title: HiC_CTCF-AID_auxin_48hr_rep1

data_processing:
fastq: Illumina's HiSeq Control Software
Hi-C reads were aligned as single end reads using BWA with default parameters. Uniquely mapping reads were manually paired using in an in house pipeline. PCR duplicate reads were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (HIC) were generated useing juicebox pre (Neva et al., 2016).

extract_protocol:
Hi-C experiments were conducted using Mbo1 according to previous publication (Rao et al., 2014).
Hi-C library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).

treatment_protocol: To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24 or 48 hours after stating auxin treatment. Neural cell differentiation treatment was performed with or without auxin treatment, and the neural precursor cells were harvested on day 4 or 2 days after washing out auxin from the day 4 sample.


title: 5080_55670_KLF4 E18.5 CONT 13: Epidermis, control 1

status: Public on Aug 23 2020

type: RNA

city: New York

first: Sarah

middle: E

last: Millar

state: NY

address: Icahn Building, Floor 13 Room 020C, 1425 Madison Ave

department: Developmental, Cell and Regenerative Biology

country: USA

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Cel files were RMA normalized in Transcriptome Analysis Console (TAC, v4.0.2, ThermoFisher)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: E18.5 epidermis

label_protocol: 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: Pregnant dams were placed on 1g/kg doxycycline chow from gestational age E8.5 to E18.5

extract_protocol: Trizol extraction of total RNA was performed using the Qiagen RNeasy kit

treatment_protocol: Dorsal skin was floated dermis side down on dispase solution and incubated at 37ºC until the epidermis could be easily removed. Epidermis was stored in Trizol following the manufacturer's instructions

tag: tissue

value: epidermis

tag: age

tag: genotype

value: control

tag: litter

value: litter 1


title: Adult-Stomach3-1

status: Public on Feb 10 2020

type: SRA

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

library_source: transcriptomic

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Homo_sapiens. GRCh38 assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Homo_sapiens. GRCh38
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

organism: Homo sapiens

source_name: Microwell-seq analysis

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

tag: Sex

value: Male

value: Stomach


title: KLF4 E18.5 CONT 4: Epidermis, control 6

value: litter 2


title: Adult-Stomach2


title: CTCF-AID_rna_auxin_0hr_rep2

status: Public on Mar 06 2020

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
fastq: Illumina's HiSeq Control Software
RNA-seq reads were aligned against the mouse mm10 genome assembly using STAR (Dobin et al., 2013). The processed data was created using HTseq (Anders et al., 2015) and used for differential expression analysis by edgeR (Robinson et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: The processed file include all sample data of the number of read counts in each gene that were calculated using HTseq (Anders et al., 2015).

source_name: embryonic stem cells

growth_protocol: Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2

extract_protocol: RNA-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).

treatment_protocol: To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24, 48 or 96 hours after stating auxin treatment. Neural progenitor cell differentiation treatment was performed with or without auxin treatment, and harvested on day 2, 4, 6 and 2 days after washing out auxin from day 4 and day 6 samples.

tag: cell line

value: F123 mouse ES cell


title: HiC_CTCF-AID_auxin_48hr_rep2

library_source: genomic

molecule: genomic DNA


title: Adult-Stomach3-2


title: Adult-Stomach3-3


title: HiC_CTCF-AID_auxin_0hr_rep1


title: HiC_CTCF-AID_auxin_0hr_rep2


title: 5080_55669_KLF4 E18.5 MUT 12: Epidermis, Klf4 mutant 2

value: Klf4 mutant


title: Adult-Stomach1


title: KLF4 E18.5 CONT 1: Epidermis, control 3


title: kidney biopsy 1230

status: Public on Nov 07 2019

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: archetype cluster (1,2,3,4,5,6,7)

value: yes

tag: in n=102? (yes, no)

value: no

tag: mmdx (abmr, pabmr, mixed, tcmr, ptcmr, nr, na)

value: TCMR


title: kidney biopsy 1723

value: Mixed


title: kidney biopsy 1481

tag: in n=321? (yes, no)

value: ABMR


title: kidney biopsy 360

value: NR


title: kidney biopsy 1149


title: kidney biopsy 1485


title: kidney biopsy 1644


title: kidney biopsy 477


title: kidney biopsy 1609

value: pABMR


title: kidney biopsy 1433


title: kidney biopsy 375


title: kidney biopsy 147


title: kidney biopsy 226


title: kidney biopsy 1083


title: kidney biopsy 481


title: kidney biopsy 1105


title: kidney biopsy 432


title: kidney biopsy 1499


title: kidney biopsy 308


title: kidney biopsy 519


title: kidney biopsy 1719


title: kidney biopsy 525


title: kidney biopsy 762


title: kidney biopsy 1361


title: kidney biopsy 1223


title: kidney biopsy 1188


title: kidney biopsy 1492


title: kidney biopsy 1267


title: kidney biopsy 1162


title: kidney biopsy 668


title: kidney biopsy 1102


title: kidney biopsy 571


title: kidney biopsy 648


title: kidney biopsy 1265


title: kidney biopsy 851


title: kidney biopsy 112


title: kidney biopsy 1156


title: kidney biopsy 806


title: kidney biopsy 746


title: kidney biopsy 930


title: kidney biopsy 1107


title: kidney biopsy 83


title: kidney biopsy 14


title: kidney biopsy 457


title: kidney biopsy 675

value: pTCMR


title: kidney biopsy 1222


title: kidney biopsy 1281


title: kidney biopsy 1166


title: kidney biopsy 1194


title: kidney biopsy 340


title: kidney biopsy 1358


title: kidney biopsy 1333


title: kidney biopsy 475


title: kidney biopsy 285


title: kidney biopsy 959

tag: hprt (positive, negative)

