title: GDT_Control_5h_Rep1

tag: growth medium

value: GDT (Growth-to-development transition)

tag: agent

value: Control

tag: time point


title: Littermates rep1

status: Public on May 22 2019

type: SRA

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: polysome mRNAs

library_source: transcriptomic

data_processing:
Illumina bcl2fastq 1.8.4 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-alpha5. Before mapping, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from Ensembl version 75) using the STAR mapper (version 2.4.0j, default parameters). Alignments from reads matching more than once on the genome were removed. Mus musculus GFF3 genome annotation from from Ensembl version mm10-ens75 was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: mm10 version Ensembl 75
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Hypocampus

extract_protocol:
BAC array purification
Ovation RNA-Seq system NuGEN

tag: strain

value: tg:Aldh1L1-RPL10aGFP/ Cx43 fl/fl

tag: age

value: 6 weeks


title: HGF

city: Taipei, Taiwan

first: Yaw-dong

last: lang

state: Taiwan

address: 28 Sec. 2, Academia Rd. Nankang, Taipei 115

department: Institute of biomedical science

country: Taiwan

institute: Academia Sinica

description: HGF induction from Huh-7

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC contentthe clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Qualified reads after filtering low-quality data were analyzed using   TopHat  v2.0.  12. and HTSeq v0.6.1 for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: Huh-7 cells induced with HGF

growth_protocol: Huh-7 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted from cancer cell lines by NucleoSpin RNA XS (Macherey Nagel, Duren, Germany).
A total amount of 3 μg RNA per sample was used as in put material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library 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（RNase H. Second strandcDNA 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 37°C for 15 min followed by 5 min at 95 °C 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: Huh7 cells treated with 10 ng/ml HGF for 48 h

tag: cell line

tag: cell type

value: human hepatocellular carcinoma cell line

tag: genotype/variation

value: HGF induction


title: GDT_Starvation_2h_Rep1

city: Bethesda

first: Cameron

last: Palmer

state: MD

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

country: USA

institute: National Institutes of Health

data_processing:
Illumina HiSeq2500 sequencing, 50bp reads.
Adapter removal with cutadapt v1.16
Alignment to Dictyostelium discoideum genome with hisat v2.1.0
Assignment of reads to gene features with Subread featureCounts v1.6.1
Signal detection via differential expression analysis between triplicate groups with DESeq2 1.18.1
Genome_build: ENSEMBL 2.7.33
Supplementary_files_format_and_content: Number of reads assigned to gene features, as computed by Subread featureCounts v1.6.1

molecule: polyA RNA

organism: Dictyostelium discoideum

growth_protocol: Dictyostelium discoideum AX3 strain cells were grown axenically in HL5 medium with glucose (ForMedium) containing 100 μg/ml of ampicillin and 100 μg/ml streptomycin, at 22˚C in suspension culture, shaking at ~180 rpm, to a density of 1-1.5 x 106 cells/ml.

extract_protocol:
Total RNA from the growing or developing cells were isolated using the RNAeasy mini preparation kit [Qiagen; see Key Resource Table] and following the manufacturer’s protocol.
RNA integrity was checked by running a denaturing MOPS-formaldehyde gel and with the Agilent bioanalyzer. 4 µg of total RNA was used for poly(A) enrichment, followed by mRNA sequencing library preparations using the Truseq mRNA library preparation kit.

treatment_protocol: To examine Dictyostelium multicellular development in starvation condition, log phase growth cells (1-1.5×106 cells/ml) were adhered in six well plates (3.5 x 106 cells/well; or 0.4 x 106 cells/cm2), replenished with fresh full growth media or GDT-growth media (see below) and incubated for 2 hours. Followed by washing cells (2 times) with Developmental Buffer (DB; 5 mM Na2HPO4, 5 mM NaH2PO4, 1 mM CaCl2, 2 mM MgCl2, adjust to pH-6.6) to remove any sticking media components, filled wells with 2.0 ml of DB and monitored developmental progress at regular intervals during starvation. To examine growth-to-development transition induced by rapamycin without nutrient withdrawal, cells adhered in six well plates (see above), washed with GDT growth media (2 times), replenished with 2 ml of GDT media [50% Glc[—] (HL5 media without glucose, Formedium), 27 mM glucose, 1 mM MgCl2, 0.5 mM CaCl2, adjust to pH-6.6] media and incubated at 22°C for 2 hours, followed with rapamycin treatment to the GDT-media adapted cells for acquiring growth-to-development transition.

value: Starvation

value: 2 hours


title: Control

description: Control from Huh-7

source_name: Huh-7 control cells

value: control


title: Mut

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC contentthe clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Qualified reads after filtering low-quality data were analyzed using   TopHat  v2.0.  12. and HTSeq v0.6.1 for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Overexpression of NLS mutation of PSPC1 from Mahlavu

growth_protocol: SK-Hep1 and Mahlavu cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen).

value: Mahlavu

value: Overexpression of NLS mutation of PSPC1


title: GDT_Rapamycin_2h_Rep1

value: Rapamycin


title: GDT_Control_2h_Rep1


title: CT131

source_name: Overexpression of c-terminal of PSPC1 from Mahlavu

value: Overexpression of c-terminal of PSPC1


title: E

source_name: Mock control from Mahlavu

value: Mock control


title: CB primary cells chronic hypoxia

type: RNA

city: Heidelberg

first: Matias

last: Mosqueira

state: Baden-Wuttenberg

address: Im Neuenheimer Feld, 326 R414

department: Institute of Physiology and Pathop

country: Germany

institute: Heidelberg University Hospital

description:
This GEO Sample represents 3 replicates.
CH
CB_CH_1, CB_CH_2, CB_CH_3

hyb_protocol: Membranes were prehybridized in ExpressHyb hybridization buffer, containing the sheared salmon testes DNA for 30 min at 68 ºC in a rotating hybridization oven. The heat-denatured probe (95 ºC for 5 min) was hybridized overnight at 68 ºC with continuous agitation followed by three washing steps [twice at room temperature for 5 min with Sodium Chloride/ Sodium Citrate solution (1 X SSC = 150 mM NaCl/15 mM sodium citrate, pH 7.0), twice with 2 X SSC plus 1% SDS at 68 ºC for 30 min, and twice with 0.1 X SSC plus 0.5% SDS at room temperature for 30 min].

scan_protocol: The membranes were exposed on phosphoimager up to 3 hours at room temperature.

data_processing: Image acquisition and quantification of the average of three membranes under Nx and three under CH were performed using the software AtlasImage V2.0 (Clontech). The normalization was performed to each experiment using a coefficient of normalization (adding the averaging of the signal of all genes to the signal values for all the genes that are above the background signal). The parameters used for the data analysis were the ratio threshold (TR) and the difference threshold (TD). Here, we defined the criterion to classified as a significant change in gene expression for TR of 1.5 and TD of 1,000 pixels, respectively. The TR was defined as the ratio between the CH normalized and averaged of the adjusted intensity signal over the Nx normalized and averaged of the adjusted intensity signal of the same gene. TD was defined as the difference between CH normalized and averaged of the adjusted intensity signal minus the Nx normalized and averaged of the adjusted intensity signal of the same gene.

label: [α-32P] dCTP (3000 Ci/mmol)

organism: Rattus norvegicus

source_name: carotid body primary cultured cells

label_protocol: Radiolabeled cDNA probes were synthesized from 6 μg of RNA amplified in the presence of dATP, dTTP, dGTP, [α-32P] dCTP (3000 Ci/mmol), poly T, Superscript II Reverse transcriptase (Invitrogen) and the purified (Atlas NucleoSpin Extraction Spin Columns, BD Biosciences Clontech).

growth_protocol: The experiments were performed on CB cultured cells from Sprague Dawley rats (ca. 100 g) anesthetized with sodium pentobarbital (40 mg/kg i.p.). The neck was opened and the carotid bifurcations were exposed. Sixteen CBs per primary culture were excised and placed in ice-chilled Ca2+ -Mg2+ -free Hank´s solution and then enzymatically dissociated under soft shaking with 0.1% collagenase and 150U/ml DNase at 37ºC for 1 h. The cells were centrifugated at 1500 rpm for 10 min and re-suspended in culture medium (HEPES-modified Ham´s F-12 nutrient mixture supplemented with 10% horse serum, 10% fetal bovine serum and 15 ng/ml nerve growth factor). The cells were plated into 35 mm Petri-dishes coated with poly-L-lysine (0.1mg/ml).

extract_protocol: Total RNA from CB cultured primary rat cells was isolated by adding 1.0 ml of Trizol (Invitrogen) following manufacturer's instructions.

treatment_protocol: The cells were maintained at 37ºC in water-saturated, 5% CO2 denominated in Nx conditions. A chronic hypoxic (CH) environment was generated in a 5-liters Billups-Rothenberg hypoxia chamber (Del Mar, CA, USA) (Allen et al., 2001) where cultured cells were maintained in the incubator at 37ºC after being flushed for 20 minutes with 5% CO2 - 95% N2. The gas mixture and the culture medium were changed every day.

tag: strain/background

value: Sprague Dawley

tag: tissue

value: carotid body

tag: number of organ/ culture

tag: treatment

value: Chronic hypoxia

tag: oxygen level

tag: days of culture

value: 7 days


title: S3_2

city: Tianjin

first: Bin

last: Jia

state: Tianjin

address: No 92, Weijin Road

department: School of chemical engineering and technology

country: China

institute: Tianjin University

data_processing:
Quality control
Reads mapping to the reference genome Saccharomyces cerevisiae S288C
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Differential expression analysis was performed using the DESeq R package (1.18.0).
Supplementary_files_format_and_content: processed data (read counts) contained RPKM for each gene in different samples

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: 12 h cultivation in flask, 250 rpm, 30 ℃

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agelent, USA)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to each sample.

treatment_protocol: Saccharomyces cerevisiae cells were pelleted and quickly frozen by liquid nitrogen.

tag: genotype

value: S.cerevisiae with synV

tag: variation

value: Genome rearrangement


title: S3_1


title: GDT_Rapamycin_30min_Rep1

value: GDT (Growth-to-development transition)

value: 30 minutes


title: YF_P

source_name: Overexpression of PSPC1  YF mutation with PTK6

value: human hepatocellular carcinoma cell line


title: YF

source_name: Overexpression of PSPC1 YF mutation

value: Overexpression of PSPC1 YF mutation


title: GDT_Control_30min_Rep1

value: Control


title: H0_3


title: GDT_Starvation_30min_Rep1

value: Starvation


title: knockout of fourth LTA exon_rep3

city: Berlin

first: Marina

last: Kolesnichenko

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Center

hyb_protocol: 73 µl hybridization cocktail was added to 2.5 µg fragmented and labled ss-cDNA and 80 µl of this cocktail was applied to the Human Clariom S arrays (Affymetrix) and hybridized for 16 hours at 45°C in a Genechip Hybridization Oven 640 (Affymetrix). After hybridization the arrays were washed and stained with a Genechip Fluidics Station 450 (Affymetrix) using the genechip hybridization wash and stain kit according to protocol FS450_0007.

scan_protocol: Arrays were scanned using the Affymetrix Scanner 3000 7G.

data_processing: Affymetrix CEL files were normalized using RMA. Data analysis was performed with the Transcriptome Analysis Console 4.0 (ThermoFisher Scientific).

label: Biotin

source_name: L-1236_knockout of fourth LTA exon

label_protocol: 250 ng RNA was amplified, fragmented and biotin-labelled using the GeneChipTM WT PLUS Reagent kit (ThermoFisher Scientific) according to the manufacturer’s instructions.

growth_protocol: L-1236-LTA knockout clones were cultivated in L-1236 conditioned medium. For expression analysis, the conditioned medium was removed and the clones were cultivated in RPMI+ 10% heat inactivated FCS for 72 h. RNA was prepared from about 1.5 x 106 cells.

