title: DSSd12_2

status: Public on May 11 2019

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

data_processing:
Basecalling was performed using Illumina Casava v.1.7 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequences.
Read quality was accessed using FASTQC.
Read counts were estimated at the transcript level using kallisto: kallisto quant -i /$input_directory/transcripts.idx -o /$output_directory/$sample_name -b 100 -t 6 --single -l 180 -s 20 $sample_name
Genome_build: mm10
Supplementary_files_format_and_content: We provided individual tab-separated text files containing Kallisto estimated counts (est_counts) and transcript per million (tpm) for each Sample. We also included a matrix contating rounded estimated counts (kallisto_counts.csv) and a log2-normalized counts (cpm, log2_counts_per_million.csv), summarized at the gene level.

extract_protocol:
Colon samples were stored in RNAlater (Ambion) at -80˚C until further use. Colonic samples were homogenized using bead-beating system (Precellys) for total RNA purification using RNAeasy kit (Qiagen) following manufacturers recommendations. RNA purity and quantity was measured by NanoDrop spectrophotometer (ThermoFisher). All samples were screened for RNA integrity check and presented RIN values above 8 on 2100 Bioanalyzer instrument (Agilent).
Samples were submitted to Novogene for library preparation using TruSeq Stranded mRNA Library Prep Kit (poly-A selection) and sequencing using Illumina HISEQ 2500 platform (Illumina). Samples were sequenced using single-end 50bp sequencing, aiming a minimum coverage of 20M reads.

treatment_protocol: Female 8-12 weeks old C57BL/6J mice were obtained from ScanBur (Charles River, Germany) and housed in environmentally enriched ventilated cages under specific pathogen free conditions (SPF) at Astrid Fagræus laboratory (AFL, Karolinska Institutet) under 12h light cycle and receiving water and ration ad libitum (RM1(P), Special Diet Services). For induction of colitis, 2.5% w/v dextran sulfate sodium (DSS; Affymetrics) was supplemented in drinking water and given to mice for 7 consecutive days, with a change on day 3. After the treatment was ceased, mice returned to receive standard water. Mice were monitored everyday for alterations in body weight, disease activity index (DAI) 1. Mice were anesthetized with isofluorane and sacrificed for blood and tissue sampling at different time points.

tag: Sex

value: Female

value: 9 weeks old

tag: replicate

tag: group

tag: tissue

value: Proximal Colon

tag: cage

value: B

tag: flowcell


title: DSSd14_2

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain


title: DSSd12_3

value: C


title: DSSd14_3


title: DSSd14_1

value: A


title: DSSd12_1


title: DSSd10_3


title: DSSd10_2


title: genomic DNA from monocytes 19

status: Public on Jun 20 2019

type: genomic

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

country: USA

institute: ASRC-CUNY

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

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing: GenomeStudio v2011.1 and Methylation module (within GenomeStudio) v1.9 was used.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: RRMS patient with Low BMI

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from CD14+ sorted blood monocytes using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: M

tag: age

tag: bmi

tag: therapy

value: Naive

tag: disease state

value: CIS

tag: cell type

value: blood monocytes


title: DSSd08_3


title: DSSd08_2


title: DSSd08_1


title: DSSd07_3


title: DSSd07_2

value: HLNYHBCXX


title: DSSd06_2


title: DSSd06_3


title: DSSd07_1


title: DSSd04_3


title: DSSd04_2


title: DSSd04_1


title: DSSd06_1


title: genomic DNA from monocytes 15

value: F

value: RRMS


title: DSSd02_2


title: DSSd02_1


title: DSSd00_2


title: DSSd02_3


title: genomic DNA from monocytes 12


title: DSSd00_1


title: HC-4

status: Public on May 10 2019

city: Pittsburgh

last: Fuschiotti

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
Chromium scRNA-seq data produced by the 10X Chromium Platform were processed to generate sample-specific fastq files.
Processed reads were then examined by quality metrics, mapped to a reference human genome using RNA-seq aligner STAR and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger pipeline (10X Genomics).
To ensure that PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level 10. In this way, cell x gene UMI counting matrices were generated for downstream analyses.
Seurat, an R package developed for single-cell analysis,11 was used to identify distinct cell populations and visualize cell clusters in graphs as in. 8 Specifically, the UMI matrix was filtered such that only cells expressing at least 200 genes were utilized in downstream analysis.
Unwanted sources of variation were regressed out of the data by constructing linear models to predict gene expression based on the number of UMIs per cell as well as the percentage of mitochondrial gene content.
Genome_build: GrCh38 genome
Supplementary_files_format_and_content: Raw dataframe csv files

molecule: polyA RNA

source_name: Skin tissue

extract_protocol:
Skin biopsies were minced and digested enzymatically (Whole Dissociation Skin Kit, Miltenyi Biotec) for 2 hours at 37°C and further dispersed using the Miltenyi gentleMACS Octo Dissociator. Experimental procedures followed established techniques7 using the Chromium Single Cell 3’ Library V2  kit (10x Genomics). Cell suspensions were separated by the Chromium System (10X Genomics)7,8 into  mini-reaction "partitions" or GEMs formed by oil micro-droplets, each containing a gel bead and a cell. A  1000-fold excess of partitions compared to cells assured that most partitions/GEMs had only one cell per  GEM. Gel beads contained an oligonucleotide scaffold composed of an oligo-dT section for priming  reverse transcription, and barcodes for each cell (10X Genomics) and each transcript (unique molecular   identifier, UMI), as described.9 7,000 cells were loaded into the instrument to obtain data on ~4,000 cells  with a rate of ~3.1% of partitions showing more than one cell/partition. The following steps were all  performed using reagents and protocols developed by 10X Genomics.
The emulsions were transferred from the Chromium chip to a PCR cycler for cDNA synthesis. The emulsion was then broken using a recovery agent, and following Dynabead and SPRI clean up, cDNAs were amplified by PCR (C1000, Bio-Rad). cDNAs were sheared enzymatically into lengths of ~200bp. DNA fragment ends were repaired, A-tailed, and adaptors ligated.

value: Healthy control


title: HC-3


title: HC-2


title: CTCL-12

source_name: Skin tumor

tag: tumor stage

value: CTCL tumor


title: HC-1


title: genomic DNA from monocytes 16

source_name: RRMS patient with High BMI


title: CTCL-8

value: IIB T3N0B0M0


title: DSSd00_3


title: genomic DNA from monocytes 11


title: genomic DNA from monocytes 3


title: genomic DNA from monocytes 17


title: genomic DNA from monocytes 7


title: CTCL-6

value: F IIB T3NxB0M0


title: genomic DNA from monocytes 6


title: genomic DNA from monocytes 18


title: genomic DNA from monocytes 2


title: genomic DNA from monocytes 5


title: genomic DNA from monocytes 10


title: genomic DNA from monocytes 14


title: genomic DNA from monocytes 4


title: genomic DNA from monocytes 1


title: genomic DNA from monocytes 13


title: BrTuRefMix vs. 130B BrTuB07

status: Public on May 08 2019

type: RNA

city: Santa Monica

first: HSIAOWANG

last: CHEN

state: CA

address: 2825 Santa Monica Blvd

department: Medicine

institute: UCLA

hyb_protocol: In comparison of expression between each breast tumor sample and a reference mix pool composed of equal amount of 19 breast tumor contains ER+, HER2 amplified, and triple negative samples. 825 ng each of labeled reference mix  (BrTuRefMix,cy3 label) and individual Breast tumor baseline sample(cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol.

scan_protocol: Slides were read on an Agilent Microarray scanner (G2565CA) with extended dynamic range applied. Images were quantified using Agilent Feature Extraction Software version A.10.7 or version 11.0 refer to raw data file column.

data_processing:
Agilent Feature Extraction Software was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used  to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extracted data was imported into Rosetta Resolver version 7.2  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging.
In Rosetta analysis, setting for cluster Algoritm is list here and applies to both sample experiment and sequence.  Algorithm=Agglomerative, Algorithm parameters: Heuristic criteria=Average link, Similarity measure metric type=Cosine correlation.
In Rosetta analysis, setting for statistical cuts is list here to generate the cluster.  Thresholds=equal or bigger than 2 fold change with P-vaule equal or less than 0.01. Number of experiment cut is not applied.

source_name: BrTuRefMix

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions.

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit following manufacturer's protocol.

tag: sample type

value: tumor reference mix

source_name: 130B BrTuB07

value: Breast tumor baseline

tag: er status (ihc staining results)

value: Neg

tag: pr_status (ihc staining results)

