H0037956

description: PAXgene whole blood mRNA


title: H0037935

description: PAXgene whole blood mRNA


title: H0037943

description: PAXgene whole blood mRNA


title: H0037941

description: PAXgene whole blood mRNA


title: H0037966

description: PAXgene whole blood mRNA


title: H0037900

description: PAXgene whole blood mRNA


title: H0037947

description: PAXgene whole blood mRNA


title: H0037918

description: PAXgene whole blood mRNA


title: H0037914

description: PAXgene whole blood mRNA


title: H0037907

description: PAXgene whole blood mRNA


title: H0037912

description: PAXgene whole blood mRNA


title: H0037936

description: PAXgene whole blood mRNA


title: H0037964

description: PAXgene whole blood mRNA


title: H0037920

description: PAXgene whole blood mRNA


title: H0037896

description: PAXgene whole blood mRNA


title: H0037897

description: PAXgene whole blood mRNA


title: H0037960

description: PAXgene whole blood mRNA


title: H0037895

description: PAXgene whole blood mRNA


title: H0037888

description: PAXgene whole blood mRNA


title: H0037883

description: PAXgene whole blood mRNA


title: H0037894

description: PAXgene whole blood mRNA


title: H0037882

description: PAXgene whole blood mRNA


title: H0037962

description: PAXgene whole blood mRNA


title: H0037881

description: PAXgene whole blood mRNA


title: H0037879

description: PAXgene whole blood mRNA


title: H0037893

description: PAXgene whole blood mRNA


title: H0037880

description: PAXgene whole blood mRNA


title: H0037890

description: PAXgene whole blood mRNA


title: H0037878

description: PAXgene whole blood mRNA


title: H0037856

description: PAXgene whole blood mRNA


title: H0037873

description: PAXgene whole blood mRNA


title: H0037874

description: PAXgene whole blood mRNA


title: H0037871

description: PAXgene whole blood mRNA


title: H0037876

description: PAXgene whole blood mRNA


title: H0037846

description: PAXgene whole blood mRNA


title: H0037858

description: PAXgene whole blood mRNA


title: H0037862

description: PAXgene whole blood mRNA


title: H0037842

description: PAXgene whole blood mRNA


title: H0037847

description: PAXgene whole blood mRNA


title: H0037840

description: PAXgene whole blood mRNA


title: H0037838

description: PAXgene whole blood mRNA


title: H0037853

description: PAXgene whole blood mRNA


title: H0037864

description: PAXgene whole blood mRNA


title: H0037849

description: PAXgene whole blood mRNA


title: H0037839

description: PAXgene whole blood mRNA


title: H0037850

description: PAXgene whole blood mRNA


title: H0037836

description: PAXgene whole blood mRNA


title: acta2/foxc1b-negative rep1

status: Public on Sep 10 2019

city: Worcester

first: Nathan

middle: D.

last: Lawson

state: MA

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
For mural cellls, raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 (Illumina) to generate fastq files for each sample. For kdrl cells, raw HiSeq2000 data files were processed with CASAVA 1.8.2 (Illumina) to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples, if index sequences were non-redundant, we allowed for 1 mismatch or N in the index.
Paired-end reads were aligned to 26 chromosomes and  967 primary assembly scaffolds of the zebrafish genome GRCz11, with star_2.5.3a (Dobin et al., 2013).
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts_1.5.2 (Liao, Smyth, & Shi, 2014).
Normalization and differential expression (DE) analysis was performed with  DESeq2_1.20.0 (Love, Huber, & Anders, 2014).
For DE analysis, the original DESeq2 shrinkage estimator was used to estimate log2 fold change (LFC) for each comparison.
Genome_build: GRCz11, Refseq GCF_000002035.6
Supplementary_files_format_and_content: comma-separated text file

molecule: polyA RNA

organism: Danio rerio

source_name: non-mural cells

growth_protocol: zebrafish embryos were grown to 4 or 5 days post fertilization

extract_protocol:
total RNA was isolated using TRIzol
oligo dT -primed cDNA was amplified (REPLI-G) followed by library construction using TruSeq adapters

treatment_protocol: embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.

value: embryonic vascular smooth muscle cells

tag: cell population

value: non-mural cells

tag: Stage

value: 4 days post fertilization

tag: genotype/variation

tag: sorting

value: FACS-isolated cells


title: acta2-positive rep1

source_name: mural cells

tag: tissue

value: mural cells


title: acta2/foxc1b-positive rep1


title: acta2/foxc1b-negative rep3


title: acta2/foxc1b-positive rep2


title: acta2-positive rep2


title: acta2-negative rep3


title: acta2-positive rep3


title: acta2-negative rep1


title: acta2-negative rep2


title: kdrl-negative rep2

source_name: non-endothelial cells

extract_protocol:
total RNA was isolated using TRIzol
oligo dT primed libraries were constructed using the TotalScript kit (Epicentre)

treatment_protocol: embryos were dissociated and single cell suspensions were fixed acccording to the MARIS protocol; transgene expressing cells were isolated by fluorescence activated cell sorting.

