title: DKO0-p5_MuERVL

data_processing:
Library strategy: BS-Amplicon
CpG methylation states were determined using BiQAnalyzerHT, filtering for a sequence identity of >= 0.8 (reference sequence for IAP and IAPez have been shortened in order to obtain a better mapping of the sequencing reads) and strand-specific methylation patterns were obtained using Hairpinanalyzer V0.3 (Mathias Bader and Julia Arand, available under: https://github.com/PascalGiehr/Hairpinanalyzer), filtering for a linker conversion rate of >= 0.8. H(O)TA was applied in order to determine enzyme efficiencies.
Genome_build: mm9
processed data files format and content: csv containing read count statistics

extract_protocol:
Genomic DNA was isolated from cells through phenol-chloroform extraction
200 ng of genomic DNA was digested with 10 U of BsaWI (NEB), DdeI (NEB), Eco47I (Thermo Fisher Sc.) or MspI (Thermo Fisher Sc.), incubated for 16 h at 60°C (BsaWI) or 37°C (DdeI, Eco47I and MspI) and afterwards heat inactivated. 50 pmol of endonuclease specific hairpin-linker was ligated in a 20 µl reaction at 16 °C for 3 h. Bisulfite conversion was done using Zymo’s EZ DNA Methylation-Gold Kit according to manufacturer’s instructions. Bisulfite treated Hairpin-DNA was eluted in 20 µl Elution Buffer. PCR was performed in 30 µl reactions with 2 µl of Hairpin-Bisulfite template and 37 PCR cycles using HotFirePol®DNA Polymerase (Solis BioDyne) or HotStarTaq DNA Polymerase (Qiagen). PCR products were purified from a 1.2% agarose gel using Avegene’s GenepHlow™ Gel/PCR Kit according to manufacturer’s instructions and eluted in 20 µl 0.1x TE buffer. Amplicons were indexed in a 50 µl PCR using specific TruSeq indices and 6 PCR cycles. Index PCRs were purified with 1.1x AMPure XP beads (Beckman Coulter). Amplicons were sequenced on an Illumina MiSeq in a 2x250 bp sequencing mode

treatment_protocol: Passaged five times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid

value: mESC


title: PC-3_DMSO_H3K27ac_Rep2

status: Public on Jul 24 2021

type: SRA

city: Rochester

first: Ting

last: Wei

state: MN

address: 507 3rd St SW

country: USA

institute: Mayo Clinic

library_source: genomic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7.
Raw sequences were mapped to reference genome (hg38) using BWA (v0.5.9) with default parameters.
Peak calling was performed using MASC2 (v2.0.10).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: prostate

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: PC-3 cells were treated with vehicle (DMSO) or 5μM Palbociclib for 24 hours.

tag: cell line

tag: passages

tag: treatment

value: DMSO

tag: chip antibody

value: Rabbit monoclonal anti-Acetyl Histone H3 (Lys27) Abcam Cat# ab4729, RRID:AB_2118291anti-STAT2 #72604S, Cell Signaling Technology


title: PC-3_shHDAC5_Palbociclib_Rep3

library_source: transcriptomic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7.
Raw sequences were mapped to reference genome (hg38) using STAR (2.5.2b).
RseQC was used to calculate gene expression.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: FPKM

molecule: total RNA

extract_protocol:
RNA-Seq: Total RNA was isolated from cells using the RNeasy Plus Mini Kit (QIAGEN). High-quality (Agilent Bioanalyzer RIN > 7.0) total RNA was employed for the preparation of sequencing libraries using the Illumina TruSeq Stranded Total RNA/Ribo-Zero Sample Prep Kit.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: PC-3 cells infected with shNC or shHDAC5 were treated with vehicle (DMSO) or 5μM Palbociclib for 24 hours.

tag: shRNA

value: Palbociclib


title: Endo_B_cell_sample_9

city: Oxford

first: Jen

last: Southcombe

address: John Radcliffe Hospital, Headington, Oxford OX3 9RR

department: Nuffield Department of Women's and Reproductive Health

country: United Kingdom

institute: University of Oxford

data_processing:
Raw reads of fastq format were firstly processed through Novogene Co., Ltd. in-house  perl scripts. In this step, probability of an incorrect base call 1 in 100 times (Q20),  probability of an incorrect base call 1 in 1000 times (Q30), raw reads number, error  rate and A/T/G/C content distribution were calculated. Accordingly, clean data (clean  reads) were obtained by removing reads containing adapter, reads containing ploy-N and  low quality reads from raw data. Read trimming was also performed to remove bases  towards read ends with high error rate and distorted GC contents. All the downstream  analyses were based on the obtained clean data.
Raw reads were mapped to Ensembl Homo sapiens cDNA database release 94 (http://  ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/cdna/) using TopHat v2.0.12. Appropriate parameters are also set (e.g. the longest intron length). Only  filtered reads were used to analyse mapping status of RNA-seq data to the reference  genome.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. The non-normalised count table generated was then used for downstream  analysis.
Genome_build: Homo sapiens cDNA database release 94 (http://  ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/cdna/)
Supplementary_files_format_and_content: Tab-delimited text file containing normalized abundance measurements for each sample, output from DESeq2
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for each sample

source_name: endometrium

extract_protocol:
Immediately after sorting, cells were pelleted by centrifugation and re-suspended in RLT  buffer (Qiagen, USA) and RNA was extracted using QIAGEN RNeasy Micro Kits (Qiagen,  USA) according to the manufacturer’s protocol ’Purification of Total RNA from Animal  and Human Cells’. The procedure enriches for mRNA; all RNA molecules longer than  200 nucleotides are purified.
Samples were treated as single cells using Smart-Seq2  protocol for cDNA conversion. The library was prepared using Standard  Nextera Illumina Library Prep kit according to manufacturer’s protocol.

treatment_protocol: Frozen endometrial cell digests were thawed into HS-media (RPMI1640 supplemented with 10%FCS, 1% Human Serum, 2mM glutamine, 100 IU/ml penicillin and 100 ug/ml streptomycin) at 37C and centrifuged at 300 x g. Endometrial cells were re-suspended in HS-Media and transferred to a 25cm2 flask for 30 minutes at 37C/ 5% CO2, then supernatants containing non-adherent cells were further transferred to a fresh flask for an  additional 30 minutes incubation, for stromal and epithelial cell depletion. Supernatants were then removed and transferred onto a lymphoprep layer with centrifugation at 800 x g for 20 minutes. Cells in the interface were washed in PBS and prepared for cell sorting on an Aria III (BD Biosciences, USA) using 85 micrometer nozzle. Briefly, endometrial cells were stained with Zombie AquaTM Viability Dye (Biolegend, USA) then incubated  with antibodies CD3 APC FIRETM750, CD45 BV650TM, CD4 FITC, CD25 PE, CD8 BV711TM, CD19 PE-Cy7 and CD127 APC (all from Biolegend, USA). CD19+ B cells were isolated as singlet cells (FSC-H vs FSC-A), Zombie Aqua-,CD45+, CD19+

tag: tissue

value: endometrium

tag: age

tag: cell type

value: B cells

tag: menstrual phase

value: mid-luteal


title: TKO-L-p0_MuERVL

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

organism: Mus musculus

source_name: J1 mESC

growth_protocol: mES cells were cultured in Knock Out DMEM media (Gibco) containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF. For ES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CD1 mouse embryonic fibroblasts (MEFs) were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells per well of a six-well plate and were split every 3–4 days.

tag: strain

tag: genotype

value: Dnmt3a + Dnmt3b KO + Dnmt1 shRNA


title: lung, vehicle treatment C2

type: RNA

city: Daegu

first: Eok-Cheon

last: Kim

address: hyunchung-ro 170

department: Biochemistry and Molecular Biology

country: South Korea

institute: College of Medicine, Yeungnam University

description: Gene expression data from lung tissue

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)
Affymetrix Power Tools (affymetrix-power-tools.html) R 3.5.1 (https://www.r-project.org/)

label: biotin

source_name: lung tissue of vehicle-treated mouse

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Animals were housed in a light- and temperature-controlled room and had free access to drinking water and standard rodent diet.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Male C57BL/6J mice (8 weeks old) were anesthetized and received intratracheal instillation of PBS or 2 U/kg bleomycin. After 5 days, HHT (0.545 mg/kg) or vehicle was administered intraperitoneally 2 times a week for 15 days.