tag: treatment group

value: TCHTy

tag: drug response

value: PCR


title: BrTuRefMix vs. 128B BrTuB07

source_name: 128B BrTuB07

value: Pos

value: TCTy

value: RD


title: BrTuRefMix vs. 125B BrTuB07

source_name: 125B BrTuB07


title: BrTuRefMix vs. 124B BrTuB07

source_name: 124B BrTuB07

value: TCH


title: genomic DNA from monocytes 9

value: M

value: Naive

value: blood monocytes


title: BrTuRefMix vs. 120B BrTuB07

source_name: 120B BrTuB07


title: BrTuRefMix vs. 127B BrTuB07

source_name: 127B BrTuB07


title: BrTuRefMix vs. 119B BrTuB07

source_name: 119B BrTuB07


title: BrTuRefMix vs. 122B BrTuB07

source_name: 122B BrTuB07


title: BrTuRefMix vs. 121B BrTuB07

source_name: 121B BrTuB07


title: BrTuRefMix vs. 123B BrTuB07

source_name: 123B BrTuB07


title: BrTuRefMix vs. 118B BrTuB07

source_name: 118B BrTuB07


title: BrTuRefMix vs. 113B BrTuB07

source_name: 113B BrTuB07


title: BrTuRefMix vs. 116B BrTuB07

source_name: 116B BrTuB07


title: BrTuRefMix vs. 115B BrTuB07

source_name: 115B BrTuB07


title: BrTuRefMix vs. 111B BrTuB07

source_name: 111B BrTuB07


title: BrTuRefMix vs. 110B BrTuB07

source_name: 110B BrTuB07


title: BrTuRefMix vs. 112B BrTuB07

source_name: BrTuRefMix

source_name: 112B BrTuB07


title: BrTuRefMix vs. 106B BrTuB07

source_name: 106B BrTuB07


title: BrTuRefMix vs. 105B BrTuB07

source_name: 105B BrTuB07


title: genomic DNA from monocytes 8

source_name: RRMS patient with High BMI

value: F

value: RRMS


title: BrTuRefMix vs. 107B BrTuB07

source_name: 107B BrTuB07


title: BrTuRefMix vs. 103B BrTuB07

source_name: 103B BrTuB07


title: BrTuRefMix vs. 129B BrTuB07

source_name: 129B BrTuB07


title: BrTuRefMix vs. 104B BrTuB07

source_name: 104B BrTuB07


title: BrTuRefMix vs. 100B BrTuB07

source_name: 100B BrTuB07


title: BrTuRefMix vs. 95B BrTuB07

source_name: 95B BrTuB07


title: BrTuRefMix vs. 93B BrTuB07

source_name: 93B BrTuB07


title: BrTuRefMix vs. 90B BrTuB07

source_name: 90B BrTuB07


title: BrTuRefMix vs. 89B BrTuB07

source_name: 89B BrTuB07


title: BrTuRefMix vs. 91B BrTuB07

source_name: 91B BrTuB07


title: BrTuRefMix vs. 97B BrTuB07

source_name: 97B BrTuB07


title: BrTuRefMix vs. 86B BrTuB07

source_name: 86B BrTuB07


title: BrTuRefMix vs. 98B BrTuB07

source_name: BrTuRefMix

source_name: 98B BrTuB07


title: BrTuRefMix vs. 88B BrTuB07

source_name: 88B BrTuB07


title: BrTuRefMix vs. 92B BrTuB07

source_name: 92B BrTuB07


title: BrTuRefMix vs. 102B BrTuB07

source_name: 102B BrTuB07


title: BrTuRefMix vs. 85B BrTuB07

source_name: 85B BrTuB07


title: BrTuRefMix vs. 83B BrTuB07

source_name: 83B BrTuB07


title: BrTuRefMix vs. 81B BrTuB07

source_name: 81B BrTuB07


title: BrTuRefMix vs. 80B BrTuB07

source_name: 80B BrTuB07


title: BrTuRefMix vs. 87B BrTuB07

source_name: 87B BrTuB07


title: BrTuRefMix vs. 78B BrTuB07

source_name: 78B BrTuB07


title: BrTuRefMix vs. 82B BrTuB07

source_name: 82B BrTuB07


title: BrTuRefMix vs. 84B BrTuB07

source_name: 84B BrTuB07


title: BrTuRefMix vs. 77B BrTuB07

source_name: 77B BrTuB07


title: BrTuRefMix vs. 76B BrTuB07

source_name: 76B BrTuB07


title: BrTuRefMix vs. 79B BrTuB07

source_name: 79B BrTuB07


title: BrTuRefMix vs. 75B BrTuB07

source_name: 75B BrTuB07


title: BrTuRefMix vs. 71B BrTuB07

source_name: BrTuRefMix

source_name: 71B BrTuB07


title: BrTuRefMix vs. 73B BrTuB07

source_name: 73B BrTuB07


title: BrTuRefMix vs. 70B BrTuB07

source_name: 70B BrTuB07


title: BrTuRefMix vs. 114B BrTuB07

source_name: 114B BrTuB07


title: BrTuRefMix vs. 68B BrTuB07

source_name: 68B BrTuB07


title: BrTuRefMix vs. 64B BrTuB07

source_name: 64B BrTuB07


title: BrTuRefMix vs. 66B BrTuB07

source_name: 66B BrTuB07


title: BrTuRefMix vs. 58B BrTuB07

source_name: 58B BrTuB07


title: BrTuRefMix vs. 65B BrTuB07

source_name: 65B BrTuB07


title: BrTuRefMix vs. 67B BrTuB07

source_name: 67B BrTuB07


title: BrTuRefMix vs. 52B BrTuB07

source_name: 52B BrTuB07


title: BrTuRefMix vs. 69B BrTuB07

source_name: 69B BrTuB07


title: BrTuRefMix vs. 74B BrTuB07

source_name: 74B BrTuB07


title: BrTuRefMix vs. 57B BrTuB07

source_name: 57B BrTuB07


title: BrTuRefMix vs. 47B BrTuB07

source_name: 47B BrTuB07


title: BrTuRefMix vs. 54B BrTuB07

source_name: 54B BrTuB07


title: BrTuRefMix vs. 60B BrTuB07

source_name: BrTuRefMix

source_name: 60B BrTuB07


title: BrTuRefMix vs. 53B BrTuB07

source_name: 53B BrTuB07


title: BrTuRefMix vs. 51B BrTuB07

source_name: 51B BrTuB07


title: BrTuRefMix vs. 63B BrTuB07

source_name: 63B BrTuB07


title: BrTuRefMix vs. 61B BrTuB07

source_name: 61B BrTuB07


title: BrTuRefMix vs. 44B BrTuB07

source_name: 44B BrTuB07


title: BrTuRefMix vs. 42B BrTuB07

source_name: 42B BrTuB07


title: BrTuRefMix vs. 62B BrTuB07

source_name: 62B BrTuB07


title: BrTuRefMix vs. 43B BrTuB07

source_name: 43B BrTuB07


title: BrTuRefMix vs. 59B BrTuB07

source_name: 59B BrTuB07


title: BrTuRefMix vs. 40B BrTuB07

source_name: 40B BrTuB07


title: BrTuRefMix vs. 48B BrTuB07

source_name: 48B BrTuB07


title: BrTuRefMix vs. 39B BrTuB07

source_name: 39B BrTuB07


title: BrTuRefMix vs. 38B BrTuB07

source_name: 38B BrTuB07


title: BrTuRefMix vs. 34B BrTuB07

source_name: 34B BrTuB07


title: BrTuRefMix vs. 30B BrTuB07

source_name: 30B BrTuB07


title: BrTuRefMix vs. 33B BrTuB07

source_name: BrTuRefMix

source_name: 33B BrTuB07


title: BrTuRefMix vs. 32B BrTuB07

source_name: 32B BrTuB07


title: BrTuRefMix vs. 41B BrTuB07

source_name: 41B BrTuB07


title: BrTuRefMix vs. 27B BrTuB07

source_name: 27B BrTuB07


title: BrTuRefMix vs. 31B BrTuB07

source_name: 31B BrTuB07


title: BrTuRefMix vs. 26B BrTuB07

source_name: 26B BrTuB07


title: BrTuRefMix vs. 22B BrTuB07

source_name: 22B BrTuB07


title: BrTuRefMix vs. 24B BrTuB07

source_name: 24B BrTuB07


title: BrTuRefMix vs. 19B BrTuB07

source_name: 19B BrTuB07


title: BrTuRefMix vs. 28B BrTuB07

source_name: 28B BrTuB07


title: BrTuRefMix vs. 20B BrTuB07

source_name: 20B BrTuB07


title: BrTuRefMix vs. 13B BrTuB07

source_name: 13B BrTuB07


title: BrTuRefMix vs. 14B BrTuB07

source_name: 14B BrTuB07


title: BrTuRefMix vs. 25B BrTuB07

source_name: 25B BrTuB07


title: BrTuRefMix vs. 18B BrTuB07

source_name: 18B BrTuB07


title: BrTuRefMix vs. 35B BrTuB07

source_name: 35B BrTuB07


title: BrTuRefMix vs. 37B BrTuB07

source_name: BrTuRefMix

source_name: 37B BrTuB07


title: BrTuRefMix vs. 16B BrTuB07

source_name: 16B BrTuB07


title: BrTuRefMix vs. 29B BrTuB07

source_name: 29B BrTuB07


title: BrTuRefMix vs. 9B BrTuB07

source_name: 9B BrTuB07


title: BrTuRefMix vs. 8B BrTuB07

source_name: 8B BrTuB07


title: BrTuRefMix vs. 12B BrTuB07

source_name: 12B BrTuB07


title: BrTuRefMix vs. 21B BrTuB07

source_name: 21B BrTuB07


title: BrTuRefMix vs. 11B BrTuB07

source_name: 11B BrTuB07


title: BrTuRefMix vs. 7B BrTuB07

source_name: 7B BrTuB07


title: Root RNA seq Lib 2

status: Public on Dec 23 2018

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

data_processing:
Sequenced reads were aligned to the TAIR10 Arabidopsis genome using STAR.
Htseq was used to count reads on genes and rpkm values were calculated using EdgeR
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with RPKM

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: Arabidopsis plant (Col-0) was grown under long day conditions at 22C on vertical agar plates. Roots were harvested from 14-day old plants, and RNA-seq was performed.

extract_protocol:
RNA was extracted using TRIZOL (Life Technologies) reagent and cleaned with RNA Clean & Concentrator™-5 (Zymo).
Libraries were prepared for NGS sequencing with NEBNext RNA library prep kit (module E7530-E7490).

value: roots

tag: background ecotype

tag: genotype

value: expressing INTACT

value: 14 days


title: Root RNA seq Lib 1

tag: tissue


title: HKC_day0_RUNX1 ChIP-Seq input DNA

status: Public on Dec 18 2018

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the self-generated hg19 reference genome using STAR 2.5.0. The code to generate the reference genome: STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /home/self_generated_genome/ --genomeFastaFiles /home/hg19.fa --sjdbGTFfile /home/Homo_sapiens.GRCh37.75_new.gtf --sjdbOverhang 100  The code for mapping: STAR  --runThreadN 16 --quantMode GeneCounts  --outSAMstrandField intronMotif  --outFilterIntronMotifs RemoveNoncanonical  --outFilterType BySJout  --outSAMtype BAM SortedByCoordinate  --outWigType wiggle  --outWigStrand Unstranded   --genomeDir /home/self_generated_genome  --readFilesCommand zcat  --readFilesIn $r1file $r2file  --outFileNamePrefix /home/mapping
wigToBigWig from UCSC geome browser is used to generate the bigwig files from the wiggle files
peaks.bed files are generated with MACS2 and contain all the peak information.
Genome_build: hg19, Homo_sapiens.GRCh37.75_new.gtf

source_name: keratinocytes

growth_protocol: primary keratinocytes were cultured in Keratinocyte Basal Medium (KBM, Lonza #CC-4131) supplemented with 100 U/mL Penicillin/Streptomycin (Gibco Life Technology #15140122), 0.1 mM ethanolamine (Sigma Aldrich #141-43-5), 0.1 mM O-phosphoethanolamine (Sigma Aldrich #1071-23-4), 0.4% (vol/vol) bovine pituitary extract, 0.5 μg/mL hydrocortisone, 5 μg/mL insulin and 10 ng/mL epidermal growth factor (Lonza #CC-4131). Medium was refreshed every other day. When cells were more than 90% confluent (day 0), differentiation was induced by depletion of growth factors in addition to cell contact inhibition. Cells were collected at four differentiation stages, proliferation (day 0), early differentiation (day 2), mid differentiation (day 4), and late differentiation (day 7) for subsequent experiment. No mycoplasma contamination is found during cell culture.

extract_protocol:
Chromatin was incubated overnight at 4 °C in 1× incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES) supplemented with protease inhibitors and 0.1% BSA. A 50:50 mix of Protein A and G Dynabeads (Invitrogen) were added. Antibodies against H3K4me3 (Diagenode, C15410003, 1 μg), H3K27me3 (Diagenode, C15410069, 1.5 μg) and RUNX1 (ab23980, abcam, 4 μg) were used in each ChIP assay. The beads were washed twice with wash buffer 1 (0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), once with wash buffer 2 (wash buffer 1 with 500 mM NaCl), once with wash buffer 3 (250 mM LiCl, 0.5% sodium deoxycholate, 0.5% NP-50, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), and twice with wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES). After the washing steps, beads were rotated for 20 min at room temperature in elution buffer (1% SDS and 0.1 M NaHCO3). The supernatant was de-cross-linked with 200 mM NaCl and 100 μg/mL proteinase K for 4 h at 65 °C. De-cross-linked DNA was purified with MinElute PCR Purification columns (Qiagen). DNA amounts were determined with Qubit fluorometric quantification (ThermoFisher Scientific).
The pulled down DNA fragments were proceeded on with library construction using KAPA Hyper Prep Kit (Kapa Biosystems #KK8504) according to the standard protocol. The prepared libraries were then sequenced using the NextSeq 500 (Illumina) according to standard Illumina protocols.

tag: cell line

tag: Stage

value: day0 (proliferation)

tag: antibody


title: Root ATAC seq Lib 2

data_processing:
Sequenced reads were aligned to the TAIR10 Arabidopsis genome using bowtie.
Only unique mapped reads were used. Peaks were called by applying MACS2, with the parameters: -g 135000000 --nomodel --extsize 75 --shift -30
Genome_build: TAIR10
Supplementary_files_format_and_content: Bedgraph files were generated using sliding windows of 100 bp with steps of 25 bp. Reads from each sample were count in the windows.

source_name: root

growth_protocol: Arabidopsis plant (Col-0) was grown under long day conditions at 22C on vertical agar plates. Roots were harvested from 14-day old plants, and ATAC-seq was performed.

extract_protocol:
INTACT based protocol.
ATAC-seq: purified nuclei were transposed with 2.5 ul of Tn5 from the Illumina Nextera kit, followed by DNA purification with the EX-GP200 kit ( hy-labs). To generate libraries for sequencing, DNA was amplified and double sided cleaning was performed with Agencourt AMPure XP beads.

tag: age

value: 14 days old

tag: nuclei purification method

value: streptavidin affinity purification


title: BrTuRefMix vs. 6B BrTuB07

value: tumor reference mix

source_name: 6B BrTuB07

value: Breast tumor baseline

value: Neg

value: TCHTy


title: HKC_day0_RUNX1 ChIP-Seq

value: abcam #ab23980


title: HKC_day7_H3K27me3 ChIP-Seq

value: day7 (late differentiation)

value: Diagenode #C15410069


title: BrTuRefMix vs. 1B BrTuB07

source_name: 1B BrTuB07

value: RD


title: BrTuRefMix vs. 2B BrTuB07

source_name: 2B BrTuB07

value: Pos


title: BrTuRefMix vs. 4B BrTuB07

source_name: 4B BrTuB07

value: PCR


title: HKC_day7_H3K4me3 ChIP-Seq

value: Diagenode #C15410003


title: HKC_day0_H3K4me3 ChIP-Seq


title: HKC_day4_H3K27me3 ChIP-Seq

value: day4 (mid differentiation)


title: HKC_day7-1_RNA-Seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the self-generated hg19 reference genome using STAR 2.5.0. The code to generate the reference genome: STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /home/self_generated_genome/ --genomeFastaFiles /home/hg19.fa --sjdbGTFfile /home/Homo_sapiens.GRCh37.75_new.gtf --sjdbOverhang 100  The code for mapping: STAR  --runThreadN 16 --quantMode GeneCounts  --outSAMstrandField intronMotif  --outFilterIntronMotifs RemoveNoncanonical  --outFilterType BySJout  --outSAMtype BAM SortedByCoordinate  --outWigType wiggle  --outWigStrand Unstranded   --genomeDir /home/self_generated_genome  --readFilesCommand zcat  --readFilesIn $r1file $r2file  --outFileNamePrefix /home/mapping
wigToBigWig from UCSC geome browser is used to generate the bigwig files from the wiggle files
ReadsPerGene.out.tab file is generated with STAR 2.5.0 with the option of  --quantMode GeneCounts
ReadsPerGene.out.tab file is generated with STAR 2.5.0 and contains the information of read counts per gene.
Genome_build: hg19, Homo_sapiens.GRCh37.75_new.gtf