extract_protocol: RNA extraction was performed according to manufacturer’s protocol using the RNeasy kit (Qiagen). RNA concentrations were measured using the NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies) and RNA quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were transducted with the lentiCRIPSPR v2 vector containing gRNAs which target the second (g2) and the fourth exon (g3) of LTA. Following single cell clone selection, L-1236 control cells (v2) and two LTA KO clones g2_1 and g3_4 were cultured in normal culture medium for 72 h.

value: Hodgkin’s lymphoma cell line

tag: phenotype

value: CRISPR/Cas9 mediated knockout of fourth LTA exon

tag: rin


title: wild type_rep1

source_name: L-1236_wild type

value: wild type phenotype


title: GDT_Control_0min_Rep1

tag: growth medium

tag: agent

value: 0 minutes


title: wild type_rep2


title: P

source_name: Overexpression of PSPC1 from SK-Hep1

value: Overexpression of PSPC1


title: H0_2


title: knockout of fourth LTA exon_rep1


title: knockout of second LTA exon_rep3

source_name: L-1236_knockout of second LTA exon

value: CRISPR/Cas9 mediated knockout of second LTA exon


title: Peripheral_blood_Daughter_Healthy

type: genomic

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer IBMCC-CIC

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: ChAS console from Affymetrix was used to assess genome wide copy number frequencies

label: biotin

molecule: genomic DNA

source_name: Peripheral blood

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix

growth_protocol: Not applicable

extract_protocol: Total RNA from disgregated cells was extracted using Buffer RLT plus (Qiagen, CA, USA) and purified with All prep DNA/RNA mini Kit (Qiagen, CA, USA).

treatment_protocol: Not applicable

tag: disease

value: Healthy

value: Peripheral blood


title: wild type_rep3


title: knockout of second LTA exon_rep2


title: All trans retinoic acid (atRA) treatment

city: Baltimore

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

description: Gene expression data from wounded skin of TLR3KO mice with or without atRA

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
probe group file: Clariom_S_Mouse.r1.pgf
meta-probeset file: Clariom_S_Mouse.na36.mm10.transcript.csv

source_name: wounded back skin

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip 3' IVT Plus Kit per manufacturer's instructions.

growth_protocol: Inbred TLR3KO mice were maintained in the specific pathogen free (SPF) zone of animal facility at Johns Hopkins

extract_protocol: Total RNA was isolated from cells using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: TLR3KO mice at telogen stage were wounded on back skin with 1.2 cm2 size. Next day (wound day 1-WD1), 30 ul including 0.1 ug of atRA were locally treated onto wounded skin of TLR3KO mice. Equal volume of EtOH (30 ul) was treated as a vehicle.

tag: age

value: 22 days old mice

value: wounded back skin

value: All trans retinoic acid


title: A_P

source_name: Overexpression of PSPC1 with PTK6 from Sk-Hep1

tag: cell line

value: Overexpression of PSPC1 with PTK6


title: H0_1

value: S.cerevisiae with synV

value: Genome rearrangement


title: M

source_name: Mock control from SK-Hep1

tag: cell type

value: human hepatocellular carcinoma cell line

value: Mock control


title: Peripheral_blood_Affected_Son_Epileptic_Encephalopathy

value: Epileptic encephalopathy


title: Peripheral_blood_Father_Healthy


title: Ethanol (EtOH) treatment

tag: genotype/variation

value: 21 days old mice

value: Ethanol


title: Peripheral_blood_Mother_Healthy


title: Mosaic MLH1-epimutation carrier. Genomic DNA (FFPE)

city: L'Hospitalet de Llobregat

first: Estela

last: Damaso

state: Barcelona

address: Av.Gran Via de l'Hospitalet, 199-203

department: Hereditary Cancer Program

institute: Catalan Institute of Oncology (ICO)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: HiScan platform (Illumina)

data_processing: GenomeStudio software (Methylation Module)

source_name: FFPE normal colon mucosa

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from blood sample using Wizard Genomic DNA Purification Kit  (Promega) according to standard instructions. Genomic DNA from FFPE sample was extracted using QIAmp DNA FFPE Tissue Kit (Qiagen) and Deparaffinization Solution (Qiagen) according to the manufacturer's instructions

tag: gender

value: Female

tag: personal history of cancer

value: Colorectal cancer, small bowel cancer, gastric cancer

tag: age at diagnosis

tag: molecular characteristics of tumors

value: Microsatellite instability, BRAF wildtype, MLH1 methylation

tag: other available files from patient


title: knockout of second LTA exon_rep1

value: Hodgkin’s lymphoma cell line

value: CRISPR/Cas9 mediated knockout of second LTA exon


title: 4553CD823wPB

status: Public on May 21 2019

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Arrays were washed, stained and scanned as described in the Affymetrix GeneChip® Expression Analysis Technical Manual

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data from .CEL files were analyzed using R Bioconductor.

organism: Macaca mulatta

label_protocol: Five µg of the amplified cDNA was fragmented, biotinylated, and hybridized to arrays using the NuGEN Ovation Encore Biotin Module, according to kit instructions.

extract_protocol: Total RNA extraction was performed using the RNeasy mini kit (QIAGEN, Hilden, Germany)

tag: animal id

tag: vaccine

tag: protection

value: Susceptible


title: W4372CD823wPB


title: W4372CD423wPB


title: W4372CD42wPB


title: knockout of fourth LTA exon_rep2

tag: phenotype

value: CRISPR/Cas9 mediated knockout of fourth LTA exon


title: 4553CD822wPP


title: Mosaic MLH1-epimutation carrier Genomic DNA (Blood)

source_name: total blood


title: 4774CD823wPB

value: Resistant


title: 4553CD423wPB


title: W4372CD82wPB


title: 4553CD422wPP


title: 4774CD423wPB


title: 4553CD82wPB


title: 4774CD42wPB


title: 4553CD42wPB


title: 4552CD823wPB


title: 4552CD423wPB


title: 4552CD42wPB


title: W4400CD823wPB


title: 4774CD822wPP


title: 4773CD423wPB


title: 4552CD82wPB


title: W4372CD422wPP


title: 4552CD822wPP


title: 4774CD422wPP


title: 4552CD422wPP


title: 4773CD823wPB


title: W4394CD423wPB


title: 4395CD823wPB


title: W4394CD823wPB


title: 4395CD423wPB


title: 4777CD423wPB


title: 4778CD823wPB


title: 4778CD82wPB


title: W4381CD42wPB


title: 4778CD423wPB


title: 4777CD823wPB


title: W4394CD42wPB


title: W4394CD422wPP


title: 4778CD822wPP


title: W4381CD423wPB


title: 4778CD42wPB


title: 4777CD82wPB


title: 4777CD822wPP


title: W4381CD823wPB


title: 4776CD823wPB


title: W4381CD422wPP


title: 4781CD823wPB


title: 4777CD422wPP


title: 4773CD42wPB


title: 4777CD42wPB


title: 4395CD82wPB


title: 4776CD423wPB


title: 4395CD42wPB


title: 4776CD82wPB


title: S3_3

tag: genotype

tag: variation


title: 4778CD422wPP


title: 4781CD423wPB


title: 4776CD42wPB


title: 4781CD422wPP


title: 4781CD42wPB


title: 4779CD423wPB


title: 4776CD422wPP


title: 4776CD822wPP


title: 4547CD823wPB


title: 4547CD422wPP


title: 4547CD423wPB


title: 4779CD822wPP


title: 4770CD82wPB


title: 4770CD423wPB


title: 4779CD422wPP


title: 4770CD42wPB


title: W4400CD422wPP


title: 4395CD822wPP


title: Het_input

city: San Francisco

first: Michael

middle: Robert

last: Waterfield

state: CA

address: 513 Parnassus Ave MSB S-1076

department: Diabetes Center

institute: UCSF

library_source: genomic

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings)(Li and Durbin, 2009). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome
ChIP-seq reads were aligned to the mm10 genome assembly
The resulting histograms (genomic “signal maps”) were stored in bigWig files. H3K9me3 enriched regions were identified using the SICER algorithm(Zang et al., 2009) at a cutoff of FDR 1E-10 and a max gap parameter of 600 bp. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Genome_build: mm10

source_name: Lymph nodes and spleen

extract_protocol:
Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer
ChIP-Seq and subsequent data analysis was performed by Active Motif. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: Primary naïve T-cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.

value: Naive T Lymphocytes

tag: strain

tag: chip antibody


title: Het2_H3K9me3_mm10

value: H3K9me3 (Active Motif, cat# 39161, Lot# 2)


title: KO_input


title: KO1_H3K9me3_mm10


title: KO2_H3K9me3_mm10


title: Het1_H3K9me3_mm10


title: 4547CD822wPP


title: 4770CD823wPB


title: W4400CD42wPB


title: 4779CD823wPB


title: W4400CD822wPP


title: 4770CD822wPP


title: 4779CD42wPB


title: 4773CD822wPP


title: 4770CD422wPP


title: 4773CD422wPP


title: 16_Post

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software v3.8

source_name: breast cancer tumor

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: patient id

tag: time

value: Post

tag: tumor size

tag: lymph node status

value: pos

tag: estrogen receptor

tag: progesteron receptor

tag: grade

value: III

tag: clinical dimension


title: 17_Pre

value: Pre

value: neg


title: 16_Pre


title: 4395CD422wPP


title: 15_Pre


title: 15_Post


title: 13_Post


title: 12_Post


title: 17_Post


title: 10_Post

value: II


title: 9_Pre


title: 9_Post


title: 11_Post


title: 14_Post


title: 12_Pre


title: 10_Pre


title: 4_Pre


title: 11_Pre


title: 6_Pre


title: 14_Pre


title: 8_Pre


title: 8_Post


title: 7_Pre


title: 5_Pre


title: 13_Pre


title: 5_Post


title: SM-HCQ (54-59, 5A-5C)

city: Cincinnati

first: Soma

last: Sengupta

state: OH

address: 3125 Eden Avenue

department: Neurology

institute: University of Cincinnati

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_8

data_processing:
aligned to the hg19 human reference genome using STAR (v 2.4.1a)
featureCounts tool was used to count the reads of the mapped bam files (featureCounts -p -a hg19.gtf -o paircounts.txt *.bam)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: metastatic brain tumor tissue

extract_protocol:
RNA will be extracted from the FFPE sample using Qiagen’s AllPrep FFPE kit.  The sample will be added to lysis buffer containing proteinase and then centrifuged to create a pellet and a supernatant.  The RNA will be purified from the Supernatant. RNA is quantified via RiboGreen and RNA quality is measured by the DV200 score (fraction of RNA fragments whose length is > 200nts). Due to the inherent nature of samples derived from FFPE to contain degraded and cross-linked nucleic acids, all FFPE samples will be accepted into the workflows at risk and will be billed accordingly.
RNA will be processed for Transcriptome Capture. Library preparation utilizes a stranded cDNA library from isolated RNA, then hybridizes the library to a set of DNA oligonucleotide probes to enrich the library for coding region transcript fragments. Transcriptome Capture targets 21,415 genes, representing 98.3% of the RefSeq exome. Due to the inherent nature of samples derived from FFPE to contain degraded and cross-linked nucleic acids, all FFPE samples will be accepted into the workflows at risk and will be billed accordingly.