value: lung

tag: gender

value: male

value: 11 weeks old

value: vehicle-treated


title: Endo_B_cell_sample_8


title: PC-3_DMSO_H3K27ac_Rep1


title: v65-WT_MuERVL

source_name: V65 mESC

value: WT


title: PC-3_shHDAC5_Palbociclib_Rep2


title: lung, vehicle treatment C1

description: Gene expression data from lung tissue


title: DKO0-p1_mSat

treatment_protocol: Passaged once after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid

value: Dnmt3a + Dnmt3b KO


title: Unpaired_AA_V2_Patient UP45 D7

type: protein

city: Stanford

first: Allan

last: Feng

state: CA

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

description: Antibodies in patient serum samples bind to conjugated beads in protein array. The fluorescence measured as MFI from the secondary antibody was used to determine serum antibody reactivity.

hyb_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from serum samples.

scan_protocol: A Luminex FlexMAP 3D instrument was used to measure fluorescence (in MFI) from each  barcoded bead.

data_processing: Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

source_name: Hospitalized COVID-19

extract_protocol: Blood was collected from patients and healthy controls from 3 different centers. The blood was then processed into serum which was then run on our arrays.

value: serum

tag: condition

value: Hospitalized COVID-19


title: PC-3_shHDAC5_Palbociclib_Rep1


title: Endo_B_cell_sample_6


title: Endo_B_cell_sample_5


title: PC-3_shNC_Palbociclib_Rep3

value: shNC


title: DKO0-p1_MuERVL

value: mESC


title: v65-WT_mSat


title: Endo_B_cell_sample_7


title: DKO0-p5_IAPez


title: PC-3_shNC_Palbociclib_Rep1


title: Endo_B_cell_sample_3


title: TKO-L-p0_mSat


title: Endo_B_cell_sample_2


title: PC-3_shNC_Palbociclib_Rep2


title: PC-3_shHDAC5_DMSO_Rep3

value: DMSO


title: 7OSF: Oral Submucous fibrosis

type: genomic

city: Bangalore

first: Ruchi

last: Jain

state: Karnataka

address: C V Raman Road

department: Molecular Reproduction Development and Genetics

country: India

institute: Indian Institute of Science

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Not provided

data_processing: Average Beta

label: Cy5 and Cy3

source_name: OSF

label_protocol: Not provided

extract_protocol: Samples extracted using Qiagen Genomic DNA Kit according to manufacturer's instructions.

value: Oral Submucous fibrosis


title: Endo_B_cell_sample_4


title: DKO0-p1_IAPez


title: PC-3_shHDAC5_DMSO_Rep2


title: Endo_B_cell_sample_1


title: TKO-L-p0_IAPez


title: MV4-11_sgKDSR#2

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description:
Eukaryotic mRNA directional library
FKRN190313852

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run)
Sequenced reads were mapped to hg19 whole genome using STAR_2.6.0a
Aligned reads was normalized by edgeR bioconductor package and outputed as rpkm.txt file
Genome_build: Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: raw count table in txt format for all 8 samples

source_name: Leukemia

growth_protocol: MV4-11 and MOLM13 cells were cultured in RPMI 1640 (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS), penicillin/streptomycin (Gibco), GlutaMax (Gibco) and plasmocin (0.5 g/ml; Invitrogen). Cells were cultured in 37C incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN)
Eukaryotic mRNA directional library prep at Novogene Inc.
HiSeq PE150 at Novogene Inc.

treatment_protocol: Cells stably expressing the Cas9 endonuclease were established via transduction of LentiCas9-blast (Addgene) lentivirus and select by blasticidin (20 g/ml; Gibco). The lentiviral sgRNA transduced cells were selected by puromycin (1 μg/ml; Gibco).

tag: manipulation

tag: sgrna


title: v65-WT_IAPez


title: 5OSF: Oral Submucous fibrosis


title: 6OSF: Oral Submucous fibrosis


title: PC-3_shHDAC5_DMSO_Rep1


title: 4OSF: Oral Submucous fibrosis


title: MV4-11_sgCtrl#2

description:
Eukaryotic mRNA directional library
FKRN190313850


title: WT_WGBS

description: WGBS

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm9 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads).
Genome_build: mm9
processed data files format and content: bigWig file of 10X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

extract_protocol:
Purelink Genomic DNA mini kit (Invitrogen)
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)


title: PC-3_shNC_DMSO_Rep1


title: TKO-L-p0_IAP


title: PC-3_shNC_DMSO_Rep2


title: MV4-11_sgKDSR#1

description:
Eukaryotic mRNA directional library
FKRN190313851


title: DKO0_singlecell_9_P5

data_processing:
Library strategy: BS-Amplicon
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the IAPEz-int and LTR1 sequence with bsmap using the following parameter: -v 0.1 -s 16 -w 100 -S 1 -R -u -q 20
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads).
Genome_build: IAP sequence
processed data files format and content: bigWig file of 10X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

treatment_protocol: Passaged 5 times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid


title: PC-3_shNC_DMSO_Rep3


title: DKO0-p5_IAP


title: DKO0_singlecell_6_P5


title: MV4-11_sgCtrl#1

description:
Eukaryotic mRNA directional library
FKRN190313849


title: MOLM13_sgKDSR#2

description:
Eukaryotic mRNA directional library
FKRN190313848


title: DKO0_singlecell_8_P5


title: 3OSF: Oral Submucous fibrosis


title: DKO0_singlecell_5_P5


title: DKO0-p1_IAP


title: C-3

city: Gui'yang

first: hu

middle: li

last: juan

address: 116 Baoshan North Road, Guiyang City, Guizhou Province, China

country: China

institute: Guizhou Normal University

description:
Brassica napus L
C_3

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ZS11 genome using HISAT2.
The FPKM (Fragments per Kilobase of transcript per Million mapped reads) was calculated.
The GO annotations for the DEGs in leaf were determined by using Blast2GO.
Genome_build: ZS11
Supplementary_files_format_and_content: gene.fpkm.matrix.annot.txt:Matrix table with raw gene counts for every gene and every sample.

organism: Brassica napus

source_name: Leaves

extract_protocol:
The leaves were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: aneuploidy Brassica napus cv. "null"

value: Leaves

value: 30 days after planting


title: 1OSF: Oral Submucous fibrosis


title: v65-WT_IAP


title: 2OSF: Oral Submucous fibrosis


title: MOLM13_sgCtrl#2

description:
Eukaryotic mRNA directional library
FKRN190313846


title: DKO0_singlecell_7_P5


title: 5N: normal buccal mucosa

source_name: normal mucosa

value: normal buccal mucosa


title: DKO0-p5_L1mdT


title: MOLM13_sgKDSR#1

description:
Eukaryotic mRNA directional library
FKRN190313847


title: DKO0_singlecell_2_P5


title: C-1

description:
Brassica napus L
C_1


title: C-2

description:
Brassica napus L
C_2


title: DKO0_singlecell_3_P5


title: DKO0-p1_L1mdT


title: O-2

description:
Brassica napus L
A_2

value: euploid Brassica napus cv. "Oro"


title: DKO0-p5_L1mdA


title: TKO-L-p0_L1mdT

value: Dnmt3a + Dnmt3b KO + Dnmt1 shRNA


title: O-3

description:
Brassica napus L
A_3


title: Nano_2

city: Tianjin

first: Shuai

last: Li

state: Tianjin

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

description:
PCR amplicon
Nanobody library generated by ldsDNA

data_processing:
Paired-end reads were assigned to each sample according to the unique barcodes.
Reads were filtered by QIIME quality filters.
Paired-end reads from the original DNA fragments were merged using FLASH, a very fast and accurate analysis tool which was designed to merge paired-end reads when there are overlaps between reads 1 and reads 2.
Supplementary_files_format_and_content: fasta files, containing nucleotide sequence of the nanobody library, were generated for each sample.

growth_protocol: HEK293T cell line was maintained in Dulbecco’s modified Eagle medium (DMEM) (Thermo Fisher) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution at 37℃ with 5% CO2.