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA kit (MACHEREY-NAGEL #740955.250).
RNA-Seq experiment was performed with the starting material of 500 ng total RNA, to obtain double-strand cDNA (ds-cDNA). After purification with the MinElute Reaction Cleanup Kit (Qiagen #28206), 3 ng ds-cDNA was processed for library construction using KAPA Hyper Prep Kit (Kapa Biosystems #KK8504) according to the standard protocol except that a 15-minute USER enzyme (BioLab # M5505L) incubation step was added before library amplification. The prepared libraries were quantified with the KAPA Library Quantification Kit (Kapa Biosystems #KK4844), and then sequenced in a paired-ended manner using the NextSeq 500 (Illumina) according to standard Illumina protocols.


title: BrTuRefMix vs. 5B BrTuB07

source_name: BrTuRefMix

source_name: 5B BrTuB07


title: HKC_day0-1_RNA-Seq


title: HKC_day0-2_RNA-Seq


title: HKC_day2-2_RNA-Seq

value: day2 (early differentiation)


title: Root ATAC seq Lib 3

value: roots

value: expressing INTACT


title: HKC_day2-1_RNA-Seq


title: HKC_day2_H3K27me3 ChIP-Seq


title: Root ATAC seq Lib 1

value: 14 days old


title: HKC_day4-1_RNA-Seq


title: HKC_day4-2_RNA-Seq


title: HKC_day7-2_RNA-Seq


title: HKC_day2_H3K4me3 ChIP-Seq


title: HESC 30 EPC siWNK1 (FD39855)

status: Public on Aug 20 2018

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
Raw reads of 101 nucleotides were trimmed (10 nucleotides from the 5' end and 1 nucleotide from the 3' end) to generate 90-nucleotide pair-ended reads.
Reads were mapped to the human genome (UCSC hg19) using Tophat. NCBI RefSeq genes were used as reference and up to 2 possible mismatches were allowed. Read duplicates were removed using Picard tools. Htseq was used to determine the number of reads falling in known genes.
EdgeR was used to analyze gene-based read counts to determine differentially expressed genes. siNT and siWNK1-treated samples from the same patient (identified as HESC line ID) were treated as paired samples for statistical analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file of differential gene expression analysis.

source_name: HESC 30 EPC siWNK1

extract_protocol:
RNA was isolated from cultured cells using the Qiagen Rneasy Mini kit.
Libraries were prepared using the Illumina TruSeq RNA library prep kit v2 with polyA selection per the manufacturer's instructions.

treatment_protocol: HESCs were transfected with non-targeting siRNA (siNT) or with siRNA targeting WNK1 (siWNK1) for 48 hours, then subjected to in vitro decidualization in medium containing 17 beta-estradiol, medroxyprogesterone acetate, and db-cAMP.

value: Primary human endometrial stromal cells

tag: epc treatment

value: EPC day 3

tag: sirna treatment

value: siRNA targeting WNK1 (siWNK1)

value: HESC


title: HESC 42 EPC siNT (FD39846)

source_name: HESC 42 EPC siNT

value: non-targeting siRNA (siNT)

tag: cell type


title: HKC_day4_H3K4me3 ChIP-Seq


title: HESC 34 EPC siWNK1 (FD39851)

source_name: HESC 34 EPC siWNK1


title: HESC 30 EPC siNT (FD39854)

source_name: HESC 30 EPC siNT


title: HESC 42 EPC siWNK1 (FD39928)

source_name: HESC 42 EPC siWNK1


title: Sox17 f/f Sox17_ChIPSeq

status: Public on Aug 09 2018

data_processing:
36-nt sequence reads were identified by the Sequencing Service (using Illumina’s Genome Analyzer 2).
Reads were mapped to the mouse genome mm9 using the BWA algorithm.
Only tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Bigwig generated using bedGraphToBigWig from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig

source_name: Uterus

extract_protocol:
Chromatin samples were prepared by Active Motif Services - Factor Path assays
Libraries were prepared by Active Motif Services - Factor Path assays

tag: strain

value: uterus

value: WT

tag: gender

value: female

tag: chip antibody

value: SOX17 (R&D Systems AF1924)


title: HESC 34 EPC siNT (FD39850)

source_name: HESC 34 EPC siNT


title: HKC_day0_H3K27me3 ChIP-Seq

value: day0 (proliferation)

value: Diagenode #C15410069


title: BrTuRefMix vs. 101B BrTuB07

tag: sample type

value: tumor reference mix

source_name: 101B BrTuB07

value: Breast tumor baseline

tag: er status (ihc staining results)

value: Neg

tag: pr_status (ihc staining results)

value: Pos

value: TCH

value: PCR


title: E6E7

status: Public on Apr 23 2018

city: Bordeaux

first: Nicolas

middle: J.

last: Tourasse

address: 146 rue Leo Saignat

department: INSERM U1212, CNRS UMR5320

country: France

institute: University of Bordeaux

description:
SAMN06660772
SRX2690697

data_processing:
Raw FASTQ files were generated by the sequencing platform using Illumina Casava 1.8 basecalling software.
We estimated general read quality using FastQC (v0.10.1), trimmed low-quality 5' and 3' ends (Phred score <20) using Sickle (v1.2), removed remaining adapters and merged overlapping reads (at least 10 bp) using SeqPrep (v1.1) and split merged reads in half with a home-made "awk" routine. Finally, paired-ends with one read shorter than 30 bp were discarded.
Gene expression levels were computed following the protocol of Haas et al. (Nature Protocols 2013, 8:1494-1512) using tools from the Trinity (v2.2.0) and RSEM (v1.3.0) packages. RSEM was employed to estimate gene-level abundances by aligning RNA-Seq reads onto the cDNA sequences of the protein-coding transcripts obtained from the Ensembl (release 87) database, which are based on assembly hg38 (GRCh38) of the human genome. Bowtie (v2.2.5) was used as read aligner. Abundances were then transformed into TMM (trimmed mean of M-values)-normalized FPKM (fragments per kb per million mapped reads) gene expression values.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: One Microsoft Excel spreadsheet with normalized abundance measurements calculated using RSEM and Trinity

source_name: fibroblast cells

growth_protocol: IMR90 cells were grown in modified DMEM supplemented with 15 % fetal calf serum and 100 U/ml Penicillin and 100µg/ml Streptomycin. Plasmids employed for establishing cell lines that stably express pBabe-ras and pBabe-TERT were kindly provided, respectively, by Scott Lowe and Robert Weinberg. pZIPSV40 was obtained from Parmjit Jat. The gene encoding SV40 small t was amplified by PCR from pZIPSV40 and cloned into the pBabe-puro vector. E6 and E7 were amplified by PCR from HPV16 genomic DNA and cloned into the pBabe-neo vector. pBabe constructs were co-transfected with the pCL-10A1 (IMGENEX) vector into 293 cells and the retrovirus-containing supernatant was collected after 48 hours, 0.45 µm-filtered, supplemented with 8µg/ml Sequabrene and incubated with IMR90 cells or the appropriate transformation intermediates. Cells that had incorporated the respective construct were identified by adding the appropriate selection marker for 5 days to 4 weeks (400 µg/ml G418; 2µg/ml puromycin; 100 µg/ml hygromycin).

extract_protocol:
Total RNA was isolated by mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed at the Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.

tag: cell line background

value: primary embryonic fibroblast

tag: intermediate cell line

value: IMR90 E6/E7


title: IMR90

description:
SAMN06660771
SRX2690604


title: E6E7R

description:
SAMN06660773
SRX2690698

value: IMR90 E6/E7/RAS


title: E6E7RS

description:
SAMN06660775
SRX2690700

value: IMR90 E6/E7/RAS/small t


title: E6E7RST

description:
SAMN06660776
SRX2690701

value: IMR90 E6/E7/RAS/small t/TERT


title: E6E7S

description:
SAMN06660774
SRX2690699

value: IMR90 E6/E7/small t


title: Sox17 f/f GD3.5 rep2

hyb_protocol: Approximately 480ng of fragmented cRNA samples were loaded onto each of the Mouse G3 8x60K Expression arrays. The arrays were hybridized in an Agilent Hybridization Chamber for 17 hours at 65C with rotation at 10rpm.

scan_protocol: Once dry, the slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C and Scan Control software version A.8.5.1. Data extraction and quality assessment of the microarray data was completed using Agilent Feature Extraction Software Version 11.0.1.1.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Array data were analyzed using Bioconductor for with quantile normalization.

source_name: uterus, day 3.5 natural pregnancy

label_protocol: Twenty-five nanograms of total RNA, combined with RNA spike mix, were reverse transcribed using a T7 Primer Mix to produce cDNA. The cDNA product was transcribed using T7 RNA Polymerase, producing cyanine-3-labeled cRNA. The labeled cRNA was purified using a Qiagen RNeasy Mini Kit. Purified products were quantified using the NanoDrop spectrophotometer for yield and dye incorporation, and tested for integrity on the Agilent Bioanalyzer. Six hundred nanograms of the labeled cRNA were fragmented.

growth_protocol: Female mice were fed normal chow and were mated to male mice of proven fertility at 8-10 weeks of age.

extract_protocol: RNA was isolated from frozen tissue using Trizol and aqueous phase separation techniques with the Qiagen RNEasy prep kit.

treatment_protocol: Female mice at breeding age were mated to males of proven fertility and sacrificed 3 days after the presence of the post-coital plug. Uteri without embryos were harvested and frozen.

tag: tissue

value: whole uterine tissue

tag: genotype

value: WT


title: LtfiCre/+ Sox17 f/f GD3.5 rep2

value: Sox17 KO

value: female


title: LtfiCre/+ Sox17 f/f GD3.5 rep1


title: Sox17 f/f GD3.5 rep1


title: GATA2_ChIPseq

status: Public on Jan 02 2018

data_processing:
36-nt sequence reads were identified by the Sequencing Service (using Illumina’s Hi-Seq).
Reads were mapped to the human genome hg19 using the BWA algorithm.
Only tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
The number of unique alignments without duplicate reads was totaled and MACS analysis was performed at a pvalue 1e-7.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig files were generated using bedGraphToBigWig from UCSC.

source_name: Endometrial biopsy from healthy women

growth_protocol: Human endometrial stromal cells (HESCs) were cultured in 150-mm culture dishes with HESC growth media (DMEM/F12 containing 10% of fetal bovine serum and 1% antibiotic-antimycotic)

extract_protocol:
Cells were fixed for 15 min with 1/10 volume of freshly prepared formaldehyde solution (11% formaldehyde, 0.1 M NaCl, 1 mM EDTA, and 50 mM HEPES). The fixation was stopped by adding 1/20 volume 2.5 M glycine for 5 min. Fixed HESCs were collected and pelleted at 800 x g for 10 min at 4 oC. Cell pellets were washed two times with cold PBS-Igepal (0.5% Igepal, 1 mM PMSF).  HESCs from six patients were pooled before genomic DNA isolation. NR2F2 immunoprecipitation and DNA library generation were performed by Active Motif.
ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit. Briefly, DNA ends were polished and 59-phosphorylated using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. Addition of 3’-adenine to blunt ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size fractionated to 175–225 bp on a 2% agarose gel. After amplification for 18 cycles with Phusion polymerase, the resulting DNA libraries were tested by RT-qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.