tag: tumor type

value: Metastatic Melanoma

tag: timing of immunotherapy use relative to rt (1 - after only, 2 - before and after)

tag: status (alive - 0; dead/hospice - 1)

tag: months to death or last fu


title: SM-HCQ (4G-4K)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_4


title: SM-HCP (YP-YX)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_37


title: 1_Post


title: SM-HCP (ZZ, Q11-Q14)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_46


title: SM-HCP (YJ-YO)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_36


title: 3_Post


title: 2_Pre


title: 7_Post


title: 1_Pre


title: SM-HCP (YF-YI)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_35


title: 2_Post


title: SM-HCP (Y4-Y8)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_33


title: 3_Pre


title: 6_Post


title: 4_Post


title: SM-HCP (XP-XT)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_30


title: SM-HCP (WC-WF)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_22


title: SM-HCQ (1D-1H)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_48


title: SM-HC (Q14-Q19, Q1A-Q1C)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_47


title: SM-HCP (WL-WP)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_24


title: SM-HCQ6 (S-V)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_16


title: SM-HCP (YY, YZ, Z1)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_38


title: SM-HCP (VZ, W1-W7)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_20


title: SM-HCP (ZA-ZD)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_41


title: Human adult liver  (H7_201#1375)

city: London

first: Joe

middle: M

last: Segal

address: 28 floor Tower wing, Great Maze pond

department: Centre of Stem Cell and Regenerative Medicine

country: United Kingdom

institute: Kings college London

data_processing:
Raw sequencing reads were aligned using STAR and per gene counts were calculated using HTSEQ
Gene counts were further analyzed using the R package SCATER for pre-processing, quality control and normalization
To filter out bad cells from scRNA-seq analysis we used median absolute deviations (MADs) on library size, total genes detected, mitochondrial gene percentage and artificial ERCC spike in percentage. Two deviations from the median were used to remove cell outliers. For library size and total genes the lower tail outliers were excluded. For mitochondrial and ERCC spike in percentage upper tail outliers were excluded.
T-SNE analysis, clustering and gene expression performed in R
Genome_build: GRCh38
Supplementary_files_format_and_content: [Series_count_matrix.csv] Raw HTSEQ counts for all samples and feature date
[Series_feature_matrix.csv]   MetaData including FACS gating population for each sample

source_name: Human adult liver

extract_protocol:
Commercially obtained fresh human hepatocytes were stained with the following primary antibodies, CD235a (349104, FITC, mouse; Biolegend), EpCAM (324208, APC, mouse; Biolegend) and ASGPR1 (563655, PE, mouse, BD Pharmingen™), all at 1:100 dilution and incubated for 30mins at 4˚C. DAPI (D1306, ThermoFisher Scientific) at 1:1000 dilution was used for live/dead staining. Briefly, cells were sorted using a BD FACS Aria II instrument and deposited as single cells into 96-well plates, pre-loaded with lysis buffer (1% Triton X-100, 1mM dNTP, 1μM oligo-dT30, 1:1.2x106 ERCC ExFold RNA spike-in, Recombinant RNase Inhibitor (2313B, Takara Clontech). Single-cell sequencing was performed using SmartSeq2.
RNA was converted into cDNA using SMARTScribe Reverse Transcriptase (639538, Takara Clontech) and amplified for 21 cycles (Kapa HiFi HotStart ReadyMix 2x, KK2602, KAPA Biosystems). Successful single cell libraries were identified by capillary gel electrophoresis (DNF-474-1000, High Sensitivity NGS Fragment Analysis Kit, AATI) and converted into sequencing libraries using a Nextera XT DNA Sample Preparation Kit (FC-131-1096, Illumina). Barcoded libraries were pooled and subjected to 75 base pair paired-end sequencing on a Illumina HiSeq 2500 instrument.

tag: sample type

value: Fresh human hepatocytes

tag: sample id

value: Human adult liver 1

tag: Sex

value: Male

tag: age

value: 7 years

tag: developmental stage

value: adult


title: Human adult liver  (H9_201#1407)


title: Human adult liver  (H8_201#1390)


title: Human adult liver  (H6_201#1359)


title: Human adult liver  (H3_201#1313)


title: Human adult liver  (H4_201#1329)


title: Human adult liver  (H3_201#1314)


title: Human adult liver  (H1_201#1285)


title: Human adult liver  (G9_201#1251)


title: Human adult liver  (H10_201#1423)


title: Human adult liver  (G8_201#1236)


title: Human adult liver  (G6_201#1209)


title: Human adult liver  (G2_201#1146)


title: Human adult liver  (G10_201#1265)


title: Human adult liver  (G6_201#1208)


title: Human adult liver  (G5_201#1192)


title: Human adult liver  (G4_201#1177)


title: Human adult liver  (G7_201#1223)


title: Human adult liver  (G3_201#1162)


title: Human adult liver  (G1_201#1131)


title: Human adult liver  (G12_201#1273)


title: SM-HCQ7 (D-L)

description:
Found within the matrix table counts.txt under column with given sample name
sample name:
Specimen_19


title: Human adult liver  (F9_201#1066)


title: Human adult liver  (F8_201#1050)


title: Human adult liver  (G1_201#1130)


title: Human adult liver  (F7_201#1034)


title: Human adult liver  (F5_201#1001)


title: Human adult liver  (F6_201#1017)


title: Human adult liver  (H5_201#1345)


title: Human adult liver  (H2_201#1300)


title: Human adult liver  (F4_201#990)


title: Human adult liver  (F2_201#961)


title: Human adult liver  (F3_201#975)


title: Human adult liver  (F4_201#989)


title: Human adult liver  (F11_201#1099)


title: Human adult liver  (F12_201#1115)


title: Human adult liver  (F10_201#1082)


title: Human adult liver  (F1_201#945)


title: Human adult liver  (E9_201#883)


title: Human adult liver  (E8_201#868)


title: Human adult liver  (E5_201#819)


title: Human adult liver  (E2_201#773)


title: Human adult liver  (E6_201#835)


title: Human adult liver  (E5_201#818)


title: Human adult liver  (D9_201#695)


title: Human adult liver  (E12_201#930)


title: Human adult liver  (E1_201#757)


title: Human adult liver  (E4_201#804)


title: Human adult liver  (E10_201#897)


title: Human adult liver  (E11_201#913)


title: Human adult liver  (D7_201#664)


title: Human adult liver  (D8_201#679)


title: Human adult liver  (D6_201#648)


title: Human adult liver  (D4_201#617)


title: Human adult liver  (D4_201#616)


title: Human adult liver  (D5_201#634)


title: Human adult liver  (D3_201#601)


title: Human adult liver  (D2_201#586)


title: Human adult liver  (D12_201#742)


title: Human adult liver  (D1_201#570)


title: Human adult liver  (D10_201#709)


title: Human adult liver  (C9_201#505)


title: Human adult liver  (C7_201#474)


title: Human adult liver  (E12_201#929)


title: Human adult liver  (C6_201#457)


title: Human adult liver  (C5_201#442)


title: Human adult liver  (C3_201#409)


title: Human adult liver  (C4_201#425)


title: Human adult liver  (C10_201#523)


title: Human adult liver  (C11_201#539)


title: Human adult liver  (C1_201#380)


title: Human adult liver  (B8_201#299)


title: Human adult liver  (B9_201#315)


title: Human adult liver  (C12_201#555)


title: Human adult liver  (B3_201#222)


title: Human adult liver  (B7_201#283)


title: Human adult liver  (B12_201#366)


title: Human adult liver  (B2_201#206)


title: Human adult liver  (B1_201#191)


title: Human adult liver  (B10_201#331)


title: Human adult liver  (B11_201#348)


title: Human adult liver  (A9_201#129)


title: Human adult liver  (D11_201#726)


title: Human adult liver  (C8_201#490)


title: Human adult liver  (A8_201#115)


title: Human adult liver  (A7_201#102)


title: Human adult liver  (A6_201#87)


title: Human adult liver  (A5_201#71)


title: Human adult liver  (A4_201#56)


title: Human adult liver  (A2_201#24)


title: Human adult liver  (A3_201#40)


title: Human adult liver  (A11_201#163)


title: Human adult liver  (A10_201#146)


title: Human adult liver  (B5_201#252)


title: Human adult liver  (B6_201#268)


title: Human adult liver  (C2_201#395)


title: Human adult liver  (H8_202#1391)


title: Human adult liver  (H7_202#1376)


title: Human adult liver  (H6_202#1360)


title: Human adult liver  (H4_202#1330)


title: Human adult liver  (H2_202#1301)


title: Human adult liver  (H5_202#1346)


title: Human adult liver  (H3_202#1315)


title: Human adult liver  (H10_202#1424)


title: Human adult liver  (G4_202#1178)


title: Human adult liver  (G2_202#1147)


title: Human adult liver  (G7_202#1224)


title: Human adult liver  (G3_202#1163)


title: Human adult liver  (H9_202#1408)


title: Human adult liver  (G10_202#1266)


title: Human adult liver  (G1_202#1132)


title: Human adult liver  (F9_202#1067)


title: Human adult liver  (F6_202#1018)


title: Human adult liver  (F7_202#1035)


title: Human adult liver  (A12_201#177)


title: Human adult liver  (F8_202#1051)


title: Human adult liver  (F5_202#1002)


title: Human adult liver  (F4_202#991)


title: Human adult liver  (A1_201#9)


title: Human adult liver  (C4_201#426)


title: Human adult liver  (F2_202#962)


title: Human adult liver  (F12_202#1116)


title: Human adult liver  (G8_202#1237)


title: Human adult liver  (E3_202#789)


title: Human adult liver  (E12_202#931)


title: Human adult liver  (E2_202#774)


title: Human adult liver  (F10_202#1083)


title: Human adult liver  (E6_202#836)


title: Human adult liver  (F1_202#946)


title: Human adult liver  (D3_202#602)


title: Human adult liver  (D8_202#680)


title: Human adult liver  (E7_202#852)


title: Human adult liver  (E4_202#805)


title: Human adult liver  (D5_202#635)


title: Human adult liver  (D7_202#665)


title: Human adult liver  (E11_202#914)


title: Human adult liver  (D2_202#587)


title: Human adult liver  (E5_202#820)


title: Human adult liver  (D12_202#743)


title: Human adult liver  (E1_202#758)


title: Human adult liver  (C9_202#506)


title: Human adult liver  (D11_202#727)


title: Human adult liver  (D10_202#710)


title: Human adult liver  (C8_202#491)


title: Human adult liver  (C7_202#475)


title: Human adult liver  (D1_202#571)


title: Human adult liver  (C4_202#427)


title: Human adult liver  (C6_202#458)


title: Human adult liver  (C2_202#396)


title: Human adult liver  (E10_202#898)


title: Human adult liver  (D4_202#618)


title: Human adult liver  (C12_202#556)


title: Human adult liver  (C10_202#524)


title: Human adult liver  (A9_202#130)


title: Human adult liver  (B5_202#253)


title: Human adult liver  (B12_202#367)


title: Human adult liver  (A8_202#116)


title: Human adult liver  (B2_202#207)


title: Human adult liver  (B7_202#284)


title: Human adult liver  (B10_202#332)


title: Human adult liver  (B8_202#300)


title: Human adult liver  (B4_202#236)


title: Human adult liver  (A6_202#88)


title: Human adult liver  (C1_202#381)


title: Human adult liver  (C11_202#540)


title: Human adult liver  (A5_202#72)


title: Human adult liver  (H9_211#1409)

value: Human adult liver 2

value: 43 years


title: Human adult liver  (A3_202#41)


title: Human adult liver  (C3_202#410)


title: Human adult liver  (A2_202#25)


title: Human adult liver  (B11_202#349)


title: Human adult liver  (B3_202#223)


title: Human adult liver  (A10_202#147)


title: Human adult liver  (B1_202#192)


title: Human adult liver  (H6_211#1361)


title: Human adult liver  (A12_202#178)


title: Human adult liver  (A1_202#10)


title: Human adult liver  (A4_202#57)


title: Human adult liver  (H5_211#1347)


title: Human adult liver  (H8_211#1392)


title: Human adult liver  (H4_211#1331)


title: Human adult liver  (H3_211#1316)


title: Human adult liver  (H10_211#1425)


title: Human adult liver  (H7_211#1377)


title: Human adult liver  (H1_211#1286)


title: Human adult liver  (G4_211#1179)


title: Human adult liver  (G3_211#1164)


title: Human adult liver  (G7_211#1225)


title: Human adult liver  (G10_211#1267)


title: Human adult liver  (H2_211#1302)


title: Human adult liver  (G8_211#1238)


title: Human adult liver  (F7_211#1036)


title: Human adult liver  (G6_211#1210)