value: non-endothelial cells

value: 5 days post fertilization


title: kdrl positive rep3

source_name: endothelial cells

value: endothelial cells


title: acta2/foxc1b-negative rep2


title: kdrl positive rep2


title: kdrl-negative rep3


title: H0037826

description: PAXgene whole blood mRNA


title: H0037833

description: PAXgene whole blood mRNA


title: kdrl-negative rep1


title: H0037832

description: PAXgene whole blood mRNA


title: H0037828

description: PAXgene whole blood mRNA


title: H0037831

description: PAXgene whole blood mRNA


title: wt_FAIRE_44h_rep2

status: Public on May 31 2019

city: Salt Lake City

first: Bruce

last: Edgar

state: UT

address: 2000 Cir of Hope Dr.

department: Department of Oncological Sciences

institute: University of Utah

data_processing:
FAIRE-Seq sequencing reads were aligned to  reference genome using Bowtie2. Merged bam files were generated for each genotype by combining replicates. The  Z-scores were calculated using the mean and standard deviation per chromosome arm
RNA-Seq sequencing reads were aligned to thereference genome using STAR and further counted using HTSeq
Genome_build: dm6
Supplementary_files_format_and_content: bigwig, count

organism: Drosophila melanogaster

source_name: wing

growth_protocol: female fly wings from wildtype or transgenic flies expressing flippase control, E2F1+DP (E2F) and CycD+Cdk4+E2F1+DP (CycD_E2F) were dissected at corresponding timepoints

extract_protocol:
For FAIRE- samples, fly wings were dissected in PBS and brifely fixed before sonication and pheno-chloroform extraction; For RNA collections, fly wings were dissected and harvested in Trizol
FAIRE-Seq libraries were constructed using the Rubicon Thruplex DNA-seq kit; RNA-Seq libraries  were generated using the stranded mRNA sequencing kit from KAPA Biosystems

value: wildtype

tag: Sex

value: female

tag: developmental stage

value: 44h APF


title: wt_FAIRE_44h_rep1


title: wt_FAIRE_44h_rep3


title: H0037835

description: PAXgene whole blood mRNA


title: H0037830

description: PAXgene whole blood mRNA


title: wt_FAIRE_24h_rep3

value: 24h APF


title: wt_FAIRE_24h_rep2


title: H0037827

description: PAXgene whole blood mRNA


title: wt_FAIRE_24h_rep1


title: kdrl positive rep1


title: wt_FAIRE_36h_rep1

value: 36h APF


title: wt_FAIRE_18h_rep3

value: 18h APF


title: wt_FAIRE_18h_rep1


title: wt_FAIRE_L3_rep2


title: wt_FAIRE_L3_rep3


title: wt_FAIRE_6h_rep3

value: 6h APF


title: wt_FAIRE_36h_rep3


title: wt_FAIRE_L3_rep1


title: DNase-seq_ILCP_rep2_GB3059

status: Public on May 30 2019

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description:
DNase-seq
ILCP_WT_DHS_peaks.txt
ILCP_WT_DHS.se-W100-normalized.wig.gz

data_processing:
Library strategy: DNAse-seq
Basecalling by RTA 1.18.66.3, Illumina instrument run time analysis software
Sequencing reads were aligned to mouse genome (mm9) with default parameters.
Reads from replicates were merged and redundant reads were removed from further analysis.
Peak calling were performed using MACS2 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Called peaks generated by MACS2. Wig files contain normalized tag density, which can be uploaded to UCSC genome browser for visulization.

source_name: ILCP

growth_protocol: Samples were isolated by cell sorting from bone marrow single cell suspensions

extract_protocol:
For DNase I digestion, 300 cells from each cell type were collected by FACS sorting. 0.3 unit of DNase I (Roche, 04716728001) was added to each cell type and incubated at 37 °C for 5 minutes. Reaction were stop by adding 80 μl of stop buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.15% SDS, 10 mM EDTA) containing 1 μl of 20 mg/ml proteinase K. Samples were incubated at 55 °C for overnight and DNA purified by phenol–chloroform extraction, followed by precipitation with ethanol in the presence of 20 μg glycogen.
The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10"; 67°C, 30"; 72°C, 30" for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10"; 68°C, 30"; 72°C, 30" for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq3000.

value: bone marrow

value: ILCP

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1+ IL-7Ra+

tag: antibody


title: DNase-seq_ILCP_rep3_GB7348


title: DNase-seq_EILP_rep3_GB7347

description:
DNase-seq
EILP_WT_DHS_peaks.txt
EILP_WT_DHS.se-W100-normalized.wig.gz