treatment_protocol: Cells grow to reach approximately 90% confluency, starting to treat with decidual media (Opti-MEM media containing 2% charcoal-stripped FBS, 1% antibiotic-antimycotic, 1 µM Medroxyprogesterone acetate, 10 nM E2, and 50 µM cAMP). Decidual media was changed every 48 h. After 72h of treatment, cells were fixed.

value: Primary endometrial stromal cells

tag: passage

value: GATA2 (Santa Cruz Biotechnologies, sc-9008)


title: #67 D0 siGA

description: Gene expression data from day 0 of gata2 siRNA treated human decidual stromal cells

hyb_protocol: The fragmented, labeled cRNA (15 ug) was hybridized to Human Genome U133 Plus 2.0 arrays.

scan_protocol: Scanning was done using an Affymetrix 3000 with autoloading scanner performed using Affymetrix protocols.

data_processing: A DNA-Chip analyzer dChIP version 1.3 was utilized to adjust arrays to a common baseline using invariant set normalization. All Genechips (n=6) were normalized together to the same baseline and modeled together.

label: biotin

source_name: human primary endometrial stromal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human primary endometrial stromal cells were cultured in growth media consisting of DMEM/F12 containing 10% of fetal bovine serum (FBS) and 1% antibiotic-antimycotic.

extract_protocol: QIAGEN RNeasy total RNA isolation kit.

treatment_protocol: Human primary stromal cells from three different patients were grown to approximately 70% confluence and subsequently treated with 100nM medroxyprogesterone acetate, and 1mM 8-bromo-cAMP and transfected with 60nM scrambled, non-targeting (siNT), or GATA2-targeting (siGATA2) siRNA using Lipofectamine RNAiMax lipid per the manufacturer’s instructions. After 72 hours of transfection exposure cells were harvested and RNA isolated using the RNAeasy Mini kit as per manufacterer’s instructions.

value: human decidual stromal cells

tag: Stage

value: Female proliferative phase


title: #54 D3 siGA

description: Gene expression data from day 3 of gata2 siRNA treated human decidual stromal cells


title: #67 D3 siGA


title: #67 D3 siNT

description: Gene expression data from day 3 of non-targeting siRNA treated human decidual stromal cells


title: #35 D0 siNT

description: Gene expression data from day 0 of non-targeting siRNA treated human decidual stromal cells


title: Sox17 f/f GD3.5 rep3


title: #54 D0 si2


title: #67 D0 siNT


title: #54 D3 siNT


title: #35 D3 NT1


title: #35 D3 siGA


title: LtfiCre/+ Sox17 f/f GD3.5 rep3


title: #54 D0 NT2


title: #35 D0 siGA


title: Input


title: Control_1

status: Public on Nov 17 2017

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description:
6929742081_R04C01_Grn.idat
6929742081_R04C01_Red.idat
sample name: LPZ_CTR

hyb_protocol: Infinium HD Assay for Methylation (Illumina)

scan_protocol: Illumina HiScan SQ system (Illumina)

data_processing: Beta value.  The methylation β values were normalized using the BMIQ normalization method

label: Cy5 and Cy3

source_name: CD34+ enriched mobilized peripheral blood

extract_protocol: QiaAmp DNA Blood Mini kit (Quagen)

value: blood

value: Female

tag: diagnosis

value: Healthy


title: Control_4

description:
8363800249_R01C01_Grn.idat
8363800249_R01C01_Red.idat
sample name: AJOB_CTR

label_protocol: Infinium HD Assay for Methylation (Illumina)

value: Male


title: sample_57

description:
200308800008_R01C01_Grn.idat
200308800008_R01C01_Red.idat
sample name: 2032

source_name: bone marrow total cells

value: bone marrow

value: CMML


title: Control_9

description:
8359026002_R05C01_Grn.idat
8359026002_R05C01_Red.idat
sample name: TEI_CTR


title: sample_59

description:
8359018041_R05C02_Grn.idat
8359018041_R05C02_Red.idat
sample name: HX_DX


title: sample_62

description:
8359018041_R04C01_Grn.idat
8359018041_R04C01_Red.idat
JLLP_DX


title: Control_5

description:
8359018048_R02C01_Grn.idat
8359018048_R02C01_Red.idat
sample name: MGG_CTR


title: Control_6

description:
8363800249_R04C02_Grn.idat
8363800249_R04C02_Red.idat
sample name: IGP_CTR


title: sample_64

description:
8359018048_R05C01_Grn.idat
8359018048_R05C01_Red.idat
sample name: RMR_DX


title: sample_56

description:
200308800008_R02C01_Grn.idat
200308800008_R02C01_Red.idat
sample name: 1998


title: Control_8

description:
8363800249_R05C02_Grn.idat
8363800249_R05C02_Red.idat
sample name: DLG_CTR


title: sample_53

description:
200308800008_R02C02_Grn.idat
200308800008_R02C02_Red.idat
sample name: 1555


title: Control_2

description:
8363800211_R05C02_Grn.idat
8363800211_R05C02_Red.idat
sample name: JPR_CTR


title: sample_48

description:
200308800008_R04C02_Grn.idat
200308800008_R04C02_Red.idat
sample name: 632


title: sample_63

description:
7310440007_R05C02_Grn.idat
7310440007_R05C02_Red.idat
sample name: PPC_DX


title: sample_58

description:
9904796134_R05C01_Grn.idat
9904796134_R05C01_Red.idat
sample name: ACC_DX


title: sample_55

description:
200308800008_R06C01_Grn.idat
200308800008_R06C01_Red.idat
sample name: 1847


title: sample_50

description:
200308800008_R01C02_Grn.idat
200308800008_R01C02_Red.idat
sample name: 1261


title: sample_49

description:
200308800008_R03C01_Grn.idat
200308800008_R03C01_Red.idat
sample name: 1222


title: sample_66

description:
7310440007_R04C02_Grn.idat
7310440007_R04C02_Red.idat
sample name: AHI_C0


title: sample_54

description:
200308800008_R05C01_Grn.idat
200308800008_R05C01_Red.idat
sample name: 1824


title: Control_3

description:
8363800211_R06C02_Grn.idat
8363800211_R06C02_Red.idat
sample name: AGP_CTR


title: sample_61

description:
7310440007_R06C01_Grn.idat
7310440007_R06C01_Red.idat
sample name: JGR_DX


title: sample_60

description:
7310440007_R03C01_Grn.idat
7310440007_R03C01_Red.idat
sample name: JBG_DX


title: Control_10

description:
7310440007_R02C01_Grn.idat
7310440007_R02C01_Red.idat
sample name: COR_C1


title: sample_52

description:
200308800008_R04C01_Grn.idat
200308800008_R04C01_Red.idat
sample name: 1554


title: sample_51

description:
101032570180_R06C02_Grn.idat
101032570180_R06C02_Red.idat
sample name: 1336


title: Control_7

description:
8359018048_R03C01_Grn.idat
8359018048_R03C01_Red.idat
sample name: MCJV_CTR


title: sample_65

description:
7310440007_R01C01_Grn.idat
7310440007_R01C01_Red.idat
sample name: SLH_DX


title: sample_47

description:
200308800008_R03C02_Grn.idat
200308800008_R03C02_Red.idat
sample name: 67


title: sample_43

description:
3999431129_R01C02_Grn.idat
3999431129_R01C02_Red.idat
sample name: 43


title: sample_40

description:
3999431129_R04C01_Grn.idat
3999431129_R04C01_Red.idat
40


title: sample_42

description:
3999431129_R06C01_Grn.idat
3999431129_R06C01_Red.idat
sample name: 42


title: sample_46

description:
3999431129_R04C02_Grn.idat
3999431129_R04C02_Red.idat
sample name: 46


title: sample_33

description:
3999431089_R03C02_Grn.idat
3999431089_R03C02_Red.idat
sample name: 33


title: sample_38

description:
3999431129_R02C01_Grn.idat
3999431129_R02C01_Red.idat
sample name: 38


title: sample_27

description:
3999431089_R03C01_Grn.idat
3999431089_R03C01_Red.idat
sample name: 27


title: sample_37

description:
3999431129_R01C01_Grn.idat
3999431129_R01C01_Red.idat
sample name: 37


title: sample_24

description:
3999431014_R06C02_Grn.idat
3999431014_R06C02_Red.idat
sample name: 24


title: sample_44

description:
3999431129_R02C02_Grn.idat
3999431129_R02C02_Red.idat
sample name: 44


title: sample_39

description:
3999431129_R03C01_Grn.idat
3999431129_R03C01_Red.idat
sample name: 39


title: sample_34

description:
3999431089_R04C02_Grn.idat
3999431089_R04C02_Red.idat
sample name: 34


title: sample_28

description:
3999431089_R04C01_Grn.idat
3999431089_R04C01_Red.idat
sample name: 28


title: sample_21

description:
3999431014_R03C02_Grn.idat
3999431014_R03C02_Red.idat
sample name: 21


title: sample_41

description:
3999431129_R05C01_Grn.idat
3999431129_R05C01_Red.idat
sample name: 41


title: sample_36

description:
3999431089_R06C02_Grn.idat
3999431089_R06C02_Red.idat
sample name: 36


title: sample_30

description:
3999431089_R06C01_Grn.idat
3999431089_R06C01_Red.idat
sample name: 30


title: sample_45

description:
3999431129_R03C02_Grn.idat
3999431129_R03C02_Red.idat
sample name: 45


title: sample_35

description:
3999431089_R05C02_Grn.idat
3999431089_R05C02_Red.idat
sample name: 35


title: sample_18

description:
3999431014_R06C01_Grn.idat
3999431014_R06C01_Red.idat
sample name: 18


title: sample_31

description:
3999431089_R01C02_Grn.idat
3999431089_R01C02_Red.idat
sample name: 31


title: sample_29

description:
3999431089_R05C01_Grn.idat
3999431089_R05C01_Red.idat
29


title: sample_25

description:
3999431089_R01C01_Grn.idat
3999431089_R01C01_Red.idat
sample name: 25


title: sample_17

description:
3999431014_R05C01_Grn.idat
3999431014_R05C01_Red.idat
sample name: 17


title: sample_23

description:
3999431014_R05C02_Grn.idat
3999431014_R05C02_Red.idat
sample name: 23


title: sample_22

description:
3999431014_R04C02_Grn.idat
3999431014_R04C02_Red.idat
sample name: 22


title: sample_32

description:
3999431089_R02C02_Grn.idat
3999431089_R02C02_Red.idat
sample name: 32


title: sample_20

description:
3999431014_R02C02_Grn.idat
3999431014_R02C02_Red.idat
sample name: 20


title: sample_16

description:
3999431014_R04C01_Grn.idat
3999431014_R04C01_Red.idat
sample name: 16


title: sample_26

description:
3999431089_R02C01_Grn.idat
3999431089_R02C01_Red.idat
sample name: 26


title: sample_19

description:
3999431014_R01C02_Grn.idat
3999431014_R01C02_Red.idat
sample name: 19


title: input_myotube_DM_day_5

status: Public on Aug 18 2017

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment with mouse genome (NCBIM37/mm9) using Bowtie2 version 2.2.6 (Langmead et al. 2012),
To detect genomic region with significant enrichment we used SICER  software version 1.1 (Zang, et al. 2009). For peak calling we use a Window parameter of 600 and a Gap parameter of 1200 and a FDR of 1%.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files are created using file Extended tag pileup from MACS version 1.4.2 (Zhang et al. 2008)  for every 10 bp

source_name: C2C12 cell line

growth_protocol: C2C12 myoblasts were grown in growth medium (GM) consisting of DMEM (Gibco) containing 20% FBS (Invitrogen) and 1% Penicillin-Streptomycin (Gibco). Primary myoblasts were maintained in Ham’s F10 (Gibco) medium complemented with 20% FBS (Invitrogen), 10 ng/ml of bFGF (Invitrogen), 0,1% Fungizone (Invitrogen), Penicillin-Streptomycin.

extract_protocol:
extract protocol was performed essentially as previously described (Creppe et al. 2014).
library construction protocol was performed essentially as previously described (Creppe et al. 2014).

treatment_protocol: For differentiation, cell culture plates were Matrigel-treated (BD Biosciences) for 1h at 37ºC. Differentiation medium (DM) for all cell cultures was DMEM supplemented with 2% Horse serum (Gibco) and Penicillin-Streptomycin. To induce differentiation, cells seeded at high confluence were washed once with PBS and DM was added.