value: Negative


title: kidney biopsy 1706


title: kidney biopsy 1296


title: kidney biopsy 896


title: kidney biopsy 1507


title: kidney biopsy 786


title: kidney biopsy 833


title: kidney biopsy 1712


title: kidney biopsy 1462


title: kidney biopsy 409


title: kidney biopsy 1101


title: kidney biopsy 1643


title: kidney biopsy 825


title: kidney biopsy 719


title: kidney biopsy 220


title: kidney biopsy 84


title: kidney biopsy 400


title: kidney biopsy 410


title: kidney biopsy 1493


title: kidney biopsy 727


title: kidney biopsy 620


title: kidney biopsy 1158


title: kidney biopsy 445


title: kidney biopsy 1616


title: kidney biopsy 101


title: kidney biopsy 884


title: kidney biopsy 1012


title: kidney biopsy 816


title: kidney biopsy 441


title: kidney biopsy 690


title: kidney biopsy 524


title: kidney biopsy 991


title: kidney biopsy 149


title: kidney biopsy 255


title: kidney biopsy 1363


title: kidney biopsy 209


title: kidney biopsy 520


title: kidney biopsy 1008


title: kidney biopsy 883


title: kidney biopsy 858


title: kidney biopsy 1344


title: kidney biopsy 347


title: kidney biopsy 316


title: kidney biopsy 1183


title: kidney biopsy 171


title: kidney biopsy 827


title: kidney biopsy 1390


title: kidney biopsy 1745


title: kidney biopsy 908


title: kidney biopsy 557


title: kidney biopsy 48


title: kidney biopsy 1035


title: kidney biopsy 346


title: kidney biopsy 960


title: kidney biopsy 859


title: kidney biopsy 1495


title: kidney biopsy 692


title: kidney biopsy 36


title: kidney biopsy 995


title: kidney biopsy 903


title: kidney biopsy 1513


title: kidney biopsy 396


title: kidney biopsy 1488


title: kidney biopsy 1244


title: kidney biopsy 1478


title: kidney biopsy 979


title: kidney biopsy 383


title: kidney biopsy 1652


title: kidney biopsy 291


title: kidney biopsy 449


title: kidney biopsy 498


title: kidney biopsy 1534


title: kidney biopsy 444


title: kidney biopsy 353


title: kidney biopsy 472


title: kidney biopsy 198


title: kidney biopsy 1242


title: kidney biopsy 1146


title: kidney biopsy 1342


title: kidney biopsy 576


title: kidney biopsy 612


title: kidney biopsy 1306


title: kidney biopsy 1234


title: kidney biopsy 313


title: kidney biopsy 99


title: kidney biopsy 487


title: kidney biopsy 1400


title: kidney biopsy 745


title: kidney biopsy 1612


title: kidney biopsy 921


title: kidney biopsy 1514


title: kidney biopsy 1293


title: kidney biopsy 785

value: Positive


title: kidney biopsy 505


title: kidney biopsy 174


title: kidney biopsy 1710


title: kidney biopsy 1435


title: kidney biopsy 1528


title: kidney biopsy 27


title: kidney biopsy 1057


title: kidney biopsy 743


title: kidney biopsy 779


title: kidney biopsy 479


title: kidney biopsy 1184


title: kidney biopsy 78


title: kidney biopsy 1411


title: kidney biopsy 587


title: kidney biopsy 1640


title: kidney biopsy 355


title: kidney biopsy 1651


title: kidney biopsy 929


title: kidney biopsy 45


title: kidney biopsy 622


title: kidney biopsy 453


title: kidney biopsy 638


title: kidney biopsy 211


title: kidney biopsy 442


title: kidney biopsy 710


title: kidney biopsy 492


title: kidney biopsy 596


title: kidney biopsy 339


title: kidney biopsy 1634


title: kidney biopsy 1531


title: kidney biopsy 615


title: kidney biopsy 547


title: kidney biopsy 1033


title: kidney biopsy 194


title: kidney biopsy 905


title: kidney biopsy 793


title: kidney biopsy 110


title: kidney biopsy 421


title: kidney biopsy 1240


title: kidney biopsy 893


title: kidney biopsy 560


title: kidney biopsy 1252


title: kidney biopsy 1498


title: kidney biopsy 366


title: kidney biopsy 1574


title: kidney biopsy 1075


title: kidney biopsy 1000


title: kidney biopsy 1500


title: kidney biopsy 1442


title: kidney biopsy 1422


title: kidney biopsy 235


title: kidney biopsy 1354


title: kidney biopsy 1734


title: kidney biopsy 1458


title: kidney biopsy 1042


title: kidney biopsy 290


title: kidney biopsy 1675


title: kidney biopsy 1204


title: kidney biopsy 1069


title: kidney biopsy 764


title: kidney biopsy 51


title: kidney biopsy 881


title: kidney biopsy 1419


title: kidney biopsy 870


title: kidney biopsy 589


title: kidney biopsy 1613


title: kidney biopsy 1286


title: kidney biopsy 1722


title: kidney biopsy 286


title: kidney biopsy 999


title: kidney biopsy 644


title: kidney biopsy 1693


title: kidney biopsy 1529


title: kidney biopsy 973


title: kidney biopsy 1065


title: kidney biopsy 595


title: kidney biopsy 783


title: kidney biopsy 1208


title: kidney biopsy 1053


title: kidney biopsy 634


title: kidney biopsy 928


title: kidney biopsy 169


title: kidney biopsy 273


title: kidney biopsy 747


title: kidney biopsy 898


title: kidney biopsy 887


title: kidney biopsy 754


title: kidney biopsy 911


title: kidney biopsy 122


title: kidney biopsy 1336


title: kidney biopsy 818


title: kidney biopsy 1690


title: kidney biopsy 1298


title: kidney biopsy 1662


title: kidney biopsy 65


title: kidney biopsy 759


title: kidney biopsy 422


title: kidney biopsy 935


title: kidney biopsy 247


title: kidney biopsy 712


title: kidney biopsy 1560


title: kidney biopsy 1314


title: kidney biopsy 232


title: kidney biopsy 1329


title: kidney biopsy 1715


title: kidney biopsy 495


title: kidney biopsy 15


title: kidney biopsy 1319


title: kidney biopsy 1694


title: kidney biopsy 5


title: kidney biopsy 933


title: kidney biopsy 332


title: kidney biopsy 562


title: kidney biopsy 1457


title: kidney biopsy 1725


title: kidney biopsy 1301


title: kidney biopsy 312


title: kidney biopsy 1257


title: kidney biopsy 4


title: kidney biopsy 1232


title: kidney biopsy 321


title: kidney biopsy 342


title: kidney biopsy 1238


title: kidney biopsy 1489


title: kidney biopsy 1425


title: kidney biopsy 1550


title: kidney biopsy 770


title: kidney biopsy 238


title: kidney biopsy 972


title: kidney biopsy 1338


title: kidney biopsy 1299


title: kidney biopsy 438


title: kidney biopsy 713


title: kidney biopsy 187


title: kidney biopsy 604


title: kidney biopsy 1623


title: kidney biopsy 203


title: kidney biopsy 1067


title: kidney biopsy 50


title: kidney biopsy 1098


title: kidney biopsy 927


title: kidney biopsy 82


title: kidney biopsy 61


title: kidney biopsy 1622


title: kidney biopsy 548


title: kidney biopsy 482


title: kidney biopsy 269


title: kidney biopsy 399


title: kidney biopsy 1297


title: kidney biopsy 1190


title: kidney biopsy 1186


title: kidney biopsy 878


title: kidney biopsy 894


title: kidney biopsy 429


title: kidney biopsy 807


title: kidney biopsy 244


title: kidney biopsy 839


title: kidney biopsy 236


title: kidney biopsy 1071


title: kidney biopsy 1526


title: kidney biopsy 1637


title: kidney biopsy 156


title: kidney biopsy 1732


title: kidney biopsy 382


title: kidney biopsy 1405


title: kidney biopsy 1629


title: kidney biopsy 900


title: kidney biopsy 1271


title: kidney biopsy 873


title: kidney biopsy 594


title: kidney biopsy 1355


title: kidney biopsy 849


title: kidney biopsy 558


title: kidney biopsy 798


title: kidney biopsy 728


title: kidney biopsy 55


title: kidney biopsy 134


title: kidney biopsy 264


title: kidney biopsy 1630


title: kidney biopsy 165


title: kidney biopsy 153


title: kidney biopsy 502


title: kidney biopsy 185


title: kidney biopsy 1191


title: kidney biopsy 1251


title: kidney biopsy 120


title: kidney biopsy 1592


title: kidney biopsy 1388


title: kidney biopsy 309


title: kidney biopsy 812


title: kidney biopsy 1229


title: kidney biopsy 1665


title: kidney biopsy 186


title: kidney biopsy 1667


title: kidney biopsy 1541


title: kidney biopsy 1524


title: kidney biopsy 1744


title: kidney biopsy 1459


title: kidney biopsy 706


title: kidney biopsy 108


title: kidney biopsy 190


title: kidney biopsy 527


title: kidney biopsy 1677


title: kidney biopsy 301


title: kidney biopsy 1090


title: kidney biopsy 1438


title: kidney biopsy 1128


title: kidney biopsy 822


title: kidney biopsy 1155


title: kidney biopsy 195


title: kidney biopsy 41


title: kidney biopsy 1660


title: kidney biopsy 140


title: kidney biopsy 1636


title: kidney biopsy 1283


title: kidney biopsy 602


title: kidney biopsy 1077


title: kidney biopsy 566


title: kidney biopsy 574


title: kidney biopsy 287


title: kidney biopsy 1351


title: kidney biopsy 164


title: kidney biopsy 1292


title: kidney biopsy 600


title: kidney biopsy 567


title: kidney biopsy 305


title: kidney biopsy 523


title: kidney biopsy 748


title: kidney biopsy 486


title: kidney biopsy 434


title: kidney biopsy 1530


title: kidney biopsy 73


title: kidney biopsy 1617


title: kidney biopsy 1727


title: kidney biopsy 1741


title: kidney biopsy 484


title: kidney biopsy 737


title: kidney biopsy 469


title: kidney biopsy 913


title: kidney biopsy 1409


title: kidney biopsy 1583


title: kidney biopsy 687


title: kidney biopsy 1118


title: kidney biopsy 1135


title: kidney biopsy 1549


title: kidney biopsy 1066


title: kidney biopsy 1056


title: kidney biopsy 262


title: kidney biopsy 1653


title: kidney biopsy 992


title: kidney biopsy 1581


title: kidney biopsy 405


title: kidney biopsy 953


title: kidney biopsy 398


title: kidney biopsy 160


title: kidney biopsy 371


title: kidney biopsy 1141


title: kidney biopsy 522


title: kidney biopsy 1015


title: kidney biopsy 1661


title: kidney biopsy 1032


title: kidney biopsy 966


title: kidney biopsy 384


title: kidney biopsy 18


title: kidney biopsy 1593


title: kidney biopsy 521


title: kidney biopsy 411


title: kidney biopsy 956


title: kidney biopsy 943


title: kidney biopsy 1317


title: kidney biopsy 494


title: kidney biopsy 769


title: kidney biopsy 1187


title: kidney biopsy 504


title: kidney biopsy 808


title: kidney biopsy 1332


title: kidney biopsy 1099


title: kidney biopsy 167


title: kidney biopsy 1054


title: kidney biopsy 279


title: kidney biopsy 613


title: kidney biopsy 1010


title: kidney biopsy 1112


title: kidney biopsy 1516