title: Human adult liver  (G9_211#1252)


title: Human adult liver  (F3_211#976)


title: Human adult liver  (F5_211#1003)


title: Human adult liver  (F4_211#992)


title: Human adult liver  (G5_211#1193)


title: Human adult liver  (F6_211#1019)


title: Human adult liver  (F10_211#1084)


title: Human adult liver  (G2_211#1148)


title: Human adult liver  (G12_211#1274)


title: Human adult liver  (E8_211#869)


title: Human adult liver  (E9_211#884)


title: Human adult liver  (F2_211#963)


title: Human adult liver  (F12_211#1117)


title: Human adult liver  (E5_211#821)


title: Human adult liver  (F8_211#1052)


title: Human adult liver  (G1_211#1133)


title: Human adult liver  (E4_211#806)


title: Human adult liver  (F1_211#947)


title: Human adult liver  (E3_211#790)


title: Human adult liver  (F11_211#1100)


title: Human adult liver  (E2_211#775)


title: Human adult liver  (E10_211#899)


title: Human adult liver  (D7_211#666)


title: Human adult liver  (D8_211#681)


title: Human adult liver  (E11_211#915)


title: Human adult liver  (E1_211#759)


title: Human adult liver  (D9_211#696)


title: Human adult liver  (D4_211#619)


title: Human adult liver  (D2_211#588)


title: Human adult liver  (D5_211#636)


title: Human adult liver  (D12_211#744)


title: Human adult liver  (D11_211#728)


title: Human adult liver  (C9_211#507)


title: Human adult liver  (D1_211#572)


title: Human adult liver  (C7_211#476)


title: Human adult liver  (C8_211#492)


title: Human adult liver  (C6_211#459)


title: Human adult liver  (E6_211#837)


title: Human adult liver  (E12_211#932)


title: Human adult liver  (C5_211#443)


title: Human adult liver  (C4_211#428)


title: Human adult liver  (D6_211#649)


title: Human adult liver  (E7_211#853)


title: Human adult liver  (C3_211#411)


title: Human adult liver  (D3_211#603)


title: Human adult liver  (C2_211#397)


title: Human adult liver  (C11_211#541)


title: Human adult liver  (C12_211#557)


title: Human adult liver  (C10_211#525)


title: Human adult liver  (B6_211#269)


title: Human adult liver  (D10_211#711)


title: Human adult liver  (B5_211#254)


title: Human adult liver  (B2_211#208)


title: Human adult liver  (B7_211#285)


title: Human adult liver  (B12_211#368)


title: Human adult liver  (B8_211#301)


title: Human adult liver  (B4_211#237)


title: Human adult liver  (B9_211#316)


title: Human adult liver  (A9_211#131)


title: Human adult liver  (B10_211#333)


title: Human adult liver  (A8_211#117)


title: Human adult liver  (A7_211#103)


title: Human adult liver  (B1_211#193)


title: Human adult liver  (A5_211#73)


title: Human adult liver  (A6_211#89)


title: Human adult liver  (A4_211#58)


title: Human adult liver  (A12_211#179)


title: Human adult liver  (A11_211#164)


title: Human adult liver  (A1_211#11)


title: Human adult liver  (A10_211#148)


title: Human adult liver  (A3_211#42)


title: Human adult liver  (A2_211#26)


title: Human adult liver  (E5_212#822)


title: Human adult liver  (E6_212#838)


title: Human adult liver  (E4_212#807)


title: Human adult liver  (E3_212#791)


title: Human adult liver  (B11_211#350)


title: Human adult liver  (C1_211#382)


title: Human adult liver  (D6_212#650)


title: Human adult liver  (D7_212#667)


title: Human adult liver  (D8_212#682)


title: Human adult liver  (D9_212#697)


title: Human adult liver  (E1_212#760)


title: Human adult liver  (D4_212#620)


title: Human adult liver  (D12_212#745)


title: Human adult liver  (D5_212#637)


title: Human adult liver  (D11_212#729)


title: Human adult liver  (D1_212#573)


title: Human adult liver  (C9_212#508)


title: Human adult liver  (C7_212#477)


title: Human adult liver  (C6_212#460)


title: Human adult liver  (C4_212#429)


title: Human adult liver  (C3_212#412)


title: Human adult liver  (C2_212#398)


title: Human adult liver  (E2_212#776)


title: Human adult liver  (C1_212#383)


title: Human adult liver  (B3_211#224)


title: Human adult liver  (C11_212#542)


title: Human adult liver  (C12_212#558)


title: Human adult liver  (B9_212#317)


title: Human adult liver  (B7_212#286)


title: Human adult liver  (D10_212#712)


title: Human adult liver  (D2_212#589)


title: Human adult liver  (A3_212#43)


title: Human adult liver  (B10_212#334)


title: Human adult liver  (B4_212#238)


title: Human adult liver  (A2_212#27)


title: Human adult liver  (A5_212#74)


title: Human adult liver  (B1_212#194)


title: Human adult liver  (A6_212#90)


title: Human adult liver  (B6_212#270)


title: Human adult liver  (B5_212#255)


title: Human adult liver  (B2_212#209)


title: Human adult liver  (B3_212#225)


title: Human adult liver  (A9_212#132)


title: Human adult liver  (B12_212#369)


title: Human adult liver  (A4_212#59)


title: Human adult liver  (A10_212#149)


title: Human adult liver  (A1_212#12)


title: Human adult liver  (A11_212#165)


title: Human adult liver  (A8_212#118)


title: Human adult liver  (B11_212#351)


title: Human adult liver  (A12_212#180)


title: Human adult liver  (H6_221#1362)

value: Human adult liver 3

value: 57 years


title: Human adult liver  (H7_221#1378)


title: Human adult liver  (H9_221#1410)


title: Human adult liver  (H5_221#1348)


title: Human adult liver  (H8_221#1393)


title: Human adult liver  (H4_221#1332)


title: Human adult liver  (B8_212#302)


title: Human adult liver  (A7_212#104)


title: Human adult liver  (H3_221#1317)


title: Human adult liver  (H10_221#1426)


title: Human adult liver  (H1_221#1287)


title: Human adult liver  (G5_221#1194)


title: Human adult liver  (G3_221#1165)


title: Human adult liver  (G4_221#1180)


title: Human adult liver  (G1_221#1134)


title: Human adult liver  (G10_221#1268)


title: Human adult liver  (F8_221#1053)


title: Human adult liver  (G2_221#1149)


title: Human adult liver  (F9_221#1068)


title: Human adult liver  (F6_221#1020)


title: Human adult liver  (F7_221#1037)


title: Human adult liver  (F2_221#964)


title: Human adult liver  (F5_221#1004)


title: Human adult liver  (F4_221#993)


title: Human adult liver  (F11_221#1101)


title: Human adult liver  (E8_221#870)


title: Human adult liver  (E3_221#792)


title: Human adult liver  (F12_221#1118)


title: Human adult liver  (E5_221#823)


title: Human adult liver  (E2_221#777)


title: Human adult liver  (F1_221#948)


title: Human adult liver  (E9_221#885)


title: Human adult liver  (E6_221#839)


title: Human adult liver  (E4_221#808)


title: Human adult liver  (E7_221#854)


title: Human adult liver  (E11_221#916)


title: Human adult liver  (G6_221#1211)


title: Human adult liver  (E12_221#933)


title: Human adult liver  (E10_221#900)


title: Human adult liver  (D7_221#668)


title: Human adult liver  (F10_221#1085)


title: Human adult liver  (D6_221#651)


title: Human adult liver  (D4_221#621)


title: Human adult liver  (D2_221#590)


title: Human adult liver  (D9_221#698)


title: Human adult liver  (D12_221#746)


title: Human adult liver  (E1_221#761)


title: Human adult liver  (D10_221#713)


title: Human adult liver  (D5_221#638)


title: Human adult liver  (D1_221#574)


title: Human adult liver  (D11_221#730)


title: Human adult liver  (C8_221#493)


title: Human adult liver  (C9_221#509)


title: Human adult liver  (C7_221#478)


title: Human adult liver  (C4_221#430)


title: Human adult liver  (C5_221#444)


title: Human adult liver  (C11_221#543)


title: Human adult liver  (C12_221#559)


title: Human adult liver  (C2_221#399)


title: Human adult liver  (C6_221#461)


title: Human adult liver  (C3_221#413)


title: Human adult liver  (B9_221#318)


title: Human adult liver  (C10_221#526)


title: Human adult liver  (B7_221#287)


title: Human adult liver  (B8_221#303)


title: Human adult liver  (B5_221#256)


title: Human adult liver  (D3_221#604)


title: Human adult liver  (B4_221#239)


title: Human adult liver  (B3_221#226)


title: Human adult liver  (B12_221#370)


title: Human adult liver  (B2_221#210)


title: Human adult liver  (B10_221#335)


title: Human adult liver  (B11_221#352)


title: Human adult liver  (A9_221#133)


title: Human adult liver  (B1_221#195)


title: Human adult liver  (A7_221#105)


title: Human adult liver  (A8_221#119)


title: Human adult liver  (A6_221#91)


title: Human adult liver  (A4_221#60)


title: Human adult liver  (A2_221#28)


title: Human adult liver  (A10_221#150)


title: Human adult liver  (C1_221#384)


title: Human adult liver  (A11_221#166)


title: Human adult liver  (H4_222#1333)


title: Human adult liver  (H3_222#1318)


title: Human adult liver  (H8_222#1394)


title: Human adult liver  (H7_222#1379)


title: Human adult liver  (H6_222#1363)


title: Human adult liver  (H10_222#1427)


title: Human adult liver  (H5_222#1349)


title: Human adult liver  (H1_222#1288)


title: Human adult liver  (G4_222#1181)


title: Human adult liver  (G3_222#1166)


title: Human adult liver  (G5_222#1195)


title: Human adult liver  (G2_222#1150)


title: Human adult liver  (G10_222#1269)


title: Human adult liver  (G8_222#1239)


title: Human adult liver  (G1_222#1135)


title: Human adult liver  (F7_222#1038)


title: Human adult liver  (F8_222#1054)


title: Human adult liver  (F9_222#1069)


title: Human adult liver  (F4_222#994)


title: Human adult liver  (F5_222#1005)


title: Human adult liver  (F2_222#965)


title: Human adult liver  (F11_222#1102)


title: Human adult liver  (F12_222#1119)


title: Human adult liver  (G6_222#1212)


title: Human adult liver  (E9_222#886)


title: Human adult liver  (F1_222#949)


title: Human adult liver  (E4_222#809)


title: Human adult liver  (E6_222#840)


title: Human adult liver  (E3_222#793)


title: Human adult liver  (E5_222#824)


title: Human adult liver  (E2_222#778)


title: Human adult liver  (F6_222#1021)


title: Human adult liver  (E12_222#934)


title: Human adult liver  (E11_222#917)


title: Human adult liver  (E1_222#762)


title: Human adult liver  (D8_222#683)


title: Human adult liver  (D9_222#699)


title: Human adult liver  (D6_222#652)


title: Human adult liver  (E10_222#901)


title: Human adult liver  (D4_222#622)


title: Human adult liver  (F3_222#977)


title: Human adult liver  (F10_222#1086)


title: Human adult liver  (D2_222#591)


title: Human adult liver  (D12_222#747)


title: Human adult liver  (E8_222#871)


title: Human adult liver  (D10_222#714)


title: Human adult liver  (E7_222#855)


title: Human adult liver  (C9_222#510)


title: Human adult liver  (D1_222#575)


title: Human adult liver  (C6_222#462)


title: Human adult liver  (C7_222#479)


title: Human adult liver  (C5_222#445)


title: Human adult liver  (C4_222#431)


title: Human adult liver  (C2_222#400)


title: Human adult liver  (C3_222#414)


title: Human adult liver  (C11_222#544)


title: Human adult liver  (D11_222#731)


title: Human adult liver  (B9_222#319)


title: Human adult liver  (D3_222#605)