value: mouse myotube

tag: cell line


title: input_myoblast_DM_day_0

value: mouse myoblast


title: C2C12_myotube_DM_day_5

value: MacroH2A (Buschbeck et al., 2009)


title: C2C12_myoblast_DM_day_0


title: sample_15

description:
3999431014_R03C01_Grn.idat
3999431014_R03C01_Red.idat
sample name: 15


title: expr_ko_r2

status: Public on Jul 18 2017

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description:
RNA-Seq
GA4876-rpkm.gz

data_processing:
Basecalls performed using CASAVA 1.0
Short reads were mapped to the mouse genome by using Bowtie2 with default parameters (PMID: 22388286 ). Later analysis excluded short reads mapped to multiple genomic positions and kept only one read for each genomic site when it received multiple reads.
ChIP-Seq read enriched regions were identified with SICER (PMID: 19505939) with a window size of 200 bps and a gap size of 400 bps27. A conservative set of MLL4 binding sites were identified with stringent parameters and input control: E value = 1,000 and FDR = 0.001. To have a conservative prediction on genomic regions that were not bound by MLL4, we increased the E-value for MLL4 peak call until the ChIP-Seq signal of the additionally called peaks was indistinguishable from the input signal; for this purpose, non-stringent parameters were set: E value = 100,000 and FDR = 0.05. ChIP-Seq peaks for histone modifications H3K4me1, H3K27me3 and H3K27ac without inputs were called with an E-value of 10. Differential H3K4me1 peaks between Mll4 deletion and control cells were predicted by EdgerR (FDR < 0.001; FC > 2) (PMID: 19910308).
The mRNA expression level of a gene is quantified by RPKM (reads per kilo-base of exon model per million reads; PMID 18516045) with in-house script.
For Hi-C data analysis, in-house scripts were used to exclude pair-end tags/reads (PETs) with each end mapped to different chromosomes or showing low mapping quality (MAPQ < 10). For PETs mapped to exactly the same positions, only one PET was kept. To speed up calculation, we divided the genome into r = 1K bps bins to generate an interaction matrix to record the number of PETs linking any two genomic bins for each sample where HiC data was generated; PETs spanning below 1K bps and over 2M bps were excluded from the counting.
Genome_build: mm9
Supplementary_files_format_and_content: *rpkm.gz: zipped text file for gene expression. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
Supplementary_files_format_and_content: *.sicerdiff.gz: zipped peak file reacording differential peak call from SICER. Columns from left to right denonte: chrom, start, end,  Readcount_A,  Normalized_Readcount_A, ReadcountB, Normalized_Readcount_B, Fc_A_vs_B, pvalue_A_vs_B, FDR_A_vs_B, Fc_B_vs_A, pvalue_B_vs_A, FDR_B_vs_A.
Supplementary_files_format_and_content: *FDR0.05.gz or *FDR0.001.gz: zipped peak file recording peak call from SICER with input control. Columns from left to right denote: chrom, start, end, chipseq_island_read_count, control_island_read_count, p-value, fold-change, and FDR.
Supplementary_files_format_and_content: *.scoreisland.gz: zipped peak file recoding peak call from SICER without control. Columns from left to right denote: chrom, start, end, score.
Supplementary_files_format_and_content: *.III.gz: zipped txt file recording # of Hi-C PETs linking two 1K-bp regions. Column from left to right: chrom, start of one region, start of the other region, number of PETs.
Supplementary_files_format_and_content: *.edger3.gz prediction from edger3. Columns from left to right: peak region, logFC, logCPM, Pvalue and FDR

source_name: Naive CD4 T cells

extract_protocol:
For RNA-Seq: the total RNAs were purified using Qiagen's miRNeasy micro kit (Qiagen cat# 217084) plus Qiagen’s DNase set (Qiagen cat# 79254) for on-column DNase digestion option. PolyA-tailed RNAs were purified from pure total RNA using Dynabeads® mRNA DIRECT™ Kit (ambion life technologies cat# 61012). ChIP and Hi-C follow the protocols described previously in (PMID: 17512414) and (PMID: 25497547 ) with minor modifications.
Library constructions for ChIP-Seq, RNA-Seq and Hi-C follow the protocols described previously in (PMID: 17512414), (PMID: 19528076) and (PMID: 25497547 ) with minor modifications.

value: lymph nodes

tag: treatment

value: Mll4 KO


title: sample_12

description:
3999423014_R06C02_Grn.idat
3999423014_R06C02_Red.idat
sample name: 12


title: expr_wt_r2

description:
RNA-Seq
GA4874-rpkm.gz

value: wild type


title: sample_11

description:
3999423014_R05C02_Grn.idat
3999423014_R05C02_Red.idat
sample name: 11


title: sample_13

description:
3999431014_R01C01_Grn.idat
3999431014_R01C01_Red.idat
sample name: 13


title: expr_wt_r1

description:
RNA-Seq
GA5043-rpkm.gz


title: expr_ko_r1

description:
RNA-Seq
GA5044-rpkm.gz


title: C2C12_si_Ctrl_rep4

description: Gene expression of C2C12 cell lines

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ÂºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ÂºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturers protocol, (DNase 500 ng)

value: control


title: C2C12_si_Ctrl_rep3

description: Gene expression of C2C12 cell lines


title: C2C12_si_mH2A1.1_rep2

description: Gene expression of C2C12 cell lines


title: MLL4_r1

description:
ChIP-Seq
GA5963-TGACCA-ChIPSeq-mouse-MLL3ppMLL4FF-Naiv-CD4-MLL4.sam_noDup-W200-G400-islands-summary-FDR0.001.gz

value: MLL4 (PMCID:PMC3869375)


title: Input


title: C2C12_si_mH2A1.1_rep3

description: Gene expression of C2C12 cell lines


title: sample_14

description:
3999431014_R02C01_Grn.idat
3999431014_R02C01_Red.idat
sample name: 14


title: C2C12_si_Ctrl_rep2

description: Gene expression of C2C12 cell lines


title: C2C12_si_mH2A1.1_rep1

description: Gene expression of C2C12 cell lines


title: C2C12_si_Ctrl_rep1

description: Gene expression of C2C12 cell lines


title: sample_10

description:
3999423014_R04C02_Grn.idat
3999423014_R04C02_Red.idat
sample name: 10


title: sample_9

description:
3999423014_R03C02_Grn.idat
3999423014_R03C02_Red.idat
sample name: 9


title: C2C12_si_mH2A1.1_rep4

description: Gene expression of C2C12 cell lines


title: sample_2

description:
3999423014_R02C01_Grn.idat
3999423014_R02C01_Red.idat
sample name: 2


title: sample_3

description:
3999423014_R03C01_Grn.idat
3999423014_R03C01_Red.idat
sample name: 3


title: sample_6

description:
3999423014_R06C01_Grn.idat
3999423014_R06C01_Red.idat
sample name: 6


title: kidney biopsy, archetype985

status: Public on Jul 10 2017

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

country: Canada

institute: University of Alberta

hyb_protocol: 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 (Affymetrix, Santa Clara, CA).

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

extract_protocol: Tissue was homogenized in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the RNeasy Micro Kit (Qiagen, 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.

value: kidney

tag: archetype cluster

value: AKI

tag: g

tag: cg

tag: i

tag: ci

tag: t

tag: ct

tag: v

tag: cv

tag: ah

tag: ptc

tag: in i-ifta set n=234?

tag: mmdx


title: kidney biopsy, archetype992

tag: tissue

value: Bord.

value: NR


title: sample_4

description:
3999423014_R04C01_Grn.idat
3999423014_R04C01_Red.idat
sample name: 4

tag: gender

tag: diagnosis


title: kidney biopsy, archetype990

value: IFTA


title: kidney biopsy, archetype991

value: ABMR


title: sample_8

description:
3999423014_R02C02_Grn.idat
3999423014_R02C02_Red.idat
sample name: 8

value: Female


title: kidney biopsy, archetype982

value: GN


title: kidney biopsy, archetype995


title: kidney biopsy, archetype986


title: kidney biopsy, archetype997

value: TCMR


title: kidney biopsy, archetype998


title: kidney biopsy, archetype996


title: kidney biopsy, archetype999

value: NOMOA


title: kidney biopsy, archetype984


title: kidney biopsy, archetype994

value: Mixed


title: kidney biopsy, archetype987

value: Other


title: kidney biopsy, archetype988


title: kidney biopsy, archetype981


title: kidney biopsy, archetype989


title: kidney biopsy, archetype980


title: kidney biopsy, archetype993


title: sample_5

description:
3999423014_R05C01_Grn.idat
3999423014_R05C01_Red.idat
sample name: 5

value: bone marrow

value: Male

value: CMML


title: kidney biopsy, archetype98


title: kidney biopsy, archetype983


title: kidney biopsy, archetype99


title: sample_7

description:
3999423014_R01C02_Grn.idat
3999423014_R01C02_Red.idat
sample name: 7


title: sample_1

description:
3999423014_R01C01_Grn.idat
3999423014_R01C01_Red.idat
sample name: 1


title: kidney biopsy, archetype979


title: kidney biopsy, archetype978


title: kidney biopsy, archetype974

value: ABMRsusp


title: kidney biopsy, archetype976


title: kidney biopsy, archetype971


title: kidney biopsy, archetype965


title: kidney biopsy, archetype964

value: Neg


title: kidney biopsy, archetype958

value: kidney


title: kidney biopsy, archetype970

value: BK


title: kidney biopsy, archetype972


title: kidney biopsy, archetype963


title: kidney biopsy, archetype977


title: kidney biopsy, archetype966


title: kidney biopsy, archetype956


title: kidney biopsy, archetype955

value: Not done


title: kidney biopsy, archetype973

value: Bord.

value: NR


title: kidney biopsy, archetype975


title: kidney biopsy, archetype967

value: AKI


title: kidney biopsy, archetype953

value: ABMR


title: kidney biopsy, archetype952

value: GN


title: kidney biopsy, archetype96


title: kidney biopsy, archetype968


title: kidney biopsy, archetype969


title: kidney biopsy, archetype960


title: kidney biopsy, archetype957

value: TCMR


title: kidney biopsy, archetype962


title: kidney biopsy, archetype961


title: kidney biopsy, archetype954


title: kidney biopsy, archetype97

value: NOMOA


title: kidney biopsy, archetype959


title: kidney biopsy, archetype951


title: kidney biopsy, archetype950


title: kidney biopsy, archetype940


title: kidney biopsy, archetype95


title: kidney biopsy, archetype947


title: kidney biopsy, archetype941


title: kidney biopsy, archetype942


title: kidney biopsy, archetype945


title: kidney biopsy, archetype939


title: kidney biopsy, archetype944


title: kidney biopsy, archetype94

value: Mixed


title: kidney biopsy, archetype946


title: kidney biopsy, archetype948

value: TG


title: kidney biopsy, archetype943


title: kidney biopsy, archetype931

value: trace


title: kidney biopsy, archetype936


title: kidney biopsy, archetype938

value: Pos


title: kidney biopsy, archetype929

value: IFTA


title: kidney biopsy, archetype935


title: kidney biopsy, archetype949

value: ABMRsusp


title: kidney biopsy, archetype937


title: kidney biopsy, archetype934


title: kidney biopsy, archetype933

value: DiabNeph


title: kidney biopsy, archetype93

value: kidney


title: kidney biopsy, archetype932

value: BK


title: kidney biopsy, archetype925


title: kidney biopsy, archetype928


title: kidney biopsy, archetype926


title: kidney biopsy, archetype930


title: kidney biopsy, archetype927


title: kidney biopsy, archetype924


title: kidney biopsy, archetype92


title: kidney biopsy, archetype915


title: kidney biopsy, archetype913


title: kidney biopsy, archetype914


title: kidney biopsy, archetype917


title: kidney biopsy, archetype920


title: kidney biopsy, archetype918


title: kidney biopsy, archetype922

value: Other


title: kidney biopsy, archetype916

value: Bord.