title: kidney biopsy 306


title: kidney biopsy 1428


title: kidney biopsy 62


title: kidney biopsy 250


title: kidney biopsy 1455


title: kidney biopsy 1256


title: kidney biopsy 819


title: kidney biopsy 341


title: kidney biopsy 412


title: kidney biopsy 1668


title: kidney biopsy 34


title: kidney biopsy 1494


title: kidney biopsy 998


title: kidney biopsy 1127


title: kidney biopsy 386


title: kidney biopsy 1736


title: kidney biopsy 718


title: kidney biopsy 1325


title: kidney biopsy 1349


title: kidney biopsy 1164


title: kidney biopsy 882


title: kidney biopsy 1447


title: kidney biopsy 585


title: kidney biopsy 208


title: kidney biopsy 1575


title: kidney biopsy 21


title: kidney biopsy 534


title: kidney biopsy 1542


title: kidney biopsy 799


title: kidney biopsy 1315


title: kidney biopsy 30


title: kidney biopsy 1571


title: kidney biopsy 39


title: kidney biopsy 193


title: kidney biopsy 143


title: kidney biopsy 106


title: kidney biopsy 1579


title: kidney biopsy 944


title: kidney biopsy 491


title: kidney biopsy 331


title: kidney biopsy 89


title: kidney biopsy 1648


title: kidney biopsy 990


title: kidney biopsy 658


title: kidney biopsy 447


title: kidney biopsy 1133


title: kidney biopsy 315


title: kidney biopsy 1394


title: kidney biopsy 464


title: kidney biopsy 1094


title: kidney biopsy 623


title: kidney biopsy 1483


title: kidney biopsy 1589


title: kidney biopsy 512


title: kidney biopsy 684


title: kidney biopsy 1415


title: kidney biopsy 394


title: kidney biopsy 701


title: kidney biopsy 265


title: kidney biopsy 131


title: kidney biopsy 299


title: kidney biopsy 717


title: kidney biopsy 1620


title: kidney biopsy 952


title: kidney biopsy 1285


title: kidney biopsy 1658


title: kidney biopsy 385


title: kidney biopsy 397


title: kidney biopsy 926


title: kidney biopsy 1021


title: kidney biopsy 787


title: kidney biopsy 1471


title: kidney biopsy 670


title: kidney biopsy 1109


title: kidney biopsy 699


title: kidney biopsy 1002


title: kidney biopsy 837


title: kidney biopsy 1279


title: kidney biopsy 679


title: kidney biopsy 40


title: kidney biopsy 781


title: kidney biopsy 861


title: kidney biopsy 74


title: kidney biopsy 871


title: kidney biopsy 430


title: kidney biopsy 1273


title: kidney biopsy 1276


title: kidney biopsy 248


title: kidney biopsy 1139


title: kidney biopsy 210


title: kidney biopsy 564


title: kidney biopsy 1138


title: kidney biopsy 1372


title: kidney biopsy 1467


title: kidney biopsy 12


title: kidney biopsy 128


title: kidney biopsy 125


title: kidney biopsy 1215


title: kidney biopsy 7


title: kidney biopsy 729


title: kidney biopsy 1595


title: kidney biopsy 1738


title: kidney biopsy 1197


title: kidney biopsy 1318


title: kidney biopsy 1038


title: kidney biopsy 606


title: kidney biopsy 376


title: kidney biopsy 1050


title: kidney biopsy 1322


title: kidney biopsy 17


title: kidney biopsy 633


title: kidney biopsy 955


title: kidney biopsy 234


title: kidney biopsy 814


title: kidney biopsy 413


title: kidney biopsy 1389


title: kidney biopsy 476


title: kidney biopsy 722


title: kidney biopsy 133


title: kidney biopsy 853


title: kidney biopsy 239


title: kidney biopsy 1642


title: kidney biopsy 1089


title: kidney biopsy 711


title: kidney biopsy 270


title: kidney biopsy 1572


title: kidney biopsy 1699


title: kidney biopsy 847


title: kidney biopsy 1704


title: kidney biopsy 983


title: kidney biopsy 300


title: kidney biopsy 886


title: kidney biopsy 1259


title: kidney biopsy 539


title: kidney biopsy 204


title: kidney biopsy 1


title: kidney biopsy 168


title: kidney biopsy 1201


title: kidney biopsy 1473


title: kidney biopsy 1080


title: kidney biopsy 734


title: kidney biopsy 1408


title: kidney biopsy 1312


title: kidney biopsy 554


title: kidney biopsy 278


title: kidney biopsy 683


title: kidney biopsy 1379


title: kidney biopsy 1743


title: kidney biopsy 333


title: kidney biopsy 971


title: kidney biopsy 76


title: kidney biopsy 967


title: kidney biopsy 1548


title: kidney biopsy 1635


title: kidney biopsy 584


title: kidney biopsy 1600


title: kidney biopsy 240


title: kidney biopsy 1682


title: kidney biopsy 283


title: kidney biopsy 298


title: kidney biopsy 1515


title: kidney biopsy 1502


title: kidney biopsy 228


title: kidney biopsy 184


title: kidney biopsy 1562


title: kidney biopsy 23


title: kidney biopsy 163


title: kidney biopsy 846


title: kidney biopsy 408


title: kidney biopsy 311


title: kidney biopsy 1136


title: kidney biopsy 1374


title: kidney biopsy 1304


title: kidney biopsy 406


title: kidney biopsy 56


title: kidney biopsy 1740


title: kidney biopsy 1059


title: kidney biopsy 343


title: kidney biopsy 592


title: kidney biopsy 951


title: kidney biopsy 1196


title: kidney biopsy 1302


title: kidney biopsy 530


title: kidney biopsy 1148


title: kidney biopsy 889


title: kidney biopsy 1134


title: kidney biopsy 555


title: kidney biopsy 552


title: kidney biopsy 439


title: kidney biopsy 182


title: kidney biopsy 145


title: kidney biopsy 94


title: kidney biopsy 241


title: kidney biopsy 655


title: kidney biopsy 1611


title: kidney biopsy 832


title: kidney biopsy 437


title: kidney biopsy 918


title: kidney biopsy 166


title: kidney biopsy 836


title: kidney biopsy 1288


title: kidney biopsy 381


title: kidney biopsy 1555


title: kidney biopsy 1557


title: kidney biopsy 1437


title: kidney biopsy 1178


title: kidney biopsy 1310


title: kidney biopsy 934


title: kidney biopsy 1095


title: kidney biopsy 1504


title: kidney biopsy 598


title: kidney biopsy 1449


title: kidney biopsy 981


title: kidney biopsy 1005


title: kidney biopsy 1465


title: kidney biopsy 465


title: kidney biopsy 1663


title: kidney biopsy 1262


title: kidney biopsy 800


title: kidney biopsy 1004


title: kidney biopsy 136


title: kidney biopsy 1702


title: kidney biopsy 1684


title: kidney biopsy 1088


title: kidney biopsy 172


title: kidney biopsy 965


title: kidney biopsy 607


title: kidney biopsy 742


title: kidney biopsy 691


title: kidney biopsy 1046


title: kidney biopsy 1340


title: kidney biopsy 636


title: kidney biopsy 561


title: kidney biopsy 1311


title: kidney biopsy 231


title: kidney biopsy 154


title: kidney biopsy 1659


title: kidney biopsy 450


title: kidney biopsy 551


title: kidney biopsy 90


title: kidney biopsy 1497


title: kidney biopsy 1404


title: kidney biopsy 1074


title: kidney biopsy 1496


title: kidney biopsy 1117


title: kidney biopsy 1392


title: kidney biopsy 1359


title: kidney biopsy 696


title: kidney biopsy 1527


title: kidney biopsy 216


title: kidney biopsy 11


title: kidney biopsy 680


title: kidney biopsy 349


title: kidney biopsy 749


title: kidney biopsy 471


title: kidney biopsy 662


title: kidney biopsy 1626


title: kidney biopsy 1518


title: kidney biopsy 1614


title: kidney biopsy 1733


title: kidney biopsy 146


title: kidney biopsy 499


title: kidney biopsy 950


title: kidney biopsy 217


title: kidney biopsy 127


title: kidney biopsy 546


title: kidney biopsy 568


title: kidney biopsy 841


title: kidney biopsy 1161


title: kidney biopsy 109


title: kidney biopsy 1615


title: kidney biopsy 757


title: kidney biopsy 123


title: kidney biopsy 1385


title: kidney biopsy 191


title: kidney biopsy 1300


title: kidney biopsy 1108


title: kidney biopsy 1250


title: kidney biopsy 1132


title: kidney biopsy 1207


title: kidney biopsy 1395


title: kidney biopsy 575


title: kidney biopsy 782


title: kidney biopsy 252


title: kidney biopsy 1450


title: kidney biopsy 1717


title: kidney biopsy 681


title: kidney biopsy 1246


title: kidney biopsy 1472


title: kidney biopsy 1628


title: kidney biopsy 352


title: kidney biopsy 1072


title: kidney biopsy 776


title: kidney biopsy 631


title: kidney biopsy 949


title: kidney biopsy 532


title: kidney biopsy 1713


title: kidney biopsy 645


title: kidney biopsy 70


title: kidney biopsy 28


title: kidney biopsy 1393


title: kidney biopsy 155


title: kidney biopsy 824


title: kidney biopsy 368


title: kidney biopsy 817


title: kidney biopsy 1412


title: kidney biopsy 1461


title: kidney biopsy 838


title: kidney biopsy 1685


title: kidney biopsy 996


title: kidney biopsy 1386


title: kidney biopsy 317


title: kidney biopsy 510


title: kidney biopsy 826


title: kidney biopsy 790


title: kidney biopsy 1399


title: kidney biopsy 274


title: kidney biopsy 1295


title: kidney biopsy 1044


title: kidney biopsy 1097


title: kidney biopsy 1598


title: kidney biopsy 435


title: kidney biopsy 326


title: kidney biopsy 1260


title: kidney biopsy 452


title: kidney biopsy 796


title: kidney biopsy 1321


title: kidney biopsy 1263


title: kidney biopsy 1565


title: kidney biopsy 1731


title: kidney biopsy 251


title: kidney biopsy 909


title: kidney biopsy 328


title: kidney biopsy 698


title: kidney biopsy 1688


title: kidney biopsy 272


title: kidney biopsy 515


title: kidney biopsy 954


title: kidney biopsy 1546


title: kidney biopsy 1645


title: kidney biopsy 1060


title: kidney biopsy 976


title: kidney biopsy 1151


title: kidney biopsy 59


title: kidney biopsy 1124


title: kidney biopsy 702


title: kidney biopsy 138


title: kidney biopsy 266


title: kidney biopsy 1533


title: kidney biopsy 1011


title: kidney biopsy 1353


title: kidney biopsy 219


title: kidney biopsy 714


title: kidney biopsy 1217


title: kidney biopsy 780


title: kidney biopsy 1236


title: kidney biopsy 1173


title: kidney biopsy 307


title: kidney biopsy 1119


title: kidney biopsy 183


title: kidney biopsy 1370


title: kidney biopsy 1195


title: kidney biopsy 591


title: kidney biopsy 550


title: kidney biopsy 1410


title: kidney biopsy 1728


title: kidney biopsy 102


title: kidney biopsy 1708


title: kidney biopsy 1739


title: kidney biopsy 137


title: kidney biopsy 1427


title: kidney biopsy 553


title: kidney biopsy 667


title: kidney biopsy 282


title: kidney biopsy 1013


title: kidney biopsy 840


title: kidney biopsy 1563


title: kidney biopsy 97


