title: WT-5

city: La Jolla

first: Timothy

last: Huang

address: 10901 N Torrey Pines Rd.

institute: Sanford Burnham Prebys Medical Discovery Institute

description: fpkm_genename.txt (G10)

data_processing:
Illumina CASAVA1.8 used for base calling.
Sequenced reads were trimmed for adaptor sequence, reads containing N > 10% (N represents base that cannot be determined) were removed; remove low quality reads: the quality value of over 50% bases of the read is <=20.
Differential expression significant analysis of two conditions/groups by using the DESeq2 R package, while the significant criterion is padj<0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample

source_name: Motor cortex

extract_protocol:
Total RNA was extracted from postnatal day 22 mouse motor cortex tissue using the RNA Extraction from Tissue kit (Kurabo, RT-S2).
NEBNext® UltraTM RNA library construction

value: Motor cortex

value: postnatal day 22

tag: genotype

value: wild type


title: EZH2_H3K27ac_rep2

status: Public on May 07 2019

type: SRA

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

country: USA

institute: University of Southern California

description:
EZH2_H3K27ac.narrowPeak
EZH2_H3K27ac.tracks.bedGraph

library_source: genomic

data_processing:
Short sequence reads (SR50) were aligned to the hg19 genome assembly using BWA and data was preprocessed using the ENCODE3 ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/). ChIP-seq peaks were called using MACS2 from each replicate first and then reproducible peaks were selected using the naïve overlap tool, as suggested in the ENCODE3 ChIP-seq standards document (https://www.encodeproject.org/pages/pipelines/) and previously described.
Genome_build: GRCh37

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HCT116 cells (ATCC #CCL-247) were maintained in McCoy's 5A medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
HCT116 cells were transfected with D3A-dCas9/D3L and either KRAB-dCas9 or Ezh2-dCas9 and three gRNAs targeting the HER2 promoter. Control cells were transfected with dCas9 and the same three gRNAs. For transient repression timepoints, cells were cross-linked 5 days after transfection and growth in puromycin-containing media. For persistent repression timepoints, cells were sorted as described above and dCas9 control cells were cross-linked 24 days after transfection. Cross-linking was carried out in 1% formaldehyde for 10 min at room temperature and was stopped with 0.125 M glycine. Cross-linked cells were lysed with ChIP lysis buffer (5 mM PIPES pH8, 85 mM KCl, 1% Igepal) with a protease inhibitor (PI) cocktail (Roche). Nuclei were collected by centrifugation at 2,000 rpm. for 5 min at 4 °C and lysed in nuclei lysis buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS) supplemented with PI cocktail. Chromatin was fragmented using the Bioruptor 2000 (Diagenode) and diluted with 5 vol RIPA buffer (50 mM Tris pH 7.6, 150 mM NaCl, 1 mM EDTA pH8, 1% Igepal, 0.25% Deoxycholic acid). ChIP enrichment was performed by incubation with 3 µg H3K9me3 antibody (Diagenode C15410056), 2 µg H3K27me3 antibody (MP07–449), 2 µg H3K27ac antibody (Active Motif #39133) or 2 µg normal rabbit IgG (Abcam ab46540) for 16 h at 4°C. Immune complexes were bound to 20 µl magnetic protein A/G beads (ThermoFisher) for 2 hours at 4°C. Beads were washed 2x with RIPA and 3x with ChIP wash buffer (100 mM Tris pH8, 500 mM LiCl, 1% Deoxycholic acid). The final wash was performed in ChIP wash buffer with 150 mM NaCl. Cross-links were then reversed by heating beads in 100 µl ChIP elution buffer (50 mM NaHCO3, 1% SDS) overnight at 65°C and DNA was purified using the QIAquick PCR Purification Kit (Qiagen).
Each entire ChIP sample was used to prepare Illumina sequencing libraries using the KAPA Hyper Prep Kit (Roche) and NEXTflex DNA barcodes (BIOO Scientific). Illumina sequencing libraries were pooled and sequenced using the HiSeq 4000 platform (Illumina) at the UC Davis DNA Technologies Sequencing Core.

treatment_protocol: Cells of 60-70% confluency were transfected using Lipofectamine 3000 (Life Technologies) following the manufacturer’s instructions. Transfections were performed in 12-well plates using 625 ng individual or combinations of dCas9 expression vector, 500 ng of equimolar pooled gRNA expression vectors. All experiments were cotransfected with 125 ng of puromycin-resistant plasmid pBABE-puro to select for transfected cells. Transfection medium was replaced 24 hours post-transfection with growth medium containing 3 µg /mL puromycin to enrich for transfected cells. After 72 hours of puromycin selection, HER2 negative cell population was collected by flow cytometry and cells were maintained in standard growth media for a total of 24 day and cross-linked for ChIP assays.

tag: disease state

value: colorectal carcinoma

tag: antibody

tag: transfection

value: Ezh2-dCas9+D3A-dCas9+D3L + HER2 gRNAs 1,2+3


title: CTRL_rep1

type: genomic

description: 17 days post transfection

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Samples were normalized (background corrected) using the ‘noob’ function in the minfi software program in R computing language. For each probe, methylated (M) and unmethylated (U) signal intensities were recorded as well as the beta value (M/(M+U)).

label: Cy3, Cy5

label_protocol: Genomic DNA was bisulfite converted and EPIC DNA methylation array data were processed in the USC Molecular Genomics Core

extract_protocol: HCT116 cells were transfected with D3A-dCas9/D3L and either KRAB-dCas9 or Ezh2-dCas9 and three gRNAs targeting the HER2 promoter. Each replicate (n = 2) was performed as an entirely separate transfection experiment. Transfected cells were sorted by flow cytometry as described above and genomic DNA was extracted. Control cells were transfected with three HER2 gRNAs and dCas9 (no effector domain). Genomic DNA from sorted and control cells was isolated 17 and 24 days after transfection using the Quick-gDNA MiniPrep kit (ZYMO). The Infinium Human MethylationEPIC BeadChip (Illumina) was used to analyze global DNA methylation.

tag: cell line

value: dCas9-noED + HER2 gRNAs 1,2+3


title: EZH2_24d_rep2

description: 24 days post transfection


title: Per11 year 6

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

description:
Per11
CpG methylation
Sample22

hyb_protocol: Bisulphite converted DNA hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Illumina scaner

data_processing: Raw intensity data files (idat files) for both mouse and human samples were processed using the R package Minfi.

source_name: buffy coat

label_protocol: Illumina

extract_protocol: DNA provided by Health ABC biorepository; standard DNA extraction protocol

tag: year (visit year when sample was collected)

tag: baseline age

tag: self reported race

value: African American

tag: self sex

value: Female


title: At2+_2-1

city: Durham

first: Paul

middle: William

last: Denny

state: Durham

address: Lower Mountjoy

department: Biosciences

country: United Kingdom

institute: Durham University

library_source: transcriptomic

data_processing:
Fastq files were aligned to Arabidopsis genome (Arabidopsis Araport 2017) using  STAR
BAM files resulting from the alignments were summarized to genes using the HTSeq package
Expression data was normalized using the DESeq package from bioconductor in R
Differentially expressed genes (³2-fold and £5% false discovery rate) were identified using the DESeq package
Genome_build: Arabidopsis thaliana genome (Arabidopsis Araport 2017)
Supplementary_files_format_and_content: Tab-delimited text files include log2 counts per million (CPM) values for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana plants were grown on 0.8% Murashige and Skoog (MS) agar for 10 days. Plants were grown at 20°C under 16h day/8 h night photoperiod.

extract_protocol:
RNA was isolated using the ReliaPrep™ RNA Tissue Miniprep System (Promega) and processed as per manufacturer’s instructions.
Libraries were prepared using the Illumina Truseq stranded mRNA sample preparation kit, according to the manufacturer’s instructions.

treatment_protocol: Seedling were untreated

tag: tissue

value: seedlings

tag: developmental stage

value: 10 day old seedlings

tag: background strain

value: AtIPCS2 over expressing line

tag: treatment

value: untreated


title: At2++_9-2


title: EZH2_24d_rep1

description: 24 days post transfection


title: CSC1_A5

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Mus musculus

source_name: Mouse skin squamous cell carcinoma

extract_protocol:
Mouse skin squamous cell carcinoma cells including tumor initiating cells before and after adoptive cell transfer (ACT)-based immunotherapy were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC
Single cells were lysed by incubating at 72oC for 3 min. Revers transcritpion reaction and whole transcriptome amplification were perforemd according to Smart-seq2 protocol with a few modifications (Yang et al., Cell, 2017). The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was perforemd by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequecned on Illumina Nextseq 500 with mid-output 75cycles paired-end mode.

tag: Sex

value: Mixed

tag: age

tag: strain

tag: cell type

value: skin squamous cell carcinoma

tag: sorting markers

value: Before ACT immunotherapy


title: EZH2_H3K27ac_rep1

tag: disease state


title: CTRL_rep2

description: 17 days post transfection


title: Per3 year 1

description:
Per3
CpG methylation
Sample5


title: CSC1_A4


title: At3+_4-1

tag: genotype

value: AtIPCS3 over expressing line


title: CSC1_A9


title: EZH2_17d_rep2

description: 17 days post transfection

tag: transfection


title: At1++_7-3

value: AtIPCS1 over expressing line


title: A3

type: RNA

city: Fuzhou

first: Fei

last: He

address: No.1 Xuefubei Road

country: China

institute: Fujian Medical University

hyb_protocol: Total RNAs were hybridized using mRNA + lncRNA Human Gene Expression Microarray V4.0 (4×180K format, CapitalBio Corp, Beijing, China)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: lung adenocarcinoma tissues

label_protocol: The purity and concentration of RNA was determined by Nano Drop ND-1000 spectrophotometer according to OD260/280 reading.

extract_protocol: Tumor samples were microdissected to ensure the purity of the tumor. From the same patient, adjacent normal tissue samples were collected from resected, located approximately 3.5-5 cm away from the tumor site.

treatment_protocol: Samples were fresh frozen and were shipped on ice for subsequent RNA extraction

value: lung adenocarcinoma


title: CTRL_H3K27ac_rep2

description:
CTRL_H3K27ac.narrowPeak
CTRL_H3K27ac.tracks.bedGraph

tag: antibody


title: Per8 year 1

description:
Per8
CpG methylation
Sample15

tag: year (visit year when sample was collected)


title: CSC1_A3


title: Per6 year 6

description:
Per6
CpG methylation
Sample12

tag: baseline age

value: Caucasian

value: Male


title: At1++_7-2


title: CTRL_H3K27ac_rep1

value: colorectal carcinoma


title: Astro-mem KO4

description: fpkm_genename.txt (G7)

value: Motor cortex

value: postnatal day 22

value: membralin astrocyte conditional knockout


title: At1++_7-1


title: Astro-mem KO3

description: fpkm_genename.txt (G6)


title: At1+_3-3


title: CSC1_A2


title: WT-3

description: fpkm_genename.txt (G5)

value: wild type


title: CSC1_A1


title: At1+_3-1

value: seedlings


title: CSC1_A12


title: EZH2_17d_rep1

description: 17 days post transfection

tag: cell line

value: Ezh2-dCas9+D3A-dCas9+D3L + HER2 gRNAs 1,2+3


title: At1+_3-2

value: 10 day old seedlings


title: At2+_2-2

value: AtIPCS2 over expressing line

value: untreated


title: Astro-mem KO2

description: fpkm_genename.txt (G4)


title: SW480_sh-PIPKIγ_rep3

city: Shanghai

first: Junli

last: Xue

address: 1800 Yuntai Road, Pudong District

department: Department of Oncology

institute: Shanghai East Hospital, Tongji University School of Medicine

description: Gene expression data from sh-PIPKIγ SW480 colon cancer cell lines

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned on the Agilent Scanner G2505C using one color scan setting for 4x40K array slides (Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Background subtraction and normalization of probe set intensities were performed using Robust Multiarray Analysis (RMA). Gene set enrichment analysis (GSEA) was performed on the Broad Institute Platform and statistical significance (false discovery rate, FDR) was set at 0.25.