title: kidney biopsy, archetype921


title: kidney biopsy, archetype912


title: kidney biopsy, archetype911


title: kidney biopsy, archetype923


title: kidney biopsy, archetype919


title: kidney biopsy, archetype909

value: NR


title: kidney biopsy, archetype91


title: kidney biopsy, archetype910


title: kidney biopsy, archetype907


title: kidney biopsy, archetype906


title: kidney biopsy, archetype905


title: kidney biopsy, archetype904


title: kidney biopsy, archetype900


title: kidney biopsy, archetype903


title: kidney biopsy, archetype90


title: kidney biopsy, archetype902


title: kidney biopsy, archetype908


title: kidney biopsy, archetype901

value: AKI


title: kidney biopsy, archetype899

value: ABMR


title: kidney biopsy, archetype896


title: kidney biopsy, archetype9


title: kidney biopsy, archetype897


title: kidney biopsy, archetype892


title: kidney biopsy, archetype893


title: kidney biopsy, archetype883


title: kidney biopsy, archetype882


title: kidney biopsy, archetype881

value: GN


title: kidney biopsy, archetype89


title: kidney biopsy, archetype895

value: pos


title: kidney biopsy, archetype890


title: kidney biopsy, archetype886


title: kidney biopsy, archetype879


title: kidney biopsy, archetype877

value: TCMR


title: kidney biopsy, archetype888


title: kidney biopsy, archetype891


title: kidney biopsy, archetype88


title: kidney biopsy, archetype885

value: NOMOA


title: kidney biopsy, archetype878


title: kidney biopsy, archetype884


title: kidney biopsy, archetype876


title: kidney biopsy, archetype894


title: kidney biopsy, archetype880


title: kidney biopsy, archetype873


title: kidney biopsy, archetype887


title: kidney biopsy, archetype898


title: kidney biopsy, archetype889


title: kidney biopsy, archetype872


title: kidney biopsy, archetype875


title: kidney biopsy, archetype874


title: kidney biopsy, archetype871


title: kidney biopsy, archetype870


title: kidney biopsy, archetype865


title: kidney biopsy, archetype869


title: kidney biopsy, archetype87


title: kidney biopsy, archetype86


title: kidney biopsy, archetype855


title: kidney biopsy, archetype849


title: kidney biopsy, archetype864


title: kidney biopsy, archetype867


title: kidney biopsy, archetype850


title: kidney biopsy, archetype868


title: kidney biopsy, archetype853


title: kidney biopsy, archetype852

value: Mixed


title: kidney biopsy, archetype862


title: kidney biopsy, archetype859


title: kidney biopsy, archetype863


title: kidney biopsy, archetype861


title: kidney biopsy, archetype858


title: kidney biopsy, archetype848


title: kidney biopsy, archetype85


title: kidney biopsy, archetype866


title: kidney biopsy, archetype860


title: kidney biopsy, archetype857


title: kidney biopsy, archetype845


title: kidney biopsy, archetype854


title: kidney biopsy, archetype847


title: kidney biopsy, archetype846


title: kidney biopsy, archetype844


title: kidney biopsy, archetype851


title: kidney biopsy, archetype837


title: kidney biopsy, archetype843


title: kidney biopsy, archetype836


title: kidney biopsy, archetype830


title: kidney biopsy, archetype840


title: kidney biopsy, archetype835


title: kidney biopsy, archetype828


title: kidney biopsy, archetype832

value: Neg


title: kidney biopsy, archetype841


title: kidney biopsy, archetype856


title: kidney biopsy, archetype84


title: kidney biopsy, archetype83


title: kidney biopsy, archetype838


title: kidney biopsy, archetype826

value: TG


title: kidney biopsy, archetype829

value: IFTA


title: kidney biopsy, archetype839


title: kidney biopsy, archetype833


title: kidney biopsy, archetype834


title: kidney biopsy, archetype842


title: kidney biopsy, archetype827


title: kidney biopsy, archetype831


title: kidney biopsy, archetype825


title: kidney biopsy, archetype824


title: kidney biopsy, archetype823


title: kidney biopsy, archetype819


title: kidney biopsy, archetype816


title: kidney biopsy, archetype822


title: kidney biopsy, archetype814


title: kidney biopsy, archetype811


title: kidney biopsy, archetype818


title: kidney biopsy, archetype813


title: kidney biopsy, archetype810


title: kidney biopsy, archetype821


title: kidney biopsy, archetype807


title: kidney biopsy, archetype820


title: kidney biopsy, archetype815


title: kidney biopsy, archetype809


title: kidney biopsy, archetype806

value: focal mild


title: kidney biopsy, archetype81


title: kidney biopsy, archetype808


title: kidney biopsy, archetype812


title: kidney biopsy, archetype803


title: kidney biopsy, archetype82


title: kidney biopsy, archetype817


title: kidney biopsy, archetype801


title: kidney biopsy, archetype800


title: kidney biopsy, archetype80


title: kidney biopsy, archetype805


title: kidney biopsy, archetype804


title: kidney biopsy, archetype8


title: kidney biopsy, archetype799


title: kidney biopsy, archetype796


title: kidney biopsy, archetype798


title: kidney biopsy, archetype797


title: kidney biopsy, archetype795


title: kidney biopsy, archetype802


title: kidney biopsy, archetype791


title: kidney biopsy, archetype794


title: kidney biopsy, archetype793


title: kidney biopsy, archetype789


title: kidney biopsy, archetype782


title: kidney biopsy, archetype784


title: kidney biopsy, archetype785


title: kidney biopsy, archetype787


title: kidney biopsy, archetype783


title: kidney biopsy, archetype781


title: kidney biopsy, archetype79


title: kidney biopsy, archetype778


title: kidney biopsy, archetype776


title: kidney biopsy, archetype779


title: kidney biopsy, archetype788


title: kidney biopsy, archetype790


title: kidney biopsy, archetype78


title: kidney biopsy, archetype792


title: kidney biopsy, archetype780


title: kidney biopsy, archetype786


title: kidney biopsy, archetype775


title: kidney biopsy, archetype777


title: kidney biopsy, archetype774


title: kidney biopsy, archetype768


title: kidney biopsy, archetype77

value: Pending


title: kidney biopsy, archetype773

value: kidney


title: kidney biopsy, archetype767


title: kidney biopsy, archetype771


title: kidney biopsy, archetype762


title: kidney biopsy, archetype769


title: kidney biopsy, archetype764


title: kidney biopsy, archetype772


title: kidney biopsy, archetype761


title: kidney biopsy, archetype766


title: kidney biopsy, archetype760


title: kidney biopsy, archetype770


title: kidney biopsy, archetype765


title: kidney biopsy, archetype763


title: kidney biopsy, archetype755


title: kidney biopsy, archetype758


title: kidney biopsy, archetype76

value: Pos


title: kidney biopsy, archetype754


title: kidney biopsy, archetype759

value: DiabNeph


title: kidney biopsy, archetype756

value: Bord.