title: kidney biopsy 281


title: kidney biopsy 121


title: kidney biopsy 1114


title: kidney biopsy 57


title: kidney biopsy 915


title: kidney biopsy 297


title: kidney biopsy 1669


title: kidney biopsy 336


title: kidney biopsy 1211


title: kidney biopsy 1029


title: kidney biopsy 528


title: kidney biopsy 415


title: kidney biopsy 982


title: kidney biopsy 773


title: kidney biopsy 1597


title: kidney biopsy 1212


title: kidney biopsy 115


title: kidney biopsy 1678


title: kidney biopsy 940


title: kidney biopsy 514


title: kidney biopsy 1143


title: kidney biopsy 1674


title: kidney biopsy 310


title: kidney biopsy 1350


title: kidney biopsy 507


title: kidney biopsy 1737


title: kidney biopsy 189


title: kidney biopsy 835


title: kidney biopsy 1120


title: kidney biopsy 716


title: kidney biopsy 454


title: kidney biopsy 1407


title: kidney biopsy 664


title: kidney biopsy 275


title: kidney biopsy 869


title: kidney biopsy 632


title: kidney biopsy 1588


title: kidney biopsy 1159


title: kidney biopsy 1414


title: kidney biopsy 723


title: kidney biopsy 483


title: kidney biopsy 1476


title: kidney biopsy 1192


title: kidney biopsy 132


title: kidney biopsy 71


title: kidney biopsy 325


title: kidney biopsy 876


title: kidney biopsy 66


title: kidney biopsy 823


title: kidney biopsy 8


title: kidney biopsy 789


title: kidney biopsy 736


title: kidney biopsy 578


title: kidney biopsy 485


title: kidney biopsy 1096


title: kidney biopsy 150


title: kidney biopsy 673


title: kidney biopsy 1556


title: kidney biopsy 1474


title: kidney biopsy 1182


title: kidney biopsy 141


title: kidney biopsy 1087


title: kidney biopsy 1378


title: kidney biopsy 268


title: kidney biopsy 1357


title: kidney biopsy 261


title: kidney biopsy 760


title: kidney biopsy 1243


title: kidney biopsy 761


title: kidney biopsy 401


title: kidney biopsy 1347


title: kidney biopsy 854


title: kidney biopsy 1327


title: kidney biopsy 1676


title: kidney biopsy 302


title: kidney biopsy 968


title: kidney biopsy 335


title: kidney biopsy 148


title: kidney biopsy 686


title: kidney biopsy 1254


title: kidney biopsy 1167


title: kidney biopsy 293


title: kidney biopsy 1707


title: kidney biopsy 1573


title: kidney biopsy 1543


title: kidney biopsy 1048


title: kidney biopsy 732


title: kidney biopsy 1214


title: kidney biopsy 1126


title: kidney biopsy 327


title: kidney biopsy 891


title: kidney biopsy 68


title: kidney biopsy 420


title: kidney biopsy 1721


title: kidney biopsy 1016


title: kidney biopsy 1001


title: kidney biopsy 9


title: kidney biopsy 1058


title: kidney biopsy 1051


title: kidney biopsy 63


title: kidney biopsy 518


title: kidney biopsy 1373


title: kidney biopsy 1510


title: kidney biopsy 1172


title: kidney biopsy 541


title: kidney biopsy 538


title: kidney biopsy 1284


title: kidney biopsy 938


title: kidney biopsy 693


title: kidney biopsy 880


title: kidney biopsy 588


title: kidney biopsy 257


title: kidney biopsy 379


title: kidney biopsy 752


title: kidney biopsy 611


title: kidney biopsy 771


title: kidney biopsy 879


title: kidney biopsy 916


title: kidney biopsy 1249


title: kidney biopsy 1439


title: kidney biopsy 1657


title: kidney biopsy 463


title: kidney biopsy 1567


title: kidney biopsy 1287


title: kidney biopsy 289


title: kidney biopsy 1228


title: kidney biopsy 1680


title: kidney biopsy 460


title: kidney biopsy 180


title: kidney biopsy 1585


title: kidney biopsy 456


title: kidney biopsy 724


title: kidney biopsy 1145


title: kidney biopsy 545


title: kidney biopsy 848


title: kidney biopsy 467


title: kidney biopsy 1430


title: kidney biopsy 1584


title: kidney biopsy 451


title: kidney biopsy 227


title: kidney biopsy 1040


title: kidney biopsy 1387


title: kidney biopsy 830


title: kidney biopsy 543


title: kidney biopsy 378


title: kidney biopsy 263


title: kidney biopsy 1308


title: kidney biopsy 617


title: kidney biopsy 64


title: kidney biopsy 425


title: kidney biopsy 1692


title: kidney biopsy 1413


title: kidney biopsy 1289


title: kidney biopsy 1218


title: kidney biopsy 958


title: kidney biopsy 1024


title: kidney biopsy 230


title: kidney biopsy 570


title: kidney biopsy 750


title: kidney biopsy 1241


title: kidney biopsy 1085


title: kidney biopsy 656


title: kidney biopsy 1610


title: kidney biopsy 367


title: kidney biopsy 1604


title: kidney biopsy 1199


title: kidney biopsy 1122


title: kidney biopsy 1724


title: kidney biopsy 256


title: kidney biopsy 104


title: kidney biopsy 1670


title: kidney biopsy 490


title: kidney biopsy 1569


title: kidney biopsy 424


title: kidney biopsy 1331


title: kidney biopsy 1689


title: kidney biopsy 1330


title: kidney biopsy 139


title: kidney biopsy 1023


title: kidney biopsy 1081


title: kidney biopsy 1129


title: kidney biopsy 395


title: kidney biopsy 1052


title: kidney biopsy 1142


title: kidney biopsy 924


title: kidney biopsy 330


title: kidney biopsy 1696


title: kidney biopsy 351


title: kidney biopsy 526


title: kidney biopsy 345


title: kidney biopsy 1220


title: kidney biopsy 500


title: kidney biopsy 1401


title: kidney biopsy 1508


title: kidney biopsy 87


title: kidney biopsy 784


title: kidney biopsy 1041


title: kidney biopsy 292


title: kidney biopsy 1275


title: kidney biopsy 91


title: kidney biopsy 1210


title: kidney biopsy 374


title: kidney biopsy 1482


title: kidney biopsy 726


title: kidney biopsy 1303


title: kidney biopsy 370


title: kidney biopsy 1003


title: kidney biopsy 672


title: kidney biopsy 1484


title: kidney biopsy 446


title: kidney biopsy 206


title: kidney biopsy 805


title: kidney biopsy 912


title: kidney biopsy 685


title: kidney biopsy 1671


title: kidney biopsy 740


title: kidney biopsy 1443


title: kidney biopsy 542


title: kidney biopsy 271


title: kidney biopsy 901


title: kidney biopsy 640


title: kidney biopsy 603


title: kidney biopsy 756


title: kidney biopsy 1261


title: kidney biopsy 788


title: kidney biopsy 388


title: kidney biopsy 1356


title: kidney biopsy 468


title: kidney biopsy 708


title: kidney biopsy 962


title: kidney biopsy 666


title: kidney biopsy 1130


title: kidney biopsy 1469


title: kidney biopsy 1586


title: kidney biopsy 902


title: kidney biopsy 221


title: kidney biopsy 1397


title: kidney biopsy 253


title: kidney biopsy 829


title: kidney biopsy 1202


title: kidney biopsy 1045


title: kidney biopsy 895


title: kidney biopsy 423


title: kidney biopsy 1280


title: kidney biopsy 1346


title: kidney biopsy 1445


title: kidney biopsy 700


title: kidney biopsy 1061


title: kidney biopsy 362


title: kidney biopsy 1729


title: kidney biopsy 142


title: kidney biopsy 1368


title: kidney biopsy 766


title: kidney biopsy 1735


title: kidney biopsy 1532


title: kidney biopsy 850


title: kidney biopsy 1335


title: kidney biopsy 1047


title: kidney biopsy 1627


title: kidney biopsy 158


title: kidney biopsy 1705


title: kidney biopsy 597


title: kidney biopsy 795


title: kidney biopsy 803


title: kidney biopsy 831


title: kidney biopsy 626


title: kidney biopsy 860


title: kidney biopsy 642


title: kidney biopsy 337


title: kidney biopsy 1106


title: kidney biopsy 758


title: kidney biopsy 653


title: kidney biopsy 1213


title: kidney biopsy 175


title: kidney biopsy 1683


title: kidney biopsy 1216


title: kidney biopsy 1578


title: kidney biopsy 1454


title: kidney biopsy 170


title: kidney biopsy 426


title: kidney biopsy 188


title: kidney biopsy 872


title: kidney biopsy 1641


title: kidney biopsy 1687


title: kidney biopsy 1203


title: kidney biopsy 259


title: kidney biopsy 114


title: kidney biopsy 117


title: kidney biopsy 1313


title: kidney biopsy 657


title: kidney biopsy 1697


title: kidney biopsy 904


title: kidney biopsy 242


title: kidney biopsy 433


title: kidney biopsy 431


title: kidney biopsy 42


title: kidney biopsy 1506


title: kidney biopsy 877


title: kidney biopsy 1307


title: kidney biopsy 1591


title: kidney biopsy 1007


title: kidney biopsy 1466


title: kidney biopsy 986


title: kidney biopsy 223


title: kidney biopsy 1599


title: kidney biopsy 820


title: kidney biopsy 621


title: kidney biopsy 1380


title: kidney biopsy 6


title: kidney biopsy 768


title: kidney biopsy 1375


title: kidney biopsy 199


title: kidney biopsy 1121


title: kidney biopsy 459


title: kidney biopsy 373


title: kidney biopsy 20


title: kidney biopsy 601


title: kidney biopsy 466


title: kidney biopsy 1605


title: kidney biopsy 1343


title: kidney biopsy 1464


title: kidney biopsy 590


title: kidney biopsy 1039


title: kidney biopsy 1554


title: kidney biopsy 1382


title: kidney biopsy 1219


title: kidney biopsy 1290


title: kidney biopsy 946


title: kidney biopsy 984


title: kidney biopsy 1078


title: kidney biopsy 1116


title: kidney biopsy 1545


title: kidney biopsy 1436


title: kidney biopsy 1512


title: kidney biopsy 741


title: kidney biopsy 304


title: kidney biopsy 1153


title: kidney biopsy 517


title: kidney biopsy 1034


title: kidney biopsy 402


title: kidney biopsy 1028


title: kidney biopsy 276


title: kidney biopsy 1716


title: kidney biopsy 295


title: kidney biopsy 1110


title: kidney biopsy 455


title: kidney biopsy 1030


title: kidney biopsy 1477


title: kidney biopsy 212


title: kidney biopsy 496


title: kidney biopsy 1205


title: kidney biopsy 1233


title: kidney biopsy 88


title: kidney biopsy 1672


title: kidney biopsy 885


title: kidney biopsy 1070


title: kidney biopsy 1547


title: kidney biopsy 774


title: kidney biopsy 354


title: kidney biopsy 416


title: kidney biopsy 318


title: kidney biopsy 777


title: kidney biopsy 580


title: kidney biopsy 224


title: kidney biopsy 1381


title: kidney biopsy 1601


title: kidney biopsy 1027


title: kidney biopsy 1147


title: kidney biopsy 975


title: kidney biopsy 864


title: kidney biopsy 1043


title: kidney biopsy 95


title: kidney biopsy 1111


title: kidney biopsy 98


title: kidney biopsy 834


title: kidney biopsy 1421


title: kidney biopsy 389