source_name: SW480 Colorectal Cancer Cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: SW480 cells were maintained in DMEM medium with 2 mM glutamine, 5 mM glucose supplemented with 1% penicillin, and streptomycin and tested for mycoplasma contamination.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cells were stably transfected with sh-Ctrl or sh-PIPKIγ.

value: sh-PIPKIγ


title: CSC1_A10

value: Mixed

value: skin squamous cell carcinoma

value: Before ACT immunotherapy


title: Exp110

city: Pleasanton

first: Maeve

last: Ohuallachain

state: CALIFORNIA

address: 4300 Hacienda Drive

institute: ROCHE SEQUENCING SOLUTIONS INC

data_processing:
FLASH-1.2.11 was used to merge the paired end reads.
seqtk-v1.2 was used to convert merged fastq file to fasta format.
The reads were then parsed to identify cell-id and marker-id based on the white-list info in the associated qdata folder, deduplicated based on cell-id and marker-ids and finally chimeric reads were filtered out.
Expression counts were then used to remove putative debris and doublets cells based on the criteria listed in Singlet_settings.txt in the corresponding qdata folder.
Expression counts matrix was then normalized by scaling the counts by row-means and multiplying by a factor of 10.
Genome_build: A github repository for the software used to process the raw-fastqs is available at the following location: https://github.com/bioinform/QBC_Single_Cell_Analysis_NGS
Supplementary_files_format_and_content: Tab separated text files containing jittered expression counts (both normalized and un-normalized) for different markers for each individual cell
The *tar.gz contains various files containing white-list information for cell-barcode ids, anchor-sequence info, marker-sequence info and settings information for removal of cell-debris and cell-doublets. The files in this folder is used to process the raw fastqs for each of the experiment.

source_name: Jurkat cell line

growth_protocol: Jurkat cells and Nalm-6 cells were obtained from America Type Tissue Collection (ATCC). Cells at a density of ~1×106/mL were fixed in RPMI medium without serum in 1.6% paraformaldehyde (Electronic Microscopy Sciences) for 10 min at room temperature under gentle agitation. Cells were pelleted and permeabilized with ice-cold methanol for at least 10 min on ice. Once in methanol cells can be stored at −80 °C for several weeks without loss of antibody signal or RNA degradation.

extract_protocol:
QIAquick Gel Extraction Kit (Qiagen, 28704).
PCR with Illumina dual index primers
Single cell barcoding by split-pool synthesis via ligation

value: cell line

value: Jurkat

tag: molecule type

value: various targeted RNA transcripts


title: SW480_sh-PIPKIγ_rep2


title: WT-2

description: fpkm_genename.txt (G3)

tag: tissue


title: CSC1_A11


title: SW480_sh-PIPKIγ_rep1


title: Astro-mem KO1

description: fpkm_genename.txt (G2)


title: WT-1

description: fpkm_genename.txt (G1)


title: CD44_H9


title: exp108

source_name: Jurkat cell line and Nalm-6 cell line

value: cell lines

value: Jurkat  and Nalm-6


title: SW480_sh-Ctrl_rep3

description: Gene expression data from control SW480 colon cancer cell lines

value: sh-Ctrl


title: CSC1_B11


title: exp113_5_S5_L008

source_name: PBMC

growth_protocol: Cells at a density of ~1×106/mL were fixed in RPMI medium without serum in 1.6% paraformaldehyde (Electronic Microscopy Sciences) for 10 min at room temperature under gentle agitation. Cells were pelleted and permeabilized with ice-cold methanol for at least 10 min on ice. Once in methanol cells can be stored at −80 °C for several weeks without loss of antibody signal or RNA degradation.

value: primary cells from donor

value: PBMC


title: KOTS_ATAC_rep2

city: Fukuoka

first: Takashi

last: Ishiuchi

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

data_processing:
For RNA-seq, reads were aligned using TopHat (v2.1.1) with the option ‘--segment-length 34 --library-type fr-secondstrand’, and the Cufflinks program (v2.2.1) with the option ‘-u --library-type fr-secondstrand’ was used to calculate the fragments per kilobase of exon per million mapped fragments (fpkm) value.
For H3K4 ChIP-seq, reads were aligned to the mouse genome (mm9) using Bowtie2 (v2.2.9) with the option ‘-N 1’after removing adaptor sequences and low quality reads by TrimGalore. The enrichment of H3K4me3 was analyzed through the normalization with input samples.
ATAC-seq reads were aligned  aligned to the mouse genome (mm9) using Bowtie2 (v2.2.9) with the option ‘-N 1 -L 25’.
Genome_build: mm9, hg38
Supplementary_files_format_and_content: Text files include FPKM values for each sample. BigWig files include the information of genomic distributions of ChIP or ATAC reads.

source_name: TS cells

growth_protocol: Mouse TS cells were cultured in RPMI medium containing 70% feeder-consitioned medium, FGF4, heparin and Activin A (Peprotech). Human TS cells were cultured as described previously (Okae et al, Cell Stem Cell, 2018).

extract_protocol:
Total RNA was extracted with RNeasy Mini kit (QIAGEN). For ChIP-seq, chromatin was sonicated with Covaris S2. ATAC-seq was carried out with a standard protocol.
150 ng of total RNA from each sample was used for library preparation. mRNA was purified with NEBnext poly(A) mRNA magnetic isolation module (NEB), and sequence libraries were prepared with NEBnext Ultra II Directional RNA library prep kit (NEB) following the manufacturer’s protocol. ChIPmentation was carried out for H3K4me3 ChIP-seq library construction with 7 min incubation with a Tn5 tagmentation enzyme solution (Schmidl et al., 2015). ATAC-seq was carried out as described previously (Buenrostro et al., 2013).

value: trophoblast stem (TS) cells

tag: genotype/variation

value: Zfp281 knockout


title: exp120-1


title: CD44_H8


title: CD44_H7


title: SW480_sh-Ctrl_rep2


title: WT-4

description: fpkm_genename.txt (G8)

value: Motor cortex

value: postnatal day 22

value: wild type


title: WTTS_ATAC_rep2

value: wild-type


title: KOTS_ATAC_rep1


title: CD44_H6

value: Mixed


title: 100-2

source_name: K562 cell line and SK-MEL-2 cell line

growth_protocol: K562 cells and SK-MEL-2 cells were obtained from America Type Tissue Collection (ATCC). K562 cells were grown in IMDM media (from Invitrogen) with 10% FBS and 1% Pen Strep Glut. SK-MEL-2 were grown in EMEM (from ATCC) with 10% FBA and 1% PenStrep Glut. Cells to be analyzed for only mRNA expression or both protein and mRNA expression were stored in methanol at -80°C until staining.

value: K562 and SK-MEL-2


title: Astro-mem KO5

description: fpkm_genename.txt (G9)

value: membralin astrocyte conditional knockout


title: SW480_sh-Ctrl_rep1


title: 100-1


title: CD44_H5

value: skin squamous cell carcinoma

value: Before ACT immunotherapy


title: WTTS_ATAC_rep1


title: Zfp281ChIP_rep2

data_processing:
For RNA-seq, reads were aligned using TopHat (v2.1.1) with the option ‘--segment-length 34 --library-type fr-secondstrand’, and the Cufflinks program (v2.2.1) with the option ‘-u --library-type fr-secondstrand’ was used to calculate the fragments per kilobase of exon per million mapped fragments (fpkm) value.
For ChIP-seq, reads were aligned to the mouse genome (mm9) using Bowtie2 (v2.2.9) with the option ‘-N 0’, and peaks were called using MACS (v2.1.1.20160309) with the option ‘--to-large --nomodel’.
Genome_build: mm9
Supplementary_files_format_and_content: Text files include FPKM values for each sample. narrowPeak files include the information for the positions of Zfp281 ChIP peaks.

growth_protocol: For ChIP assay, mouse TS cells were cultured in N2B27 medium containing FGF2, Activin A (Peprotech), Y27632 and XAV939 (Calbiochem) (FAXY medium)  using fibronectin-coated plates (Ohinata and Tsukiyama, 2014).

extract_protocol:
Total RNA was extracted with RNeasy Mini kit (QIAGEN). For ChIP-seq, chromatin was sonicated with Covaris S2.
150 ng of total RNA from each sample was used for library preparation. mRNA was purified with NEBnext poly(A) mRNA magnetic isolation module (NEB), and sequence libraries were prepared with NEBnext Ultra II Directional RNA library prep kit (NEB) following the manufacturer’s protocol with 10 cycles of PCR amplification. ChIPmentation was carried out for the ChIP-seq library construction with 7 min incubation with a Tn5 tagmentation enzyme solution (Schmidl et al., 2015).

tag: strain background

tag: chip antibody


title: Anaef4B_RPF

city: San Francisco

first: Darienne

middle: Ross

last: Myers

address: 513 Parnassus Ave, HSW 1330A, Box 0452

department: Anatomy

institute: UCSF

description:
ribosome protected fragement (RPF)
Anaef4B_rpf_masked in processed data file

data_processing:
Demultiplexing (UCSF CAT)
Genome alignment (TopHat v.1.4.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text file, each column is the read counts per gene for each sample (column naming samplename#_totRNA)
RPF Samples
Demultiplexing (UCSF CAT)
Adapter removal (Fastx toolkit)
rRNA contaminant removal (Bowtie v.0.2.17)
Genome alignment (TopHat v.1.4.1)
first and last 3 codons were masked (Plastid)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text file, each column is the read counts per gene for each sample with the first and last 3 codons for each gene masked (column naming samplename#_rpf_masked)

source_name: purified lymph node CD4+ T cell, 12 week old Anaef/Anaef mouse

extract_protocol:
Total RNA was isolated from 20,000 cells per sample using the Dynabeads mRNA DIRECT Purification Kit (Thermo Fishcer Scientific).
RPF: The bulk pool of purified CD4 T cells (60-100 million cells) were washed in RNase-free PBS, treated with 100ug/ml cycloheximide (CHX) for 1 minute, and then lysed in polysome lysis buffer as described (Stern-Ginossar et al., 2012). Lysate was clarified by centrifugation (10 minutes, 20000g, 4ºC), snap-frozen, and RNA content was measured using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific). Ribosome protected fragments (RPFs) were prepared by digesting samples for 1 hour at room temperature with 8ug micrococcal nuclease (MNase) per ug of RNA, 5mM CaCl2, 1:10 SuperAseIn (Invitrogen), and reactions were stopped with 6.25mM EGTA. RPFs were purified by sucrose cushion by overlaying MNase-digested lysate onto sucrose solution (34% sucrose, 5X polysome buffer, 50mg/ml CHX, 1M DTT) and ultracentrifugation was performed in a TLA-100.3 rotor (Beckman-Coulter) for 1 hour at 100,000rpm, 4ºC.
Total RNA libraries were prepared using the Nugen/Nextera XT kit (Illumina) and single-end 50pb RNA sequencing was performed using a HiSeq 4000 (Illumina).
RPF: Subsequent sample clean up and library preparation was performed using the TruSeq Ribo Profile (Mammalian) kit (Illumina) and libraries were sequenced on a HiSeq 4000 (Illumina) in the UCSF Center for Advanced Technology Core.