extract_protocol:
48 h after transfection, total RNAs were extracted with RNAiso Plus (TaKaRa) reagent. cDNA was synthesized by PrimeScript TM RT reagent Kit with gDNA Eraser (TaKaRa) following standard protocol. KOD DNA polymerase was used to amplify the CDR1-3 encoding sequences .
Library construction and high-throughput sequencing were conducted by Novogene (Tianjin, China). Sequencing libraries were generated using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina) following the manufacturer’s recommendations, and the index codes were added.
The library quality was assessed on the Qubit Fluorometer and Agilent Bioanalyzer 2100 system. At last, the library was sequenced on an Illumina NovaSeq 6000 system and 250-bp paired-end (PE) reads were generated.

treatment_protocol: HEK293T cells were seeded into 6-well plates the day before transfection (60% - 70% confluency). 500 ng/well of each input amplicons (1000ng/well in total) were co-transfected into HEK293T cells with Lipofectamine 2000 (Invitrogen) reagent following standard protocol.

tag: barcode 1

value: GGCTAC

tag: barcode 2

value: CGGAAT


title: DKO0_singlecell_1_P5


title: Pf_CDP_Input

city: Chennai

first: Arumugam

last: Rajavelu

state: Tamil Nadu

address: Adayar

institute: IITM

data_processing:
FastQC for quality analysis and Cutadapt for adaptor trimming
ChIP seq reads were aligned to PlasmoDB-37 using Bowtie2-build
Peak calling was performed using MACS3 tool
ChIP-seq signals were background subtracted using MACS3 bdgcmp tool
multiBigwigSummary
Genome_build: PlasmoDB-37
Supplementary_files_format_and_content: Deeptools was used for viualization
Supplementary_files_format_and_content: Bamcoverage tool was used to generate bigwig files from the normalized ChIP datasets

organism: Plasmodium falciparum NF54

source_name: Plasmodium falciparum culture

growth_protocol: Asexual blood stages of P. falciparum 3D7 strain was cultured at 5% hematocrit using advanced RPMI 1640 supplemented with 2 mM L- glutamine, 0.6% Albumax II and 10% human O+ Serum.

extract_protocol:
The parasites were released from infected RBCs by lysis with 0.15 % saponin. Crosslinked chromatin was prepared by adding 1% formaldehyde to the culture for 5 min followed by the addition of glycine to 0.125 M final concentration for 5 minutes to stop the cross-linking. Chromatin was sheared by sonication in a Bioruptor UCD-200 (Diagenode) for 10 min at 30 s intervals, power setting high, to a size of 300–800 bp. ChIP was performed by adding 1.8 µg of H3K64me3 antibodies to ChIP buffer (100 mM NaCl, 20 mM Tris pH-7.5, 6 mM EDTA, 1% Triton X- 100). The three respective RBC stage samples of wild-type 3D7 were added to the mixture and incubated at 4 °C for overnight, followed by the addition of 15 μl protein A Dynabeads and further incubated for 4 h. After washing with buffers containing 180 mM NaCl, immuno-precipitated DNA was eluted and purified using PCR purification columns.
Libraries for ChIP sequencing were prepared using NEB Next Ultra II DNA Library preparation kit. In brief, ChIP DNA and the Input DNA are subjected to various enzymatic steps for repair the ends and tailing with dA-tail followed by ligation of adapter sequences. These adapter ligated fragments are then size selected using SPRI beads. Next, the size selected fragments are indexed during limited cycle PCR to generate final libraries for paired-end sequencing. The resulting libraries are quantified before getting sequenced on Illumina HiSeq 2500/4000 system to generate 2X50 bp sequence reads.

value: input

value: Untreated


title: DKO0_singlecell_4_P5

value: Dnmt3a + Dnmt3b KO


title: Nano_3

value: CTAGCT


title: O-1

description:
Brassica napus L
A_1


title: 4N: normal buccal mucosa


title: 3N: normal buccal mucosa


title: MOLM13_sgCtrl#1

description:
Eukaryotic mRNA directional library
FKRN190313845

tag: cell line


title: DKO0_Uhrf1_C5_P15

description:
DKO_UHRF1_C5_P15_10X.bw
WGBS

treatment_protocol: CRISPR Cas9 mediated knockout of Uhrf1, passaged 15 times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid

value: Dnmt3a + Dnmt3b + Uhrf1 KO


title: Nano_1

value: CCAACA


title: MPRA plasmid library - chimp HAR sequences

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

data_processing:
Library strategy: MPRA
To identify HAR barcodes, the sequence immediately preceding the adapter sequence was isolated, and the occurrence of each barcode counted
To compare to the reference 10,690 barcodes, each barcode’s Levenstein distance was calculated with respect to all reference barcodes using the stringdist package, and the minimum value was taken for each barcode
Multiple probes were summarized by taking the mean of each probe
Data was normalized to account for effective logFC differences across uneven library sizes by using the Trimmed Means of M normalization as implemented in the edgeR package
The RNA matrix was created by dividing each sample’s RNA value by the respective plasmid DNA
HARs with significant enhancer activity were identified using a one-sided one-sample T-test of the three biological replicates to identify HARs with log2 mRNA/DNA>0. This T-test was performed independently using the human and chimpanzee orthologs as well as the data from N2A and SH-SY5Y cells, and those with a p-value <0.05 in at least one of these samples were considered to have significant enhancer activity. False discovery rates were also identified by shuffling the MPRA data between HARs and samples and recomputing the p-values, to identify the proportion of enhancers identified at a given p-value threshold that may be the result of a falsely identified enhancer. A two-sided paired T-test was used to identify HARs with significantly different log2(mRNA/DNA) ratios between the human and chimpanzee orthologs.
Supplementary_files_format_and_content: tab-delimited file of normalized reporter expression from human or chimp sequence of each assayed HAR

organism: unidentified plasmid

source_name: plasmid library for transfection

growth_protocol: Neuro2A/N2A cells (ATCC, CCL-131) were grown in 10% fetal bovine serum, Dulbecco’s Modified Eagle Medium, and 1% Penicillin-Streptomycin. SH-SY5Y cell (ATCC, CRL-2266) medium was 10% fetal bovine serum, Dulbecco’s Modified Eagle Medium/F12, and 1% Penicillin-Streptomycin. Both cell lines were maintained in a 5% CO2 incubator at 37oC.

extract_protocol:
mRNA was isolated using TRIzol reagent (Invitrogen, 15596018)
Resulting Tag-seq amplified cDNA was deep sequenced using the Illumina Hi-Seq X with 150-bp paired-end reads.

treatment_protocol: Molecular Inversion Probes (MIPs) targeting flanking regions of all HAR sequences were designed using the MIPgen program (Boyle et al., 2014) and manufactured as a pool by CustomArray (Bothell, WA). Target genomic sequences from both human (Promega, G1521) and chimpanzee DNA (Coriell, NS03489) were captured as previously described (Cantsilieris et al., 2017) and purified using Agencourt AMPure XP beads at 0.9X concentration (Beckman-Coulter, A63881). The MPRA assay then was conducted as previously described (Melnikov et al., 2014). Briefly, the captures were cloned into modified pMPRA1 vector (Addgene, 49349). The only modification to the pMPRA1 vector was the addition of an AsiSI restriction site used for inserting our captured DNA fragments. The luciferase gene and minimal promoter (pMPRA_donor2, Addgene, 49353) was then cloned into the pMPRA1_Capture construct pool. The transfection of the MPRA libraries was performed with five replicates per condition, and the experiment was conducted in triplicate. The cells (N2A and SH-SY5Y) were grown as adherent cultures for 24hr in 15 cm plates. Then, 20ug of MPRA constructs and 4ug of a fluorescent reporter construct per plate were transfected into cells with Lipofectamine LTX reagent (Thermo Fisher, A12621). The cells were checked for fluorescent reporter expression at 24hr and harvested 48hr post-transfection.