title: kidney biopsy 1062


title: kidney biopsy 22


title: kidney biopsy 618


title: kidney biopsy 755


title: kidney biopsy 46


title: kidney biopsy 1686


title: kidney biopsy 573


title: kidney biopsy 1294


title: kidney biopsy 1274


title: kidney biopsy 1666


title: kidney biopsy 218


title: kidney biopsy 1517


title: kidney biopsy 948


title: kidney biopsy 1730


title: kidney biopsy 1104


title: kidney biopsy 1434


title: kidney biopsy 1157


title: kidney biopsy 364


title: kidney biopsy 767


title: kidney biopsy 1631


title: kidney biopsy 237


title: kidney biopsy 1570


title: kidney biopsy 96


title: kidney biopsy 284


title: kidney biopsy 1536


title: kidney biopsy 1448


title: kidney biopsy 544


title: kidney biopsy 1224


title: kidney biopsy 531


title: kidney biopsy 1460


title: kidney biopsy 1540


title: kidney biopsy 480


title: kidney biopsy 258


title: kidney biopsy 549


title: kidney biopsy 474


title: kidney biopsy 957


title: kidney biopsy 350


title: kidney biopsy 85


title: kidney biopsy 1309


title: kidney biopsy 537


title: kidney biopsy 899


title: kidney biopsy 47


title: kidney biopsy 1180


title: kidney biopsy 207


title: kidney biopsy 267


title: kidney biopsy 77


title: kidney biopsy 201


title: kidney biopsy 1711


title: kidney biopsy 79


title: kidney biopsy 10


title: kidney biopsy 462


title: kidney biopsy 516


title: kidney biopsy 1076


title: kidney biopsy 196


title: kidney biopsy 844


title: kidney biopsy 811


title: kidney biopsy 682


title: kidney biopsy 637


title: kidney biopsy 1603


title: kidney biopsy 458


title: kidney biopsy 26


title: kidney biopsy 628


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title: kidney biopsy 1170


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title: kidney biopsy 1031


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title: kidney biopsy 2


title: kidney biopsy 1082


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title: kidney biopsy 892


title: kidney biopsy 1169


title: kidney biopsy 1175


title: kidney biopsy 1376


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title: kidney biopsy 93


title: kidney biopsy 1701


title: kidney biopsy 129


title: kidney biopsy 1742


title: kidney biopsy 608


title: kidney biopsy 1564


title: kidney biopsy 1115


title: kidney biopsy 863


title: kidney biopsy 654


title: kidney biopsy 86


title: kidney biopsy 1152


title: kidney biopsy 428


title: kidney biopsy 1403


title: kidney biopsy 1049


title: kidney biopsy 1103


title: kidney biopsy 72


title: kidney biopsy 536


title: kidney biopsy 387


title: kidney biopsy 1174


title: kidney biopsy 1064


title: kidney biopsy 1144


title: kidney biopsy 181


title: kidney biopsy 1503


title: kidney biopsy 1316


title: kidney biopsy 358


title: kidney biopsy 865


title: kidney biopsy 936


title: kidney biopsy 1537


title: kidney biopsy 1055


title: kidney biopsy 33


title: kidney biopsy 977


title: kidney biopsy 1544


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title: kidney biopsy 100


title: kidney biopsy 616


title: kidney biopsy 980


title: kidney biopsy 652


title: kidney biopsy 478


title: kidney biopsy 715


title: kidney biopsy 828


title: kidney biopsy 897


title: kidney biopsy 1367


title: kidney biopsy 1022


title: kidney biopsy 676


title: kidney biopsy 1168


title: kidney biopsy 914


title: kidney biopsy 985


title: kidney biopsy 1291


title: kidney biopsy 1068


title: kidney biopsy 419


title: kidney biopsy 1519


title: kidney biopsy 1221


title: kidney biopsy 1424


title: kidney biopsy 111


title: kidney biopsy 577


title: kidney biopsy 923


title: kidney biopsy 802


title: kidney biopsy 868


title: kidney biopsy 1420


title: kidney biopsy 323


title: kidney biopsy 260


title: kidney biopsy 641


title: kidney biopsy 619


title: kidney biopsy 440


title: kidney biopsy 493


title: kidney biopsy 363


title: kidney biopsy 1227


title: kidney biopsy 246


title: kidney biopsy 866


title: kidney biopsy 630


title: kidney biopsy 1402


title: kidney biopsy 1163


title: kidney biopsy 791


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title: kidney biopsy 605


title: kidney biopsy 43


title: kidney biopsy 689


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title: kidney biopsy 862


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title: kidney biopsy 1580


title: kidney biopsy 202


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title: kidney biopsy 1337


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title: kidney biopsy 38


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title: kidney biopsy 1084


title: kidney biopsy 1026


title: kidney biopsy 380


title: kidney biopsy 1625


title: kidney biopsy 1339


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title: kidney biopsy 669


title: kidney biopsy 1446


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title: kidney biopsy 1383


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title: kidney biopsy 1225


title: kidney biopsy 1278


title: kidney biopsy 540


title: kidney biopsy 470


title: kidney biopsy 643


title: kidney biopsy 488


title: kidney biopsy 1441


title: kidney biopsy 243


title: kidney biopsy 867


title: kidney biopsy 113


title: kidney biopsy 361


title: kidney biopsy 501


title: kidney biopsy 393


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title: kidney biopsy 322


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title: kidney biopsy 1695


title: kidney biopsy 572


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title: kidney biopsy 1479


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title: kidney biopsy 29


title: kidney biopsy 151


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title: kidney biopsy 1535


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title: kidney biopsy 778


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title: kidney biopsy 1006


title: kidney biopsy 509


title: kidney biopsy 1398


title: kidney biopsy 624


title: kidney biopsy 1113


title: kidney biopsy 627


title: kidney biopsy 674


title: kidney biopsy 52


title: kidney biopsy 1655


title: kidney biopsy 245


title: kidney biopsy 288


title: kidney biopsy 365


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title: kidney biopsy 357


title: kidney biopsy 176


title: kidney biopsy 1091


title: kidney biopsy 1523


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title: kidney biopsy 1646


title: kidney biopsy 119


title: kidney biopsy 1423


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title: kidney biopsy 1451


title: kidney biopsy 1305


title: kidney biopsy 130


title: kidney biopsy 1324


title: kidney biopsy 1714


title: kidney biopsy 1406


title: kidney biopsy 1371


title: kidney biopsy 1079


title: kidney biopsy 945


title: kidney biopsy 1266


title: kidney biopsy 703


title: kidney biopsy 344


title: kidney biopsy 707


title: kidney biopsy 229


title: kidney biopsy 974


title: kidney biopsy 436


title: kidney biopsy 254


title: kidney biopsy 3


title: kidney biopsy 225


title: kidney biopsy 1552


title: kidney biopsy 961


title: kidney biopsy 1505


title: kidney biopsy 1709


title: kidney biopsy 997


title: kidney biopsy 559


title: kidney biopsy 1073


title: kidney biopsy 1703


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title: kidney biopsy 1698


title: kidney biopsy 919


title: kidney biopsy 931


title: kidney biopsy 709


title: kidney biopsy 792


title: kidney biopsy 987


title: kidney biopsy 1551


title: kidney biopsy 16


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title: kidney biopsy 497


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title: kidney biopsy 233


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title: kidney biopsy 1440


title: kidney biopsy 44


title: kidney biopsy 1154


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title: kidney biopsy 1619


title: kidney biopsy 569


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title: kidney biopsy 324


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title: kidney biopsy 334


title: kidney biopsy 994


title: kidney biopsy 1432


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title: kidney biopsy 1100


title: kidney biopsy 144


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title: kidney biopsy 173


title: kidney biopsy 60


title: kidney biopsy 116


title: kidney biopsy 200


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title: kidney biopsy 1258


title: kidney biopsy 1185


title: kidney biopsy 1664


title: kidney biopsy 1624


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title: kidney biopsy 414


title: kidney biopsy 1480


title: kidney biopsy 625


title: kidney biopsy 969


title: kidney biopsy 1426


title: kidney biopsy 635


title: kidney biopsy 197


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title: kidney biopsy 1165


title: kidney biopsy 1621


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title: kidney biopsy 294


title: kidney biopsy 650


title: kidney biopsy 329


title: kidney biopsy 1341


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title: kidney biopsy 609


title: kidney biopsy 53


title: kidney biopsy 738


title: kidney biopsy 448


title: kidney biopsy 1264


title: kidney biopsy 1150


title: kidney biopsy 1568


title: kidney biopsy 593


title: kidney biopsy 1017


title: kidney biopsy 1226


title: kidney biopsy 1345


title: kidney biopsy 303


title: kidney biopsy 1231


title: kidney biopsy 1323


title: kidney biopsy 731


title: kidney biopsy 1348


title: kidney biopsy 1209


title: kidney biopsy 1429


title: kidney biopsy 910


title: kidney biopsy 1125


title: kidney biopsy 753


title: kidney biopsy 1277


title: kidney biopsy 922


title: kidney biopsy 1475


title: kidney biopsy 1160


title: kidney biopsy 348


title: kidney biopsy 391


title: kidney biopsy 797


title: kidney biopsy 739


title: kidney biopsy 506


title: kidney biopsy 1522


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title: kidney biopsy 19


title: kidney biopsy 920


title: kidney biopsy 678