treatment_protocol:
none (Total RNA)
1 minute CHX (RPF)

value: lymph node CD4+ T cell

value: 12 week old

value: Anaef/Anaef

tag: extract protocol

value: 1 min CHX, polysome buffer lysis, Mnase digest, sucrose cushion

tag: library contstruction protocol


title: Anaef3B_RPF

description:
ribosome protected fragement (RPF)
Anaef3B_rpf_masked in processed data file

tag: age

tag: strain

value: TruSeq Ribo Profile (Mammalian) kit (Illumina)


title: CD44_H4

tag: Sex

tag: cell type

tag: sorting markers

tag: treatment


title: WT2B_RPF

description:
ribosome protected fragement (RPF)
WT2B_rpf_masked in processed data file

source_name: purified lymph node CD4+ T cell, 12 week old WT/WT mouse

tag: genotype

value: WT/WT


title: CD44_H3


title: WT1B_RPF

description:
ribosome protected fragement (RPF)
WT1B_rpf_masked in processed data file


title: CD44_H2


title: ILC1a_4

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

hyb_protocol: Products were hybridized to Affymetrix Human Gene 1.0 ST arrays according to the manufacturer’s protocol

data_processing: Data were analyzed with GenePattern software (Broad Institute). Raw data were normalized using standard RMA workflow.

label: biotin

source_name: tonsil

label_protocol: Purified RNA was amplified using Nugen Ovation Pico SL or Ovation Pico kits and labeled using Nugen Encore Biotin kit.

extract_protocol: Briefly, tissue was mechanically disrupted, passed through 0.0059 inches opening sieve, and filtered extensively through 70μm cell strainers. CD56+ cells were enriched via positive selection with CD56 microbeads (Myltenyi), according to manufacturer’s recommendations. RNAs from the sorted ILC subsets were prepared by using RNeasy Plus Micro kit (Qiagen), following manufacturer instructions.

value: tonsil

tag: markers


title: Input_rep2

value: trophoblast stem (TS) cells


title: ILC1a_2


title: CD44_H12


title: CD44_H1


title: WT HLCs [AR3098_02]

city: Suita

first: Tomoki

last: Yamashita

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

description: WT HLCs

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: FCL-iPS, hepatocyte-like cells, iPSC-derived, WT

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The two groups of human iPS cells (CYP2C19-deficient iPS cells and wild type iPS cells) were maintained on iMatrix-511 (Nippi)-coated plates with StemFit AK02N medium (Ajinomoto).

extract_protocol: RNA was extracted using RNeasy Mini Kit.

treatment_protocol: Hepatic differentiation: Before the initiation of hepatic differentiation, human iPS cells were enzymatically dissociated into clamps by using dispase (Roche), and the clamps were plated onto BD Matrigel Basement Membrane Matrix Growth Factor Reduced (BD Biosciences). These cells were cultured in the MEF-conditioned medium until the cells reach approximately 80% confluence. The differentiation protocol for the induction of definitive endoderm (DE) cells, hepatoblast-like cells, and HLCs was based on our previous reports with some modifications. Briefly, in the DE differentiation, human iPS cells were cultured for 4 days in RPMI1640 medium (Sigma), which contained 100 ng/ml Activin A (R&D Systems), 1×GlutaMAX (Thermo Fisher Scientific), and 1×B27 Supplement Minus Vitamin A (Thermo Fisher Scientific). For the induction of hepatoblast-like cells, the DE cells were cultured for 5 days in RPMI1640 medium (Sigma) which contained 20 ng/ml bone morphogenetic protein (BMP) 4 (R&D Systems), 20 ng/ml FGF4 (R&D Systems), 1×GlutaMAX, and 1×B27 Supplement Minus Vitamin A. To perform the hepatic differentiation, the hepatoblast-like cells were cultured for 5 days in RPMI1640 medium (Sigma), which contained 20 ng/ml hepatocyte growth factor (HGF), 1×GlutaMAX, and 1×B27 Supplement Minus Vitamin A. Finally, the cells were cultured for 11 days in Hepatocyte Culture Medium (HCM, Lonza) without epidermal growth factor (EGF) but with 20 ng/ml oncostatin M (OsM).

value: FCL-iPS

value: iPS cell-derived hepatocyte-like cells (iPSC-HLCs)


title: Anaef8_totalRNA

description: Anaef8_totRNA in processed data file

value: Dynabeads mRNA DIRECT Purification Kit

value: Nugen/Nextera XT kit (Illumina)


title: Input_rep1


title: ILC1a_3


title: Zfp281 KO2_RNA-seq

description:
KO_rep2_FPKM
KO6_S4_L001
processed data file: genes.fpkm_tracking.diff.txt

source_name: homozygous Zfp281

tag: developmental stage

value: homozygous Zfp281 mutant

value: Placenta


title: Anaef7_totalRNA

description: Anaef7_totRNA in processed data file


title: CYP2C19-KO HLCs [AR3098_01]

description: CYP2C19-KO HLCs

source_name: FCL-iPS, hepatocyte-like cells, iPSC-derived, CYP2C19-KO

tag: cell line


title: ILC1a_1


title: ILC1b_4


title: Zfp281 KO1_RNA-seq

description:
KO_rep1_FPKM
KO5_S3_L001
processed data file: genes.fpkm_tracking.diff.txt


title: CD44_H10

value: Mixed


title: CD44_H11

value: skin squamous cell carcinoma


title: Zfp281 Het2_RNA-seq

description:
Het_rep2_FPKM
Het2_S2_L001
processed data file: genes.fpkm_tracking.diff.txt

source_name: heterozygous Zfp281

value: heterozygous Zfp281 mutant


title: WT4_totalRNA

description: WT4_totRNA in processed data file

value: lymph node CD4+ T cell


title: Zfp281ChIP_rep1


title: Anaef5_totalRNA

description: Anaef5_totRNA in processed data file

value: 12 week old


title: ILC1b_3


title: CD44_G9

value: Before ACT immunotherapy


title: Zfp281 Het1_RNA-seq

description:
Het_rep1_FPKM
Het1_S1_L001
processed data file: genes.fpkm_tracking.diff.txt


title: ILC1b_2


title: WT3_totalRNA

description: WT3_totRNA in processed data file


title: Anaef6_totalRNA

description: Anaef6_totRNA in processed data file

value: Anaef/Anaef


title: CD44_G8


title: ILC1b_1


title: ILC3b_3


title: uuo-day14-2

type: protein

city: Boston

first: Lorena

last: Pantano

state: MA

address: 655 Huntington Ave

department: Biostatistics

institute: Harvard Chan School of Public Health

data_processing:
Raw data was converted to mzXML
searched via Sequest against Uniprot version 28
Variable modifications of oxidized methionine and over-labelling of TMT on serine, threonine and tyrosine were considered
linear discriminant analysis was used to distinguish forward and reverse hits and reverse hits were filtered to an FDR of 1% at the protein level
using rules of parsimony shared peptides were collapsed into the minimally sufficient number of proteins
Quantitation filters of > 200 sum reporter ion S:N and > 0.7 isolation specificity were incorporated
version 28  Uniprot (UniProt Consortium 2018) database downloaded 02/04/2014

label: 10-plex TMT proteomics

molecule: protein

growth_protocol: Male BALC/c mice were obtained from Charles River Laboratories (USA). All experimental protocols concerning the use of laboratory animals were performed according to the NIH guidelines for the care and use of laboratory animals, and approved by the Institutional Animal Care and Use Committees (IACUC) of Harvard Medical School. Mice were housed in groups of three on a 12-h light/dark cycle with access to food and water ad libitum. At the age of 8-10 weeks they entered the experiment.

extract_protocol: Kidney samples were mechanically homogenized in lysis buffer (8 M urea, 1% SDS, Roche complete protease inhibitors and phosphatase inhibitors, 50 mM Tris pH 8.5). Approximately one third of a kidney was used for sample preparation.  Protein concentration was determined using the BCA assay (Pierce, Rockford, IL).  The homogenate was reduced with 5 mM DTT and alkylated with 15 mM iodoacetamide (Sigma, St. Louis, MO). 0.15 mg of protein was precipitated using chloroform:methanol. Pellets were washed twice with cold methanol and re-solubilized in 8M urea with 20 mM EPPS, pH 8.5.  After diluting the samples to 4M urea using 20 mM EPPS, they were digested with Lys-C (Wako Chemicals, Richmond, VA) overnight at room temperature. On the next day, samples were further diluted to 1.5 M urea using 20 mM EPPS and digested for 6h at 37°C using Trypsin (Promega, Madison, WI). 60 µg of each sample were then brought to 10% (v/v) acetonitrile and labeled with 2:1 (TMT:Peptide) by mass of TMT-10 reagent (Pierce). The reaction was quenched with hydroxylamine (0.5% final volume). Afterwards, samples were acidified by adding formic acid to 2% final volume, combined, and desalted using a C18 Sep-Pak (Waters, Milford, MA). The now combined sample was fractionated using basic pH reversed phase chromatography using a 1200 HPLC (Agilent; Santa Clara, CA) equipped with a UV-DAD detector and fraction collection system. Then, the resulting 12 fractions were desalted using the C18 StageTip procedure.  Each fraction was loaded onto a 100 µm id, 35 cm long column packed with 1.8 µm beads (Sepax, Newark DE) and separated using a 3h gradient from 8-27% buffer B (99% acetonitrile and 1% formic acid) and buffer A (96% water, 3% acetonitrile and 1% formic acid) using an Easy 1000 nano-LC (Thermo-Fisher Scientific, San Jose, CA). All MS analyses were performed on an Orbitrap Fusion Lumos mass spectrometer (Thermo-Fisher Scientific, San Jose, CA) applying a multi-notch MS3 method.

treatment_protocol: Unilateral ureter obstruction (UUO) model: Before surgery, mice were anaesthetized with an intraperitoneal injection of sodium pentobarbital (50 mg/kg of body weight), the left kidney was exposed via a flank incision and 3.0 silk suture thread was used to tie off the ureter at the lower pole. Before the obstruction and 3, 7, and 14 days later, mice were sacrificed, kidneys were removed and immediately snap frozen in liquid nitrogen.

value: BALC/c

value: male

value: 14 days after unilateral ureter obstruction

value: kidney


title: CD44_G6


title: CD44_G7


title: WT1_totalRNA

description: WT1_totRNA in processed data file

value: WT/WT


title: ILC3b_1

value: tonsil


title: WT2_totalRNA

description: WT2_totRNA in processed data file

value: Dynabeads mRNA DIRECT Purification Kit


title: ILC3b_2


title: uuo-day14-1

source_name: Unilateral ureter obstruction (UUO) model


title: CD44_G5


title: CD44_G4


title: ILC3a_4


title: CD44_G3


title: uuo-day7-3

value: 7 days after unilateral ureter obstruction


title: uuo-day7-2


title: CD44_G2


title: ILC3a_3


title: uuo-day7-1


title: CD44_G1


title: At2+_2-3

source_name: seedlings

value: seedlings

value: 10 day old seedlings

tag: background strain

value: AtIPCS2 over expressing line

value: untreated


title: uuo-day3-3

value: 3 days after unilateral ureter obstruction

tag: tissue


title: ILC3a_2


title: bKO rep3

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

country: Germany

institute: German cancer research center (DKFZ)

data_processing:
base calling bcl2fastq 2.19.0.316
low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90% of the read needing a quality phred score > 20. Homertools 4.7 33 were used for PolyA-tail trimming, and reads with a length < 17 were removed.
With STAR 2.3 34, the filtered reads were mapped against mouse genome 38 (mm10) using default parameters
Count data were generated using featureCounts 35(parameters --minReadOverlap 3 -T 3 -M -O) for the genes annotated in the gencode.vM16.gtf file.
Genome_build: mm10

source_name: Tcell

extract_protocol:
Tregs cells were FACS-purified. RNA was prepared using the QIAGEN RNeasy Mini Kit. DNA was removed using the QIAGEN RNase-Free DNase Set
SmarTer Ultra Low Input RNA and NEBNext ChIP-Seq was used for library construction. libraries were pooled with six samples in each lane and sequenced (Illumina HiSeq 2000 v4 Single-Read 50 bp)

treatment_protocol: we created a mouse strain with Treg-specific ablation of Junb (Foxp3YFP-Cre×JunbFlox/Flox) by crossing the Foxp3YFP-Cre mice and the JunbFlox/Flox strain

value: T cell

value: 3 month


title: bKO rep2


title: uuo-day3-2


title: bKO rep1


title: CD44_G11

source_name: Mouse skin squamous cell carcinoma

value: Mixed

value: skin squamous cell carcinoma

value: Before ACT immunotherapy


title: ILC3a_1


title: WT_N_8h_1

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

description: Gene expression after 8 hours of ammonium addition to cells growing without combined nitrogen