value: EILP

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-


title: DNase-seq_EILP_rep1_GB3053


title: Peripheral donor 2

status: Public on May 17 2019

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build hg19 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF and the following parameter: --expect-cells=8000.
The six samples were collectively aggregated with the cellranger aggr function with the following parameter: --normalized=mapped.
Cells were filtered with Seurat (v2.3.4) FilterCells function. Cells with nUMIs less than 200 (to remove cells with poor read quality) or greater than 2500 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: mito.genes <- grep(pattern = "^MT-", x = rownames(x = seurat_object@data), value = TRUE).
Aggregated reads were normalized with Seurat (v2.3.4) with the following command: NormalizeData(object = seurat_object, normalization.method = "LogNormalize",  scale.factor = 10000). Variable genes were identified from downstream normalization with: FindVariableGenes(object = seurat_object, mean.function = ExpMean, dispersion.function = LogVMR,  x.low.cutoff = 0.0125, x.high.cutoff = 3, y.cutoff = 0.5). Cell-to-cell variation regression was performed to minimize any batch effect introduced in the sample preparation process with: ScaleData(object = seurat_object, vars.to.regress = c("nUMI", "percent.mito")).
Clustering was performed with Seurat (v2.3.4) FindClusters. In order to generate the shared nearest neighbor (SNN) graph, the principal component analysis reduction technique was utilized for the first 10 principal components. A granularity resolution value of 0.6 was used to discriminate clusters.
Genome_build: hg19
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format. Log-normalized expression values (from the seurat_object@data slot) were appended to relevant metadata (barcode and cluster label from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values.

source_name: Retina

extract_protocol:
A 2-mm foveal centered and a 4-mm peripheral punch from the inferotemporal region were acquired from three clinically normal human donors. Tissue was dissociated using the Papain Dissociation System (Worthington Biochemical Corporation, Lakewood NJ). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Single-cell RNA libraries were prepared for sequencing using standard 10X genomics protocols. Briefly, cryopreserved samples were thawed, and single cells were captured and barcoded using the Chromium System with the v3 single cell-reagent kit (10x Genomics, Pleasanton CA). Sequencing was performed on pooled libraries using the Illumina HiSeq 4000 platform (San Diego, CA), generating 150 base pair paired-end reads.

tag: location

value: Periphery

tag: donor

value: Donor 2


title: DNase-seq_ALP_rep3_GB7346

description:
DNase-seq
ALP_WT_DHS_peaks.txt
ALP_WT_DHS.se-W100-normalized.wig.gz

source_name: ALP

tag: cell type

value: ALP

value: Lin- Kit+ 2B4+ a4b7- Flt3high IL-7Ra+


title: Peripheral donor 1

value: Donor 1


title: Fovea donor 2

value: Fovea


title: Fovea donor 3

value: Donor 3


title: DNase-seq_ALP_rep2_GB3057


title: Peripheral donor 3


title: Fovea donor 1


title: DNase-seq_ALP_rep1_GB3052


title: DNase-seq_EILP_rep2_GB3058


title: wt_FAIRE_18h_rep2

value: wildtype

value: female


title: Wild-type ChIP rep2

status: Public on Apr 03 2019

first: Richard

middle: E

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

description:
macs_WT-1_peaks.narrowPeak
macs_WT_mean_treat_pileup.bedGraph

data_processing:
Basecalls performed using Illumina RTA v2.4.11
ChIP-seq reads were aligned to the sacCer3 genome assembly using Bowtie version 1.0.0 with the following parameters: -n2 -3 40 -m3 --best --strata -S
Peaks were called using MACS version 2.1.1.20160226 in paired-end mode with the following settings:  -g 1.21e7 --keep-dup auto -B --SPMR
Pileups were generated during peak calling. Correlation between replicates was found to be greater than 0.98 by UCSC wigCorrelate
Genome_build: sacCer3
Supplementary_files_format_and_content: narrowPeak files were generated during peak calling; scores are -10*log10qvalue
Supplementary_files_format_and_content: Averaged bedGraph files were generated using macs2 cmbreps; scores are reads per million total reads.

organism: Saccharomyces cerevisiae

source_name: sonicated spheroplasts

growth_protocol: Cells grown at 25 degrees C in YEPD broth

extract_protocol:
Spheroplasts were prepared, washed, and lysed in detergent containing  buffer with protease inhibitors. Lysate was sonicated to obtain DNA fragments of average size 100 bp,
Libraries were prepared using Illumina Nextera DNA Library Kit #FC-121-1031

value: S. cerevisiae S288C

tag: genetic background

tag: ab name

value: anti-HA agarose beads (A2220, Sigma)


title: Wild-type ChIP rep1

description:
macs_WT-2_peaks.narrowPeak
macs_WT_mean_treat_pileup.bedGraph

tag: strain


title: Stages 3 to 6, Protocol x1, Stage 6 complete

status: Public on May 10 2019

city: Cambridge

first: Adrian

last: Veres

state: Massachusetts

address: 7 Divinity Ave

institute: Harvard University

data_processing:
All processing steps from raw fastq files to count matrices were performed using the custom pipeline for inDrops data analysis (www.github.com/indrops/indrops) using the the following parameters specified in the YAML file: [trimmomatic arguments]: LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "30". [output_arguments]: filter_alignments_to_softmasked_regions: True. All other parameters were used as in the default_parameters file in the repository github.com/indrops/indrops, commit hash 8a9167.
Genome_build: GRCh38.88
Supplementary_files_format_and_content: '*.raw_indrops_counts.*' files are the raw, unfiltered output from the Indrops processing pipeline. The first column indicates the barcode label using the Indrops pipeline nomenclature, all folllowing columns are UMIFM counts as defined in Klein et al. (2015). The gene corresponding to each column is listed in the header line.
Supplementary_files_format_and_content: '*.processed_counts.*' are filtered counts files, removing undetected genes and filtering cells using the thresholds described in the methods section of Veres et al. 2019. The first column indicates the cell label, all following columns are UMIFM counts for the gene indicated in the header row.
Supplementary_files_format_and_content: '*.cell_metadata.*' files contain metadata associated for all filtered cells in the each dataset. The first row is a header detailing the type of data in each column. These include TSNE coordinates, cluster label annotations and pseudotime values (as appropriate).
Supplementary_files_format_and_content: code_analysis_files.tar is a tarball of all files (primarily loom-formatted) used in generating the analysis, with the accompanying code at https://github.com/meltonlab/scbeta_indrops