title: kidney biopsy 1633


title: kidney biopsy 215


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title: kidney biopsy 917


title: kidney biopsy 1396


title: kidney biopsy 845


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title: kidney biopsy 813


title: kidney biopsy 214


title: kidney biopsy 947


title: kidney biopsy 1538


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title: kidney biopsy 941


title: kidney biopsy 1607


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title: kidney biopsy 1123


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title: kidney biopsy 1018


title: kidney biopsy 1491


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title: kidney biopsy 159


title: kidney biopsy 32


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title: kidney biopsy 24


title: kidney biopsy 925


title: kidney biopsy 1632


title: kidney biopsy 1553


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title: kidney biopsy 639


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title: kidney biopsy 721


title: kidney biopsy 58


title: kidney biopsy 314


title: kidney biopsy 855


title: kidney biopsy 461


title: kidney biopsy 529


title: kidney biopsy 192


title: kidney biopsy 473


title: kidney biopsy 1253


title: kidney biopsy 35


title: kidney biopsy 1235


title: kidney biopsy 178


title: kidney biopsy 1365


title: kidney biopsy 1037


title: kidney biopsy 775


title: kidney biopsy 1239


title: kidney biopsy 179


title: kidney biopsy 1245


title: kidney biopsy 1681


title: kidney biopsy 1391


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title: kidney biopsy 418


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title: kidney biopsy 533


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title: kidney biopsy 135


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title: kidney biopsy 1255


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title: kidney biopsy 815


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title: kidney biopsy 801


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title: kidney biopsy 1520


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title: kidney biopsy 1700


title: kidney biopsy 888


title: kidney biopsy 735


title: kidney biopsy 1198


title: kidney biopsy 213


title: kidney biopsy 1720


title: kidney biopsy 356


title: kidney biopsy 369


title: kidney biopsy 1691


title: kidney biopsy 205


title: kidney biopsy 1558


title: kidney biopsy 1328


title: kidney biopsy 1020


title: kidney biopsy 704


title: kidney biopsy 1171


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title: kidney biopsy 54


title: kidney biopsy 1237


title: kidney biopsy 906


title: kidney biopsy 1248


title: kidney biopsy 407


title: kidney biopsy 280


title: kidney biopsy 1594


title: kidney biopsy 1511


title: kidney biopsy 1673


title: kidney biopsy 663


title: kidney biopsy 404


title: kidney biopsy 1352


title: kidney biopsy 1418


title: kidney biopsy 1649


title: kidney biopsy 939


title: kidney biopsy 1431


title: kidney biopsy 1726


title: kidney biopsy 1444


title: kidney biopsy 1364


title: kidney biopsy 763


title: kidney biopsy 513


title: kidney biopsy 1326


title: kidney biopsy 599


title: kidney biopsy 1177


title: kidney biopsy 695


title: kidney biopsy 1463


title: kidney biopsy 963


title: kidney biopsy 964


title: kidney biopsy 809


title: kidney biopsy 124


title: kidney biopsy 730


title: kidney biopsy 1140


title: kidney biopsy 511


title: kidney biopsy 614


title: kidney biopsy 1647


title: kidney biopsy 1576


title: kidney biopsy 1577


title: kidney biopsy 1369


title: kidney biopsy 988


title: kidney biopsy 821


title: kidney biopsy 1417


title: kidney biopsy 665


title: kidney biopsy 1521


title: kidney biopsy 372


title: kidney biopsy 1654


title: kidney biopsy 1366


title: kidney biopsy 586


title: kidney biopsy 67


title: kidney biopsy 1539


title: 213_C19

status: Public on Aug 13 2019

city: Chikusa-ku

first: Hitoshi

last: Ohtani

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

data_processing:
Sequencing reads were aligned against the human hg19 reference genome using TopHat2 v.2.1.0.
The number of overlapping mapped reads with transposable elements were obtained using Bedtool
The definitions of transposable elements were based on RepeatMasker
Genome_build: hg19
Supplementary_files_format_and_content: csv file. Expression level of codig genes and transposable elements.

extract_protocol:
Mononuclear cells were isolated immediately upon sample collection. The cells were thawed and immediately isolated into either CD14+ monocytes, CD3+ T cells or CD34+ progenitor cells. Total RNA was extracted directly from PB mononuclear cells.
cDNA linraries were prepared using KAPA RNA HyperPrep Kits and pooled using standard illumina protocols.
single-end 75 bases on a NextSeq 500 instrument (Illumina).

treatment_protocol: Hematological cancer patients were treated with 100mg/m2 5-azacytidine for five consecutive days on a 28 day schedule.

tag: disease

value: MDS

value: CD34+ bone Marrow

tag: treatment

tag: treatment response

value: Responder


title: 9_C4D1

value: Peripheral blood Mononuclear cell


title: 1344_C1D1

value: Pre-treatment

value: Non-responder


title: 213_C1D1


title: 9_C2D1


title: 9_C1D1


title: 213_C7D23


title: 1344_C2D2


title: 9_C3D1


title: kidney biopsy 810


title: kidney biopsy 697


title: kidney biopsy 804


title: 9_C4D1_CD3

value: CD3+ Tcell


title: 9_C2D1_CD3


title: 9_C1D1_CD3


title: 9_C3D1_CD3


title: 7_C4D1

value: AML


title: 7_C2D1


title: kidney biopsy 647

value: yes

value: no


title: kidney biopsy 392

value: TCMR


title: 7_C1D1


title: kidney biopsy 1650


title: 7_C4D1_CD3


title: 7_C3D1_CD3


title: 7_C1D1_CD3


title: 1_C3D5


title: 141_C3D1

value: Monocyte precursor cell


title: 25_C4D1_CD14

value: CMML

value: CD14+ Monocyte


title: 25_C1D1_CD14


title: 141_C1D1


title: 131_C3D1


title: 141_C5D1


title: 1_C2D1


title: 25_C1D1_CD3


title: 1_C3D1


title: 1_C1D1


title: 131_C5D5


title: 25_C4D1_CD3


title: 131_C5D1


title: 141_C5D5


title: K2_C2D1


title: 131_C1D1


title: K2_C3D1


title: K2_C1D5


title: K1_C2D1


title: 7_C3D1


title: K1_C3D1


title: 7_C2D1_CD3


title: K1_C1D1


title: K2_C1D1


title: O34_C8D5_CD14


title: K1_C1D5


title: O34_C1D5_CD14


title: O34_C1D1_CD14


title: O34_C1D5_CD3


title: O4_C14D5_CD14


title: O34_C1D1_CD3


title: O4_C7D5_CD14


title: O4_C7D1_CD14


title: O4_C14D1_CD14


title: O4_C1D5_CD14


title: O4_C14D5_CD3


title: O4_C1D5_CD3


title: O4_C1D1_CD3


title: O4_C1D1_CD14


title: O4_C14D1_CD3


title: O34_C8D5_CD3


title: YF-M15-640_Naïve

status: Public on Dec 13 2017

city: Palo Alto

first: Bin

last: Hu

state: California

address: 3801 Miranda Avenue

department: School of Medicine

institute: Stanford University

data_processing:
Reads were aligned to hg19 using bowtie2, discarding pairs with mapping quality less than 20. The reads from all samples were pooled, and a peak file was generated using MACS2.
Peaks that overlapped with repetitive regions or low complexity DNA regions, such as satellite DNA or retrotransposons, were removed from the analysis.
Peaks were visualized using IGV, with the y-axis set at the scale of reads per base pair. Gene and TSS annotations were based on the RefSeq database. ChIP-seq results in GM12878 were downloaded from the ENCODE project. The ability of the peaks to discriminate between subpopulations was assessed by calculating Spearman correlation coefficients on the 5,000 peaks with the greatest overall variance following a regularized-log transform.
To assess differential openness, we ran DESeq2 on the matrix of insertions in peaks by sample. Peaks were considered to be differentially open if the Wald test was less than 0.05, following multiple hypothesis correction with the Benjamini-Hochberg procedure.

source_name: PBMC

extract_protocol:
DNA from the transposase reaction was purified via a Qiagen MinElute kit.
PCR amplification was performed using Nextera PCR primers. The final libraries were quantified using a KAPA Library Quantification Kit and sequenced on an Illumina HiSeq 2500 by ELIM Biopharm.

treatment_protocol: YFV tetramer- positive and naïve CD8 T cells were sorted from PBMC at indicated time points after vaccination. Pellets from 20,000 cells were washed with cold PBS, then with RSB buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2) and lastly with lysis buffer (RSB buffer + 0.1% NP40 + 0.1% Tween 20). The pellet obtained was then resuspended in the transposase reaction mix (25μL 2× TD buffer, 1μL Illumina transposase and 24μL nuclease-free water) and incubated at 37oC for 30 min.

tag: donor

tag: days post yfv-17d

tag: cell type

value: sorted CD45RA+ CCR7+ CD8 T cells

value: PBMC


title: YF-M15-675_Naïve

tag: tissue


title: YF-M15-653_Naïve


title: YF-M15-677-D90_Naïve


title: YF-M15-678_D90_Naïve


title: YF-M15-677_Naïve


title: YF-Ig-E07 (TAD)_Naïve

value: YF Ig E07 (TAD)


title: YF-M15 -658_Naïve


title: YF-M15-661_Naïve


title: YF-M15-679_Naïve


title: YF-M15-660_Naïve


title: YF-M15-678_Naïve


title: YF-X-14-009-002_Naïve


title: YF-M15-660_D180_Naïve


title: YF-HW-11-066_Naïve


title: O4_C7D1_CD3


title: O4_C7D5_CD3


title: Hi-C_untreated_rep1

status: Public on Jun 01 2017

city: San Francisco

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

data_processing:
Hi-C. We mapped the sequence of Hi-C molecules to reference mouse genome assembly mm9 using Bowtie 2.2.8 and the iterative mapping strategy, as described in  (Imakaev et al., 2012; Lajoie et al., 2015). Upon filtering PCR duplicates and reads mapped to multiple or zero locations, we aggregated the reads pairs into 20kb and 100kb genomic bins to produce Hi-C contact matrices. To remove the short-range Hi-C artifacts - unligated and self-ligated Hi-C molecules - we ignored the contacts mapping to the same or adjacent genomic bins in all downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: 20kb and 100kb ICE corrected matrices are provided as .cool files, which can be handled with the Cooler package https://github.com/mirnylab/cooler