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: PCC7120, WT, ammonium addition, 8h, replicate 1

label_protocol: DNAse-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: Liquid culture in BG11 medium under standard illumination at 30 centigrades. Nitrogen sources are either 6 mM ammonium chloride or atmospheric nitrogen.

extract_protocol: RNA was prepared using a hot phenol-based protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Removal of combined nitrogen (for cells growing in the presence of ammonium) or addition of 10 mM ammonium to cells growing without a combined nitrogen source

value: WT


title: CD44_G10


title: WT_0h_3

description: Gene expression in medium with ammoniun as nitrogen source

source_name: PCC7120, WT, ammonium, replicate 3


title: hetR_24h_2

description: Gene expression after 24 hours of nitrogen depletion

source_name: PCC7120, hetR mutant, without combined nitrogen, 24h, replicate 2

value: hetR mutant


title: WT rep3


title: hetR_12h_2

description: Gene expression after 12 hours of nitrogen depletion

source_name: PCC7120, hetR  mutant, without combined nitrogen, 12h, replicate 2


title: WT_8h_1

description: Gene expression after 8 hours of nitrogen depletion

source_name: PCC7120, WT, without combined nitrogen, 8h, replicate 1


title: WT rep2


title: hetR_24h_1

source_name: PCC7120, hetR mutant, without combined nitrogen, 24h, replicate 1


title: hetR_12h_1

source_name: PCC7120, hetR mutant, without combined nitrogen, 12h, replicate 1


title: CD44_G12


title: LS_T2

city: Nanning

first: Dong-Liang

email: hdl666@163.com, Huangdl@gxaas.net

address: 174 Daxue Road

institute: Sugarcane Research Institure of Guangxi Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software was used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts.
Clean sequence reads were obtained by removing all adaptor sequences, empty reads and low quality reads (Q < 30 and length <50 bp) from raw reads. Clean reads were assembled by Trinity software package
Genome_build: de novo transcriptome assembly. FASTA file with transcript sequences is available on the series record.
Supplementary_files_format_and_content: text file with FPKM.

organism: Saccharum hybrid cultivar

growth_protocol: Three sugarcane genotypes with different sugar content were used for this study. They are ROC22, a high-sugar commercial variety (HS; sucrose content 15.0%)”, YT71-210, a moderate-sugar non-commercial genotype ((MS; “sucrose content 12.6%) and GT86-887, a low-sugar non-commercial genotype (LS; “sucrose content 6.0%). They were selected because of their similar growth habit and biomass production but with large differences in sugar content. Setts (stem cuttings with 2-3 buds) of these clones were obtained from disease-free plants from propagation plots and planted in the experimental farm of Sugarcane Research Institute, Nanning, China (SRI) in February 2016. They were grown till October 2016 following the best crop management practices recommended by SRI. The crops received nitrogen (360 kg/ha) fertiliser and was rain-fed with supplementary irrigation when required.

extract_protocol:
Total RNA was extracted from frozen samples using the Qiagen RNA plant mini-kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. The quality and quantity of RNA were determined by Nanodrop and Qubit, respectively, and Agilent 2100 was used to evaluate the RNA Integrity. High quality RNA samples with Integrity Number >8 were used for constructing cDNA libraries and sequencing using Illumina HiSeq 2000 platform (Beijing Novogene Bioinformatics Technology Co. Ltd., Beijing, China).
A total amount of 3μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Illumina TruseqTM RNA sample prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37oC for 15 min followed by 5 min at 95 oC before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: For all treatments the experimental unit for each clone was a 5 x 7 m rows plot with 1.2 m inter-row spacing, and they were replicated thrice. Plants were treated with 400 mg/L ethylene solution (prepared from Ethephon, a commercial preparation containing 40% 2-chloroethyl phosphonic acid in aqueous solution) or water as foliar spray till run-off from the lamina in mid-October 2016.

value: 20 cm above the node attached to the 2nd youngest fully expanded leaf

tag: phenotype

value: low-sugar (LS)

tag: cultivar


title: LS_T1


title: normal_1_uuo

value: BALC/c

value: male

value: no treatment

value: kidney


title: HiC_neutrophil

city: Chicagp

first: Yaping

last: Liu

state: IL

address: 303 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

description: Hi-C library preparation on white blood cells and neutrophils was performed using the Arima-HiC kit (Arima Genomics, Inc.; Cat # A510008), according to the manufacturer’s protocols. Briefly, WBCs (freshly isolated from whole blood) or purified neutrophils (obtained frozen from a commercial source and then thawed) were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using SPRI beads. The size-selected fragments were then enriched using Enrichment Beads (provided in Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with TruSeq adapters using the KAPA Hyper Prep kit. The purified, PCR-amplified DNA underwent standard QC (qPCR and Bioanalyzer) and was sequenced with unique dual indexes on the Illumina HiSeq X (WBC) or NovaSeq 6000 (neutrophils) Sequencing System at 2x151 base pairs..

data_processing:
Hi-C data processing: Raw fastq files from various Hi-C experiments were uniformly processed using Juicer command line tools v1.5.6 and  aligned to the human genome (GRCh38 with decoys, alt contigs, and HLA contigs). Only results after filtering reads with mapping quality score > 30 were used to generate a Pearson correlation matrix and compartment A/B eigenvector. PCA was performed using the PCA function in scikit-learn 0.19.1 in Python 3.6. The first principal component was used to segment the compartments. For each chromosome, compartments were split into two groups based on their sign. After excluding regions with mappability less than 0.75, the group of compartments with the lower mean gene density (based on Ensembl v84 annotations) was defined as compartment B; the other group was defined as compartment A. HiCCUPS loops were called by hiccups command line in Juicer with parameters “-k KR -m 512 -r 5000,10000,25000 -f .1,.1,.1 -p 4,2,1 -i 7,5,3 -t 0.02,1.5,1.75,2 -d 20000,20000,50000”.
Genome_build: hg38
Supplementary_files_format_and_content: hic

source_name: neutrophils (from Astarte Biologics Inc)

extract_protocol:
WBCs are freshly isolated from whole blood, purified neutrophils are obtained frozen from a commercial source (Astarte Biologics Inc) and then thawed
Hi-C library preparation on white blood cells and neutrophils was performed using the Arima-HiC kit (Arima Genomics, Inc.; Cat # A510008), according to the manufacturer’s protocols. Briefly, WBCs (freshly isolated from whole blood) or purified neutrophils (obtained frozen from a commercial source and then thawed) were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using SPRI beads. The size-selected fragments were then enriched using Enrichment Beads (provided in Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with TruSeq adapters using the KAPA Hyper Prep kit. The purified, PCR-amplified DNA underwent standard QC (qPCR and Bioanalyzer) and was sequenced with unique dual indexes on the Illumina HiSeq X (WBC) or NovaSeq 6000 (neutrophils) Sequencing System at 2x151 base pairs.

value: primary cell

tag: restriction enzyme

value: Arima (multi-enzyme)


title: fa-day14-2

source_name: Folic acid (FA) model

treatment_protocol: Folic acid (FA) model: Folic acid was prepared at 25 mg/ml in 0.3 M sodium bicarbonate.ice received a single dose of 250 mg/kg via intraperitoneal injection. Before the injection and 1, 2, 7, and 14 days later, mice were sacrificed, kidneys were removed and immediately snap frozen in liquid nitrogen.

value: 14 days after a single dose of 250 mg/kg folic acid via intraperitoneal injection


title: hetR_6h_1

description: Gene expression after 6 hours of nitrogen depletion

source_name: PCC7120, hetR mutant, without combined nitrogen, 6h, replicate 1


title: hetR_0h_2

source_name: PCC7120, hetR mutant, ammonium, replicate 2


title: uuo-day3-1

value: 3 days after unilateral ureter obstruction


title: fa-day14-1


title: normal_2_uuo


title: MS_T2

value: medium-sugar (MS)


title: WT_N_0h_1

description: Gene expression in medium without combined nitrogen (steady state)

source_name: PCC7120, WT, without combined nitrogen steady state, replicate 1


title: LS_CK1

source_name: developing stem tissues_control


title: fa-day7-1

value: 7 days after a single dose of 250 mg/kg folic acid via intraperitoneal injection


title: fa-day7-2


title: MS_T1


title: hetR_6h_2

source_name: PCC7120, hetR mutant, without combined nitrogen, 6h, replicate 2


title: WT rep1

value: T cell

value: 3 month


title: A56717_ACTTGA [Fn7_1 invasion]

city: Guelph

first: Kyla

last: Cochrane

state: Ontario

address: 50 Stone Road East

department: Bioinformatics

country: Canada

institute: NuBiyota

data_processing:
BWA alignment version 0.5.7 was used to generate global alignments on the paired-end reads24.  BWA was run with the default parameter settings used for alignments, except that the "-s" option (to disable Smith-Waterman alignment) was used because this feature was not designed to handle the insert size distribution that occurs in paired-end RNA-Seq data.  In the final stage of the initial alignment, all reads were excluded that failed Illumina's Chastity filter and turned on bit 512 in that record's bitwise flag to indicate the read failed platform/vendor quality checks.   For stranded gene coverage analysis, the annotations came from NCBI (GCF_000158275.2_ASM15827v2_genomic.Fna) and correspond to the annotations in v30 of bacteria.ensembl.org. These annotations all include one annotation per gene and in this case NORM_TOTAL included all reads mapped to exons (since there was no mito sequence used for alignment). To determine each gene’s raw read count (each exons total unique reads) the RPKM strategy was used with the following formula25: (number of reads mapped to all exons in a gene x 1,000,000,000)/(NORM_TOTAL x sum of the lengths of all exons in the gene ) where NORM_TOTAL = the total number of reads that are mapped to exons (i.e. fractional read count for exons).
Genome_build: The Illumina paired-end sequence data were analyzed with BWA alignment software to map each read pair onto the GCF_000158275.2_ASM15827v2 genomic reference fasta for the subspecies Fn 7-1, which was downloaded from the NCBI genome browser (https://www.ncbi.nlm.nih.gov) in April 2016.
Supplementary_files_format_and_content: RPKM

organism: Fusobacterium nucleatum

source_name: RNA extracted from bacteria that were invaded into human colon epithelial adenocarcinoma tissue culture cells

growth_protocol: Propagation of Fn strains was carried out on fastidious anaerobic agar (FAA) plates (Neogen) supplemented with 5% [v/v] defibrinated sheep blood (ThermoFisher), or in tryptic soy broth supplemented with hemin (5µg/mL) and menadione (1µg/mL) (TSBsupp) (Sigma-Aldrich), with incubation in a humidified anaerobic chamber (Ruskinn Bug Box) at 37°C under an atmosphere of N2:CO2:H2 90:5:5.  For infection assays, Fn 7-1 and Fn7-3 were grown in TSBsupp to late log phase and normalized for cell number using McFarland standards.  Caco-2 human colon adenocarcinoma cells (American Type Culture Collection (ATCC), Manassas, VA line HTB37™) were used for in vitro infection assays.  Cells were cultured in Dulbecco’s Modified Eagle Media (DMEM) (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS) (ThermoFisher), 10mM sodium pyruvate (Sigma-Aldrich), and 5µg/mL Plasmocin (Invitrogen) at 37°C in 5% CO2.  For consistency, and to avoid genotypic and phenotypic variation caused by genetic drift, only Caco-2 cells from passages 4-12 were used for experiments.