source_name: in vitro differentiated pluripotent stem cell

growth_protocol: Human embryonic and pluripotent stem cells were maintained and differentiated as described in the methods of (Veres et al. 2018). Differentiation was carried out using step-wise protocols aimed at gradually producing beta cells in vitro.

extract_protocol:
Differentiated clusters were prepared for single cell RNA sequencing as follows: 1-2 mL suspension culture was sampled from the spinner flask, dissociated with TrypLE Express (5-15 minutes at 37 °C), quenched with cold PBS + 1% BSA and gently dispersed with a P1000 pipette. Cells were then centrifuged (300 rpm, 3 min), resuspended in cold PBS+1% BSA and filtered through a 70 µm mesh filter. Centrifugation, resuspension and filtering was repeated a total of 3 times. Cells were then counted and resuspended to the working dilution for inDrops (100,000 cells/mL) in 1X PBS with 13% Optiprep (Sigma; D1556).
Single cell RNA sequencing was carried out using the inDrops platform, as previously described (Klein 2015, Zilionis 2016). Most samples were run using ‘inDrops v2’ barcoded hydrogel beads (1 Cell Bio, Harvard Single Cell Core), and one experiment used ‘inDrops v3’ beads (Harvard Single Cell Core). Following the inDrops protocol, each biological sample was split into several aliquots of 1000-3000 cells after encapsulation. At least two library aliquots were prepared separately from each sample, indexing using recommended index sequences, pooled and sequencing on a NextSeq 500 (Illumina).

tag: experiment

value: Stages 3 to 6 timecourse

value: SC-beta protocol x1

value: Stage 6


title: ES/iPSC comparison (3 samples)

description:
Veres2019_analysis_data.tar
Raw FASTQ represent v3 inDrops non-demultiplexed files. Indices and sample matches are the following: TATGCAGT [iPS1016/31, protocol v4]; AGGCTTAG [iPS1016/31, protocol v4];  TCTTACGC [HUES8, protocol v4]; AGAGGATA [HUES8, protocol x3], CTCCTTAC [HUES8, protocol x3]. Files can de demultiplexed using the inDrops pipeline (https://github.com/indrops/).

value: in vitro differentiated pluripotent stem cell

value: ES/iPSC comparison

value: SC-beta protocol x3 or v4


title: DNase-seq_ILCP_rep1_GB3054

value: bone marrow

value: ILCP

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1+ IL-7Ra+


title: Wild-type input rep2


title: Met30 ChIP rep2

description:
macs_MT-1_peaks.narrowPeak
macs_MT_mean_treat_pileup.bedGraph

value: CSE4-HA met30-6


title: Wild-type input rep1


title: Cdc4 ChIP rep1

description:
macs_CD-1_peaks.narrowPeak
macs_CD_mean_treat_pileup.bedGraph

value: CSE4-HA cdc4-1


title: WaGa

status: Public on Apr 26 2019

city: Essen

first: Jan

last: Gravemeyer

address: Universitätstraße 1

country: Germany

institute: DKZF

data_processing:
The Cell Ranger Single Cell Software Suite version 2.1.1 (http://10xgenomics.com/) was used  with default settings to align cDNA reads to the hg19 human reference genome. For quality control, cells with less than 1000 UMI  counts, less than 200 genes or expressing more than 10% mitochondrial genes were removed  from analyses leaving in total 4187 cells. The Seurat R package was used for normalization and  biological analysis (Butler et al., 2018)
Genome_build: hg19
Supplementary_files_format_and_content: normalized and filtered expression count matrix without imputation (comma separated)

source_name: Merkel cell carcinoma

growth_protocol: WaGa cells were maintained RPMI culturing medium

extract_protocol:
Since WaGa cells are growing in suspension no isolation step was required and cells were  directly single cell barcoded using the 10x Genomics 3’ Chromium v2.0 platform
Library preparation was performed according to  the 10x Genomics protocol and the library afterwards sequenced on an Illumina HiSeq 4000  (Illumina)

treatment_protocol: no treatment was applied prior to RNA isolaiton

tag: cell line

value: WaGa


title: Met30 input rep2


title: Cdc4 ChIP rep2

description:
macs_CD-2_peaks.narrowPeak
macs_CD_mean_treat_pileup.bedGraph


title: Met30 input rep1


title: Cdc4 input rep2


title: Cdc4 input rep1


title: CD45+ cells: aPD1

status: Public on Dec 11 2018

city: Boston

first: Seth

middle: B

last: Garren

address: 185 Cambridge St

department: Systems Biology

institute: Massachusetts General Hospital

data_processing:
Cellranger v2.1 cellrangercount
Genome_build: mm10
Supplementary_files_format_and_content: unfiltered gene-barcode matrix