title: kidney biopsy, archetype749


title: kidney biopsy, archetype750


title: kidney biopsy, archetype751


title: kidney biopsy, archetype753


title: kidney biopsy, archetype748


title: kidney biopsy, archetype752


title: kidney biopsy, archetype757


title: kidney biopsy, archetype75

value: NR


title: kidney biopsy, archetype744


title: kidney biopsy, archetype745


title: kidney biopsy, archetype747


title: kidney biopsy, archetype746


title: kidney biopsy, archetype742


title: kidney biopsy, archetype736


title: kidney biopsy, archetype738


title: kidney biopsy, archetype74


title: kidney biopsy, archetype740


title: kidney biopsy, archetype733


title: kidney biopsy, archetype737


title: kidney biopsy, archetype739


title: kidney biopsy, archetype741


title: kidney biopsy, archetype732


title: kidney biopsy, archetype743


title: kidney biopsy, archetype73

value: AKI


title: kidney biopsy, archetype725


title: kidney biopsy, archetype730


title: kidney biopsy, archetype734

value: ABMR


title: kidney biopsy, archetype722


title: kidney biopsy, archetype723


title: kidney biopsy, archetype726

value: GN


title: kidney biopsy, archetype724


title: kidney biopsy, archetype727


title: kidney biopsy, archetype731


title: kidney biopsy, archetype728


title: kidney biopsy, archetype729


title: kidney biopsy, archetype720


title: kidney biopsy, archetype718


title: kidney biopsy, archetype719


title: kidney biopsy, archetype721


title: kidney biopsy, archetype716


title: kidney biopsy, archetype72


title: kidney biopsy, archetype711

value: Other


title: kidney biopsy, archetype712


title: kidney biopsy, archetype71


title: kidney biopsy, archetype708


title: kidney biopsy, archetype717

value: TCMR


title: kidney biopsy, archetype714


title: kidney biopsy, archetype703

value: NOMOA


title: kidney biopsy, archetype705


title: kidney biopsy, archetype707


title: kidney biopsy, archetype710


title: kidney biopsy, archetype713


title: kidney biopsy, archetype706


title: kidney biopsy, archetype715


title: kidney biopsy, archetype700


title: kidney biopsy, archetype702

value: Not done


title: kidney biopsy, archetype7


title: kidney biopsy, archetype698


title: kidney biopsy, archetype70


title: kidney biopsy, archetype699


title: kidney biopsy, archetype701


title: kidney biopsy, archetype697


title: kidney biopsy, archetype704


title: kidney biopsy, archetype709


title: kidney biopsy, archetype696


title: kidney biopsy, archetype692


title: kidney biopsy, archetype694


title: kidney biopsy, archetype69


title: kidney biopsy, archetype691


title: kidney biopsy, archetype686


title: kidney biopsy, archetype687


title: kidney biopsy, archetype681

value: Neg


title: kidney biopsy, archetype678


title: kidney biopsy, archetype679


title: kidney biopsy, archetype695


title: kidney biopsy, archetype688


title: kidney biopsy, archetype690

value: Mixed


title: kidney biopsy, archetype676

value: IFTA


title: kidney biopsy, archetype683


title: kidney biopsy, archetype680

value: TG


title: kidney biopsy, archetype677


title: kidney biopsy, archetype682


title: kidney biopsy, archetype684


title: kidney biopsy, archetype674


title: kidney biopsy, archetype675


title: kidney biopsy, archetype68


title: kidney biopsy, archetype693


title: kidney biopsy, archetype735


title: kidney biopsy, archetype673


title: kidney biopsy, archetype671


title: kidney biopsy, archetype67


title: kidney biopsy, archetype685


title: kidney biopsy, archetype669


title: kidney biopsy, archetype666


title: kidney biopsy, archetype660


title: kidney biopsy, archetype668


title: kidney biopsy, archetype665


title: kidney biopsy, archetype689

value: BK


title: kidney biopsy, archetype664

value: kidney


title: kidney biopsy, archetype663


title: kidney biopsy, archetype66


title: kidney biopsy, archetype667


title: kidney biopsy, archetype662


title: kidney biopsy, archetype656


title: kidney biopsy, archetype659


title: kidney biopsy, archetype654


title: kidney biopsy, archetype658


title: kidney biopsy, archetype653


title: kidney biopsy, archetype657


title: kidney biopsy, archetype661


title: kidney biopsy, archetype649


title: kidney biopsy, archetype652


title: kidney biopsy, archetype65


title: kidney biopsy, archetype655


title: kidney biopsy, archetype650


title: kidney biopsy, archetype646


title: kidney biopsy, archetype647


title: kidney biopsy, archetype648


title: kidney biopsy, archetype672


title: kidney biopsy, archetype651


title: kidney biopsy, archetype645


title: kidney biopsy, archetype640


title: kidney biopsy, archetype642


title: kidney biopsy, archetype639


title: kidney biopsy, archetype643


title: kidney biopsy, archetype634


title: kidney biopsy, archetype670


title: kidney biopsy, archetype637


title: kidney biopsy, archetype638


title: kidney biopsy, archetype635


title: kidney biopsy, archetype641


title: kidney biopsy, archetype633


title: kidney biopsy, archetype630


title: kidney biopsy, archetype631


title: kidney biopsy, archetype64


title: kidney biopsy, archetype636


title: kidney biopsy, archetype629


title: kidney biopsy, archetype63


title: kidney biopsy, archetype644


title: kidney biopsy, archetype627


title: kidney biopsy, archetype626


title: kidney biopsy, archetype625


title: kidney biopsy, archetype614


title: kidney biopsy, archetype621


title: kidney biopsy, archetype620


title: kidney biopsy, archetype622


title: kidney biopsy, archetype619


title: kidney biopsy, archetype623


title: kidney biopsy, archetype618


title: kidney biopsy, archetype617


title: kidney biopsy, archetype632


title: kidney biopsy, archetype628


title: kidney biopsy, archetype610


title: kidney biopsy, archetype615


title: kidney biopsy, archetype61


title: kidney biopsy, archetype611


title: kidney biopsy, archetype612


title: kidney biopsy, archetype616


title: kidney biopsy, archetype613


title: kidney biopsy, archetype609


title: kidney biopsy, archetype62


title: kidney biopsy, archetype624


title: kidney biopsy, archetype608


title: kidney biopsy, archetype607


title: kidney biopsy, archetype606


title: kidney biopsy, archetype605


title: kidney biopsy, archetype6


title: kidney biopsy, archetype60


title: kidney biopsy, archetype603


title: kidney biopsy, archetype600


title: kidney biopsy, archetype598


title: kidney biopsy, archetype597


title: kidney biopsy, archetype602


title: kidney biopsy, archetype601


title: kidney biopsy, archetype596


title: kidney biopsy, archetype599


title: kidney biopsy, archetype590


title: kidney biopsy, archetype59


title: kidney biopsy, archetype593


title: kidney biopsy, archetype589


title: kidney biopsy, archetype592


title: kidney biopsy, archetype591


title: kidney biopsy, archetype594


title: kidney biopsy, archetype582


title: kidney biopsy, archetype585


title: kidney biopsy, archetype584


title: kidney biopsy, archetype587


title: kidney biopsy, archetype588


title: kidney biopsy, archetype586


title: kidney biopsy, archetype580


title: kidney biopsy, archetype581


title: kidney biopsy, archetype583


title: kidney biopsy, archetype579


title: kidney biopsy, archetype58


title: kidney biopsy, archetype578


title: kidney biopsy, archetype577


title: kidney biopsy, archetype575


title: kidney biopsy, archetype570


title: kidney biopsy, archetype565


title: kidney biopsy, archetype573


title: kidney biopsy, archetype574


title: kidney biopsy, archetype57


title: kidney biopsy, archetype572

value: ABMRsusp


title: kidney biopsy, archetype571


title: kidney biopsy, archetype604


title: kidney biopsy, archetype569


title: kidney biopsy, archetype567


title: kidney biopsy, archetype568


title: kidney biopsy, archetype564


title: kidney biopsy, archetype566


title: kidney biopsy, archetype563


title: kidney biopsy, archetype555


title: kidney biopsy, archetype576


title: kidney biopsy, archetype561


title: kidney biopsy, archetype56


title: kidney biopsy, archetype554


title: kidney biopsy, archetype562


title: kidney biopsy, archetype558


title: kidney biopsy, archetype549


title: kidney biopsy, archetype55


title: kidney biopsy, archetype552


title: kidney biopsy, archetype560


title: kidney biopsy, archetype553


title: kidney biopsy, archetype551


title: kidney biopsy, archetype559


title: kidney biopsy, archetype557


title: kidney biopsy, archetype556


title: kidney biopsy, archetype550


title: kidney biopsy, archetype547


title: kidney biopsy, archetype546


title: kidney biopsy, archetype541


title: kidney biopsy, archetype548


title: kidney biopsy, archetype543


title: kidney biopsy, archetype542

value: positive


title: kidney biopsy, archetype54


title: kidney biopsy, archetype595


title: kidney biopsy, archetype545


title: kidney biopsy, archetype544


title: kidney biopsy, archetype538


title: kidney biopsy, archetype535


title: kidney biopsy, archetype539


title: kidney biopsy, archetype536


title: kidney biopsy, archetype540


title: kidney biopsy, archetype537


title: kidney biopsy, archetype533


title: kidney biopsy, archetype532

value: Bord.


title: kidney biopsy, archetype530


title: kidney biopsy, archetype531


title: kidney biopsy, archetype53

value: NR


title: kidney biopsy, archetype526

value: Pos


title: kidney biopsy, archetype522

value: ABMR


title: kidney biopsy, archetype534


title: kidney biopsy, archetype521


title: kidney biopsy, archetype525


title: kidney biopsy, archetype524

value: GN


title: kidney biopsy, archetype529

value: AKI


title: kidney biopsy, archetype523


title: kidney biopsy, archetype528


title: kidney biopsy, archetype527


title: kidney biopsy, archetype520


title: kidney biopsy, archetype511


title: kidney biopsy, archetype515


title: kidney biopsy, archetype517


title: kidney biopsy, archetype513

value: Other


title: kidney biopsy, archetype516


title: kidney biopsy, archetype519

value: NOMOA


title: kidney biopsy, archetype512


title: kidney biopsy, archetype514


title: kidney biopsy, archetype518


title: kidney biopsy, archetype52


title: kidney biopsy, archetype51


title: kidney biopsy, archetype508


title: kidney biopsy, archetype510


title: kidney biopsy, archetype509

value: Not done


title: kidney biopsy, archetype5

value: TCMR


title: kidney biopsy, archetype507

value: Mixed

value: pos


title: kidney biopsy, archetype502


title: kidney biopsy, archetype500


title: kidney biopsy, archetype504


title: kidney biopsy, archetype503


title: kidney biopsy, archetype505


title: kidney biopsy, archetype501


title: kidney biopsy, archetype506


title: kidney biopsy, archetype50


title: kidney biopsy, archetype495

value: IFTA


title: kidney biopsy, archetype499


title: kidney biopsy, archetype494


title: kidney biopsy, archetype487


title: kidney biopsy, archetype491

value: TG


title: kidney biopsy, archetype488

value: kidney


title: kidney biopsy, archetype483


title: kidney biopsy, archetype484


title: kidney biopsy, archetype492


title: kidney biopsy, archetype489


title: kidney biopsy, archetype485

value: DiabNeph


title: kidney biopsy, archetype497


title: kidney biopsy, archetype486


title: kidney biopsy, archetype49


title: kidney biopsy, archetype482


title: kidney biopsy, archetype493


title: kidney biopsy, archetype490


title: kidney biopsy, archetype480


title: kidney biopsy, archetype481


title: kidney biopsy, archetype478


title: kidney biopsy, archetype48


title: kidney biopsy, archetype479


title: kidney biopsy, archetype472


title: kidney biopsy, archetype476


title: kidney biopsy, archetype474


title: kidney biopsy, archetype473


title: kidney biopsy, archetype477


title: kidney biopsy, archetype475


title: kidney biopsy, archetype470

value: ABMRsusp


title: kidney biopsy, archetype469


title: kidney biopsy, archetype471


title: kidney biopsy, archetype47


title: kidney biopsy, archetype468


title: kidney biopsy, archetype466


title: kidney biopsy, archetype463

value: BK


title: kidney biopsy, archetype467


title: kidney biopsy, archetype465


title: kidney biopsy, archetype458


title: kidney biopsy, archetype459

value: NR


title: kidney biopsy, archetype454

value: Bord.


title: kidney biopsy, archetype460


title: kidney biopsy, archetype455


title: kidney biopsy, archetype461

value: ABMR


title: kidney biopsy, archetype457


title: kidney biopsy, archetype464


title: kidney biopsy, archetype462


title: kidney biopsy, archetype456


title: kidney biopsy, archetype453


title: kidney biopsy, archetype46


title: kidney biopsy, archetype449


title: kidney biopsy, archetype447


title: kidney biopsy, archetype452


title: kidney biopsy, archetype451


title: kidney biopsy, archetype498


title: kidney biopsy, archetype443


title: kidney biopsy, archetype445


title: kidney biopsy, archetype450


title: kidney biopsy, archetype496


title: kidney biopsy, archetype448


title: kidney biopsy, archetype441


title: kidney biopsy, archetype439


title: kidney biopsy, archetype446

value: GN


title: kidney biopsy, archetype442


title: kidney biopsy, archetype45


title: kidney biopsy, archetype44


title: kidney biopsy, archetype437


title: kidney biopsy, archetype438


title: kidney biopsy, archetype444


title: kidney biopsy, archetype440

value: AKI


title: kidney biopsy, archetype433


title: kidney biopsy, archetype436


title: kidney biopsy, archetype431


title: kidney biopsy, archetype434


title: kidney biopsy, archetype435


title: kidney biopsy, archetype429


title: kidney biopsy, archetype43


title: kidney biopsy, archetype430


title: kidney biopsy, archetype424


title: kidney biopsy, archetype432


title: kidney biopsy, archetype427


title: kidney biopsy, archetype426


title: kidney biopsy, archetype421


title: kidney biopsy, archetype419


title: kidney biopsy, archetype422


title: kidney biopsy, archetype420


title: kidney biopsy, archetype409


title: kidney biopsy, archetype417


title: kidney biopsy, archetype404


title: kidney biopsy, archetype418


title: kidney biopsy, archetype413


title: kidney biopsy, archetype42


title: kidney biopsy, archetype408


title: kidney biopsy, archetype423

value: Other


title: kidney biopsy, archetype425


title: kidney biopsy, archetype405


title: kidney biopsy, archetype415


title: kidney biopsy, archetype411


title: kidney biopsy, archetype41


title: kidney biopsy, archetype410

value: NOMOA


title: kidney biopsy, archetype402


title: kidney biopsy, archetype403

value: Pos


title: kidney biopsy, archetype414


title: kidney biopsy, archetype412


title: kidney biopsy, archetype407

value: TCMR


title: kidney biopsy, archetype428


title: kidney biopsy, archetype416


title: kidney biopsy, archetype406


title: kidney biopsy, archetype401


title: kidney biopsy, archetype400


title: kidney biopsy, archetype40


title: kidney biopsy, archetype397


title: kidney biopsy, archetype398


title: kidney biopsy, archetype39


title: kidney biopsy, archetype387


title: kidney biopsy, archetype4


title: kidney biopsy, archetype393


title: kidney biopsy, archetype391


title: kidney biopsy, archetype384

value: Mixed


title: kidney biopsy, archetype390


title: kidney biopsy, archetype396


title: kidney biopsy, archetype399


title: kidney biopsy, archetype394


title: kidney biopsy, archetype386


title: kidney biopsy, archetype382


title: kidney biopsy, archetype381


title: kidney biopsy, archetype383


title: kidney biopsy, archetype378


title: kidney biopsy, archetype379


title: kidney biopsy, archetype389


title: kidney biopsy, archetype388


title: kidney biopsy, archetype385


title: kidney biopsy, archetype395


title: kidney biopsy, archetype392


title: kidney biopsy, archetype380


title: kidney biopsy, archetype376


title: kidney biopsy, archetype377


title: kidney biopsy, archetype375


title: kidney biopsy, archetype374


title: kidney biopsy, archetype371


title: kidney biopsy, archetype37


title: kidney biopsy, archetype367


title: kidney biopsy, archetype372


title: kidney biopsy, archetype365


title: kidney biopsy, archetype373


title: kidney biopsy, archetype369


title: kidney biopsy, archetype366


title: kidney biopsy, archetype38


title: kidney biopsy, archetype364


title: kidney biopsy, archetype362


title: kidney biopsy, archetype370


title: kidney biopsy, archetype360


title: kidney biopsy, archetype363


title: kidney biopsy, archetype361


title: kidney biopsy, archetype36


title: kidney biopsy, archetype356

value: Not done


title: kidney biopsy, archetype358

value: IFTA


title: kidney biopsy, archetype368


title: kidney biopsy, archetype357


title: kidney biopsy, archetype355


title: kidney biopsy, archetype354


title: kidney biopsy, archetype351


title: kidney biopsy, archetype352


title: kidney biopsy, archetype359


title: kidney biopsy, archetype353


title: kidney biopsy, archetype350


title: kidney biopsy, archetype349


title: kidney biopsy, archetype35


title: kidney biopsy, archetype348


title: kidney biopsy, archetype346


title: kidney biopsy, archetype347

value: pos


title: kidney biopsy, archetype341

value: kidney


title: kidney biopsy, archetype345


title: kidney biopsy, archetype343


title: kidney biopsy, archetype342


title: kidney biopsy, archetype336


title: kidney biopsy, archetype338


title: kidney biopsy, archetype34


title: kidney biopsy, archetype344


title: kidney biopsy, archetype335

value: DiabNeph


title: kidney biopsy, archetype340


title: kidney biopsy, archetype334


title: kidney biopsy, archetype337

value: trace


title: kidney biopsy, archetype333


title: kidney biopsy, archetype339


title: kidney biopsy, archetype332


title: kidney biopsy, archetype330


title: kidney biopsy, archetype326


title: kidney biopsy, archetype327


title: kidney biopsy, archetype328


title: kidney biopsy, archetype331


title: kidney biopsy, archetype329


title: kidney biopsy, archetype323


title: kidney biopsy, archetype32


title: kidney biopsy, archetype33


title: kidney biopsy, archetype319


title: kidney biopsy, archetype322


title: kidney biopsy, archetype324


title: kidney biopsy, archetype320


title: kidney biopsy, archetype325


title: kidney biopsy, archetype313


title: kidney biopsy, archetype314

value: BK


title: kidney biopsy, archetype312


title: kidney biopsy, archetype31


title: kidney biopsy, archetype318


title: kidney biopsy, archetype309


title: kidney biopsy, archetype317


title: kidney biopsy, archetype321


title: kidney biopsy, archetype306

value: ABMRsusp


title: kidney biopsy, archetype308


title: kidney biopsy, archetype301

value: NR


title: kidney biopsy, archetype300

value: Bord.