tag: mpra species

value: chimp


title: DKO0_Uhrf1_A10_P15

description:
DKO_UHRF1_A10_P15_10X.bw
WGBS

value: mESC


title: PfCDP_ChIP_Replicate 1

value: PfCD-antibody, raised in mouse

tag: treatment


title: TKO-L-p0_L1mdA


title: v65-WT_L1mdA

value: WT


title: MPRA plasmid library - human HAR sequences

value: human


title: TKOL_P10

description: WGBS


title: 2N: normal buccal mucosa


title: DKO0_P25

description: WGBS

treatment_protocol: Passaged 25 times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid


title: I27695-L1

status: Public on Jul 23 2021

city: Kiel

first: Joana

middle: Pimenta

last: Bernardes

address: Am Botanischen Garten 11

department: Systems Immunology

institute: Institute of Clinical Molecular Biology

data_processing:
Merge re-sequenced FastQ files (cat)
Read QC (FastQC)
Adapter and quality trimming (Trim Galore!)
Removal of ribosomal RNA (SortMeRNA)
Alignment using  STAR
Sort and index alignments (SAMtools)
Duplicate read marking (picard MarkDuplicates)
Transcript assembly and quantification (StringTie)
Create bigWig coverage files (BEDTools, bedGraphToBigWig)
Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks (MultiQC)
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts for individual samples
Supplementary_files_format_and_content: Norm counts for individual samples

source_name: hepatic sinusoidal ECs

growth_protocol: Age and sex-matched C57BL/6J mice.

extract_protocol:
FACS-sorting of purified hepatic ECs selecting for hepatic sinusoidal ECs. Extraction of total EC RNA
Whole RNA libraries were prepared using TruSeq RNA Library Prep technology and samples were sequenced using HiSeq 4000 (1x50bp).

treatment_protocol: 5 germ-free and 6 conventionally raised mice.

value: CONV-R

tag: replicate


title: I27697-L1


title: I27702-L1

value: Germ-free


title: I27701-L1


title: I27699-L1


title: I27703-L1


title: I27692-L1


title: I27694-L1


title: I27693-L1


title: human blastocyst #4

city: London

first: Hui

last: Xiao

address: 237 Fulham Road

institute: The Institute of Cancer Research

hyb_protocol: GeneChip® Human Genome U133 Plus 2.0 Array

scan_protocol: data were visualised using MIAMIVICE software

data_processing: The raw microarray CEL files were processed and normalised by using the Robust MultiArray (RMA) normalization. Detection calls was performed on the normalised data by using the mas5calls  function provided by the R package affy

source_name: human blastocyst

label_protocol: biotin-16-dUTP labelling by using EpiLabel™

growth_protocol: Embryos were developed to blastocyst stage in undisturbed culture

extract_protocol: PolyAPCR was used to amplify all polyadenylated RNA in a single sample.

treatment_protocol: Blastocysts were developed in the EmbryoScope™ incubator (Fertilitech) at 5% O2, with remote imaging allowing embryos to remain in undisturbed culture.

value: human blastocyst


title: human blastocyst #6


title: human blastocyst #5


title: human blastocyst #3


title: human blastocyst #7


title: PfCDP_ChIP_Replicate 2

tag: chip antibody


title: human blastocyst #2


title: human blastocyst #10


title: human blastocyst #1


title: human blastocyst #8


title: human blastocyst #9


title: 1N: normal buccal mucosa

tag: tissue

value: normal buccal mucosa


title: RNA_Hai_5_S14

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description: RNA-Seq

data_processing:
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and ChIP-Seq and HiC reads were mapped using bowtie2
RNA-Seq read counting performed using HT-seq and CRISPR count tables were made using mageck
BAM to bedgraph performed using bedtools bedgraph to bigwig performed using bedGraphToBigWig v4
Genome_build: mm10
Supplementary_files_format_and_content: BigWig and count tables

source_name: MC38 cells

growth_protocol:
DMEM+10% FBS
DMEM+10% FBS

extract_protocol:
Qiagen RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
Qiagen RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA_1_S10

description: RNA-Seq

value: wild type


title: RNA_Hai_8_S16

description: RNA-Seq


title: RNA_Hai_10_S17

description: RNA-Seq


title: RNA_8_S16

description: RNA-Seq


title: RNA_5_S14

description: RNA-Seq


title: RNA_Hai_3_S12

description: RNA-Seq


title: RNA_Hai_1_S10

description: RNA-Seq


title: RNA_Hai_7_S15

description: RNA-Seq


title: RNA_Hai_4_S13

description: RNA-Seq


title: RNA_11_S18

description: RNA-Seq


title: HiC_SgSetdb1_5_S9

description: Hi-C

extract_protocol:
Arima-HiC+ kit for studying 3D genome sequence and structure
library was constructed with KAPA Hyper Prep protocol Cat no# 07962347001 Kit code: KK8502.
Qiagen RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA_Hai_11_S18

description: RNA-Seq


title: RNA_3_S12

description: RNA-Seq


title: v65-WT_L1mdT

data_processing:
Library strategy: BS-Amplicon
CpG methylation states were determined using BiQAnalyzerHT, filtering for a sequence identity of >= 0.8 (reference sequence for IAP and IAPez have been shortened in order to obtain a better mapping of the sequencing reads) and strand-specific methylation patterns were obtained using Hairpinanalyzer V0.3 (Mathias Bader and Julia Arand, available under: https://github.com/PascalGiehr/Hairpinanalyzer), filtering for a linker conversion rate of >= 0.8. H(O)TA was applied in order to determine enzyme efficiencies.
Genome_build: mm9
processed data files format and content: csv containing read count statistics

extract_protocol:
Genomic DNA was isolated from cells through phenol-chloroform extraction
200 ng of genomic DNA was digested with 10 U of BsaWI (NEB), DdeI (NEB), Eco47I (Thermo Fisher Sc.) or MspI (Thermo Fisher Sc.), incubated for 16 h at 60°C (BsaWI) or 37°C (DdeI, Eco47I and MspI) and afterwards heat inactivated. 50 pmol of endonuclease specific hairpin-linker was ligated in a 20 µl reaction at 16 °C for 3 h. Bisulfite conversion was done using Zymo’s EZ DNA Methylation-Gold Kit according to manufacturer’s instructions. Bisulfite treated Hairpin-DNA was eluted in 20 µl Elution Buffer. PCR was performed in 30 µl reactions with 2 µl of Hairpin-Bisulfite template and 37 PCR cycles using HotFirePol®DNA Polymerase (Solis BioDyne) or HotStarTaq DNA Polymerase (Qiagen). PCR products were purified from a 1.2% agarose gel using Avegene’s GenepHlow™ Gel/PCR Kit according to manufacturer’s instructions and eluted in 20 µl 0.1x TE buffer. Amplicons were indexed in a 50 µl PCR using specific TruSeq indices and 6 PCR cycles. Index PCRs were purified with 1.1x AMPure XP beads (Beckman Coulter). Amplicons were sequenced on an Illumina MiSeq in a 2x250 bp sequencing mode


title: RNA_10_S17

description: RNA-Seq


title: RNA_4_S13

description: RNA-Seq


title: HiC_lacZ_S5

description: Hi-C


title: HiC_SgSetdb1_2_S8

description: Hi-C


title: HiC_SgAtf7ip_2_S7

description: Hi-C


title: CRISPR_R2_S12

description: OTHER: CRISPR

source_name: Kras G12D/ Trp53-/- LUAD cells

growth_protocol:
RPMI+10% FBS
DMEM+10% FBS

extract_protocol:
Qiagen Dneasy Blood& Tissue Kit
350bp sgRNA cassette was amplified from gDNA of virally transduced cells.  Library contains X sgRNA; therefore (1000)X reads/sample are required to maintain 1000x representation of each sgRNA.  Each sample was prepared using unique reverse primer to incorporate indexes for multiplexing.
Qiagen RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA_2_S11

description: RNA-Seq


title: RNA_7_S15

description: RNA-Seq


title: HiC_SgAtf7ip_1_S6

description: Hi-C


title: CRISPR_R2_low_S16

description: OTHER: CRISPR

value: SIINFEKL low


title: CRISPR_R2_high_S15

description: OTHER: CRISPR

value: SIINFEKL high


title: CRISPR_R1_S11

description: OTHER: CRISPR


title: ChIP_s4blue_S10

description: ChIP-Seq

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. We used Active Motif ChIP-IT High Sensitivity protocol (catalog #53040)
library was constructed with KAPA Hyper Prep protocol Cat no# 07962347001 Kit code: KK8502.
Qiagen RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ChIP_s2blue_S9