source_name: CD45+ tumor infiltrating cells

growth_protocol: MC38 tumors cell were injected intradermally into C57BL/6J mice at 2 x 106 cells per 50 μl at 4 sites in the mouse for 7 days

extract_protocol:
On day 10, mice were euthanized and tumors were isolated, digested, and single cells sorted on a BD FACSAria to isolate viable CD45+ cells.
Libraries were prepared according to 10x Genomics 3' manufacturers instructions (CG00052 Rev A)

treatment_protocol: tumors were injected with control or antiPD-1 antibody dosed at 200 μg per mouse per day

value: CD45+ immune cells


title: CD45+ cells: Control


title: Met30 ChIP rep1

description:
macs_MT-2_peaks.narrowPeak
macs_MT_mean_treat_pileup.bedGraph


title: wt_FAIRE_36h_rep2

value: wildtype

value: 36h APF


title: Ey ChIP-seq Replicate 2

status: Public on Sep 26 2018

first: Kelvin

last: Yeung

state: TX

address: One Baylor Plaza, Room S242

department: Pathology

institute: Baylor College of Medicine

data_processing:
Raw sequencing reads were mapped to the Drosophila reference genome dm3 using Burrows-Wheeler Aligner (BWA-MEM) in Unipro UGENE (v1.29.0) software using default parameters.
The aligned reads were then used for peak-calling by Model-based Analysis of ChIP-seq with default settings (MACS v1.4.2).
Genome_build: Drosophila reference genome dm3 (Release 5)
Supplementary_files_format_and_content: *.wig

source_name: L3 eye antennal discs

growth_protocol: Flies were raised at 25°C and late L3 larvae were collected for dissection.

extract_protocol:
400 Canton S third instar larval eye-antenna discs were dissected and crosslinked with 1% formaldehyde for 15 min and quenched by 125 mM Glycine for 5 min at room temperature. After washing with PBS, discs were lysed in lysis buffer (50 mM K-Hepes pH 7.8, 140 mM NaCl, 1 mM EGTA, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, protease inhibitors) and sonicated with a Branson sonifier to shear chromatin to ~200 - 400 bp.  The chromatin lysate was precleared with protein A sepharose (GE healthcare, #17-5280-01) and incubated with antibody at 4°C overnight. Protein A sepharose was added to the lysate for 3 hours to capture chromatin complexes. After three washes with lysis buffer, once with high salt wash buffer (50 mM K-Hepes pH 7.8, 500 mM NaCl, 1 mM EGTA, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, protease inhibitors) and once with TE (10 mM Tris pH8.0, 1 mm EDTA), chromatin complexes were eluted with 1% SDS, 10 mM Tris pH 8.0, and 1 mM EDTA at 65°C for 10 min, followed by reverse-crosslinking at 65°C overnight.
ChIP samples were purified using Qiagen PCR purification kit and sequenced based on the manufacturer’s instructions (Illumina, San Diego, CA).

value: Late L3

value: eye antennal discs

value: Canton S

value: anti-ey antibody


title: Ey ChIP-seq Replicate 1


title: human_atac_pk_granule

status: Public on Oct 12 2018

city: New York

first: Xiao

last: Xu

state: NY

address: 1230 York Ave

department: Laboratory of Molecular Biology

institute: The Rockefeller University

data_processing:
Adapter sequences were trimmed and reads were filtered depending on quality using Trim Galore! (trim_galore --stringency 3 --fastqc --paired *_R1_2.fastq.gz *_R2_2.fastq.gz).
Reads that passed the filter were aligned using Bowtie2 (Langmead and Salzberg, 2012) with parameters “-X 2000 --no-mixed --no-discordant” to the Homo sapiens reference genome (hg38).
Duplicate reads were removed using SAMtools (Li et al., 2009).
Reads were normalized to 1x depth (reads per genome coverage, RPGC) and input using deepTools (Ramirez et al., 2016) bamCompare module, ignoring chrX, chrY, chrM and filtering reads for minimum mapping quality of 30.
For data visualization, tdf files were generated using igvtools.
Unique fragments under 100 nt were selected as they could not contain a nucleosome. These fragments were used to call peaks with MACS2 with parameters “--nomodel -q 0.01 --call-summits --keep-dup all”. The summits for each peak from the replicates were extended to 500bp using bedtools slop. The peaks were filtered to remove chrY and chrM peaks and peaks that overlap with the hg38 blacklist from ENCODE (Consortium, 2012; Kundaje, 2013).
Genome_build: hg38
Supplementary_files_format_and_content: tdf format for visualization in IGV
Supplementary_files_format_and_content: txt format of called peaks

source_name: ATAC-seq using nuclei from specific cell types

extract_protocol:
Nuclei were isolated from post-mortem cerebellar tissue. ATAC-seq libraries were prepared as described previously (Buenrostro et al., 2013; 2015) with the following modifications: nuclei were resuspended in ice-cold lysis buffer, omitting incubation step on ice and centrifuged. Transposition reaction was performed for 30 min at 37°C using Tn5 transposase from Nextera. DNA fragments were purified and size selected using AMPure XP beads to yield 100-700bp fragments.
Libraries were generated using the Nextera DNA Library Preparation Kit. ATAC-seq libraries were sequenced on Illumina NextSeq 500 to obtain 75bp paired-ended reads.