extract_protocol:
Total RNA was also isolated from TRIzol® -stabilized samples of homogenized bacterial/tissue culture cells from the following control experiments:  1) Fn 7-1 grown in TSBsupp;  2) Caco-2 cells, with no bacterial exposure;  and 3) Caco-2 cells infected with Fn 7-1 cells for 4 hours, collected after trypsinization but without gentamicin treatment. The parameters of control #3 will resolve for Fn 7-1 genes that are needed for bacterial invasion into the host cell.  The protocol for RNA isolation of all invasion and adhesion samples, and the respective controls were repeated with three biological replicates.
Samples were thawed, homogenized, and RNA was separated from DNA and cellular debris by adding 0.2 mL of chloroform per 1 mL of TRIzol® Reagent followed by vigorous vortexing.  Samples were then centrifuged at 12,000 x g for 15 minutes at 4°C, the aqueous phase was recovered, and RNA was precipitated by adding 100% isopropanol followed by centrifugation at 12,000 x g for 10 minutes at 4°C.  The RNA pellet was washed three times in 75% EtOH, air dried for 5 minutes and re-suspended in 50 µL nuclease-free, de-ionized H2O. Samples were treated with the Turbo DNA-free™ kit (ThermoFisher), the bacterial RNA fraction was enriched using the MICROBenrichTM kit, and the sample was then ribodepleted with the MICROBexpress™ kit (ThermoFisher), all following the manufacturer’s protocols.  Finally, the quantity and quality of each RNA sample was assessed Agilent Bioanalyzer 2100 RNA Nanochips.
cDNA libraries (including biological replicates) containing both human and fusobacterial RNA were generated and sent for sequencing. The sequencing depth required for the accurate representation of both the bacterial pathogen and the mammalian host was set at a threshold of 200 million reads using estimates from previous studies.  Library construction and Illumina sequencing were performed as previously described but with the following modifications: (1) each paired-end library was PCR-amplified for 15 cycles using the standard Illumina PE1 PCR primer; and (2) a modified PE2 primer including a unique six base insertion as an index sequence was used. Libraries were gel-purified to remove residual adapter dimers and then sequenced on the Illumina HiSeq™ 2000 platform. Four paired-end 100 nt sequence lanes were run per library for a total of 12 lanes, yielding 952.6 million raw read pairs, well above the 200 million read threshold.

treatment_protocol: Caco-2 cells were grown to 85% confluence, washed briefly with PBS and resuspended in supplemented DMEM without antibiotics.  They were then infected to a MOI of 100:1 with Fn 7-1 that had been grown to late log phase in TSBsupp, and incubated at 37°C in 5% CO2 for 4 hours 14. Cells were then washed with sterile PBS and treated with fresh DMEM containing gentamicin (0.5mg/mL) (Sigma-Aldrich) for 30 minutes at 37°C in 5% CO2 to kill any bacteria present outside of the Caco-2 cells. The Caco-2 cells were then trypsinized and quenched.  All subsequent steps were carried out using reagents at 4°C. Cells were briefly pelleted by centrifugation before lysis with 0.1% (v/v) Nonidet P-40 (Sigma-Aldrich), aided with gentle mixing to release internalized (invasive) Fusobacterium cells. Cells were once again pelleted by centrifugation and washed briefly with 1X Versene. RNA was stabilized through the addition of TRIzol® Reagent (1mL per 50-100mg of pelleted sample) (ThermoFisher), before storage at -80°C.  RNAlater® (Qiagen) was used in all buffers throughout the extraction process. Total RNA extraction was performed within 15 minutes to ensure minimal transcriptional changes during the process.

tag: growth medium

value: tryptic soy broth

tag: experimental condition

value: invasion


title: WT_24h_1

source_name: PCC7120, WT, without combined nitrogen, 24h, replicate 1

value: WT


title: A56718_GATCAG [Fn7_1 invasion]


title: WT_12h_2

source_name: PCC7120, WT, without combined nitrogen, 12h, replicate 2


title: WT_24h_2

source_name: PCC7120, WT, without combined nitrogen, 24h, replicate 2


title: hetR_0h_1

source_name: PCC7120, hetR mutant, ammonium, replicate 1

value: hetR mutant


title: LS_CK2

last: Huang

value: 20 cm above the node attached to the 2nd youngest fully expanded leaf

value: low-sugar (LS)


title: fa-day2-1

value: BALC/c

value: male

value: 2 days after a single dose of 250 mg/kg folic acid via intraperitoneal injection


title: A56715_GCCAAT [Fn7_1 adhesion]

source_name: RNA extracted from bacteria that were bound to human colon epithelial adenocarcinoma tissue culture cells

value: adhesion


title: WT_6h_2

source_name: PCC7120, WT, without combined nitrogen, 6h, replicate 2


title: WT_12h_1

source_name: PCC7120, WT, without combined nitrogen, 12h, replicate 1


title: A56714_ACAGTG [Fn7_1 adhesion]


title: MS_CK2


title: fa-day1-2

value: 1 day after a single dose of 250 mg/kg folic acid via intraperitoneal injection

value: kidney


title: HS_T2

value: high-sugar (HS)


title: CSC1_A7

source_name: Mouse skin squamous cell carcinoma

value: Mixed

tag: age

value: skin squamous cell carcinoma

value: Before ACT immunotherapy


title: A56716_CAGATC [Fn7_1 invasion]

tag: strain


title: fa-day1-1

tag: Sex


title: WT_6h_1

source_name: PCC7120, WT, without combined nitrogen, 6h, replicate 1


title: normal_2_fa

value: no treatment


title: Mycobacteriophage Trixie lysogen

city: Pittsburgh

first: Travis

last: Mavrich

state: Pennsylvania

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.8.3 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.2.6
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.2
BAM format was converted to BED format using bedtools version 2.25.0
Expression levels were computed as reads mapped per base pair per strand ("top" and "bottom") using the genomecov tool of bedtools version 2.25.0
Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Genome_build: MF140410.3 (Et2Brutus)
Genome_build: JF704097.1 (Gladiator)
Genome_build: JN408461.1 (Trixie)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("top" and "bottom" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Mycolicibacterium smegmatis MC2 155

source_name: Cells grown in liquid media

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was depleted using Ribo-Zero (Illumina)
Libraries were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: host strain

value: Mycobacterium smegmatis mc2155

tag: infection

value: Mycobacteriophage Trixie

tag: infection timepoint

value: no exogenous phage added

tag: growth phase

value: lysogenic growth


title: HS_CK2

value: 20 cm above the node attached to the 2nd youngest fully expanded leaf


title: WT_0h_2

source_name: PCC7120, WT, ammonium, replicate 2

value: WT


title: WT_0h_1

source_name: PCC7120, WT, ammonium, replicate 1


title: Mycobacteriophage Gladiator lysogen

value: Mycobacteriophage Gladiator


title: C1G1R7 [MBD-seq]

status: Public on May 06 2019

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description:
G1_290
S46

data_processing:
mapping using Bowtie2 (v2.1.0) software in end-to-end & sensitive-mode
coverage peaks were generated using MACS 14 peak caller (Zhang et al. 2008). Subsequently, peaks were aligned and sequencing reads within overlapping peak sets were counted using the DiffBind R-package v2.0.9 (Stark & Brown 2013).
statistics were performed using the DeSeq2 R package (Love et al. 2014)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: csv file with gene wise read countings

source_name: Tph2 +/+_no stress_amygdala

extract_protocol:
brains were extracted, snapfrozen in isopentane, subsequently the amygdala was dissected, amygdalae of both hemispheres were poderised at - 80 ͦC, blended and split in two equal portions. DNA was extracted from one portion, using regular phenol/chlorophorm based extraction protocol as published in (Schraut et al. 2014) [MBD-seq]
library preparation was performed by Nxt-Dx (Ghent, Belgium) [MBD-seq]
MBD seq, 50 bp; paired-end; 20 million reads/ sample [MBD-seq]

treatment_protocol: pups were separated from their respective dams for 3h per day from postnatal day 2 until postnatal day 15, adult male offspring were investigated [MBD-seq]

tag: strain background

tag: genotype

value: male

value: 4 months

tag: condition

value: no stress

value: amygdala


title: C1G1R5 [MBD-seq]

description:
G1_70
S15


title: A56719_TAGCTT [Fn7_1 control]

source_name: RNA extracted from bacteria grown in broth culture

value: tryptic soy broth

value: control


title: HS_CK1

source_name: developing stem tissues_control

value: high-sugar (HS)


title: C1G1R6 [MBD-seq]

description:
G1_74
S16


title: C1G1R4 [MBD-seq]

description:
G1_52
S13


title: A56713_TGACCA [Fn7_1 adhesion]

value: adhesion


title: A56721_CTTGTA [Fn7_1 control]


title: A56720_GGCTAC [Fn7_1 control]


title: HS_T1


title: C2G1R8 [MBD-seq]

description:
G2_263
S41

source_name: Tph2 +/+_maternal separation_amygdala

value: maternal separation


title: C2G1R7 [MBD-seq]

description:
G2_241
S40


title: C1G1R1 [MBD-seq]

description:
G1_17
S2


title: C2G1R5 [MBD-seq]

description:
G2_172
S30


title: C2G1R4 [MBD-seq]

description:
G2_158
S28


title: C2G1R3 [MBD-seq]

description:
G2_153
S26


title: fa-day2-2

source_name: Folic acid (FA) model

value: BALC/c

tag: treatment

value: 2 days after a single dose of 250 mg/kg folic acid via intraperitoneal injection

value: kidney


title: C2G1R2 [MBD-seq]

description:
G2_129
S23

tag: tissue


title: C2G1R1 [MBD-seq]

description:
G2_107
S21


title: C1G2R8 [MBD-seq]

description:
G3_294
S47

source_name: Tph2 +/-_no stress_amygdala


title: C1G2R7 [MBD-seq]

description:
G3_287
S45


title: C1G2R4 [MBD-seq]

description:
G3_40
S10


title: C1G1R2 [MBD-seq]

description:
G1_28
S5


title: C2G2R8 [MBD-seq]

description:
G4_239
S39

source_name: Tph2 +/-_maternal separation_amygdala


title: Mycobacteriophage Et2Brutus lysogen

value: Mycobacterium smegmatis mc2155

value: Mycobacteriophage Et2Brutus

value: no exogenous phage added


title: C2G2R7 [MBD-seq]

description:
G4_219
S38


title: C2G2R6 [MBD-seq]

description:
G4_192
S35


title: C2G2R1 [MBD-seq]

description:
G4_125
S22


title: C2G2R2 [MBD-seq]

description:
G4_148
S25


title: C1G2R5 [MBD-seq]

description:
G3_61
S14


title: C2G2R3 [MBD-seq]

description:
G4_156
S27


title: C2G2R4 [MBD-seq]

description:
G4_167
S29


title: C1G3R7 [MBD-seq]

description:
G5_273
S43

source_name: Tph2 -/-_no stress_amygdala


title: C1G3R8 [MBD-seq]