description: ChIP-Seq


title: ChIP_s5_S5

description: ChIP-Seq


title: ChIP_s5blue_S11

description: ChIP-Seq


title: ChIP_s4_S4

description: ChIP-Seq


title: ChIP_s2_S3

description: ChIP-Seq


title: CRISPR_R1_low_S14

description: OTHER: CRISPR


title: ChIP_lacz_S6

description: ChIP-Seq


title: CRISPR_R1_high_S13

description: OTHER: CRISPR


title: ChIP_laczblue_S12

description: ChIP-Seq


title: ChIP_a2_S2

description: ChIP-Seq


title: ChIP_a2blue_S8

description: ChIP-Seq


title: ChIP_a1blue_S7

description: ChIP-Seq


title: ChIP_a1_S1

description: ChIP-Seq


title: NA-PTB-ctrl3

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

description: Immunoprecipitated RNA

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using Ensembl GRCm38 as reference
Normalization (TMM), quantitation and differential expression analysis using EdgeR
Genome_build: mm10

source_name: Immunoprecipitation from Sciatic nerve axoplasm

extract_protocol:
For enriched axoplasm extraction Sciatic nerves (SN) or Dorsal root (DR) tissues were freshly dissected and collected in Nuclear Transport buffer (TB) at a ratio of 1 SN or 3DR / 50 ml buffer (TB: 20 mM Hepes, 110 mM KAc, 5 mM MgAc, pH 7.4 supplemented with Complete protease inhibitor EDTA free, 1/50 dilution of 1 tablet reconstituted in 1ml water, as recommended by the manufacturer (Roche 1187358000), phosphatase inhibitor cocktail 2 (1/1000, Sigma 5726), phosphatase inhibitor cocktail 3 (1/1000, Sigma P0044) and RNAse inhibitors (200U/ml, RNAseIn, Promega N251B)). Tissue was manually grinded with a micropestle in Eppendorf tube until it lost its fibrous consistency. Lysates were centrifuged 10,000 g for 10 minutes at 4°C and pellet was discarded.
approximately 200ug of axoplasm/protein lysates were incubated with 10ug antibody (anti-nucleolin: abcam, ab50279 / Anti-PTBP1: Santa Cruz Biotechnology, sc-16547) for 3 hours, then supplemented with 100ml Protein G magnetic beads (Dynabeads, Thermo Fisher Scientific 10004D), pre-blocked with salmon sperm DNA (10ul DNA per 100ul beads for 1 hour 4°C), for additional 1 hour. Incubation buffer was adjusted to final 0.1% NP40 to avoid beads aggregation. All incubation steps were done at 4°C with overhead rotation. Beads were washed with increasing NP40 concentration as follows: TB-0.1% NP40 for 3-5 minutes, TB-0.5% NP40 3-5 minutes, TB-1% NP40 1 minute, TB- no detergent 3-5 minutes, then transferred to a clean Eppendorf tube in TB without detergent.
RNA was extracted from the beads using Qiagen RNeasy micro kit (Qiagen, 74004) as following the manufacturer protocol. Briefly, samples were lysed in ± 300l RLT buffer supplemented with 400mM DTT by repeated vortexing (5 times, 4 seconds on low speed). Supernatants were kept and supplemented with 70% ethanol to reach 150% of recovered volume. Samples were loaded on columns and manufacturer protocol was followed. DNase treatment was conducted on-columns for 10 minutes. Elution of RNA from the columns was done using 13l DNase/RNase free water.
SMART-seq v4 RNA Ultra Low Input RNAK kit (10ng) and Nextera XT

treatment_protocol: Mice were anesthetized with an intraperitoneal injection of xylazine and ketamine (10 mg/kg body weight). A 1-cm-long incision was made in the skin of the thigh perpendicular to the femur. A small incision was made between the thigh muscles and the muscles were separated by insertion and opening of the tip of the scissors between the muscles. The sciatic nerve was identified and pulled out using 45º forceps. The tissue was crushed using fine forceps (Dumont no. 4) two times for 30 seconds at mid- thigh level. The sciatic was positioned back in its place by gently pulling the hind leg. The incision was closed using reflex wound clips.

tag: sample type

value: Control immunoprecipitation PTBP1

tag: injuy condition

value: Naive


title: NA-PTB1

description: Immunoprecipitated RNA

value: PTBP1 immunoprecipitation


title: NA-Nuc2

description: Immunoprecipitated RNA

value: Nucleolin immunoprecipitation


title: NA-PTB-ctrl1

description: Immunoprecipitated RNA


title: NA-PTB-ctrl2

description: Immunoprecipitated RNA


title: NA-Nuc3

description: Immunoprecipitated RNA


title: NA-Nuc1

description: Immunoprecipitated RNA


title: NA-Nuc-ctrl3

description: Immunoprecipitated RNA

value: Control immunoprecipitation nucleolin


title: NA-Nuc-ctrl1

description: Immunoprecipitated RNA


title: NA-PTB2

description: Immunoprecipitated RNA


title: NA-PTB3

description: Immunoprecipitated RNA


title: NA-Nuc-ctrl2

description: Immunoprecipitated RNA


title: ChIP_input-lacZ_S13

description: ChIP-Seq


title: NA-Input3

description: Total RNA

source_name: Sciatic nerve axoplasm

value: Input


title: NA-Input2

description: Total RNA


title: Inj-PTB-ctrl2

description: Immunoprecipitated RNA

value: 7 days post Sciatic nerve crush


title: Inj-Nuc3

description: Immunoprecipitated RNA


title: Inj-PTB2

description: Immunoprecipitated RNA


title: NA-Input1

description: Total RNA


title: Inj-PTB1

description: Immunoprecipitated RNA


title: Inj-Nuc2

description: Immunoprecipitated RNA


title: Inj-Nuc1

description: Immunoprecipitated RNA


title: Inj-Nuc-ctrl2

description: Immunoprecipitated RNA


title: Inj-Nuc-ctrl3

description: Immunoprecipitated RNA


title: Inj-Input3

description: Total RNA


title: Inj-Nuc-ctrl1

description: Immunoprecipitated RNA


title: Inj-Input2

description: Total RNA


title: Inj-Input1

description: Total RNA


title: SN-Kif5A-2

description:
Immunoprecipitated total RNA
Complete_geneList_EdgeR

source_name: IP from Sciatic Nerves

extract_protocol:
For enriched axoplasm extraction Sciatic nerves (SN) or Dorsal root (DR) tissues were freshly dissected and collected in Nuclear Transport buffer (TB) at a ratio of 1 SN or 3DR / 50 ml buffer (TB: 20 mM Hepes, 110 mM KAc, 5 mM MgAc, pH 7.4 supplemented with Complete protease inhibitor EDTA free, 1/50 dilution of 1 tablet reconstituted in 1ml water, as recommended by the manufacturer (Roche 1187358000), phosphatase inhibitor cocktail 2 (1/1000, Sigma 5726), phosphatase inhibitor cocktail 3 (1/1000, Sigma P0044) and RNAse inhibitors (200U/ml, RNAseIn, Promega N251B)). Tissue was manually grinded with a micropestle in Eppendorf tube until it lost its fibrous consistency. Lysates were centrifuged 10,000 g for 10 minutes at 4°C and pellet was discarded.
approximately 200ug of axoplasm/protein lysates were incubated with 10ug antibody for 3 hours, then supplemented with 100ml Protein G magnetic beads (Dynabeads, Thermo Fisher Scientific 10004D), pre-blocked with salmon sperm DNA (10ml DNA pwe 100ml beads for 1 hour 4°C), for additional 1 hour. Incubation buffer was adjusted to final 0.1% NP40 to avoid beads aggregation. All incubation steps were done at 4°C with overhead rotation. Beads were washed with increasing NP40 concentration as follows: TB-0.1% NP40 for 3-5 minutes, TB-0.5% NP40 3-5 minutes, TB-1% NP40 1 minute, TB- no detergent 3-5 minutes, then transferred to a clean Eppendorf tube in TB without detergent.
RNA was extracted from the beads using Qiagen RNeasy micro kit (Qiagen, 74004) as following the manufacturer protocol. Briefly, samples were lysed in ± 300l RLT buffer supplemented with 400mM DTT by repeated vortexing (5 times, 4 seconds on low speed). Supernatants were kept and supplemented with 70% ethanol to reach 150% of recovered volume. Samples were loaded on columns and manufacturer protocol was followed. DNase treatment was conducted on-columns for 10 minutes. Elution of RNA from the columns was done using 13l DNase/RNase free water.
SMART-Sq v4 RNA Ultra Low Input (10pg) + Nextera XT library