title: Human adult liver  (C1_222#385)


title: Human adult liver  (C10_222#527)


title: Human adult liver  (B7_222#288)


title: Human adult liver  (B8_222#304)


title: Human adult liver  (B4_222#240)


title: Human adult liver  (B12_222#371)


title: Human adult liver  (B6_222#271)


title: Human adult liver  (B1_222#196)


title: Human adult liver  (A9_222#134)


title: Human adult liver  (B10_222#336)


title: Human adult liver  (A7_222#106)


title: Human adult liver  (B3_222#227)


title: Human adult liver  (B11_222#353)


title: Human adult liver  (B2_222#211)


title: Human adult liver  (A3_222#44)


title: Human adult liver  (A12_222#181)


title: Human adult liver  (A4_222#61)


title: Human adult liver  (A5_222#75)


title: Human adult liver  (A6_222#92)


title: Human adult liver  (C8_222#494)


title: Human adult liver  (A11_222#167)


title: Human adult liver  (A10_222#151)


title: Human fetal liver  (D12_151#740)

source_name: Human fetal liver

extract_protocol:
Human fetal tissue was dissociated by Collagenase XI enzymatic dissociation for 25 minutes at 37˚C with agitation. Samples were stained with the following primary antibodies, CD235a (349104, FITC, mouse; Biolegend), CD45 (304050, BV711, mouse; Biolegend), EpCAM (324208, APC, mouse; Biolegend), NCAM (362524, PE, mouse; Biolegend) all at 1:100 dilution and incubated for 30mins at 4˚C. DAPI (D1306, ThermoFisher Scientific) at 1:1000 dilution was used for live/dead staining.  Cells were sorted using a BD FACS Aria II instrument and deposited as single cells into 96-well plates, pre-loaded with lysis buffer (1% Triton X-100, 1mM dNTP, 1μM oligo-dT30, 1:1.2x106 ERCC ExFold RNA spike-in, Recombinant RNase Inhibitor (2313B, Takara Clontech). Single-cell sequencing was performed using SmartSeq2.
RNA was converted into cDNA using SMARTScribe Reverse Transcriptase (639538, Takara Clontech) and amplified for 21 cycles (Kapa HiFi HotStart ReadyMix 2x, KK2602, KAPA Biosystems). Successful single cell libraries were identified by capillary gel electrophoresis (DNF-474-1000, High Sensitivity NGS Fragment Analysis Kit, AATI) and converted into sequencing libraries using a Nextera XT DNA Sample Preparation Kit (FC-131-1096, Illumina). Barcoded libraries were pooled and subjected to 75 base pair paired-end sequencing on a Illumina HiSeq 2500 instrument.

value: Freshly isolated human fetal liver homegenate

value: Human fetal liver 3

value: Unknown

value: 17 postconceptional weeks (pcw)

value: fetal


title: Human fetal liver  (D11_151#722)


title: Human fetal liver  (C9_151#502)


title: Human fetal liver  (A8_151#113)


title: Human fetal liver  (A6_151#83)


title: Human fetal liver  (B7_151#279)


title: Human fetal liver  (B12_151#362)


title: Human fetal liver  (B10_151#328)


title: Human fetal liver  (A4_151#52)


title: Human fetal liver  (A3_151#36)


title: Human fetal liver  (H3_152#1309)


title: Human fetal liver  (H4_152#1325)


title: Human fetal liver  (H2_152#1296)


title: Human fetal liver  (H5_152#1341)


title: Human fetal liver  (H6_152#1356)


title: Human fetal liver  (C10_151#519)


title: Human fetal liver  (H8_152#1387)


title: Human fetal liver  (H1_152#1281)


title: Human fetal liver  (G7_152#1219)


title: Human fetal liver  (G5_152#1188)


title: Human fetal liver  (G4_152#1173)


title: Human fetal liver  (D2_151#582)


title: Human fetal liver  (G8_152#1232)


title: Human fetal liver  (D10_151#706)


title: Human fetal liver  (G6_152#1204)


title: Human fetal liver  (G2_152#1142)


title: Human fetal liver  (H10_152#1419)


title: Human fetal liver  (G3_152#1158)


title: Human fetal liver  (G1_152#1126)


title: Human fetal liver  (G10_152#1261)


title: Human fetal liver  (H9_152#1403)


title: Human fetal liver  (F9_152#1062)


title: Human fetal liver  (F6_152#1013)


title: Human fetal liver  (F4_152#985)


title: Human fetal liver  (F3_152#971)


title: Human fetal liver  (F2_152#957)


title: Human fetal liver  (F12_152#1111)


title: Human fetal liver  (F11_152#1095)


title: Human fetal liver  (F10_152#1078)


title: Human adult liver  (A1_222#13)


title: Human fetal liver  (F7_152#1030)


title: Human fetal liver  (E8_152#864)


title: Human fetal liver  (H9_163#1406)

value: Human fetal liver 1

value: 15 postconceptional weeks (pcw)


title: Human fetal liver  (H1_163#1284)


title: Human fetal liver  (H2_163#1299)


title: Human fetal liver  (E12_152#925)


title: Human fetal liver  (E4_152#801)


title: Human fetal liver  (G7_163#1222)


title: Human fetal liver  (G4_163#1176)


title: Human fetal liver  (H10_163#1422)


title: Human fetal liver  (E7_152#848)


title: Human fetal liver  (E10_152#893)


title: Human fetal liver  (E2_152#769)


title: Human fetal liver  (H3_163#1312)


title: Human fetal liver  (H6_163#1358)


title: Human fetal liver  (H7_163#1374)


title: Human fetal liver  (H4_163#1328)


title: Human fetal liver  (E11_152#909)


title: Human fetal liver  (G9_163#1250)


title: Human fetal liver  (E9_152#879)


title: Human fetal liver  (G8_163#1235)


title: Human fetal liver  (H5_163#1344)


title: Human fetal liver  (E3_152#785)


title: Human fetal liver  (G6_163#1207)


title: Human fetal liver  (E1_152#754)


title: Human fetal liver  (G2_163#1145)


title: Human fetal liver  (H8_163#1389)


title: Human fetal liver  (G3_163#1161)


title: Human fetal liver  (G5_163#1191)


title: Human fetal liver  (F1_152#941)


title: Human fetal liver  (E6_152#831)


title: Human fetal liver  (G1_163#1129)


title: Human fetal liver  (F4_163#988)


title: Human fetal liver  (F8_163#1049)


title: Human fetal liver  (F9_163#1065)


title: Human fetal liver  (F7_163#1033)


title: Human fetal liver  (G10_163#1264)


title: Human fetal liver  (F2_163#960)


title: Human fetal liver  (F3_163#974)


title: Human fetal liver  (D9_163#694)


title: Human fetal liver  (E1_163#756)


title: Human fetal liver  (F10_163#1081)


title: Human fetal liver  (E3_163#788)


title: Human fetal liver  (D4_163#615)


title: Human fetal liver  (E6_163#834)


title: Human fetal liver  (D6_163#647)


title: Human fetal liver  (E9_163#882)


title: Human fetal liver  (E8_163#867)


title: Human fetal liver  (D5_163#633)


title: Human fetal liver  (E10_163#896)


title: Human fetal liver  (E12_163#928)


title: Human fetal liver  (F6_163#1016)


title: Human fetal liver  (D8_163#678)


title: Human fetal liver  (E5_163#817)


title: Human fetal liver  (D7_163#663)


title: Human fetal liver  (F11_163#1098)


title: Human fetal liver  (E11_163#912)


title: Human fetal liver  (E2_163#772)


title: Human fetal liver  (E7_163#851)


title: Human fetal liver  (F1_163#944)


title: Human fetal liver  (F12_163#1114)


title: Human fetal liver  (D3_163#600)


title: Human fetal liver  (D2_163#585)


title: Human fetal liver  (D11_163#725)


title: Human fetal liver  (C7_163#473)


title: Human fetal liver  (D1_163#569)


title: Human fetal liver  (C8_163#489)


title: Human fetal liver  (C5_163#441)


title: Human fetal liver  (D10_163#708)


title: Human fetal liver  (C9_163#504)


title: Human fetal liver  (C12_163#554)


title: Human fetal liver  (B6_163#267)


title: Human fetal liver  (B3_163#221)


title: Human fetal liver  (C6_163#456)


title: Human fetal liver  (B4_163#235)


title: Human fetal liver  (B2_163#205)


title: Human fetal liver  (C2_163#394)


title: Human fetal liver  (B9_163#314)


title: Human fetal liver  (B8_163#298)


title: Human fetal liver  (B12_163#365)


title: Human fetal liver  (C1_163#379)


title: Human fetal liver  (C10_163#522)


title: Human fetal liver  (C3_163#408)


title: Human fetal liver  (C4_163#424)


title: Human fetal liver  (B7_163#282)


title: Human fetal liver  (A9_163#128)


title: Human fetal liver  (B11_163#347)


title: Human fetal liver  (B1_163#190)


title: Human fetal liver  (A7_163#101)


title: Human fetal liver  (A8_163#114)


title: Human fetal liver  (C11_163#538)


title: Human fetal liver  (A6_163#86)


title: Human fetal liver  (B5_163#251)


title: Human fetal liver  (B10_163#330)


title: Human fetal liver  (A5_163#70)


title: Human fetal liver  (A4_163#55)


title: Human fetal liver  (A3_163#39)


title: Human fetal liver  (A12_163#176)


title: Human fetal liver  (A10_163#145)


title: Human fetal liver  (A11_163#162)


title: Human fetal liver  (A2_163#23)


title: Human fetal liver  (H7_161#1372)


title: Human fetal liver  (H5_161#1342)


title: Human fetal liver  (H10_161#1420)


title: Human fetal liver  (H3_161#1310)


title: Human fetal liver  (H4_161#1326)


title: Human fetal liver  (H9_161#1404)


title: Human fetal liver  (G5_161#1189)


title: Human fetal liver  (G9_161#1248)


title: Human fetal liver  (A1_163#8)


title: Human fetal liver  (H2_161#1297)


title: Human fetal liver  (G4_161#1174)


title: Human fetal liver  (G7_161#1220)


title: Human fetal liver  (G6_161#1205)


title: Human fetal liver  (G3_161#1159)


title: Human fetal liver  (H1_161#1282)


title: Human fetal liver  (G1_161#1127)


title: Human fetal liver  (G10_161#1262)


title: Human fetal liver  (F9_161#1063)


title: Human fetal liver  (F7_161#1031)


title: Human fetal liver  (F6_161#1014)


title: Human fetal liver  (G8_161#1233)


title: Human fetal liver  (F4_161#986)


title: Human fetal liver  (G2_161#1143)


title: Human fetal liver  (F3_161#972)


title: Human fetal liver  (F2_161#958)


title: Human fetal liver  (F1_161#942)


title: Human fetal liver  (E3_161#786)


title: Human fetal liver  (E10_161#894)


title: Human fetal liver  (E7_161#849)


title: Human fetal liver  (E5_161#815)


title: Human fetal liver  (E12_161#926)


title: Human fetal liver  (F11_161#1096)


title: Human fetal liver  (E2_161#770)


title: Human fetal liver  (E4_161#802)


title: Human fetal liver  (D5_161#631)


title: Human fetal liver  (E6_161#832)


title: Human fetal liver  (F12_161#1112)


title: Human fetal liver  (F10_161#1079)


title: Human fetal liver  (D9_161#692)


title: Human fetal liver  (F8_161#1047)


title: Human fetal liver  (E9_161#880)


title: Human fetal liver  (D7_161#661)


title: Human fetal liver  (D8_161#676)


title: Human fetal liver  (E8_161#865)


title: Human fetal liver  (D4_161#613)


title: Human fetal liver  (E11_161#910)


title: Human fetal liver  (D11_161#723)


title: Human fetal liver  (D3_161#598)


title: Human fetal liver  (D2_161#583)


title: Human fetal liver  (F5_161#999)