description:
G5_274
S44


title: C1G1R8 [MBD-seq]

description:
G1_295
S48


title: C1G3R4 [MBD-seq]

description:
G5_43
S11


title: C1G3R3 [MBD-seq]

description:
G5_39
S9


title: C1G3R1 [MBD-seq]

description:
G5_16
S1


title: C2G1R6 [MBD-seq]

description:
G2_181
S31


title: C1G2R3 [MBD-seq]

description:
G3_37
S8


title: C2G3R8 [MBD-seq]

description:
G6_218
S37

source_name: Tph2 -/-_maternal separation_amygdala


title: C1G2R1 [MBD-seq]

description:
G3_18
S3


title: C1G2R2 [MBD-seq]

description:
G3_29
S6


title: C1G1R3 [MBD-seq]

description:
G1_35
S7


title: C2G3R6 [MBD-seq]

description:
G6_191
S34


title: C2G3R5 [MBD-seq]

description:
G6_188
S33


title: C2G3R4 [MBD-seq]

description:
G6_133
S24


title: C2G3R3 [MBD-seq]

description:
G6_106
S20


title: C2G3R2 [MBD-seq]

description:
G6_105
S19


title: Whole blood sample from a healthy adult, 102036

city: Stanford

first: Aaron

middle: M

last: Newman

state: California

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine, Department of Biomedical Data Science

institute: Stanford University

data_processing:
To maximize linearity in the context of deconvolution analyses, raw FASTQ reads were processed with Salmon v0.8.277 using GENCODE v23 reference transcripts, the –biasCorrect flag, and otherwise default parameters. RNA-Seq quantification results were merged into a single gene-level TPM matrix using the R package, tximport.
Genome_build: GENCODE v23
Supplementary_files_format_and_content: Gene expression matrix in TPM space, txt file

source_name: whole blood

extract_protocol:
Total RNA was isolated from whole blood samples of 12 healthy adults stored in PAXgene tubes. RNA was isolated using the PAXgene Blood RNA Kit (Qiagen) according to the manufacturer’s recommendations. then quantitated and quality assessed using a 2100 Bioanalyzer (Agilent).
Library preparation was performed with the TruSeq RNA exome kit (Illumina) per the manufacturer’s recommendations. RNA-Seq libraries were multiplexed together and sequenced on a single HiSeq 4000 lane (Illumina) using 2 x 150bp reads.

value: whole blood

tag: diagnosis

value: healthy

tag: subject id


title: Whole blood sample from a healthy adult, 102051


title: Whole blood sample from a healthy adult, 102035


title: Whole blood sample from a healthy adult, 102037


title: C2G3R1 [MBD-seq]

description:
G6_103
S18

value: male


title: Whole blood sample from a healthy adult, 001162


title: C1G3R2 [MBD-seq]

description:
G5_19
S4

value: 4 months


title: Whole blood sample from a healthy adult, 001161


title: C1G2R6 [MBD-seq]

description:
G3_76
S17

value: no stress


title: Whole blood sample from a healthy adult, 001156


title: Whole blood sample from a healthy adult, 001157


title: C2G2R5 [MBD-seq]

description:
G4_182
S32

value: amygdala


title: C1G3R6 [MBD-seq]

description:
G5_272
S42


title: Whole blood sample from a healthy adult, 102038


title: Whole blood sample from a healthy adult, 102034


title: C1G3R5 [MBD-seq]

description:
G5_49
S12


title: Whole blood sample from a healthy adult, 001160


title: Whole blood sample from a healthy adult, 001159


title: FL lymph node biopsy, untreated, 991

hyb_protocol: cRNA was hybridized to HGU133 Plus 2.0 microarrays (Affymetrix) according to the manufacture's protocol.

scan_protocol: standard Affymetrix protocol

data_processing: MAS5 normalized using the affy package in R/Bioconductor.

source_name: FL lymph node biopsy, untreated, 991

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA and genomic DNA were prepared and stored using TRIzol and RNeasy Midi Kits (Qiagen, Valencia, CA). Total cellular RNA (at least 300 ng) was assessed for yield (NanoDrop 2000, Thermo Scientific) and quality (2100 Bioanalyzer, Agilent).

value: lymph node


title: FL lymph node biopsy, untreated, 993

source_name: FL lymph node biopsy, untreated, 993


title: FL lymph node biopsy, untreated, 996

source_name: FL lymph node biopsy, untreated, 996


title: FL lymph node biopsy, untreated, 999

source_name: FL lymph node biopsy, untreated, 999


title: FL lymph node biopsy, untreated, 994

source_name: FL lymph node biopsy, untreated, 994


title: FL lymph node biopsy, untreated, 984

source_name: FL lymph node biopsy, untreated, 984


title: normal_1_fa

value: no treatment


title: FL lymph node biopsy, untreated, 978

source_name: FL lymph node biopsy, untreated, 978


title: FL lymph node biopsy, untreated, 983

source_name: FL lymph node biopsy, untreated, 983


title: FL lymph node biopsy, untreated, 981

source_name: FL lymph node biopsy, untreated, 981


title: FL lymph node biopsy, untreated, 973

source_name: FL lymph node biopsy, untreated, 973


title: FL lymph node biopsy, untreated, 969

source_name: FL lymph node biopsy, untreated, 969


title: FL lymph node biopsy, untreated, 980

source_name: FL lymph node biopsy, untreated, 980


title: FL lymph node biopsy, untreated, 975

source_name: FL lymph node biopsy, untreated, 975


title: FL lymph node biopsy, untreated, 968

source_name: FL lymph node biopsy, untreated, 968


title: FL lymph node biopsy, untreated, 989

source_name: FL lymph node biopsy, untreated, 989


title: FL lymph node biopsy, untreated, 961

source_name: FL lymph node biopsy, untreated, 961


title: FL lymph node biopsy, untreated, 962

source_name: FL lymph node biopsy, untreated, 962


title: FL lymph node biopsy, untreated, 987

source_name: FL lymph node biopsy, untreated, 987


title: FL lymph node biopsy, untreated, 966

source_name: FL lymph node biopsy, untreated, 966


title: FL lymph node biopsy, untreated, 963

source_name: FL lymph node biopsy, untreated, 963


title: FL lymph node biopsy, untreated, 986

source_name: FL lymph node biopsy, untreated, 986


title: FL lymph node biopsy, untreated, 957

source_name: FL lymph node biopsy, untreated, 957


title: FL lymph node biopsy, untreated, 959

source_name: FL lymph node biopsy, untreated, 959


title: FL lymph node biopsy, untreated, 958

source_name: FL lymph node biopsy, untreated, 958


title: FL lymph node biopsy, untreated, 967

source_name: FL lymph node biopsy, untreated, 967


title: FL lymph node biopsy, untreated, 976

source_name: FL lymph node biopsy, untreated, 976


title: FL lymph node biopsy, untreated, 947

source_name: FL lymph node biopsy, untreated, 947


title: FL lymph node biopsy, untreated, 948

source_name: FL lymph node biopsy, untreated, 948


title: FL lymph node biopsy, untreated, 955

source_name: FL lymph node biopsy, untreated, 955


title: FL lymph node biopsy, untreated, 949

source_name: FL lymph node biopsy, untreated, 949


title: FL lymph node biopsy, untreated, 942

source_name: FL lymph node biopsy, untreated, 942


title: FL lymph node biopsy, untreated, 943

source_name: FL lymph node biopsy, untreated, 943


title: FL lymph node biopsy, untreated, 945

source_name: FL lymph node biopsy, untreated, 945


title: MS_CK1

source_name: developing stem tissues_control

value: 20 cm above the node attached to the 2nd youngest fully expanded leaf

tag: phenotype

value: medium-sugar (MS)

tag: cultivar


title: FL lymph node biopsy, untreated, 930

source_name: FL lymph node biopsy, untreated, 930


title: FL lymph node biopsy, untreated, 927

source_name: FL lymph node biopsy, untreated, 927


title: FL lymph node biopsy, untreated, 931

source_name: FL lymph node biopsy, untreated, 931


title: FL lymph node biopsy, untreated, 913

source_name: FL lymph node biopsy, untreated, 913


title: FL lymph node biopsy, untreated, 953

source_name: FL lymph node biopsy, untreated, 953


title: FL lymph node biopsy, untreated, 952

source_name: FL lymph node biopsy, untreated, 952


title: FL lymph node biopsy, untreated, 944

source_name: FL lymph node biopsy, untreated, 944


title: FL lymph node biopsy, untreated, 903

source_name: FL lymph node biopsy, untreated, 903


title: C2G3R7 [MBD-seq]