source_name: mouse ES cells

extract_protocol: ChIP libraries were prepared using standard Illumina protocols; RNA-seq libraries were assembled using the non-stranded kit E7530L from NEB; 5C (in situ ligation) and Hi-C (HindIII dilution ligation) were assembled based on Illumina-compatible protocols. Detailed experimental procedures can be found in the supplementary information of Nora et al. 2017 Cell

tag: strain

value: CTCF-AID, Tir1

tag: restriction enzyme

value: HindIII


title: Hi-C_auxin-2days_rep1

tag: genotype


title: Hi-C_auxin-2days_rep2


title: Hi-C_untreated_rep2


title: RNA-seq_CTCF-AID_auxin2days_rep3

status: Public on May 25 2017

description: RNA-seq

data_processing:
ChIP-seq and ChIP-exo. Fastq files were trimmed using the fastq-mcf program, aligned to the mm9 reference genome with bowtie2 (Langmead and Salzberg, 2012). Reads with a mapq score of 30 or greater were retained, using Samtools. PCR duplicates were filtered out. for CTCF peaks were called using the geome wide Event finding and Motif Discovery (GEM) algorithm. For H3K27me3 peaks that are broader we used a threshold-based method.
RNA-seq. Alignment was produced using STAR version 2.5.0a , aligned to mm9. Cufflinks version 2.2.1  with Bedtools version 2.17.0 were used as to produce input for differential expression analysis with Cuffdiff . Genes with an FPKM below 1.1 in all conditions were not considered in the differential expression analysis
Hi-C. We mapped the sequence of Hi-C molecules to reference mouse genome assembly mm9 using Bowtie 2.2.8 and the iterative mapping strategy, as described in  (Imakaev et al., 2012; Lajoie et al., 2015). Upon filtering PCR duplicates and reads mapped to multiple or zero locations, we aggregated the reads pairs into 20kb and 100kb genomic bins to produce Hi-C contact matrices. To remove the short-range Hi-C artifacts - unligated and self-ligated Hi-C molecules - we ignored the contacts mapping to the same or adjacent genomic bins in all downstream analyses.
5C. Adapters were trimmed and aligment was performed using Bowtie2 against a pseudo-genome composed of all possible Forward-Reverse pairs of 5C oligonucleotides and matrices were analyzed using my5C (Lajoie et al. 2009 Nature Methods).
Genome_build: mm9
Supplementary_files_format_and_content: 5C - for all forward-reverse possible ligation pair we provide one file with raw 5C counts (not read normalized, including anchors ultimately removed from analysis), and one file with anchor filtered symmetrical read-normalized balanced (Iterative Correction method - ICE) matrices.
Supplementary_files_format_and_content: ChIP-seq and ChIP-exo. _Peaks.bed: position of the peaks. _Footprints.bed: position of ChIP-exo footprint. _tagDensity.bw: ChIP signal.
Supplementary_files_format_and_content: RNA-seq. .bw: tagDensity of signal.

molecule: polyA RNA

source_name: mouse ES cells E14Tg2a

growth_protocol: E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and subclones were cultured in DMEM+Glutamax (ThermoFisher cat 10566-016) supplemented with 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1mM Sodium Pyruvate (ThermoFisher 11360-070), 1X non-essential amino-acids (ThermoFisher 11140-50) and 104U of Leukemia inhibitory factor (Millipore ESG1107). Cells were maintained at a density of 0.2-1.5x105 cells / cm² by passaging using TrypLE (12563011) every 24-48h on 0.1% gelatin-coated dishes (Millipore cat ES-006-B) at 37°C and 7% CO2. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative. mouse ES cells were targeted to insert an Auxin-Inducible Degron (AID) tag together with an eGFP cassette, and the auxin receptor OsTir1 was expressed from a transgene. ChIP-seq, Hi-C, 5C and RNA-seq were performed at different timepoints after adding auxin to the culture medium.

extract_protocol:
For ChIP-seq cells were  trypsinized and fixed in suspension; For Chromosome Conformation Capture cells were fixed in tissue culture plates and scrapped off; For RNA-seq cells werre washed once with PBS and lysed in Trizol in the tissue culture plate.
ChIP libraries were prepared using standard Illumina protocols; RNA-seq libraries were assembled using the non-stranded kit E7530L from NEB; 5C (in-situ ligation) and Hi-C (dilution ligation) were assembled based on Illumina-compatible protocols. Detailed experimental procedures can be found in the supplementary information of Nora et al. 2017 Cell
ChIP-seq, ChIP-exo, RNA-seq, Hi-C, 5C

treatment_protocol: For induction of the auxin-inducible degron indole-3-acetic acid (IAA, chemical analog of auxin) was added in the medium at 500µM from a 1000X stock diluted in sterile water and kept at 4°C up to 4 weeks or -20°C for long term storage.

value: 129/Ola, XY

tag: chip epitope


title: RNA-seq_CTCF-AID_untreated_rep3

description: RNA-seq


title: RNA-seq_CTCF-AID_auxin4days_rep2

description: RNA-seq


title: RNA-seq_CTCF-AID_auxin1day_rep3

description: RNA-seq


title: RNA-seq_CTCF-AID_auxin2days_rep2

description: RNA-seq


title: RNA-seq_CTCF-AID_auxin4days_rep3

description: RNA-seq


title: RNA-seq_CTCF-AID_auxin1day_rep2

description: RNA-seq


title: RNA-seq_CTCF-AID_untreated_rep2

description: RNA-seq


title: RNA-seq_CTCF-AID_auxin4days_rep1

description: RNA-seq


title: ICSIB.04

status: Public on Jul 22 2016

city: Regensburg

first: Xin

last: Lu

address: Universitätsstraße 31

country: Germany

institute: University of Regensburg

description: single cell mRNA

hyb_protocol: Labelled products were purified using PCR purification kit (Qiagen) following manufacturer's instructions. Purified Cy5-labelled DNA was denatured by incubation for 5 min at 95°C, followed by incubation on ice. Hybridization mix was prepared by mixing 42 μl of denatured Cy5-labelled DNA, 55 μl of 2x HiRPM hybridisation buffer (Agilent), 11 μl of 10x GE Blocking agent (Agilent), 4 μl of 25% Tween-20, and 4 μl of 25% Igepal.  Four samples of 100 μl of hybridisation mix were overlaid on 4 hybridisation fields of Agilent Whole Mouse Genome (4x44K) Oligo Microarray with SurePrint (G4122F) microarray slides, and incubated for 17 h at 65°C, under constant rotation. After hybridisation, slides were washed in Agilent Wash buffer 1 for 1 min, on shaker, in dark, and in Agilent Wash buffer 2 (pre-warmed to 37°C) for 1 min, on shaker, in dark. Finally, slides were dried by washing for 30 s in acetonitrile.

scan_protocol: Slides were scanned on GenePix 4400A scanner (Molecular Devices). Numerical readout of fluorescence intensities (GPR file) was generated using GenePixPro 7 (Molecular Devices)

data_processing: background correction and normalization using limma package in R

source_name: individual 2-cell stage blastomere

label_protocol: Labelling of the primary WTA product was performed by PCR using Cy5-labeled primers. Reaction mix contained 5 μl of buffer I (Expand Long Template, Roche), 3% deionized formamide, 0.35 mM each dNTP, 2.5 μM 5'-U*CAGAAU*TCAU*CCC*CCCC*CCCC*CCCC*-3' primer (* denotes nucleotides conjugated with Cy5 fluorophore; Metabion), 7.5 U of PolMix (Expand Long Template, Roche), and 1 μl of primary WTA product, in the final volume of 49 μl. PCR cycling conditions were as following: one cycle with 1 min at 95°C, 11 cycles with 15 s at 95°C, 1 min at 60°C, and 3 min 30 s at 65°C, 3 cycles where the elongation time was increased 10 s/cycle, and finally one cycle with elongation time of 7 min.

growth_protocol: Wild type, C57BL/6 x DBA/2 (B6D2F1) hybrid strains were crossed (B6D2F1 x B6D2F1) to generate embryos for array profiling.  Strains were bred from stocks in-house or otherwise supplied by Charles River (L'Arbresle, France).   Animal procedures complied with the Animals (Scientific Procedures) Act, 1986. Oocytes were collected from 8- to 12-week-old females that had been super-ovulated by 10 standard serial intraperitoneal injection of 5 IU pregnant mare serum gonadotropin (PMSG) followed 48 h later by 5 IU human chorionic gonadotropin (hCG). Oviductal metaphase II (mII) oocytes were collected in M2 medium (EMD Millipore, UK; Quinn et al., 1982) ~15 h post-hCG injection essentially as described (Yoshida and Perry, 2007). After repeated washing in M2, denuded oocytes were incubated in kalium simplex optimized medium (KSOM; Specialty Media, USA; Erbach et al., 1994) under mineral oil in humidified 5% CO2 (v/v air) at 37°C, until required. Where appropriate, mII oocytes with a degenerate first polar body were selected; by 16 h post-hCG, 71.0±2.0% (n=2,294) of first polar bodies had degenerated.  Where appropraite, SrCl2 treatment was initiated 16-17.5 h post-hCG; times are given after the start of SrCl2 treatment. For phICSI and controls, embryos were chosen that possessed a second polar body and a single pronucleus at 5~7 h.

extract_protocol: For single-cell whole transcriptome amplification, ICSI and phICSI 2-cell embryos were produced by injecting B6D2F1 sperm respectively into B6D2F1 oocytes or parthenogenotes.  For phICSI-13, 2+1 embryos (Fig. 1e) were used for blastomere separation.  Embryos were exposed to acid Tyrode's solution (pH2.5; Sigma) to dissolve the zona pellucida and allowed to recover for 1 h in KSOM in humidified 5% CO2 (v/v air) at 37°C.  Embryos were then gently triturated in Ca2+-free, Mg2+-free M2 medium to separate the blastomeres and any extant polar body.  ICSI blastomeres were collected 27 h post-ICSI and the binuclear blastomeres of phICSI 2+1 embryos 27 h after the initiation of SrCl2 exposure.  One blastomere per tube was collected in a minimal volume into 5.4 μl of lysis buffer (Active Motif) containing 10 ng of tRNA (Roche), 1 μg of protease (Active Motif), and 1 μl of 37.5 μM biotinylated oligo-dT peptide nucleic acids (PNAs; Active Motif) and flash-frozen in liquid N2 until required for processing, as previously described (Hartmann and Klein, 2006; VerMilyea et al., 2011).