title: Human fetal liver  (C8_161#487)


title: Human fetal liver  (D1_161#568)


title: Human fetal liver  (C7_161#471)


title: Human fetal liver  (C6_161#454)


title: Human fetal liver  (C4_161#422)


title: Human fetal liver  (C3_161#406)


title: Human fetal liver  (C11_161#536)


title: Human fetal liver  (C12_161#552)


title: Human fetal liver  (C1_161#377)


title: Human fetal liver  (B8_161#296)


title: Human fetal liver  (B5_161#249)


title: Human fetal liver  (B2_161#203)


title: Human fetal liver  (B6_161#265)


title: Human fetal liver  (B1_161#188)


title: Human fetal liver  (B3_161#219)


title: Human fetal liver  (B9_161#312)


title: Human fetal liver  (A7_161#99)


title: Human fetal liver  (B7_161#280)


title: Human fetal liver  (B11_161#345)


title: Human fetal liver  (B4_161#233)


title: Human fetal liver  (A4_161#53)


title: Human fetal liver  (A6_161#84)


title: Human fetal liver  (A11_161#160)


title: Human fetal liver  (A5_161#68)


title: Human fetal liver  (A3_161#37)


title: Human fetal liver  (A2_161#21)


title: Human fetal liver  (A1_161#6)


title: Human fetal liver  (H9_162#1405)


title: Human fetal liver  (A10_161#143)


title: Human fetal liver  (H8_162#1388)


title: Human fetal liver  (C10_161#520)


title: Human fetal liver  (H7_162#1373)


title: Human fetal liver  (B12_161#363)


title: Human fetal liver  (A9_161#126)


title: Human fetal liver  (H6_162#1357)


title: Human fetal liver  (H5_162#1343)


title: Human fetal liver  (H4_162#1327)


title: Human fetal liver  (H3_162#1311)


title: Human fetal liver  (H1_162#1283)


title: Human fetal liver  (H10_162#1421)


title: Human fetal liver  (G10_162#1263)


title: Human fetal liver  (G7_162#1221)


title: Human fetal liver  (G2_162#1144)


title: Human fetal liver  (H2_162#1298)


title: Human fetal liver  (G9_162#1249)


title: Human fetal liver  (F8_162#1048)


title: Human fetal liver  (G1_162#1128)


title: Human fetal liver  (G5_162#1190)


title: Human fetal liver  (G6_162#1206)


title: Human fetal liver  (F5_162#1000)


title: Human fetal liver  (F9_162#1064)


title: Human fetal liver  (G8_162#1234)


title: Human fetal liver  (G3_162#1160)


title: Human fetal liver  (G4_162#1175)


title: Human fetal liver  (F7_162#1032)


title: Human fetal liver  (F4_162#987)


title: Human fetal liver  (F3_162#973)


title: Human fetal liver  (F6_162#1015)


title: Human fetal liver  (F10_162#1080)


title: Human fetal liver  (F11_162#1097)


title: Human fetal liver  (F2_162#959)


title: Human fetal liver  (F12_162#1113)


title: Human fetal liver  (E9_162#881)


title: Human fetal liver  (E8_162#866)


title: Human fetal liver  (E5_162#816)


title: Human fetal liver  (E6_162#833)


title: Human fetal liver  (E4_162#803)


title: Human fetal liver  (E3_162#787)


title: Human fetal liver  (E2_162#771)


title: Human fetal liver  (E12_162#927)


title: Human fetal liver  (D8_162#677)


title: Human fetal liver  (D9_162#693)


title: Human fetal liver  (D3_162#599)


title: Human fetal liver  (D5_162#632)


title: Human fetal liver  (E10_162#895)


title: Human fetal liver  (D4_162#614)


title: Human fetal liver  (D6_162#646)


title: Human fetal liver  (E11_162#911)


title: Human fetal liver  (D10_162#707)


title: Human fetal liver  (D11_162#724)


title: Human fetal liver  (D2_162#584)


title: Human fetal liver  (C7_162#472)


title: Human fetal liver  (C9_162#503)


title: Human fetal liver  (C8_162#488)


title: Human fetal liver  (D12_162#741)


title: Human fetal liver  (C6_162#455)


title: Human fetal liver  (E7_162#850)


title: Human fetal liver  (F1_162#943)


title: Human fetal liver  (E1_162#755)


title: Human fetal liver  (D7_162#662)


title: Human fetal liver  (C2_162#393)


title: Human fetal liver  (C3_162#407)


title: Human fetal liver  (C12_162#553)


title: Human fetal liver  (B9_162#313)


title: Human fetal liver  (B8_162#297)


title: Human fetal liver  (C10_162#521)


title: Human fetal liver  (C1_162#378)


title: Human fetal liver  (B7_162#281)


title: Human fetal liver  (B5_162#250)


title: Human fetal liver  (B4_162#234)


title: Human fetal liver  (B2_162#204)


title: Human fetal liver  (B3_162#220)


title: Human fetal liver  (B11_162#346)


title: Human fetal liver  (B1_162#189)


title: Human fetal liver  (A7_162#100)


title: Human fetal liver  (B12_162#364)


title: Human fetal liver  (A9_162#127)


title: Human fetal liver  (B10_162#329)


title: Human fetal liver  (A5_162#69)


title: Human fetal liver  (A6_162#85)


title: Human fetal liver  (C5_162#440)


title: Human fetal liver  (C4_162#423)


title: Human fetal liver  (A4_162#54)


title: Human fetal liver  (A3_162#38)


title: Human fetal liver  (A12_162#175)


title: Human fetal liver  (A2_162#22)


title: Human fetal liver  (A11_162#161)


title: Human fetal liver  (C11_162#537)


title: Human fetal liver  (A1_162#7)


title: Human fetal liver  (A10_162#144)


title: Human fetal liver  (B6_162#266)


title: Human fetal liver  (H9_171)

value: Human fetal liver 4


title: Human fetal liver  (H7_171)


title: Human fetal liver  (H5_171)


title: Human fetal liver  (H4_171)


title: Human fetal liver  (H3_171)


title: Human fetal liver  (H2_171)


title: Human fetal liver  (G8_171)


title: Human fetal liver  (G9_171)


title: Human fetal liver  (G4_171)


title: Human fetal liver  (G6_171)


title: Human fetal liver  (G5_171)


title: Human fetal liver  (G7_171)


title: Human fetal liver  (G3_171)


title: Human fetal liver  (H10_171)


title: Human fetal liver  (G10_171)


title: Human fetal liver  (G1_171)


title: Human fetal liver  (H8_171)


title: Human fetal liver  (H6_171)


title: Human fetal liver  (G2_171)


title: Human fetal liver  (F9_171)


title: Human fetal liver  (F5_171)


title: Human fetal liver  (F4_171)


title: Human fetal liver  (F7_171)


title: Human fetal liver  (F8_171)


title: Human fetal liver  (F3_171)


title: Human fetal liver  (F2_171)


title: Human fetal liver  (F10_171)


title: Human fetal liver  (H1_171)


title: Human fetal liver  (E9_171)


title: Human fetal liver  (F1_171)


title: Human fetal liver  (F11_171)


title: Human fetal liver  (E2_171)


title: Human fetal liver  (E11_171)


title: Human fetal liver  (E12_171)


title: Human fetal liver  (H12_171)


title: Human fetal liver  (G11_171)


title: Human fetal liver  (F6_171)


title: Human fetal liver  (E1_171)


title: Human fetal liver  (E8_171)


title: Human fetal liver  (G12_171)


title: Human fetal liver  (H11_171)


title: Human fetal liver  (F12_171)


title: Human fetal liver  (E6_171)


title: Human fetal liver  (E3_171)


title: Human fetal liver  (E5_171)


title: Human fetal liver  (E4_171)


title: Human fetal liver  (E7_171)


title: Human fetal liver  (H9_124#1402)

value: Human fetal liver 5

value: 19 postconceptional weeks (pcw)


title: Human fetal liver  (H6_124#1355)


title: Human fetal liver  (H7_124#1371)


title: Human fetal liver  (H2_124#1295)


title: Human fetal liver  (H5_124#1340)


title: Human fetal liver  (H4_124#1324)


title: Human fetal liver  (G9_124#1247)


title: Human fetal liver  (E10_171)


title: Human fetal liver  (G6_124#1203)


title: Human fetal liver  (G4_124#1172)


title: Human fetal liver  (G10_124#1260)


title: Human fetal liver  (G11_124#1271)


title: Human fetal liver  (F9_124#1061)


title: Human fetal liver  (F8_124#1046)


title: Human fetal liver  (F7_124#1029)


title: Human fetal liver  (F4_124#984)


title: Human fetal liver  (F12_124#1110)


title: Human fetal liver  (F10_124#1077)


title: Human fetal liver  (E8_124#863)


title: Human fetal liver  (F11_124#1094)


title: Human fetal liver  (E2_124#768)


title: Human fetal liver  (E11_124#908)


title: Human fetal liver  (D5_124#630)


title: Human fetal liver  (D7_124#660)


title: Human fetal liver  (D12_124#739)


title: Human fetal liver  (H10_124#1418)


title: Human fetal liver  (G8_124#1231)


title: Human fetal liver  (D9_124#691)


title: Human fetal liver  (D6_124#645)


title: Human fetal liver  (G3_124#1157)


title: Human fetal liver  (C9_124#501)


title: Human fetal liver  (C6_124#453)


title: Human fetal liver  (D1_124#567)


title: Human fetal liver  (C7_124#470)


title: Human fetal liver  (C5_124#438)


title: Human fetal liver  (C12_124#551)


title: Human fetal liver  (C11_124#535)


title: Human fetal liver  (C10_124#518)


title: Human fetal liver  (B8_124#295)


title: Human fetal liver  (B7_124#278)


title: Human fetal liver  (B6_124#264)


title: Human fetal liver  (B3_124#218)


title: Human fetal liver  (B4_124#232)


title: Human fetal liver  (B5_124#248)


title: Human fetal liver  (D11_124#721)


title: Human fetal liver  (B2_124#202)


title: Human fetal liver  (B12_124#361)


title: Human fetal liver  (B11_124#344)


title: Human fetal liver  (B10_124#327)


title: Human fetal liver  (A8_124#112)


title: Human fetal liver  (A7_124#98)


title: Human fetal liver  (H9_123#1401)


title: Human fetal liver  (A2_124#20)


title: Human fetal liver  (A10_124#142)


title: Human fetal liver  (A11_124#159)


title: Human fetal liver  (H7_123#1370)


title: Human fetal liver  (H8_123#1386)


title: Human fetal liver  (H6_123#1354)


title: Human fetal liver  (H4_123#1323)


title: Human fetal liver  (H3_123#1308)


title: Human fetal liver  (H5_123#1339)


title: Human fetal liver  (G6_123#1202)


title: Human fetal liver  (G7_123#1218)


title: Human fetal liver  (H2_123#1294)


title: Human fetal liver  (H10_123#1417)


title: Human fetal liver  (G10_123#1259)


title: Human fetal liver  (G2_123#1141)


title: Human fetal liver  (G1_123#1125)


title: Human fetal liver  (G8_123#1230)


title: Human fetal liver  (F6_123#1012)


title: Human fetal liver  (F9_123#1060)


title: Human fetal liver  (F2_123#956)


title: Human fetal liver  (F12_123#1109)


title: Human fetal liver  (F11_123#1093)


title: Human fetal liver  (F8_123#1045)


title: Human fetal liver  (F7_123#1028)


title: Human fetal liver  (F10_123#1076)


title: Human fetal liver  (G9_123#1246)


title: Human fetal liver  (F1_123#940)


title: Human fetal liver  (H1_123#1280)


title: Human fetal liver  (E9_123#878)


title: Human fetal liver  (E6_123#830)


title: Human fetal liver  (E8_123#862)


title: Human fetal liver  (F5_123#998)


title: Human fetal liver  (E7_123#847)


title: Human fetal liver  (G4_123#1171)