value: Sciatic nerve

tag: antibody

value: IP with Rabbit anti Kif5A (Abacm, ab5628)


title: SN-Kif5A-1

tag: strain


title: SN-Kif5A-3


title: SN-Input-1

description:
Total RNA
Complete_geneList_EdgeR

source_name: Input Sciatic nerves

value: Input axoplasm


title: SN-IgG-3

value: IP with Rabbit IgG (Abcam, ab171870)


title: SN-Input-2

description:
Total RNA
Complete_geneList_EdgeR


title: Inj-PTB3

description: Immunoprecipitated RNA


title: Inj-PTB-ctrl3

description: Immunoprecipitated RNA


title: SN-Input-3

description:
Total RNA
Complete_geneList_EdgeR


title: Inj-PTB-ctrl1

description: Immunoprecipitated RNA


title: SN-IgG-1


title: DR-Kif5A-3

source_name: IP from dorsal root

value: Dorsal root


title: DR-Kif5A-2


title: DR-Kif5A-1


title: DR-IgG-1


title: DR-Input-1

description:
Total RNA
Complete_geneList_EdgeR

source_name: Input Dorsal roots


title: DR-IgG-2


title: DR-Input-2

description:
Total RNA
Complete_geneList_EdgeR


title: WT_CB3

source_name: Soma of cultured dorsal root ganglia neurons

extract_protocol:
RNA was extracted using Qiagen RNeasy micro kit, following the manufacturer protocol. Briefly, samples were lysed in ± 300l RLT buffer supplemented with 400mM DTT by repeated vortexing (5 times, 4 seconds on low speed). Supernatants were kept and supplemented with 70% ethanol to reach 150% of recovered volume. Samples were loaded on columns and manufacturer protocol was followed. DNase treatment was conducted on-columns for 10 minutes. Elution of RNA from the columns was done using 13ul DNase/RNase free water.
TrueSeq Stranded RNA kit with RiboZero (Illumina )

treatment_protocol: Adult total DRGs from 1 mouse were collected in Hanks’ buffered saline solution (HBSS) supplemented with 5uM Hepes, 10uM D-Glucose with antibiotics as per manufacturer instructions. DRGs were treated with 100 U of papain (P4762, Sigma) for 20 minutes, followed by treatment with 1 mg/ml collagenase-II (11179179001, Roche) and 1.2 mg/ml dispase-II (04942078001, Roche) for additional 25-30 minutes. DRGs were mechanically triturated in HBSS by aspiration in a glass Pasteur pipette whose opening was narrowed by fire polishing and was pre-covered in serum containing media. Cells were then laid on a 20% Percoll cushion (in L15 media) and recovered through centrifugation at 1000 g for 8 min. Cells were washed briefly in growth media (F12, 10 % Fetal Bovine Serum (FBS), Primocin) and plated on pre-coated Millicell 1m cell-culture inserts (MCRP06H48, Millipore) and allowed to grow for 3 days prior to extraction. Pre-coating included a first step of coating with Poly-L-Lysin (P4832, Sigma) followed by Laminin (23017-015, Invitrogen).

tag: background strain

tag: genotype

value: GAR+/+

tag: compartment

value: Soma


title: WT_CB2


title: SN-IgG-2


title: WT_CB1


title: WT_axon3

source_name: Neurites of cultured dorsal root ganglia neurons

value: Neurites


title: WT_axon2


title: WT_axon1


title: het_axon3

value: GAR+/-


title: het_CB1


title: het_axon2


title: het_CB3


title: het_CB2


title: het_axon1


title: DKO0-p1_L1mdA

source_name: J1 mESC

tag: cell type

value: mESC

value: Dnmt3a + Dnmt3b KO


title: DR-Input-3

description:
Total RNA
Complete_geneList_EdgeR


title: ZT14_HA

city: College Station

first: Paul

last: Hardin

state: Texas

address: 3258 TAMU Dept of Biology Buttler Hall room 100H

institute: Texas A&M University

data_processing:
Basecalls performed using RTA software
Immunoprecipitated DNA libraries were sequenced using Illumina Hiseq 2500 system
Sequences from the different libraries (fastq format) were first mapped to the Drosophila genome (version dm3) using bowtie2
Only those reads that mapped uniquely to the Drosophila genome were sorted using the samtools suite
Peak calling was performed using the findPeaks program from the HOMER software suite
Genome_build: dm3
Supplementary_files_format_and_content: BW files were generated for each Sample
Supplementary_files_format_and_content: Matrix table with peak scores for each peak indentified

organism: Drosophila melanogaster

source_name: Fly heads

growth_protocol: Flies were reared on standard cornmeal/agar medium supplemented with yeast and kept in 12 hr light/12 hr dark (LD) cycles at 25oC.

extract_protocol:
Fly heads were removed, flash frozen on dry ice. Nuclei were isolated and crosslinked followed by DNA sonication. The Protein-DNA complexes were immunoprecipitated and ChIPped DNA is eluted for library prep.
DNA sequencing library construction was performed using NEBNext® Ultra™ DNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s instructions for end repair, adaptor ligation and size selection.

treatment_protocol: Flies were entrained  under a condition of 12 hr light/12 hr dark (LD) cycles at 25oC for 3 days prior the collection at ZT2 and ZT14 on the fourth day.

value: Heads


title: ZT2_CLK


title: ZT14_CLK


title: ZT2_HA


title: ZT14_INPUT


title: ZT2_INPUT


title: Sample 1030 Normal

last: Khavari

state: California

address: 269 Campus Drive CCSR 2150

department: Dermatology

institute: Stanford University School of Medicine

description:
CTR516
Exome sequencing
mutations.txt

data_processing:
Library strategy: WES
Reads were aligned to the hg38 reference genome using BWA MEM (version 0.7.17) to create BAM files. BAMs were then sorted, marked for PCR duplicates, and underwent base recalibration using GATK (version 4.1.8.1). Somatic variants were called using Mutect2 from GATK (version 4.1.8.1) and filtered with FilterMutectCalls with default settings.
Somatic Variants were annotated using Variant Effect Predictor (version 99) and vcf2maf (version 1.6.17).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: mutations.txt: Tab-delimited text file containing annotated somatic variants.

source_name: Skin

extract_protocol:
Tissue was minced with a scalpel, homogenized, and digested using SDS-Proteinase K. This was followed by RNase A incubation and DNA extraction using the Qiagen DNeasy Blood and Tissue kit.
Sequencing libraries were prepared using the Agilent SureSelect Human All Exon V5 (51Mb) target enrichment for whole exome capture and sequenced on the Illumina HiSeq platform with 2x100nt paired-end reads.