description:
G6_197
S36

source_name: Tph2 -/-_maternal separation_amygdala

value: maternal separation


title: FL lymph node biopsy, untreated, 920

source_name: FL lymph node biopsy, untreated, 920


title: FL lymph node biopsy, untreated, 922

source_name: FL lymph node biopsy, untreated, 922


title: FL lymph node biopsy, untreated, 912

source_name: FL lymph node biopsy, untreated, 912


title: FL lymph node biopsy, untreated, 932

source_name: FL lymph node biopsy, untreated, 932


title: FL lymph node biopsy, untreated, 940

source_name: FL lymph node biopsy, untreated, 940


title: FL lymph node biopsy, untreated, 908

source_name: FL lymph node biopsy, untreated, 908


title: FL lymph node biopsy, untreated, 919

source_name: FL lymph node biopsy, untreated, 919


title: FL lymph node biopsy, untreated, 918

source_name: FL lymph node biopsy, untreated, 918


title: FL lymph node biopsy, untreated, 929

source_name: FL lymph node biopsy, untreated, 929


title: FL lymph node biopsy, untreated, 941

source_name: FL lymph node biopsy, untreated, 941


title: FL lymph node biopsy, untreated, 900

source_name: FL lymph node biopsy, untreated, 900


title: FL lymph node biopsy, untreated, 901

source_name: FL lymph node biopsy, untreated, 901


title: FL lymph node biopsy, untreated, 893

source_name: FL lymph node biopsy, untreated, 893


title: FL lymph node biopsy, untreated, 898

source_name: FL lymph node biopsy, untreated, 898


title: FL lymph node biopsy, untreated, 879

source_name: FL lymph node biopsy, untreated, 879


title: FL lymph node biopsy, untreated, 855

source_name: FL lymph node biopsy, untreated, 855


title: FL lymph node biopsy, untreated, 895

source_name: FL lymph node biopsy, untreated, 895


title: FL lymph node biopsy, untreated, 867

source_name: FL lymph node biopsy, untreated, 867


title: FL lymph node biopsy, untreated, 859

source_name: FL lymph node biopsy, untreated, 859


title: FL lymph node biopsy, untreated, 854

source_name: FL lymph node biopsy, untreated, 854


title: FL lymph node biopsy, untreated, 888

source_name: FL lymph node biopsy, untreated, 888


title: FL lymph node biopsy, untreated, 872

source_name: FL lymph node biopsy, untreated, 872


title: FL lymph node biopsy, untreated, 883

source_name: FL lymph node biopsy, untreated, 883


title: FL lymph node biopsy, untreated, 877

source_name: FL lymph node biopsy, untreated, 877


title: FL lymph node biopsy, untreated, 866

source_name: FL lymph node biopsy, untreated, 866


title: FL lymph node biopsy, untreated, 871

source_name: FL lymph node biopsy, untreated, 871


title: FL lymph node biopsy, untreated, 885

source_name: FL lymph node biopsy, untreated, 885


title: FL lymph node biopsy, untreated, 878

source_name: FL lymph node biopsy, untreated, 878


title: FL lymph node biopsy, untreated, 894

source_name: FL lymph node biopsy, untreated, 894


title: FL lymph node biopsy, untreated, 902

source_name: FL lymph node biopsy, untreated, 902


title: FL lymph node biopsy, untreated, 861

source_name: FL lymph node biopsy, untreated, 861


title: FL lymph node biopsy, untreated, 881

source_name: FL lymph node biopsy, untreated, 881


title: FL lymph node biopsy, untreated, 850

source_name: FL lymph node biopsy, untreated, 850


title: FL lymph node biopsy, untreated, 869

source_name: FL lymph node biopsy, untreated, 869


title: FL lymph node biopsy, untreated, 857

source_name: FL lymph node biopsy, untreated, 857


title: FL lymph node biopsy, untreated, 848

source_name: FL lymph node biopsy, untreated, 848


title: FL lymph node biopsy, untreated, 844

source_name: FL lymph node biopsy, untreated, 844


title: FL lymph node biopsy, untreated, 843

source_name: FL lymph node biopsy, untreated, 843


title: FL lymph node biopsy, untreated, 982

source_name: FL lymph node biopsy, untreated, 982


title: FL lymph node biopsy, untreated, 870

source_name: FL lymph node biopsy, untreated, 870


title: FL lymph node biopsy, untreated, 839

source_name: FL lymph node biopsy, untreated, 839


title: FL lymph node biopsy, untreated, 837

source_name: FL lymph node biopsy, untreated, 837


title: FL lymph node biopsy, untreated, 831

source_name: FL lymph node biopsy, untreated, 831


title: FL lymph node biopsy, untreated, 830

source_name: FL lymph node biopsy, untreated, 830


title: FL lymph node biopsy, untreated, 829

source_name: FL lymph node biopsy, untreated, 829


title: FL lymph node biopsy, untreated, 834

source_name: FL lymph node biopsy, untreated, 834


title: FL lymph node biopsy, untreated, 818

source_name: FL lymph node biopsy, untreated, 818


title: FL lymph node biopsy, untreated, 828

source_name: FL lymph node biopsy, untreated, 828


title: FL lymph node biopsy, untreated, 816

source_name: FL lymph node biopsy, untreated, 816


title: FL lymph node biopsy, untreated, 904

source_name: FL lymph node biopsy, untreated, 904


title: FL lymph node biopsy, untreated, 810

source_name: FL lymph node biopsy, untreated, 810


title: FL lymph node biopsy, untreated, 809

source_name: FL lymph node biopsy, untreated, 809


title: FL lymph node biopsy, untreated, 813

source_name: FL lymph node biopsy, untreated, 813


title: FL lymph node biopsy, untreated, 794

source_name: FL lymph node biopsy, untreated, 794


title: FL lymph node biopsy, untreated, 805

source_name: FL lymph node biopsy, untreated, 805


title: FL lymph node biopsy, untreated, 822

source_name: FL lymph node biopsy, untreated, 822


title: FL lymph node biopsy, untreated, 823

source_name: FL lymph node biopsy, untreated, 823


title: FL lymph node biopsy, untreated, 807

source_name: FL lymph node biopsy, untreated, 807


title: FL lymph node biopsy, untreated, 797

source_name: FL lymph node biopsy, untreated, 797


title: FL lymph node biopsy, untreated, 798

source_name: FL lymph node biopsy, untreated, 798


title: FL lymph node biopsy, untreated, 803

source_name: FL lymph node biopsy, untreated, 803


title: FL lymph node biopsy, untreated, 793

source_name: FL lymph node biopsy, untreated, 793


title: FL lymph node biopsy, untreated, 787

source_name: FL lymph node biopsy, untreated, 787


title: FL lymph node biopsy, untreated, 778

source_name: FL lymph node biopsy, untreated, 778


title: FL lymph node biopsy, untreated, 783

source_name: FL lymph node biopsy, untreated, 783


title: FL lymph node biopsy, untreated, 840

source_name: FL lymph node biopsy, untreated, 840


title: FL lymph node biopsy, untreated, 769

source_name: FL lymph node biopsy, untreated, 769


title: FL lymph node biopsy, untreated, 762

source_name: FL lymph node biopsy, untreated, 762


title: FL lymph node biopsy, untreated, 777

source_name: FL lymph node biopsy, untreated, 777


title: FL lymph node biopsy, untreated, 754

source_name: FL lymph node biopsy, untreated, 754


title: FL lymph node biopsy, untreated, 751

source_name: FL lymph node biopsy, untreated, 751


title: FL lymph node biopsy, untreated, 760

source_name: FL lymph node biopsy, untreated, 760


title: FL lymph node biopsy, untreated, 752

source_name: FL lymph node biopsy, untreated, 752


title: FL lymph node biopsy, untreated, 753

source_name: FL lymph node biopsy, untreated, 753


title: FL lymph node biopsy, untreated, 749

source_name: FL lymph node biopsy, untreated, 749


title: FL lymph node biopsy, untreated, 764

source_name: FL lymph node biopsy, untreated, 764


title: FL lymph node biopsy, untreated, 771

source_name: FL lymph node biopsy, untreated, 771


title: FL lymph node biopsy, untreated, 746

source_name: FL lymph node biopsy, untreated, 746


title: FL lymph node biopsy, untreated, 745

source_name: FL lymph node biopsy, untreated, 745


title: FL lymph node biopsy, untreated, 733

source_name: FL lymph node biopsy, untreated, 733


title: FL lymph node biopsy, untreated, 750

source_name: FL lymph node biopsy, untreated, 750


title: FL lymph node biopsy, untreated, 748

source_name: FL lymph node biopsy, untreated, 748


title: FL lymph node biopsy, untreated, 782

source_name: FL lymph node biopsy, untreated, 782


title: FL lymph node biopsy, untreated, 759

source_name: FL lymph node biopsy, untreated, 759


title: FL lymph node biopsy, untreated, 738

source_name: FL lymph node biopsy, untreated, 738


title: FL lymph node biopsy, untreated, 730

source_name: FL lymph node biopsy, untreated, 730


title: FL lymph node biopsy, untreated, 741

source_name: FL lymph node biopsy, untreated, 741


title: FL lymph node biopsy, untreated, 734

source_name: FL lymph node biopsy, untreated, 734


title: FL lymph node biopsy, untreated, 714

source_name: FL lymph node biopsy, untreated, 714


title: FL lymph node biopsy, untreated, 716

source_name: FL lymph node biopsy, untreated, 716


title: FL lymph node biopsy, untreated, 731

source_name: FL lymph node biopsy, untreated, 731


title: FL lymph node biopsy, untreated, 712

source_name: FL lymph node biopsy, untreated, 712


title: FL lymph node biopsy, untreated, 713

source_name: FL lymph node biopsy, untreated, 713


title: FL lymph node biopsy, untreated, 726

source_name: FL lymph node biopsy, untreated, 726


title: FL lymph node biopsy, untreated, 708

source_name: FL lymph node biopsy, untreated, 708


title: FL lymph node biopsy, untreated, 727

source_name: FL lymph node biopsy, untreated, 727


title: FL lymph node biopsy, untreated, 710

source_name: FL lymph node biopsy, untreated, 710


title: FL lymph node biopsy, untreated, 697

source_name: FL lymph node biopsy, untreated, 697


title: FL lymph node biopsy, untreated, 705

source_name: FL lymph node biopsy, untreated, 705


title: FL lymph node biopsy, untreated, 690

source_name: FL lymph node biopsy, untreated, 690


title: FL lymph node biopsy, untreated, 692

source_name: FL lymph node biopsy, untreated, 692


title: FL lymph node biopsy, untreated, 706

source_name: FL lymph node biopsy, untreated, 706


title: FL lymph node biopsy, untreated, 695

source_name: FL lymph node biopsy, untreated, 695


title: FL lymph node biopsy, untreated, 702

source_name: FL lymph node biopsy, untreated, 702


title: FL lymph node biopsy, untreated, 679

source_name: FL lymph node biopsy, untreated, 679


title: FL lymph node biopsy, untreated, 701

source_name: FL lymph node biopsy, untreated, 701


title: FL lymph node biopsy, untreated, 698

source_name: FL lymph node biopsy, untreated, 698


title: FL lymph node biopsy, untreated, 694

source_name: FL lymph node biopsy, untreated, 694


title: FL lymph node biopsy, untreated, 681

source_name: FL lymph node biopsy, untreated, 681


title: FL lymph node biopsy, untreated, 673

source_name: FL lymph node biopsy, untreated, 673


title: FL lymph node biopsy, untreated, 667

source_name: FL lymph node biopsy, untreated, 667


title: FL lymph node biopsy, untreated, 684

source_name: FL lymph node biopsy, untreated, 684


title: FL lymph node biopsy, untreated, 704

source_name: FL lymph node biopsy, untreated, 704


title: FL lymph node biopsy, untreated, 688

source_name: FL lymph node biopsy, untreated, 688


title: FL lymph node biopsy, untreated, 668

source_name: FL lymph node biopsy, untreated, 668


title: FL lymph node biopsy, untreated, 687

source_name: FL lymph node biopsy, untreated, 687


title: FL lymph node biopsy, untreated, 665

source_name: FL lymph node biopsy, untreated, 665


title: FL lymph node biopsy, untreated, 659

source_name: FL lymph node biopsy, untreated, 659


title: FL lymph node biopsy, untreated, 646

source_name: FL lymph node biopsy, untreated, 646


title: FL lymph node biopsy, untreated, 664

source_name: FL lymph node biopsy, untreated, 664


title: FL lymph node biopsy, untreated, 666

source_name: FL lymph node biopsy, untreated, 666


title: FL lymph node biopsy, untreated, 648

source_name: FL lymph node biopsy, untreated, 648


title: FL lymph node biopsy, untreated, 650

source_name: FL lymph node biopsy, untreated, 650


title: FL lymph node biopsy, untreated, 652

source_name: FL lymph node biopsy, untreated, 652


title: FL lymph node biopsy, untreated, 662

source_name: FL lymph node biopsy, untreated, 662


title: FL lymph node biopsy, untreated, 642

source_name: FL lymph node biopsy, untreated, 642