title: Human fetal liver  (E5_123#814)


title: Human fetal liver  (E1_123#753)


title: Human fetal liver  (E4_123#800)


title: Human fetal liver  (D9_123#690)


title: Human fetal liver  (D8_123#675)


title: Human fetal liver  (E12_123#924)


title: Human fetal liver  (E10_123#892)


title: Human fetal liver  (D7_123#659)


title: Human fetal liver  (D6_123#644)


title: Human fetal liver  (D5_123#629)


title: Human fetal liver  (D4_123#612)


title: Human fetal liver  (D11_123#720)


title: Human fetal liver  (D10_123#705)


title: Human fetal liver  (D2_123#581)


title: Human fetal liver  (D12_123#738)


title: Human fetal liver  (C8_123#486)


title: Human fetal liver  (C7_123#469)


title: Human fetal liver  (C6_123#452)


title: Human fetal liver  (C5_123#437)


title: Human fetal liver  (C2_123#391)


title: Human fetal liver  (C11_123#534)


title: Human fetal liver  (C12_123#550)


title: Human fetal liver  (C3_123#405)


title: Human fetal liver  (C4_123#421)


title: Human fetal liver  (B9_123#311)


title: Human fetal liver  (C10_123#517)


title: Human fetal liver  (B5_123#247)


title: Human fetal liver  (B12_123#360)


title: Human fetal liver  (B11_123#343)


title: Human fetal liver  (B6_123#263)


title: Human fetal liver  (B8_123#294)


title: Human fetal liver  (A9_123#125)


title: Human fetal liver  (D3_123#597)


title: Human fetal liver  (D1_123#566)


title: Human fetal liver  (A7_123#97)


title: Human fetal liver  (A8_123#111)


title: Human fetal liver  (B1_123#187)


title: Human fetal liver  (A4_123#51)


title: Human fetal liver  (A6_123#82)


title: Human fetal liver  (A5_123#67)


title: Human fetal liver  (A3_123#35)


title: Human fetal liver  (A2_123#19)


title: Human fetal liver  (A10_123#141)


title: Human fetal liver  (A11_123#158)


title: Human fetal liver  (A12_123#174)


title: Human fetal liver  (H9_121#1399)


title: Human fetal liver  (H7_121#1368)


title: Human fetal liver  (H1_121#1278)


title: Human fetal liver  (B10_123#326)


title: Human fetal liver  (H8_121#1384)


title: Human fetal liver  (H10_121#1415)


title: Human fetal liver  (H6_121#1352)


title: Human fetal liver  (B3_123#217)


title: Human fetal liver  (G9_121#1244)


title: Human fetal liver  (G3_121#1155)


title: Human fetal liver  (G6_121#1200)


title: Human fetal liver  (G1_121#1123)


title: Human fetal liver  (G5_121#1186)


title: Human fetal liver  (F8_121#1043)


title: Human fetal liver  (F7_121#1026)


title: Human fetal liver  (F4_121#982)


title: Human fetal liver  (F11_121#1091)


title: Human fetal liver  (F2_121#954)


title: Human fetal liver  (F12_121#1107)


title: Human fetal liver  (E6_121#828)


title: Human fetal liver  (E7_121#845)


title: Human fetal liver  (E4_121#798)


title: Human fetal liver  (F10_121#1074)


title: Human fetal liver  (E8_121#860)


title: Human fetal liver  (E9_121#876)


title: Human fetal liver  (F9_121#1058)


title: Human fetal liver  (E3_121#783)


title: Human fetal liver  (E2_121#766)


title: Human fetal liver  (G10_121#1257)


title: Human fetal liver  (E1_121#751)


title: Human fetal liver  (E11_121#906)


title: Human fetal liver  (D9_121#688)


title: Human fetal liver  (D8_121#673)


title: Human fetal liver  (D7_121#657)


title: Human fetal liver  (E12_121#922)


title: Human fetal liver  (D3_121#595)


title: Human fetal liver  (D5_121#627)


title: Human fetal liver  (F6_121#1010)


title: Human fetal liver  (D4_121#610)


title: Human fetal liver  (D1_121#564)


title: Human fetal liver  (F3_121#969)


title: Human fetal liver  (D12_121#736)


title: Human fetal liver  (D2_121#579)


title: Human fetal liver  (C9_121#499)


title: Human fetal liver  (C8_121#484)


title: Human fetal liver  (C6_121#450)


title: Human fetal liver  (C7_121#467)


title: Human fetal liver  (C4_121#419)


title: Human fetal liver  (C11_121#532)


title: Human fetal liver  (C3_121#403)


title: Human fetal liver  (B9_121#309)


title: Human fetal liver  (C10_121#515)


title: Human fetal liver  (C5_121#435)


title: Human fetal liver  (B7_121#276)


title: Human fetal liver  (B6_121#261)


title: Human fetal liver  (C2_121#389)


title: Human fetal liver  (B12_121#358)


title: Human fetal liver  (B4_121#230)


title: Human fetal liver  (B10_121#324)


title: Human fetal liver  (B5_121#245)


title: Human fetal liver  (A7_121#96)


title: Human fetal liver  (B11_121#341)


title: Human fetal liver  (A4_121#49)


title: Human fetal liver  (A6_121#80)


title: Human fetal liver  (B1_121#185)


title: Human fetal liver  (A12_121#172)


title: Human fetal liver  (A3_121#33)


title: Human fetal liver  (H9_122#1400)


title: Human fetal liver  (A11_121#156)


title: Human fetal liver  (A10_121#139)


title: Human fetal liver  (H8_122#1385)


title: Human fetal liver  (H6_122#1353)


title: Human fetal liver  (H7_122#1369)


title: Human fetal liver  (H3_122#1307)


title: Human fetal liver  (H5_122#1338)


title: Human fetal liver  (H2_122#1293)


title: Human fetal liver  (H10_122#1416)


title: Human fetal liver  (H1_122#1279)


title: Human fetal liver  (G9_122#1245)


title: Human fetal liver  (G7_122#1217)


title: Human fetal liver  (G8_122#1229)


title: Human fetal liver  (G5_122#1187)


title: Human fetal liver  (G2_122#1140)


title: Human fetal liver  (G10_122#1258)


title: Human fetal liver  (G1_122#1124)


title: Human fetal liver  (G3_122#1156)


title: Human fetal liver  (F9_122#1059)


title: Human fetal liver  (F4_122#983)


title: Human fetal liver  (F5_122#997)


title: Human fetal liver  (F3_122#970)


title: Human fetal liver  (F6_122#1011)


title: Human fetal liver  (F11_122#1092)


title: Human fetal liver  (F12_122#1108)


title: Human fetal liver  (F10_122#1075)


title: Human fetal liver  (F2_122#955)


title: Human fetal liver  (E9_122#877)


title: Human fetal liver  (E8_122#861)


title: Human fetal liver  (F1_122#939)


title: Human fetal liver  (G6_122#1201)


title: Human fetal liver  (G4_122#1170)


title: Human fetal liver  (E5_122#813)


title: Human fetal liver  (E4_122#799)


title: Human fetal liver  (E6_122#829)


title: Human fetal liver  (E12_122#923)


title: Human fetal liver  (F8_122#1044)


title: Human fetal liver  (E10_122#891)


title: Human fetal liver  (E11_122#907)


title: Human fetal liver  (F7_122#1027)


title: Human fetal liver  (D8_122#674)


title: Human fetal liver  (E1_122#752)


title: Human fetal liver  (D9_122#689)


title: Human fetal liver  (D7_122#658)


title: Human fetal liver  (D3_122#596)


title: Human fetal liver  (D2_122#580)


title: Human fetal liver  (D12_122#737)


title: Human fetal liver  (D5_122#628)


title: Human fetal liver  (E7_122#846)


title: Human fetal liver  (D10_122#704)


title: Human fetal liver  (D11_122#719)


title: Human fetal liver  (D4_122#611)


title: Human fetal liver  (C8_122#485)


title: Human fetal liver  (C9_122#500)


title: Human fetal liver  (E3_122#784)


title: Human fetal liver  (D1_122#565)


title: Human fetal liver  (E2_122#767)


title: Human fetal liver  (D6_122#643)


title: Human fetal liver  (C6_122#451)


title: Human fetal liver  (C4_122#420)


title: Human fetal liver  (C3_122#404)


title: Human fetal liver  (C7_122#468)


title: Human fetal liver  (C5_122#436)


title: Human fetal liver  (C2_122#390)


title: Human fetal liver  (C11_122#533)


title: Human fetal liver  (C10_122#516)


title: Human fetal liver  (C12_122#549)


title: Human fetal liver  (C1_122#376)


title: Human fetal liver  (B8_122#293)


title: Human fetal liver  (B7_122#277)


title: Human fetal liver  (B6_122#262)


title: Human fetal liver  (B4_122#231)


title: Human fetal liver  (B12_122#359)


title: Human fetal liver  (B3_122#216)


title: Human fetal liver  (B11_122#342)


title: Human fetal liver  (B1_122#186)


title: Human fetal liver  (A9_122#124)


title: Human fetal liver  (B10_122#325)


title: Human fetal liver  (A8_122#110)


title: Human fetal liver  (A6_122#81)


title: Human fetal liver  (B9_122#310)


title: Human fetal liver  (B5_122#246)


title: Human fetal liver  (B2_122#201)


title: Human fetal liver  (C5_161#439)


title: Human fetal liver  (G10_104#1256)

value: Human fetal liver 2

value: 16 postconceptional weeks (pcw)


title: Human fetal liver  (G3_104#1154)


title: Human fetal liver  (H5_104#1337)


title: Human fetal liver  (H1_104#1277)


title: Human fetal liver  (G8_104#1228)


title: Human fetal liver  (H6_104#1351)


title: Human fetal liver  (G2_104#1139)


title: Human fetal liver  (G4_104#1169)


title: Human fetal liver  (H2_104#1292)


title: Human fetal liver  (A10_122#140)


title: Human fetal liver  (H4_104#1322)


title: Human fetal liver  (A4_122#50)


title: Human fetal liver  (A3_122#34)


title: Human fetal liver  (A2_122#18)


title: Human fetal liver  (H3_104#1306)


title: Human fetal liver  (H7_104#1367)


title: Human fetal liver  (G9_104#1243)


title: Human fetal liver  (H8_104#1383)


title: Human fetal liver  (G7_104#1216)


title: Human fetal liver  (A11_122#157)


title: Human fetal liver  (H9_104#1398)


title: Human fetal liver  (H10_104#1414)


title: Human fetal liver  (A12_122#173)


title: Human fetal liver  (A1_122#5)


title: Human fetal liver  (F8_104#1042)


title: Human fetal liver  (A5_122#66)


title: Human fetal liver  (G6_104#1199)


title: Human fetal liver  (G5_104#1185)


title: Human fetal liver  (C2_161#392)


title: Human fetal liver  (F7_104#1025)


title: Human fetal liver  (F6_104#1009)


title: Human fetal liver  (F12_104#1106)


title: Human fetal liver  (F2_104#953)


title: Human fetal liver  (F4_104#981)


title: Human fetal liver  (D9_104#687)


title: Human fetal liver  (D1_104#563)


title: Human fetal liver  (D8_104#672)


title: Human fetal liver  (D10_104#703)


title: Human fetal liver  (F11_104#1090)


title: Human fetal liver  (C9_104#498)


title: Human fetal liver  (D11_104#718)


title: Human fetal liver  (D12_104#735)


title: Human fetal liver  (D7_104#656)


title: Human fetal liver  (F3_104#968)


title: Human fetal liver  (D6_104#642)


title: Human fetal liver  (E1_104#750)


title: Human fetal liver  (E9_104#875)


title: Human fetal liver  (E10_104#890)


title: Human fetal liver  (E6_104#827)


title: Human fetal liver  (E8_104#859)


title: Human fetal liver  (E3_104#782)


title: Human fetal liver  (E11_104#905)


title: Human fetal liver  (E7_104#844)