tag: gender

value: female

tag: age

tag: brain region

value: cerebellum


title: human_atac_xk_basket

value: male


title: No Antibody ChIP-seq Replicate 2


title: No Antibody ChIP-seq Replicate 1


title: Sample2439_BCellData

status: Public on Apr 18 2018

city: Newcastle upon Tyne

first: Arthur

last: Pratt

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

description:
3999319005_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis

hyb_protocol: Illumina HT12 BeadChip

scan_protocol: Illumina iScan

data_processing: Normalisation via VST (Variance Stabilising Transformation and RSN (Robust Spline Normalisation)

source_name: purified peripheral blood CD19+ B cells

label_protocol: cRNA generated from 250ng total RNA using Illumina TotalPrep RNA Amplification kit

growth_protocol: Peripheral blood mononuclear cells first isolated by density centrifugation on Lymphoprep (Axis-Shield Diagnostics, Dundee, UK) underwent positive selection using anti-CD19 magnetic microbeads (Miltenyi Biotec, Bergisch, Gladback, Germany); median cell purity was 96.4% by flow cytometry. Total B lymphocyte RNA was immediately extracted using the AllPrep DNA/RNA Mini kit (Qiagen GmbH, Germany), then quality controlled using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA). The median RNA integrity number of samples used was 9.4

extract_protocol: AllPrep RNA extraction kit (Qiagen)

treatment_protocol: No ex vivo treatment

value: peripheral blood

value: CD19+ B cells

value: Undifferentiated Inflammatory Arthritis

value: F


title: Sample2519_BCellData

description:
3999350063_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2511_BCellData

description:
3999350063_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2437_BCellData

description:
3999319005_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis

value: M


title: Sample2549_BCellData

description:
3999350063_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2476_BCellData

description:
3999350096_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2379_BCellData

description:
3999319005_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2510_BCellData

description:
3999350063_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2759_BCellData

description:
3999350089_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis

value: Rheumatoid Arthritis


title: Sample2506_BCellData

description:
3999350063_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2493_BCellData

description:
3999350063_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2507_BCellData

description:
3999350063_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2264_BCellData

description:
3999350075_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Enteropathic Arthritis

value: Enteropathic Arthritis


title: Sample2305_BCellData

description:
3999350076_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2345_BCellData

description:
3999350077_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2348_BCellData

description:
3999350077_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2367_BCellData

description:
3999319005_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2368_BCellData

description:
3999319005_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2231_BCellData

description:
3999319015_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2233_BCellData

description:
3999319015_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis

value: Other Inflammatory Arthritis


title: Sample2322_BCellData

description:
9477874154_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Crystal Arthritis

value: Crystal Arthritis


title: Sample2311_BCellData

description:
3999350076_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2330_BCellData

description:
3999350077_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2145_BCellData

description:
3999319008_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Enteropathic Arthritis


title: Sample2281_BCellData

description:
3999350075_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample2203_BCellData

description:
3999350115_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2133_BCellData

description:
3999350128_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2197_BCellData

description:
3999350115_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2390_BCellData

description:
3999319005_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2257_BCellData

description:
3999319015_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2090_BCellData

description:
9477874154_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2087_BCellData

description:
3999350128_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis

value: Psoriatic Arthritis


title: Sample2222_BCellData

description:
9477874154_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis

value: Reactive Arthritis


title: Sample2072_BCellData

description:
3999319019_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2078_BCellData

description:
3999319019_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Crystal Arthritis


title: Sample2054_BCellData

description:
3999319019_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Crystal Arthritis


title: Sample2052_BCellData

description:
3999319019_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory

value: Non-Inflammatory


title: Sample2040_BCellData

description:
3999319011_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis

value: Osteoarthritis


title: Sample2062_BCellData

description:
3999319019_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Crystal Arthritis


title: Sample2086_BCellData

description:
3999350128_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample1085_BCellData

description:
3999319034_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample1083_BCellData

description:
3999319016_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1080_BCellData

description:
3999319016_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample2010_BCellData

description:
3999319034_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2030_BCellData

description:
3999319011_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2029_BCellData

description:
3999319011_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample822_BCellData

description:
3999319011_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample1088_BCellData

description:
3999319034_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample1058_BCellData

description:
9477874154_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample2047_BCellData

description:
3999319019_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample1037_BCellData

description:
3999350082_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Crystal Arthritis


title: Sample2012_BCellData

description:
3999319034_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample2045_BCellData

description:
3999319011_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1076_BCellData

description:
3999319016_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample1028corrected_BCellData

description:
3999844005_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Crystal Arthritis


title: Sample1054_BCellData

description:
3999319016_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample1032_BCellData

description:
3999853061_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1008corrected_BCellData

description:
3999853061_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample1087_BCellData