value: Skin

tag: condition

value: Normal Skin


title: Sample 1032 Normal

description:
CTR518
Exome sequencing
mutations.txt


title: Sample 1032 Tumor

description:
T518
Exome sequencing
mutations.txt

value: cSCC


title: Sample 1033 Normal

description:
CTR520
Exome sequencing
mutations.txt


title: Sample 1033 Tumor

description:
T520
Exome sequencing
mutations.txt


title: Sample 1031 Normal

description:
CTR517
Exome sequencing
mutations.txt


title: Sample 1031 Tumor

description:
T517
Exome sequencing
mutations.txt


title: I27696-L1

value: CONV-R


title: Sample 1028 Tumor

description:
T514
Exome sequencing
mutations.txt


title: Sample 1027 Tumor

description:
T512
Exome sequencing
mutations.txt


title: Sample 1029 Tumor

description:
T515
Exome sequencing
mutations.txt


title: Sample 1029 Normal

description:
CTR515
Exome sequencing
mutations.txt


title: Sample 1026 Tumor

description:
T510
Exome sequencing
mutations.txt


title: Sample 1027 Normal

description:
CTR512
Exome sequencing
mutations.txt


title: Sample 1028 Normal

description:
CTR514
Exome sequencing
mutations.txt


title: Sample 1025 Tumor

description:
T509
Exome sequencing
mutations.txt


title: Sample 1024 Tumor

description:
T508
Exome sequencing
mutations.txt


title: Sample 1026 Normal

description:
CTR510
Exome sequencing
mutations.txt


title: Sample 1025 Normal

description:
CTR509
Exome sequencing
mutations.txt


title: Sample 1024 Normal

description:
CTR508
Exome sequencing
mutations.txt


title: Sample 1023 Tumor

description:
T506
Exome sequencing
mutations.txt


title: Sample 1022 Normal

description:
CTR505
Exome sequencing
mutations.txt


title: DR-IgG-3


title: Sample 1021 Normal

description:
CTR503
Exome sequencing
mutations.txt


title: Sample 1023 Normal

description:
CTR506
Exome sequencing
mutations.txt


title: Sample 1022 Tumor

description:
T505
Exome sequencing
mutations.txt


title: Sample 1030 Tumor

description:
T516
Exome sequencing
mutations.txt


title: Sample 1021 Tumor

description:
T503
Exome sequencing
mutations.txt


title: Sample 1020 Tumor

description:
T502
Exome sequencing
mutations.txt


title: I27698-L1

value: Germ-free


title: Sample 1020 Normal

description:
CTR502
Exome sequencing
mutations.txt


title: Sample 1017 Normal

description:
CTR253
Exome sequencing
mutations.txt


title: Sample 1018 Tumor

description:
T500
Exome sequencing
mutations.txt


title: Sample 1018 Normal

description:
CTR500
Exome sequencing
mutations.txt


title: Sample 1017 Tumor

description:
T253
Exome sequencing
mutations.txt


title: Sample 1019 Normal

description:
CTR501
Exome sequencing
mutations.txt


title: Sample 1016 Normal

description:
CTR252
Exome sequencing
mutations.txt


title: Sample 1015 Normal

description:
CTR251
Exome sequencing
mutations.txt


title: Sample 1015 Tumor

description:
T251
Exome sequencing
mutations.txt


title: Sample 1016 Tumor

description:
T252
Exome sequencing
mutations.txt


title: Sample 1013 Tumor

description:
T248
Exome sequencing
mutations.txt


title: Sample 1013 Normal

description:
CTR248
Exome sequencing
mutations.txt


title: Sample 1012 Tumor

description:
T247
Exome sequencing
mutations.txt


title: Sample 1014 Normal

description:
CTR250
Exome sequencing
mutations.txt


title: Sample 1011 Tumor

description:
T238
Exome sequencing
mutations.txt


title: Sample 1011 Normal

description:
CTR238
Exome sequencing
mutations.txt


title: Sample 1010 Tumor

description:
T206
Exome sequencing
mutations.txt


title: Sample 1010 Normal

description:
CTR206
Exome sequencing
mutations.txt


title: Sample 1009 Normal

description:
CTR205
Exome sequencing
mutations.txt


title: Sample 1009 Tumor

description:
T205
Exome sequencing
mutations.txt


title: Sample 1007 Tumor

description:
T126
Exome sequencing
mutations.txt


title: Sample 1006 Normal

description:
CTR119
Exome sequencing
mutations.txt


title: Sample 1008 Tumor

description:
T203
Exome sequencing
mutations.txt


title: Sample 1007 Normal

description:
CTR126
Exome sequencing
mutations.txt


title: Sample 1008 Normal

description:
CTR203
Exome sequencing
mutations.txt


title: Sample 1019 Tumor

description:
T501
Exome sequencing
mutations.txt


title: Sample 1005 Tumor

description:
T107
Exome sequencing
mutations.txt


title: Sample 1006 Tumor

description:
T119
Exome sequencing
mutations.txt


title: Sample 1005 Normal

description:
CTR107
Exome sequencing
mutations.txt


title: Sample 1004 Tumor

description:
T106
Exome sequencing
mutations.txt


title: Sample 1002 Tumor

description:
T102
Exome sequencing
mutations.txt


title: Sample 1004 Normal

description:
CTR106
Exome sequencing
mutations.txt


title: Sample 1014 Tumor

description:
T250
Exome sequencing
mutations.txt


title: Sample 1003 Tumor

description:
T104
Exome sequencing
mutations.txt


title: Sample 1003 Normal

description:
CTR104
Exome sequencing
mutations.txt


title: Sample 1001 Tumor

description:
T101
Exome sequencing
mutations.txt


title: RNA_Mutant_Rep_3

description:
p4-MUTANT
counts.txt

data_processing:
Samples were quantified using Salmon (version 1.4) and mapped to the hg38 reference genome to generate isoform count matrices.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file containing isoform by sample count matrix.

molecule: polyA RNA

growth_protocol: Human fibroblasts were introduced into devitalized human dermis prior to seeding keratinocytes onto the basement membrane side. Human cSCC organoids were maintained for 8 days prior to harvesting.

extract_protocol:
Total RNA was then isolated from human SCC organoids using QIAshredder (Qiagen) and Trizol (ThermoFisher) followed by DNA removal with the TURBO DNA-free kit (Ambion) according to the manufacturer’s instructions.
RNA-Seq libraries were prepared with the mRNA Seq Sample Prep Kit (Illumina, Inc.) as recommended by the manufacturer.

value: Human cSCC organoid

value: COL11A1 mutant (G598A)


title: RNA_Mutant_Rep_2

description:
p3-MUTANT
counts.txt


title: RNA_WT_Rep_2

description:
p5-WT
counts.txt

value: COL11A1 WT


title: Sample 1012 Normal

description:
CTR247
Exome sequencing
mutations.txt


title: RNA_WT_Rep_3

description:
p6-WT
counts.txt


title: Sample 1001 Normal

description:
CTR101
Exome sequencing
mutations.txt


title: RNA_WT_Rep_1

description:
p2-WT
counts.txt


title: RNA_Mutant_Rep_1

description:
p1-MUTANT
counts.txt


title: CAP2-4 within-family controls (FCs)

city: Dallas

first: Donald

last: Glass

state: TX

address: 5323 Harry Hines Blvd, Mail Code 9069

institute: UT Southwestern Medical Center

data_processing:
Raw data from the machine were de-multiplexed and converted to fastq files using bcl2fastq (v2.17, Illumina)
The fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
mapped to hg19 reference genome using STAR (v2.5.3a)
Read counts were then generated using featureCounts (subread/v1.4.6)
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts of all samples in tab delimited text file

source_name: Immortalized lymphoblastoid cell line

extract_protocol:
Lymphoblastoid cells were grown in vitro and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: EBV-immortalized

tag: race

value: non-Hispanic Caucasian

value: unaffected family control


title: CAP2-2 within-family controls (FCs)


title: DGRSDX1-1 unrelated controls (UCs).

value: unrelated unaffected control


title: CAP2-1 proband

value: proband


title: SAM24292837 UC GNE006_10_182 Pos

city: South San Francisco

first: Jason

middle: A

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were based on Refseq canonical transcripts mapped to GRCh38. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from sorted human mucosal T cells from intestinal resection.

extract_protocol: RNA was extracted using Qiagen RNeasy kit as per manufacturer's protocol. Quality control of samples was done to determine RNA quantity and quality prior to their processing by RNA-seq. The concentration of RNA samples was determined using DS-11 spectrophotometer (DeNovix) and the integrity of RNA was determined by 2100 Bioanalyzer (Agilent Technologies). Approximately few ng of total RNA was used as an input material for the library generation using SMART-seq v4 Ultra Low Input RNA kit (Clontech). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq4000 (Illumina) to generate 30M of single end 50 base pair reads.

value: UC

tag: alphae

value: Pos


title: SAM24292845 Diverticulitis GNE006_10_191 Pos

value: Diverticulitis


title: SAM24292844 Diverticulitis GNE006_10_188 Neg

value: Neg


title: SAM24292847 Diverticulitis GNE006_10_196 Pos


title: SAM24292839 Diverticulitis GNE006_10_183 Pos


title: SAM24292851 UC GNE006_10_201 Pos


title: SAM24292846 Diverticulitis GNE006_10_191 Neg


title: Sample 1002 Normal

description:
CTR102
Exome sequencing
mutations.txt

value: Skin


title: SAM24292841 UC GNE006_10_187 Pos


title: SAM24292840 Diverticulitis GNE006_10_183 Neg


title: SAM24292842 UC GNE006_10_187 Neg


title: DGRSDX1-2 unrelated controls (UCs).