title: Human fetal liver  (E4_104#797)


title: Human fetal liver  (E12_104#921)


title: Human fetal liver  (F10_104#1073)


title: Human fetal liver  (F1_104#938)


title: Human fetal liver  (D5_104#626)


title: Human fetal liver  (D4_104#609)


title: Human fetal liver  (C8_104#483)


title: Human fetal liver  (C7_104#466)


title: Human fetal liver  (C6_104#449)


title: Human fetal liver  (C4_104#418)


title: Human fetal liver  (C5_104#434)


title: Human fetal liver  (C11_104#531)


title: Human fetal liver  (C1_104#375)


title: Human fetal liver  (C10_104#514)


title: Human fetal liver  (B8_104#292)


title: Human fetal liver  (B9_104#308)


title: Human fetal liver  (C12_104#548)


title: Human fetal liver  (B6_104#260)


title: Human fetal liver  (A9_104#123)


title: Human fetal liver  (B11_104#340)


title: Human fetal liver  (B4_104#229)


title: Human fetal liver  (B2_104#200)


title: Human fetal liver  (A5_104#65)


title: Human fetal liver  (B7_104#275)


title: Human fetal liver  (A6_104#79)


title: Human fetal liver  (A7_104#95)


title: Human fetal liver  (A8_104#109)


title: Human fetal liver  (B12_104#357)


title: Human fetal liver  (A4_104#48)


title: Human fetal liver  (A3_104#32)


title: Human fetal liver  (B10_104#323)


title: Human fetal liver  (B3_104#215)


title: Human fetal liver  (A2_104#17)


title: Human fetal liver  (A11_104#155)


title: Human fetal liver  (B5_104#244)


title: Human fetal liver  (A10_104#138)


title: Human fetal liver  (A12_104#171)


title: Human fetal liver  (A1_104#4)


title: Human fetal liver  (H9_103#1397)


title: Human fetal liver  (H7_103#1366)


title: Human fetal liver  (H8_103#1382)


title: Human fetal liver  (H5_103#1336)


title: Human fetal liver  (H4_103#1321)


title: Human fetal liver  (H2_103#1291)


title: Human fetal liver  (H10_103#1413)


title: Human fetal liver  (G9_103#1242)


title: Human fetal liver  (G7_103#1215)


title: Human fetal liver  (G5_103#1184)


title: Human fetal liver  (G3_103#1153)


title: Human fetal liver  (G6_103#1198)


title: Human fetal liver  (G10_103#1255)


title: Human fetal liver  (F7_103#1024)


title: Human fetal liver  (F6_103#1008)


title: Human fetal liver  (F3_103#967)


title: Human fetal liver  (F9_103#1057)


title: Human fetal liver  (G1_103#1122)


title: Human fetal liver  (F4_103#980)


title: Human fetal liver  (E9_103#874)


title: Human fetal liver  (F2_103#952)


title: Human fetal liver  (F10_103#1072)


title: Human fetal liver  (F1_103#937)


title: Human fetal liver  (E8_103#858)


title: Human fetal liver  (F12_103#1105)


title: Human fetal liver  (E7_103#843)


title: Human fetal liver  (F11_103#1089)


title: Human fetal liver  (H3_103#1305)


title: Human fetal liver  (E4_103#796)


title: Human fetal liver  (E12_103#920)


title: Human fetal liver  (E2_103#765)


title: Human fetal liver  (E11_103#904)


title: Human fetal liver  (E3_103#781)


title: Human fetal liver  (G2_103#1138)


title: Human fetal liver  (F8_103#1041)


title: Human fetal liver  (E1_103#749)


title: Human fetal liver  (E10_103#889)


title: Human fetal liver  (D7_103#655)


title: Human fetal liver  (D6_103#641)


title: Human fetal liver  (D9_103#686)


title: Human fetal liver  (D5_103#625)


title: Human fetal liver  (D3_103#594)


title: Human fetal liver  (D4_103#608)


title: Human fetal liver  (D11_103#717)


title: Human fetal liver  (D12_103#734)


title: Human fetal liver  (D10_103#702)


title: Human fetal liver  (D1_103#562)


title: Human fetal liver  (D2_103#578)


title: Human fetal liver  (C6_103#448)


title: Human fetal liver  (C3_103#402)


title: Human fetal liver  (C9_103#497)


title: Human fetal liver  (C4_103#417)


title: Human fetal liver  (C8_103#482)


title: Human fetal liver  (C7_103#465)


title: Human fetal liver  (C5_103#433)


title: Human fetal liver  (E5_103#812)


title: Human fetal liver  (C2_103#388)


title: Human fetal liver  (C12_103#547)


title: Human fetal liver  (C11_103#530)


title: Human fetal liver  (C10_103#513)


title: Human fetal liver  (C1_103#374)


title: Human fetal liver  (B8_103#291)


title: Human fetal liver  (B9_103#307)


title: Human fetal liver  (D8_103#671)


title: Human fetal liver  (B6_103#259)


title: Human fetal liver  (B7_103#274)


title: Human fetal liver  (B3_103#214)


title: Human fetal liver  (B2_103#199)


title: Human fetal liver  (B11_103#339)


title: Human fetal liver  (B5_103#243)


title: Human fetal liver  (B12_103#356)


title: Human fetal liver  (A9_103#122)


title: Human fetal liver  (A3_103#31)


title: Human fetal liver  (A5_103#64)


title: Human fetal liver  (B1_103#184)


title: Human fetal liver  (A4_103#47)


title: Human fetal liver  (A12_103#170)


title: Human fetal liver  (A1_103#3)


title: Human fetal liver  (A11_103#154)


title: Human fetal liver  (A10_103#137)


title: Human fetal liver  (H9_101#1395)


title: Human fetal liver  (H8_101#1380)


title: Human fetal liver  (A2_103#16)


title: Human fetal liver  (H6_101#1350)


title: Human fetal liver  (H7_101#1364)


title: Human fetal liver  (H5_101#1334)


title: Human fetal liver  (H4_101#1319)


title: Human fetal liver  (H3_101#1303)


title: Human fetal liver  (H1_101#1275)


title: Human fetal liver  (H10_101#1411)


title: Human fetal liver  (H2_101#1289)


title: Human fetal liver  (G9_101#1240)


title: Human fetal liver  (G7_101#1213)


title: Human fetal liver  (B10_103#322)


title: ChIP-seq stationary phase input for rep2

city: Newyork

first: Xiangwu

last: Ju

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to E.coli genome (NC_00913.3) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Genome_build: Escherichia coli str. K-12 substr. MG1655, NC_000913.3
Supplementary_files_format_and_content: wig files

organism: Escherichia coli

source_name: E.coli cell

growth_protocol: Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity.

extract_protocol:
For the RNA-seq samples, the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer (5% phenol in ethanol) immediately to the culture medium before harvest and stay on the ice for 15 minutes. Cell pellets were collected by centrifugation (6,000 rpm, 5 minutes at 4 °C), thoroughly resuspended in 100 μl of lysozyme solution [2 mg/ml in TE buffer (10 mM Tris-HCl and 1 mM EDTA)], and incubated for 2 minutes. The cells were immediately lysed by adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and the RNA was extracted following manufacture’s instruction. For the ChIP-seq samples, the the E. coli cells were fixed with 1% formaldehyde with continued shaking at 37 °C for 10 minutes before quenching with glycine (100 mM final concentration). Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment.
A new RNA-seq method SEnd-seq was developed and used to prepare the SEnd-seq library, standard RNA-seq library was prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) following the manufacturer’s instructions, ChIP-seq library was prepared with NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645)after ChIP DNA enrichment. For SEnd_seq, the RNA was ligated to a RNA adaptor (/5Phos/rNrNrN rNrArArCrCrUrGrCrUrArUrCrArArCrUrG/3ddC/ or /5Phos/rNrNrN rNrGrCrUrUrCrCrUrGrCrUrArUrCrArArCrUrG/3ddC/). The ligated RNA was converted to cDNA with the same Biotinylated RT primer(5GGGCAG T/iBiodT/GATAGCAGG). For RNA-seq , rRNA was depleted with the Ribo-Zero rRNA Removal Kit. The sequencing library was prepared with the TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions. For ChIP-seq, the enriched ChIP DNA and input DNA sequencing libraries were prepared with NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition.

tag: grouwth stage

value: Stationary phase

tag: treatment

value: 37 °C culture

tag: strain

value: wild type

tag: chip antibody

value: Chip-seq input


title: Human fetal liver  (G6_101#1196)


title: Human fetal liver  (A6_103#78)


title: Human fetal liver  (G5_101#1182)


title: ChIP-seq stationary phase input for rep1


title: ChIP-seq stationary phase RNP Ab2 rep 2

value: RNAP β' subunit antibody ( BIolegend 662904)


title: Human fetal liver  (G4_101#1167)

value: Freshly isolated human fetal liver homegenate


title: Human fetal liver  (G2_101#1136)


title: ChIP-seq stationary phase RNP Ab2 rep 1

value: RNAP β' subunit antibody (BIolegend 662904)


title: ChIP-seq stationary phase RNP Ab1 rep 2

value: RNAP β subunit antibody ( BIolegend 663903)


title: Human fetal liver  (G10_101#1253)

value: Unknown


title: Human fetal liver  (G1_101#1120)

value: fetal


title: Human fetal liver  (F8_101#1039)


title: ChIP-seq stationary phase RNP Ab1 rep 1


title: Human fetal liver  (G8_101#1226)


title: Human fetal liver  (F7_101#1022)


title: Human fetal liver  (F6_101#1006)


title: Human fetal liver  (F5_101#995)


title: Human fetal liver  (F3_101#966)


title: Human fetal liver  (F2_101#950)


title: Human fetal liver  (F4_101#978)


title: Human fetal liver  (G3_101#1151)


title: Human fetal liver  (F12_101#1103)


title: Human fetal liver  (F11_101#1087)


title: Human fetal liver  (F10_101#1070)


title: Human fetal liver  (F9_101#1055)


title: Human fetal liver  (F1_101#935)


title: Human fetal liver  (E8_101#856)


title: Human fetal liver  (E9_101#872)


title: Human fetal liver  (E7_101#841)


title: Endometrium_intrauterine_PUL_49

city: Joint Base Lewis-McChord

first: Zachary

middle: Tyler

last: Colburn

state: WA

address: 9040A Jackson Ave

department: Department of Clinical Investigation

institute: Madigan Army Medical Center

hyb_protocol: Affymetrix GeneChip Human Gene 2.0 ST Array

scan_protocol: Affymetrix GeneChip 1300 scanner

data_processing:
Affymetrix GeneChip Command Console Software was used for initial data collection followed by RMA normalization in oligo. Data was processed to remove control probes.
probe group file: HuGene-2_0-st-v1.na35.hg19.probeset.csv
meta-probeset file: HuGene-2_0-st-v1.na36.hg19.transcript.csv

source_name: Endometrial biopsy

label_protocol: Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay

extract_protocol: Endometrial biopsy collected from women with non-viable pregnancies at Madigan Army Medical Center

tag: pregnancy location

value: Non-viable Intrauterine


title: Endometrium_ectopic_PUL_92

value: Ectopic


title: Endometrium_ectopic_PUL_98A


title: Endometrium_ectopic_PUL_79


title: Human fetal liver  (E5_101#810)


title: Human fetal liver  (E6_101#825)


title: Endometrium_ectopic_PUL_55


title: Endometrium_ectopic_PUL_58


title: Endometrium_ectopic_PUL_10


title: Endometrium_ectopic_PUL_45


title: Endometrium_ectopic_PUL_95


title: Endometrium_ectopic_PUL_65


title: Endometrium_ectopic_PUL_50


title: Endometrium_ectopic_PUL_20


title: Endometrium_ectopic_PUL_37


title: Human fetal liver  (E2_101#763)


title: Human fetal liver  (E4_101#794)


title: Human fetal liver  (E3_101#779)


title: Human fetal liver  (E12_101#918)