description:
3999319034_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Crystal Arthritis


title: Sample1010_BCellData

description:
3999319007_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1029corrected_BCellData

description:
3999853061_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1070_BCellData

description:
3999319016_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample1020corrected_BCellData

description:
3999844002_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample1022_BCellData

description:
3999844002_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Spondylo-Arthropathy

value: Undifferentiated Spondylo-Arthropathy


title: Sample1006corrected_BCellData

description:
3999853061_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample1005corrected_BCellData

description:
3999844005_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1072_BCellData

description:
3999319016_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1019corrected_BCellData

description:
3999844007_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample1000corrected_BCellData

description:
3999844002_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2034_BCellData

description:
9477874154_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample980_BCellData

description:
3999319007_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample996corrected_BCellData

description:
3999844007_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample969corrected_BCellData

description:
3999844002_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample1003corrected_BCellData

description:
3999844002_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample973corrected_BCellData

description:
3999844002_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Inflammatory Arthritis


title: Sample992_BCellData

description:
3999319021_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample995_BCellData

description:
3999319021_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample962_BCellData

description:
3999319021_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample967corrected_BCellData

description:
3999844007_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample965_BCellData

description:
3999319021_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample978corrected_BCellData

description:
3999853061_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample974corrected_BCellData

description:
3999844005_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample975corrected_BCellData

description:
3999853061_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample946corrected_BCellData

description:
3999853061_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample954_BCellData

description:
3999350082_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample932_BCellData

description:
3999319036_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample938_BCellData

description:
3999844002_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample948_BCellData

description:
3999319007_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample957_BCellData

description:
3999350082_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample937corrected_BCellData

description:
3999844007_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Crystal Arthritis


title: Sample941corrected_BCellData

description:
3999844002_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample930_BCellData

description:
3999350082_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample915corrected_BCellData

description:
3999844005_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample925corrected_BCellData

description:
3999853061_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample914corrected_BCellData

description:
3999844002_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample923_BCellData

description:
3999844005_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample912_BCellData

description:
3999844007_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample892corrected_BCellData

description:
3999844005_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample926_BCellData

description:
3999319007_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample944corrected_BCellData

description:
3999844005_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample893corrected_BCellData

description:
3999844005_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample890corrected_BCellData

description:
3999844007_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample908corrected_BCellData

description:
3999844007_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample905_BCellData

description:
3999319036_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Spondylo-Arthropathy


title: Sample896corrected_BCellData

description:
3999853061_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample884corrected_BCellData

description:
3999844007_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample898_BCellData

description:
3999319007_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample856corrected_BCellData

description:
3999844002_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample850corrected_BCellData

description:
3999844007_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample857corrected_BCellData

description:
3999844005_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample882_BCellData

description:
3999319036_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample878_BCellData

description:
9477874154_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample861corrected_BCellData

description:
3999844005_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample855corrected_BCellData

description:
3999844007_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample879_BCellData

description:
3999350082_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample845_BCellData

description:
3999319036_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample891corrected_BCellData

description:
3999844002_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample841_BCellData

description:
3999319007_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample827corrected_BCellData

description:
3999844007_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample836corrected_BCellData

description:
3999853061_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample835corrected_BCellData

description:
3999844005_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample833corrected_BCellData

description:
3999844002_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: EA2145_NRAIA

status: Public on Apr 03 2018

hyb_protocol: cRNA was hybridized to the Illumina WG6 (version 4) BeadChip (Illumina, San Diego, following the manufacturer’s protocol.

scan_protocol: Illumina BeadArray Reader as per Illumina protocol.

data_processing: Normalisation of component dataset[s] (which, in some cases included raw data extracted from Pratt AG et al 2012; GEO accession GSE20098) was first carried out by robust spline normalisation (RSN) , and variance stability transformation (VST) (Du P et al 2008 Bioinformatics; Lin SM et al 2008 Nucleic Acids Res). Unique IDs for defined analyses are listed in relevant manuscript text. Where required data were merged using InSilicoMerging Bioconductor package (Taminau J et al 2012 BMC Bioinformatics), and batch correction was carried out by linear modelling Batch correction was carried out by linear modelling  (Ritchie ME et al 2015 Nucleic Acids Res).

source_name: NRAIA_Blood CD4+ T Cells

label_protocol: 50ng RNA was reverse transcribed into cRNA, and biotin-UTP labeled, using the Illumina TotalPrep RNA Amplification Kit (Ambion, Texas).

extract_protocol: Monocytes were first depleted by immunorosetting (Rosettesep Human Monocyte depletion cocktail, Stemcell Technologies Inc., Vancouver, non-RA inflammatory arthritisanada), and remaining cells underwent positive selection using Easisep whole blood CD4+ positive selection kit reagents in conjunction with the Robosep automated cell separator (Stemcell). CD4+ T-cell purity was determined using standard flow cytometry techniques; FITC-conjugated anti-CD4 and PE-conjugated anti-CD14 antibodies were used (Beckton Dickinson, New Jersey, USA). RNA was immediately extracted from CD4+ T-cell isolates using RNeasy MINI kits (Qiagen GmbH, Germany), incorporating an “on-column” DNA digestion step.