treatment_protocol: Sperm preparation was essentially as previously described (Suzuki et al., 2010). Briefly, cauda epididymidal sperm from 8- to 12-week-old B6D2F1 males were triturated for 45 sec in nuclear isolation medium (NIM; 125 mM KCl, 2.6 mM NaCl, 7.8 mM Na2HPO4, 1.4 mM KH2PO4, 3.0 mM EDTA; pH 7.0) containing 1.0% (w/v) 3-[(3-cholamidopropyl)dimethylammonio]-1- propanesulfonate (CHAPS) at room temperature (25°C). Sperm were washed twice in NIM and pelleted (1,890 g) at ambient temperature; head-tail detachment was enhanced by trituration during pellet resuspension. Finally, sperm were resuspended in ice-cold NIM (~0.5 ml per epididymis) and stored at 4°C for up to 3 h until required. ~50 μl of each suspension was typically mixed with 20 μl of polyvinylpyrrolidone (PVP, average Mr ≈ 360,000; Sigma-Aldrich) solution (15% [w/v]) and sperm injected (ICSI) into oocytes in droplet of M2 within ~60 min, essentially as described (Yoshida and Perry, 2007). Injected oocytes were transferred to KSOM under mineral oil equilibrated in humidified 5% CO2 (v/v air) at 37°C. For phICSI, SrCl2-activated haploid parthenogenotes were injected with sperm at the times indicated after commencement of SrCl2 treatment. For phICSI-13, this was 13 h after the initiation of SrCl2 treatment of B6D2F1 oocytes, which was just after pnMBD.

tag: zygote generation

value: ICSI

tag: sample type

value: single cell whole transcriptome amplification

value: individual 2-cell stage blastomere

tag: genetic background


title: phICSI.08

description: single cell mRNA

value: phICSI


title: phICSI.12

description: single cell mRNA


title: ICSIA.04

description: single cell mRNA


title: ICSIA.07

description: single cell mRNA


title: ICSIA.13

description: single cell mRNA


title: ICSIA.02

description: single cell mRNA


title: phICSI.10

description: single cell mRNA


title: ICSIA.01

description: single cell mRNA


title: ICSIA.05

description: single cell mRNA


title: ICSIB.12

description: single cell mRNA


title: ICSIB.01

description: single cell mRNA


title: phICSI.09

description: single cell mRNA


title: ICSIB.02

description: single cell mRNA


title: CHIP_090623_IB_030_green

status: Public on Dec 02 2014

hyb_protocol: Primers were removed by digestion with 30 U BglI (Fermentas, St Leon-Rot) and the samples purified on a column (Qiagen, Hilden). Murine Operon 70mer oligonucleotide arrays (Version 4) spotted on Ultra-GAPS slides (Operon, Köln resp. Corning, Schiphol-Rijk, Netherlands) were pre-hybridized with 5*SSC, 0.1% (w/v) SDS, 0.1% (w/v) BSA at 42°C and hybridized in an Arraybooster hybstation (Implen, Munich) at 42°C overnight. Washing steps following hybridization were at 42°C twice in 2*SSC, 0.1% (w/v) SDS for 5 min, twice in 0.1*SSC, 0.1% (w/v) SDS for 10 min, and twice in 0.1*SSC for 2.5 min. Non-specific binding of labelled proteins was blocked with 1% (v/v) blocking reagent for nucleic acid hybridization (Roche) followed by a staining procedure with anti-Dig-Cy5 and streptavidin-Cy3 (Jackson Laboratories) each at 16 µg/ml. Excess antibody/streptavidin was removed with 4*SSC, 0.2% (v/v) Tween-20 and slides were scanned on a Genepix 4000A scanner (Axon Instruments, Union City).

source_name: HSC

label_protocol: Primary cDNA amplification products were labelled in the presence of 3% (v/v) formamide, 2.4 µM CP2-BGL primer, dNTPs (0.35 mM dATP and dGTP, 0.3 mM dTTP and dCTP) and 50 µM labelled nucleotides. Sample cDNA was labelled with digoxygenin-dUTP (Roche) and aminodigoxygenin- dCTP (Perkin-Elmer, Rodgau), and reference cDNA with biotin-dUTP (Roche) and biotin-dCTP (Invitrogen).

growth_protocol: All mice used are C57BL/6 background. mTerc+/− were crossed with each other to generate G1 mTerc-/-. Those mice were crossed until the third generation of the telomerase knockout G3 mTerc-/-. Mice were maintained according to protocols approved by Animal Care and Use Committee of Leibniz Institute for Age Research - Fritz Lipmann Institute e.V.

extract_protocol: Cells were stained and sorted by using the following surface markers combination: HSC (CD34lo Flt3- ScaI+ cKit+ Lineage-), MPP (CD34+ Flt3+ ScaI+ cKit+ Lineage-), myeloid cells (B220- CD11b+). Quiescent HSCs and cycling HSCs were purified by using Pyronin Y (Sigma-Aldrich, P9172) and Hoechst33342 (Sigma-Aldrich, B2261). Bone marrow cells were stained with antibodies for HSCs first, then incubated with Hoechst33342 (DNA dye, 1mg/ml) at 37℃ for 30 minutes and Pyronin Y (RNA dye, 100ug/ml) for further 15 minutes under light free condition. Samples were analyzed by LSRII (BD Biosciences).

treatment_protocol: Bone marrow cells were isolated by crushing bones from donor mice.

tag: background strain

value: HSC

tag: library


title: ICSIB.05

description: single cell mRNA


title: ICSIB.13

description: single cell mRNA


title: ICSIA.08

description: single cell mRNA


title: phICSI.06

description: single cell mRNA


title: ICSIB.07

description: single cell mRNA


title: phICSI.05

description: single cell mRNA


title: ICSIA.12

description: single cell mRNA


title: CHIP_090623_IB_033_green

source_name: Myeloid cell

value: Myeloid cell


title: phICSI.01

description: single cell mRNA


title: CHIP_090623_IB_034_green


title: ICSIB.08

description: single cell mRNA


title: CHIP_090623_IB_029_green


title: CHIP_090623_IB_032_green

source_name: MPP

value: MPP


title: phICSI.04

description: single cell mRNA


title: CHIP_090623_IB_031_green


title: CHIP_090619_IB_027_green


title: CHIP_090325_KM_018_green


title: CHIP_090619_IB_024_green


title: CHIP_090325_KM_021_green

value: WT


title: CHIP_090325_KM_019_green


title: CHIP_090619_IB_028_green


title: CHIP_090619_IB_025_green


title: CHIP_090325_KM_020_green


title: CHIP_090619_IB_026_green


title: CHIP_090313_KM_014_green


title: CHIP_090313_KM_015_green


title: CHIP_090313_KM_016_green


title: CHIP_090312_KM_010_green


title: LICR_ChipSeq_ES-Bruce4_H3K27ac_E0

status: Public on Sep 10 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: line

tag: cell organism

value: mouse

value: mouse embryonic stem cells

tag: cell sex

value: M

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

value: Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: age

tag: age description

value: Embryonic day 0 (stem cell)

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

value: Pooled & filtered

tag: softwareversion

value: MACS

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: CHIP_090304_KM_001_green

tag: background strain

tag: tissue

value: HSC

tag: library


title: LICR_ChipSeq_ES-Bruce4_H3K36me3_E0

tag: lab

value: LICR-m

tag: lab description

tag: datatype

tag: datatype description

tag: line

tag: cell organism

tag: cell sex

value: rabbit polyclonal. Antibody Target:H3K36me3

value: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.

tag: strain


title: CHIP_090304_KM_006_green


title: CHIP_090312_KM_011_green

value: WT


title: CHIP_090619_IB_023_green

value: Myeloid cell


title: CHIP_090312_KM_012_green


title: CHIP_090304_KM_008_green

value: MPP


title: CHIP_090304_KM_003_green


title: CHIP_090312_KM_009_green


title: CHIP_090325_KM_022_green


title: CHIP_090304_KM_005_green


title: CHIP_090304_KM_002_green


title: CHIP_090325_KM_017_green


title: LICR_ChipSeq_ES-Bruce4_H3K27me3_E0

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

value: mouse

value: mouse embryonic stem cells

value: M

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: age

tag: age description

tag: control


title: CHIP_090313_KM_013_green

tag: background strain

tag: tissue

tag: library


title: CHIP_090304_KM_007_green

value: old G3


title: LICR_ChipSeq_ES-Bruce4_H3K4me3

status: Public on Jul 30 2011

tag: lab

tag: lab description

tag: datatype

value: ChIP-Seq

value: rabbit polyclonal

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

value: Embryonic day 0 (stem cell)

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

tag: replicate

tag: replicate description

value: tier 1

tag: softwareversion

value: ELAND

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: CHIP_090304_KM_004_green

value: HSC


title: LICR_ChipSeq_ES-Bruce4_CTCF_E0

status: Public on Apr 19 2012

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

tag: antibody

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

tag: antibody vendorid

value: 12/23/09 SOLEXA2 Lane 5

tag: strain


title: MCF-7 MEM fraction; replicate 3

status: Public on Dec 01 2004

city: Boston

first: Carol

last: Westbrook

state: MA

address: One Boston Medical Center Pl

institute: Boston University

description: Membrane-bound polysome fraction of RNA from MCF-7 cells.

source_name: MCF-7 cell line


title: MCF-7 CYT fraction; replicate 1

description: Free polysome fraction of RNA from MCF-7 cells.


title: MCF-7 MEM fraction; replicate 1


title: MCF-7 MEM fraction; replicate 2


title: MCF-7 CYT fraction; replicate 3


title: MCF-7 CYT fraction; replicate 2