title: FL lymph node biopsy, untreated, 643

source_name: FL lymph node biopsy, untreated, 643


title: FL lymph node biopsy, untreated, 639

source_name: FL lymph node biopsy, untreated, 639


title: FL lymph node biopsy, untreated, 675

source_name: FL lymph node biopsy, untreated, 675


title: FL lymph node biopsy, untreated, 649

source_name: FL lymph node biopsy, untreated, 649


title: FL lymph node biopsy, untreated, 638

source_name: FL lymph node biopsy, untreated, 638


title: FL lymph node biopsy, untreated, 603

source_name: FL lymph node biopsy, untreated, 603


title: FL lymph node biopsy, untreated, 617

source_name: FL lymph node biopsy, untreated, 617


title: FL lymph node biopsy, untreated, 600

source_name: FL lymph node biopsy, untreated, 600


title: FL lymph node biopsy, untreated, 610

source_name: FL lymph node biopsy, untreated, 610


title: FL lymph node biopsy, untreated, 601

source_name: FL lymph node biopsy, untreated, 601


title: FL lymph node biopsy, untreated, 629

source_name: FL lymph node biopsy, untreated, 629


title: FL lymph node biopsy, untreated, 641

source_name: FL lymph node biopsy, untreated, 641


title: FL lymph node biopsy, untreated, 636

source_name: FL lymph node biopsy, untreated, 636


title: FL lymph node biopsy, untreated, 620

source_name: FL lymph node biopsy, untreated, 620


title: FL lymph node biopsy, untreated, 598

source_name: FL lymph node biopsy, untreated, 598


title: FL lymph node biopsy, untreated, 637

source_name: FL lymph node biopsy, untreated, 637


title: FL lymph node biopsy, untreated, 616

source_name: FL lymph node biopsy, untreated, 616


title: FL lymph node biopsy, untreated, 595

source_name: FL lymph node biopsy, untreated, 595


title: FL lymph node biopsy, untreated, 592

source_name: FL lymph node biopsy, untreated, 592


title: FL lymph node biopsy, untreated, 569

source_name: FL lymph node biopsy, untreated, 569


title: FL lymph node biopsy, untreated, 584

source_name: FL lymph node biopsy, untreated, 584


title: FL lymph node biopsy, untreated, 627

source_name: FL lymph node biopsy, untreated, 627


title: FL lymph node biopsy, untreated, 591

source_name: FL lymph node biopsy, untreated, 591


title: FL lymph node biopsy, untreated, 558

source_name: FL lymph node biopsy, untreated, 558


title: FL lymph node biopsy, untreated, 581

source_name: FL lymph node biopsy, untreated, 581


title: FL lymph node biopsy, untreated, 567

source_name: FL lymph node biopsy, untreated, 567


title: FL lymph node biopsy, untreated, 549

source_name: FL lymph node biopsy, untreated, 549


title: FL lymph node biopsy, untreated, 575

source_name: FL lymph node biopsy, untreated, 575


title: FL lymph node biopsy, untreated, 542

source_name: FL lymph node biopsy, untreated, 542


title: FL lymph node biopsy, untreated, 531

source_name: FL lymph node biopsy, untreated, 531


title: FL lymph node biopsy, untreated, 574

source_name: FL lymph node biopsy, untreated, 574


title: FL lymph node biopsy, untreated, 520

source_name: FL lymph node biopsy, untreated, 520


title: FL lymph node biopsy, untreated, 589

source_name: FL lymph node biopsy, untreated, 589


title: FL lymph node biopsy, untreated, 599

source_name: FL lymph node biopsy, untreated, 599


title: FL lymph node biopsy, untreated, 1170

source_name: FL lymph node biopsy, untreated, 1170


title: FL lymph node biopsy, untreated, 1171

source_name: FL lymph node biopsy, untreated, 1171


title: FL lymph node biopsy, untreated, 1175

source_name: FL lymph node biopsy, untreated, 1175


title: FL lymph node biopsy, untreated, 1165

source_name: FL lymph node biopsy, untreated, 1165


title: FL lymph node biopsy, untreated, 530

source_name: FL lymph node biopsy, untreated, 530


title: FL lymph node biopsy, untreated, 1173

source_name: FL lymph node biopsy, untreated, 1173


title: FL lymph node biopsy, untreated, 1166

source_name: FL lymph node biopsy, untreated, 1166


title: FL lymph node biopsy, untreated, 1164

source_name: FL lymph node biopsy, untreated, 1164


title: FL lymph node biopsy, untreated, 1160

source_name: FL lymph node biopsy, untreated, 1160


title: FL lymph node biopsy, untreated, 1157

source_name: FL lymph node biopsy, untreated, 1157


title: FL lymph node biopsy, untreated, 1156

source_name: FL lymph node biopsy, untreated, 1156


title: FL lymph node biopsy, untreated, 1155

source_name: FL lymph node biopsy, untreated, 1155


title: FL lymph node biopsy, untreated, 1162

source_name: FL lymph node biopsy, untreated, 1162


title: FL lymph node biopsy, untreated, 628

source_name: FL lymph node biopsy, untreated, 628


title: FL lymph node biopsy, untreated, 1153

source_name: FL lymph node biopsy, untreated, 1153


title: FL lymph node biopsy, untreated, 583

source_name: FL lymph node biopsy, untreated, 583


title: FL lymph node biopsy, untreated, 1176

source_name: FL lymph node biopsy, untreated, 1176


title: FL lymph node biopsy, untreated, 1174

source_name: FL lymph node biopsy, untreated, 1174


title: FL lymph node biopsy, untreated, 1145

source_name: FL lymph node biopsy, untreated, 1145


title: FL lymph node biopsy, untreated, 1146

source_name: FL lymph node biopsy, untreated, 1146


title: FL lymph node biopsy, untreated, 1158

source_name: FL lymph node biopsy, untreated, 1158


title: FL lymph node biopsy, untreated, 1151

source_name: FL lymph node biopsy, untreated, 1151


title: FL lymph node biopsy, untreated, 1144

source_name: FL lymph node biopsy, untreated, 1144


title: FL lymph node biopsy, untreated, 1147

source_name: FL lymph node biopsy, untreated, 1147


title: FL lymph node biopsy, untreated, 1150

source_name: FL lymph node biopsy, untreated, 1150


title: FL lymph node biopsy, untreated, 1168

source_name: FL lymph node biopsy, untreated, 1168


title: FL lymph node biopsy, untreated, 1141

source_name: FL lymph node biopsy, untreated, 1141


title: FL lymph node biopsy, untreated, 1143

source_name: FL lymph node biopsy, untreated, 1143


title: FL lymph node biopsy, untreated, 1131

source_name: FL lymph node biopsy, untreated, 1131


title: FL lymph node biopsy, untreated, 1137

source_name: FL lymph node biopsy, untreated, 1137


title: FL lymph node biopsy, untreated, 1152

source_name: FL lymph node biopsy, untreated, 1152


title: FL lymph node biopsy, untreated, 1149

source_name: FL lymph node biopsy, untreated, 1149


title: FL lymph node biopsy, untreated, 1125

source_name: FL lymph node biopsy, untreated, 1125


title: FL lymph node biopsy, untreated, 1135

source_name: FL lymph node biopsy, untreated, 1135


title: FL lymph node biopsy, untreated, 1136

source_name: FL lymph node biopsy, untreated, 1136


title: FL lymph node biopsy, untreated, 1127

source_name: FL lymph node biopsy, untreated, 1127


title: FL lymph node biopsy, untreated, 1124

source_name: FL lymph node biopsy, untreated, 1124


title: FL lymph node biopsy, untreated, 1123

source_name: FL lymph node biopsy, untreated, 1123


title: FL lymph node biopsy, untreated, 1139

source_name: FL lymph node biopsy, untreated, 1139


title: FL lymph node biopsy, untreated, 1120

source_name: FL lymph node biopsy, untreated, 1120


title: FL lymph node biopsy, untreated, 1119

source_name: FL lymph node biopsy, untreated, 1119


title: FL lymph node biopsy, untreated, 1114

source_name: FL lymph node biopsy, untreated, 1114


title: FL lymph node biopsy, untreated, 1110

source_name: FL lymph node biopsy, untreated, 1110


title: FL lymph node biopsy, untreated, 1111

source_name: FL lymph node biopsy, untreated, 1111


title: FL lymph node biopsy, untreated, 1105

source_name: FL lymph node biopsy, untreated, 1105


title: FL lymph node biopsy, untreated, 1109

source_name: FL lymph node biopsy, untreated, 1109


title: FL lymph node biopsy, untreated, 1101

source_name: FL lymph node biopsy, untreated, 1101


title: FL lymph node biopsy, untreated, 1098

source_name: FL lymph node biopsy, untreated, 1098


title: FL lymph node biopsy, untreated, 1099

source_name: FL lymph node biopsy, untreated, 1099


title: FL lymph node biopsy, untreated, 1087

source_name: FL lymph node biopsy, untreated, 1087


title: FL lymph node biopsy, untreated, 1082

source_name: FL lymph node biopsy, untreated, 1082


title: FL lymph node biopsy, untreated, 1102

source_name: FL lymph node biopsy, untreated, 1102


title: FL lymph node biopsy, untreated, 1088

source_name: FL lymph node biopsy, untreated, 1088


title: FL lymph node biopsy, untreated, 1116

source_name: FL lymph node biopsy, untreated, 1116


title: FL lymph node biopsy, untreated, 1093

source_name: FL lymph node biopsy, untreated, 1093


title: FL lymph node biopsy, untreated, 1097

source_name: FL lymph node biopsy, untreated, 1097


title: FL lymph node biopsy, untreated, 1118

source_name: FL lymph node biopsy, untreated, 1118


title: FL lymph node biopsy, untreated, 1096

source_name: FL lymph node biopsy, untreated, 1096


title: FL lymph node biopsy, untreated, 1112

source_name: FL lymph node biopsy, untreated, 1112


title: FL lymph node biopsy, untreated, 1091

source_name: FL lymph node biopsy, untreated, 1091


title: FL lymph node biopsy, untreated, 1077

source_name: FL lymph node biopsy, untreated, 1077


title: FL lymph node biopsy, untreated, 1103

source_name: FL lymph node biopsy, untreated, 1103


title: FL lymph node biopsy, untreated, 1079

source_name: FL lymph node biopsy, untreated, 1079


title: FL lymph node biopsy, untreated, 1070

source_name: FL lymph node biopsy, untreated, 1070


title: FL lymph node biopsy, untreated, 1062

source_name: FL lymph node biopsy, untreated, 1062


title: FL lymph node biopsy, untreated, 1066

source_name: FL lymph node biopsy, untreated, 1066


title: FL lymph node biopsy, untreated, 1058

source_name: FL lymph node biopsy, untreated, 1058


title: FL lymph node biopsy, untreated, 1056

source_name: FL lymph node biopsy, untreated, 1056


title: FL lymph node biopsy, untreated, 1068

source_name: FL lymph node biopsy, untreated, 1068


title: FL lymph node biopsy, untreated, 1089

source_name: FL lymph node biopsy, untreated, 1089


title: FL lymph node biopsy, untreated, 1063

source_name: FL lymph node biopsy, untreated, 1063


title: FL lymph node biopsy, untreated, 1055

source_name: FL lymph node biopsy, untreated, 1055


title: FL lymph node biopsy, untreated, 1076

source_name: FL lymph node biopsy, untreated, 1076


title: FL lymph node biopsy, untreated, 1053

source_name: FL lymph node biopsy, untreated, 1053


title: FL lymph node biopsy, untreated, 1054

source_name: FL lymph node biopsy, untreated, 1054


title: FL lymph node biopsy, untreated, 1047

source_name: FL lymph node biopsy, untreated, 1047


title: FL lymph node biopsy, untreated, 1045

source_name: FL lymph node biopsy, untreated, 1045


title: FL lymph node biopsy, untreated, 1040

source_name: FL lymph node biopsy, untreated, 1040


title: FL lymph node biopsy, untreated, 1050

source_name: FL lymph node biopsy, untreated, 1050


title: FL lymph node biopsy, untreated, 1028

source_name: FL lymph node biopsy, untreated, 1028


title: FL lymph node biopsy, untreated, 1037

source_name: FL lymph node biopsy, untreated, 1037


title: FL lymph node biopsy, untreated, 1030

source_name: FL lymph node biopsy, untreated, 1030


title: FL lymph node biopsy, untreated, 1024

source_name: FL lymph node biopsy, untreated, 1024


title: FL lymph node biopsy, untreated, 1044

source_name: FL lymph node biopsy, untreated, 1044


title: FL lymph node biopsy, untreated, 1033

source_name: FL lymph node biopsy, untreated, 1033


title: FL lymph node biopsy, untreated, 1052

source_name: FL lymph node biopsy, untreated, 1052


title: FL lymph node biopsy, untreated, 1017

source_name: FL lymph node biopsy, untreated, 1017


title: FL lymph node biopsy, untreated, 1049

source_name: FL lymph node biopsy, untreated, 1049


title: FL lymph node biopsy, untreated, 1025

source_name: FL lymph node biopsy, untreated, 1025


title: FL lymph node biopsy, untreated, 1014

source_name: FL lymph node biopsy, untreated, 1014


title: FL lymph node biopsy, untreated, 1039

source_name: FL lymph node biopsy, untreated, 1039