treatment_protocol: Between 0900 and 1200hrs during the clinic appointment, 15ml peripheral whole blood was drawn into EDTA tubes (Greiner Bio-One, ACPA- RAustria) and stored at room temperature for a maximum of 4 hours before processing.

tag: age (yrs)

tag: diagnostic category

value: Non-RA inflammatory arthritis (NRAIA) - includes Code A 4-11)

value: CD4+ T-cell


title: EA2231_ACPApRA

source_name: ACPApRA_Blood CD4+ T Cells

value: ACPA-pos RA

tag: tissue


title: EA1080_NRAIA

value: peripheral blood


title: EA1083_ACPApRA


title: EA1085_NRAIA


title: EA2148_NRAIA


title: EA2086_ACPApRA


title: EA2257_UA

source_name: UA_Blood CD4+ T Cells

value: Undifferentiated arthritis


title: EA2075_NRAIA


title: EA2042_ACPAnRA

source_name: ACPAnRA_Blood CD4+ T Cells

value: ACPA-neg RA


title: Sample826_BCellData

description:
3999844007_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis

value: CD19+ B cells

value: Undifferentiated Inflammatory Arthritis

tag: Sex

value: F


title: EA0912_NRAIA


title: EA1076_NRAIA


title: EA2067_NiA

source_name: NiA_Blood CD4+ T Cells

value: Non-inflammatory arthritis/arthalgia - includes Code A 1 & 2


title: EA2040_NiA


title: EA2044_NRAIA


title: EA2034_NRAIA


title: EA2144_NRAIA

value: M


title: EA2078_NRAIA


title: EA1022_NRAIA


title: EA2222_NRAIA


title: EA1054_NiA


title: EA2012_NRAIA


title: EA2010_ACPApRA


title: EA1032_ACPApRA


title: EA1051_ACPAnRA


title: EA1058_NRAIA


title: EA1020_UA


title: EA2140_NRAIA


title: EA2090_ACPApRA


title: EA2087_NRAIA


title: EA2029_ACPApRA


title: EA2030_ACPAnRA


title: EA2062_NRAIA


title: EA0975_ACPApRA


title: EA1042_ACPApRA


title: EA1050_NRAIA


title: EA1070_NRAIA


title: EA1008_NRAIA


title: EA2047_NRAIA


title: EA1087_NRAIA


title: EA1005_ACPAnRA


title: EA1010_ACPAnRA


title: EA1019_NiA


title: EA1037_NRAIA


title: EA0974_ACPAnRA


title: EA0978_ACPAnRA


title: EA2054_NRAIA


title: EA2052_NiA


title: EA1088_NRAIA


title: EA1072_ACPAnRA


title: EA1000_ACPAnRA


title: EA1003_ACPApRA


title: EA1094_ACPApRA


title: EA2072_ACPApRA


title: EA0915_ACPAnRA


title: EA0891_NRAIA


title: EA0946_ACPApRA


title: EA0827_ACPAnRA


title: EA0945_UA


title: EA0842_NRAIA


title: EA0815_NRAIA


title: EA0896_ACPAnRA


title: EA0814_UA


title: EA0840_ACPAnRA


title: EA0829_NRAIA


title: EA0841_NRAIA


title: EA0838_ACPApRA


title: EA0826_NiA


title: EA0992_ACPApRA


title: EA0995_ACPAnRA


title: EA0938_ACPAnRA


title: EA0980_NRAIA


title: EA0962_NRAIA


title: EA0954_NRAIA


title: EA0935_NRAIA


title: EA0967_NRAIA


title: EA0905_NRAIA


title: EA0965_NiA


title: GH infusion_14d male liver pool 1_polyA-selected_G96_M5

status: Public on Jul 14 2017

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: poly-A selected RNA, unstranded library

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene. Primary RNA transcripts (hnRNA) were quantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; this counting thus excludes sequence reads that map to an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics),
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and differential expression results comparing cGH-treated male mouse livers to sham-treated male mouse livers; The raw sequencing data for the sham-treated controls is found in GEO series GSE66140, samples GSM1612771, GSM1612772, and GSM1612773.

source_name: liver tissue

extract_protocol:
RNA was extracted from flash fozen mouse liver using Trizol per the manufacturer's instructions.
RNA was polyA-selected and sequencing libraries were prepared using the Illumina TruSeq RNA library preparation kit (Illumina, cat# RS-122-2001), according to the manufacturer's instructions.

treatment_protocol: Male CD1 mice, 8–9 weeks of age, were purchased from Charles River Laboratories  (Crl:CD1(ICR)). Alzet osmotic pumps (model 1007D) were filled with recombinant rat GH and were implanted subcutaneously under ketamine and xylazine anesthesia. GH was infused at a rate of 25 ng/g body weight/h for either 10 h or 14 d.

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: treatment

value: Continuous GH 14 days

value: Male

value: 8-9 weeks


title: EA0932_ACPApRA


title: EA0934_ACPAnRA


title: EA0930_ACPAnRA


title: EA0937_NRAIA