title: kidney biopsy, archetype316


title: kidney biopsy, archetype311


title: kidney biopsy, archetype299


title: kidney biopsy, archetype298


title: kidney biopsy, archetype302

value: ABMR


title: kidney biopsy, archetype307

value: GN


title: kidney biopsy, archetype315


title: kidney biopsy, archetype297


title: kidney biopsy, archetype303


title: kidney biopsy, archetype310


title: kidney biopsy, archetype295


title: kidney biopsy, archetype305


title: kidney biopsy, archetype296


title: kidney biopsy, archetype30


title: kidney biopsy, archetype3


title: kidney biopsy, archetype304


title: kidney biopsy, archetype293


title: kidney biopsy, archetype291


title: kidney biopsy, archetype294


title: kidney biopsy, archetype29


title: kidney biopsy, archetype289


title: kidney biopsy, archetype285


title: kidney biopsy, archetype290


title: kidney biopsy, archetype292

value: TG


title: kidney biopsy, archetype287

value: NOMOA


title: kidney biopsy, archetype288


title: kidney biopsy, archetype283


title: kidney biopsy, archetype284


title: kidney biopsy, archetype282


title: kidney biopsy, archetype28


title: kidney biopsy, archetype276


title: kidney biopsy, archetype271


title: kidney biopsy, archetype281


title: kidney biopsy, archetype275


title: kidney biopsy, archetype279


title: kidney biopsy, archetype269


title: kidney biopsy, archetype277


title: kidney biopsy, archetype278


title: kidney biopsy, archetype272


title: kidney biopsy, archetype267


title: kidney biopsy, archetype280


title: kidney biopsy, archetype266


title: kidney biopsy, archetype273


title: kidney biopsy, archetype274


title: kidney biopsy, archetype268


title: kidney biopsy, archetype270


title: kidney biopsy, archetype265


title: kidney biopsy, archetype27


title: kidney biopsy, archetype261


title: kidney biopsy, archetype262

value: AKI


title: kidney biopsy, archetype263


title: kidney biopsy, archetype260


title: kidney biopsy, archetype264


title: kidney biopsy, archetype26


title: kidney biopsy, archetype258


title: kidney biopsy, archetype259


title: kidney biopsy, archetype254


title: kidney biopsy, archetype257


title: kidney biopsy, archetype255


title: kidney biopsy, archetype252


title: kidney biopsy, archetype253


title: kidney biopsy, archetype249


title: kidney biopsy, archetype248


title: kidney biopsy, archetype251


title: kidney biopsy, archetype241


title: kidney biopsy, archetype244


title: kidney biopsy, archetype25


title: kidney biopsy, archetype247

value: TCMR


title: kidney biopsy, archetype246

value: Mixed


title: kidney biopsy, archetype239


title: kidney biopsy, archetype237


title: kidney biopsy, archetype242


title: kidney biopsy, archetype243


title: kidney biopsy, archetype245


title: kidney biopsy, archetype256


title: kidney biopsy, archetype250


title: kidney biopsy, archetype240


title: kidney biopsy, archetype24


title: kidney biopsy, archetype235


title: kidney biopsy, archetype236


title: kidney biopsy, archetype238


title: kidney biopsy, archetype234


title: kidney biopsy, archetype231


title: kidney biopsy, archetype232


title: kidney biopsy, archetype230


title: kidney biopsy, archetype23


title: kidney biopsy, archetype221


title: kidney biopsy, archetype226


title: kidney biopsy, archetype286


title: kidney biopsy, archetype224


title: kidney biopsy, archetype218


title: kidney biopsy, archetype219


title: kidney biopsy, archetype228


title: kidney biopsy, archetype225


title: kidney biopsy, archetype222


title: kidney biopsy, archetype216


title: kidney biopsy, archetype220


title: kidney biopsy, archetype22


title: kidney biopsy, archetype210


title: kidney biopsy, archetype213


title: kidney biopsy, archetype211


title: kidney biopsy, archetype214

value: Pos


title: kidney biopsy, archetype215


title: kidney biopsy, archetype21


title: kidney biopsy, archetype212


title: kidney biopsy, archetype233


title: kidney biopsy, archetype227


title: kidney biopsy, archetype205

value: IFTA


title: kidney biopsy, archetype203


title: kidney biopsy, archetype200


title: kidney biopsy, archetype208


title: kidney biopsy, archetype207


title: kidney biopsy, archetype2


title: kidney biopsy, archetype20


title: kidney biopsy, archetype192


title: kidney biopsy, archetype19


title: kidney biopsy, archetype201


title: kidney biopsy, archetype193


title: kidney biopsy, archetype198


title: kidney biopsy, archetype194


title: kidney biopsy, archetype199


title: kidney biopsy, archetype204


title: kidney biopsy, archetype191


title: kidney biopsy, archetype196


title: kidney biopsy, archetype190


title: kidney biopsy, archetype197


title: kidney biopsy, archetype229


title: kidney biopsy, archetype223


title: kidney biopsy, archetype195


title: kidney biopsy, archetype188


title: kidney biopsy, archetype187


title: kidney biopsy, archetype185


title: kidney biopsy, archetype217


title: kidney biopsy, archetype181


title: kidney biopsy, archetype177


title: kidney biopsy, archetype176


title: kidney biopsy, archetype202


title: kidney biopsy, archetype186


title: kidney biopsy, archetype175


title: kidney biopsy, archetype171


title: kidney biopsy, archetype180


title: kidney biopsy, archetype184


title: kidney biopsy, archetype173


title: kidney biopsy, archetype172


title: kidney biopsy, archetype178


title: kidney biopsy, archetype18


title: kidney biopsy, archetype209


title: kidney biopsy, archetype174


title: kidney biopsy, archetype170


title: kidney biopsy, archetype183


title: kidney biopsy, archetype169


title: kidney biopsy, archetype182


title: kidney biopsy, archetype179


title: kidney biopsy, archetype167


title: kidney biopsy, archetype17


title: kidney biopsy, archetype166


title: kidney biopsy, archetype165


title: kidney biopsy, archetype168


title: kidney biopsy, archetype189


title: kidney biopsy, archetype206


title: kidney biopsy, archetype161


title: kidney biopsy, archetype162


title: kidney biopsy, archetype159


title: kidney biopsy, archetype163


title: kidney biopsy, archetype153


title: kidney biopsy, archetype158


title: kidney biopsy, archetype16


title: kidney biopsy, archetype154


title: kidney biopsy, archetype15


title: kidney biopsy, archetype150


title: kidney biopsy, archetype151


title: kidney biopsy, archetype147


title: kidney biopsy, archetype157

value: Not done


title: kidney biopsy, archetype148

value: kidney


title: kidney biopsy, archetype142


title: kidney biopsy, archetype146


title: kidney biopsy, archetype144


title: kidney biopsy, archetype139


title: kidney biopsy, archetype14


title: kidney biopsy, archetype141


title: kidney biopsy, archetype155


title: kidney biopsy, archetype156


title: kidney biopsy, archetype164


title: kidney biopsy, archetype136

value: Other


title: kidney biopsy, archetype152


title: kidney biopsy, archetype130


title: kidney biopsy, archetype160


title: kidney biopsy, archetype132


title: kidney biopsy, archetype145


title: kidney biopsy, archetype137


title: kidney biopsy, archetype13


title: kidney biopsy, archetype134


title: kidney biopsy, archetype129


title: kidney biopsy, archetype131


title: kidney biopsy, archetype125


title: kidney biopsy, archetype126


title: kidney biopsy, archetype128


title: kidney biopsy, archetype123


title: kidney biopsy, archetype121


title: kidney biopsy, archetype135


title: kidney biopsy, archetype133


title: kidney biopsy, archetype124


title: kidney biopsy, archetype1207


title: kidney biopsy, archetype1205

value: Neg


title: kidney biopsy, archetype1206


title: kidney biopsy, archetype1208


title: kidney biopsy, archetype122

value: BK


title: kidney biopsy, archetype1201


title: kidney biopsy, archetype1203


title: kidney biopsy, archetype1204


title: kidney biopsy, archetype1202


title: kidney biopsy, archetype140


title: kidney biopsy, archetype1193


title: kidney biopsy, archetype1197

value: ABMRsusp


title: kidney biopsy, archetype120


title: kidney biopsy, archetype1198


title: kidney biopsy, archetype1192


title: kidney biopsy, archetype12


title: kidney biopsy, archetype1194


title: kidney biopsy, archetype1200


title: kidney biopsy, archetype1196


title: kidney biopsy, archetype1199


title: kidney biopsy, archetype1195


title: kidney biopsy, archetype1191

value: NR


title: kidney biopsy, archetype1189


title: kidney biopsy, archetype1186


title: kidney biopsy, archetype119


title: kidney biopsy, archetype1190


title: kidney biopsy, archetype1187


title: kidney biopsy, archetype1188


title: kidney biopsy, archetype1183

value: Bord.


title: kidney biopsy, archetype1184


title: kidney biopsy, archetype1185


title: kidney biopsy, archetype138


title: kidney biopsy, archetype149


title: kidney biopsy, archetype143


title: kidney biopsy, archetype127


title: kidney biopsy, archetype1172

value: ABMR


title: kidney biopsy, archetype1180


title: kidney biopsy, archetype1179


title: kidney biopsy, archetype1177


title: kidney biopsy, archetype118


title: kidney biopsy, archetype1175


title: kidney biopsy, archetype1170


title: kidney biopsy, archetype117


title: kidney biopsy, archetype1173


title: kidney biopsy, archetype1174

value: Pending


title: kidney biopsy, archetype1165


title: kidney biopsy, archetype1164


title: kidney biopsy, archetype1182


title: kidney biopsy, archetype1178


title: kidney biopsy, archetype1169


title: kidney biopsy, archetype1176


title: kidney biopsy, archetype1161


title: kidney biopsy, archetype1166


title: kidney biopsy, archetype1167


title: kidney biopsy, archetype1168


title: kidney biopsy, archetype1163


title: kidney biopsy, archetype1159


title: kidney biopsy, archetype116


title: kidney biopsy, archetype1157


title: kidney biopsy, archetype1158


title: kidney biopsy, archetype1162


title: kidney biopsy, archetype1156


title: kidney biopsy, archetype1154


title: kidney biopsy, archetype1160


title: kidney biopsy, archetype1153


title: kidney biopsy, archetype1155


title: kidney biopsy, archetype1151


title: kidney biopsy, archetype1152


title: kidney biopsy, archetype1149


title: kidney biopsy, archetype1150


title: kidney biopsy, archetype115


title: kidney biopsy, archetype1147


title: kidney biopsy, archetype1142


title: kidney biopsy, archetype1140


title: kidney biopsy, archetype1141


title: kidney biopsy, archetype1146


title: kidney biopsy, archetype1145


title: kidney biopsy, archetype1138


title: kidney biopsy, archetype1181


title: kidney biopsy, archetype1135


title: kidney biopsy, archetype1144

value: GN


title: kidney biopsy, archetype1132


title: kidney biopsy, archetype1137


title: kidney biopsy, archetype1136

value: NOMOA


title: kidney biopsy, archetype1139

value: AKI

value: pos


title: kidney biopsy, archetype1148


title: kidney biopsy, archetype114

value: Mixed


title: kidney biopsy, archetype1143


title: kidney biopsy, archetype1134

value: TCMR


title: kidney biopsy, archetype1133


title: kidney biopsy, archetype113


title: kidney biopsy, archetype1129


title: kidney biopsy, archetype1131


title: kidney biopsy, archetype1128


title: kidney biopsy, archetype1127


title: kidney biopsy, archetype1125


title: kidney biopsy, archetype1122


title: kidney biopsy, archetype1120

value: IFTA


title: kidney biopsy, archetype1114


title: kidney biopsy, archetype1117


title: kidney biopsy, archetype1118


title: kidney biopsy, archetype1171


title: kidney biopsy, archetype1116