title: SAM24358904 Patient170 Y M Etrolizumab Week14 Ileum Active 1.33583405016517 Almac

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. We used GENCODE basic (v.27) gene models. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Ensembl Gene IDs, counts and nRPKM statistics.

source_name: RNA from human intestinal biopsy

extract_protocol: Biopsies from the etrolizumab clinical study were thawed, removed from RNAlater, homogenized with 0.1 mm glass beads and RNA was purified using Qiagen All-prep 96 kits. Quantity and quality of the RNA was assessed with a NanoDrop 8000 (Thermo Scientific) and Bioanalyzer, respectively. Sequence libraries were prepared from 0.1 ug of RNA using TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer's instructions.

value: Y

tag: Sex

value: M

value: Etrolizumab

tag: visit

tag: location

value: Ileum

value: Active

tag: sequencingcenter

value: Almac


title: SAM24358973 Patient161 Y M Etrolizumab Screen Ileum Active 1.47981335142568 Almac

tag: treatment

value: Screen


title: SAM24358822 Patient173 Y F Etrolizumab Week14 Colon Active 1.56338982857335 Almac

value: F

value: Colon


title: SAM24359019 Patient153 Y M Etrolizumab Screen Ileum Active 1.51933414375919 Almac


title: SAM24358782 Patient162 N M Etrolizumab Week14 Ileum Inactive 1.33859515499425 Almac

value: N

value: Inactive


title: SAM24358807 Patient154 N M Placebo Screen Colon Active 1.45153418945674 Almac

value: Placebo


title: SAM24292843 Diverticulitis GNE006_10_188 Pos


title: SAM24358832 Patient179 Y F Placebo Week14 Colon Active 1.33870573015122 Almac


title: SAM24358916 Patient152 Y F Etrolizumab Screen Colon Inactive 1.40758400268284 Almac


title: SAM24359078 Patient150 N F Etrolizumab Screen Colon Active 1.43020527475794 Almac


title: SAM24358992 Patient145 Y F Etrolizumab Week14 Colon Active 1.69717501623991 Almac


title: SAM24359026 Patient12 N F Etrolizumab Week14 Ileum Inactive 1.68351790906819 Almac


title: SAM24358880 Patient146 N M Placebo Screen Ileum Active 1.4343419433774 Almac


title: SAM24358861 Patient141 N M Etrolizumab Week14 Colon Active 1.52914071371547 Almac


title: SAM24358938 Patient143 Y F Etrolizumab Screen Ileum Active 1.51187651243856 Almac


title: SAM24358906 Patient136 N M Etrolizumab Screen Colon Active 1.26367036202682 Almac


title: SAM24358911 Patient138 Y F Etrolizumab Week14 Colon Active 1.44091624243352 Almac


title: SAM24359074 Patient135 Y F Etrolizumab Screen Ileum Active 1.04890929907953 Almac


title: SAM24359015 Patient142 Y F Etrolizumab Screen NA NA 1.26228482989277 Almac


title: SAM24292848 Diverticulitis GNE006_10_196 Neg


title: SAM24359003 Patient139 N F Etrolizumab Screen Colon Active 1.94798408962427 Almac


title: SAM24358814 Patient127 Y F Etrolizumab Week14 Colon Active 1.56548076851987 Almac


title: SAM24292852 UC GNE006_10_201 Neg

value: UC


title: SAM24358912 Patient126 N M Etrolizumab Screen Ileum Inactive 1.79105173390952 Almac


title: SAM24358886 Patient19 Y F Etrolizumab Screen Ileum Active 1.79125069762535 Almac


title: SAM24292838 UC GNE006_10_182 Neg


title: SAM24358965 Patient133 Y M Etrolizumab Screen Colon Active 1.57550760946028 Almac


title: SAM24358920 Patient126 N M Etrolizumab Week14 Ileum Inactive 0.744757884791543 Almac


title: SAM24358908 Patient9 N F Etrolizumab Screen Ileum Active 1.66476810233265 Almac


title: SAM24359042 Patient123 N M Placebo Screen NA NA 1.73674442921922 Almac


title: SAM24358812 Patient121 Y F Placebo Week14 Colon Active 1.83371229281879 Almac


title: SAM24359049 Patient104 N M Etrolizumab Screen Ileum Active 1.62643177932904 Almac


title: SAM24359091 Patient113 Y F Etrolizumab Screen Ileum Active 1.70807503455487 Almac


title: SAM24358907 Patient106 Y F Etrolizumab Week14 Colon Active 1.48120609004028 Almac


title: SAM24359081 Patient111 Y M Etrolizumab Week14 Colon Inactive 1.48110326104029 Almac


title: SAM24359098 Patient108 Y M Etrolizumab Screen Ileum Inactive 1.60971117342137 Almac


title: SAM24358998 Patient99 Y M Etrolizumab Screen Ileum Active 1.54184035866109 Almac


title: SAM24359084 Patient89 N M Etrolizumab Screen Colon Inactive 1.36830559249814 Almac


title: SAM24358932 Patient92 N F Etrolizumab Screen Colon Inactive 0.989156175912907 Almac


title: SAM24358773 Patient95 N F Etrolizumab Week14 Ileum Active 1.30005214324376 Almac


title: SAM24358987 Patient86 N F Placebo Screen Ileum Active 1.35970825687319 Almac


title: SAM24358955 Patient84 Y F Placebo Screen Ileum Active 1.06924959924252 Almac


title: SAM24359029 Patient85 Y F Etrolizumab Week14 Ileum Active 1.3978003036469 Almac


title: SAM24358887 Patient82 Y F Etrolizumab Screen Ileum Inactive 1.6188344652324 Almac


title: SAM24359018 Patient81 N M Etrolizumab Week14 Colon Active 1.45989573566254 Almac


title: SAM24359106 Patient79 Y F Etrolizumab Week14 Colon Active 1.13360986476642 Almac


title: SAM24359021 Patient83 Y F Etrolizumab Week14 Ileum Active 1.73848483099913 Almac


title: SAM24359471 Patient252 Y M Etrolizumab Screen Ileum Active 1.70698451252995 Almac


title: SAM24358924 Patient76 N M Etrolizumab Screen Colon Inactive 1.48467533927858 Almac


title: SAM24358909 Patient247 Y F Placebo Screen Ileum Active 1.51496596621681 Almac


title: SAM24358934 Patient124 Y F Placebo Screen Colon Active 1.357786153983 Almac


title: SAM24359063 Patient73 Y M Etrolizumab Screen NA NA 1.64486154544362 Almac


title: SAM24358958 Patient67 Y F Etrolizumab Screen Colon Active 1.12508277534471 Almac


title: SAM24358971 Patient83 Y F Etrolizumab Screen Ileum Active 1.34534358957035 Almac


title: SAM24359066 Patient96 Y M Etrolizumab Screen NA NA 1.29510016370573 Almac


title: SAM24358915 Patient106 Y F Etrolizumab Screen Colon Active 1.28118018186059 Almac


title: SAM24358967 Patient236 N M Etrolizumab Screen Ileum Inactive 2.19256125558248 Almac


title: SAM24359033 Patient238 Y M Etrolizumab Week14 Colon Active 1.75962305441655 Almac


title: SAM24358937 Patient247 Y F Placebo Week14 Ileum Active 1.25910009395661 Almac


title: SAM24358894 Patient74 N F Etrolizumab Screen Colon Active 1.37569143895328 Almac


title: SAM24358923 Patient92 N F Etrolizumab Week14 Ileum Active 1.38319166848031 Almac


title: SAM24359090 Patient235 Y F Placebo Week14 Ileum Active 1.29368702967867 Almac


title: SAM24358931 Patient233 Y F Etrolizumab Week14 Colon Active 1.31744839919364 Almac


title: SAM24358926 Patient211 N M Etrolizumab Screen Colon Active 1.46642067497214 Almac


title: SAM24358966 Patient225 Y F Etrolizumab Screen Ileum Active 1.04497349118583 Almac


title: SAM24359017 Patient236 N M Etrolizumab Week14 Ileum Inactive 1.73433980759175 Almac


title: SAM24358897 Patient224 Y F Etrolizumab Week14 Ileum Active 1.09736702111602 Almac


title: SAM24359001 Patient197 Y F Etrolizumab Week14 Ileum Active 1.95320644156882 Almac


title: SAM24358981 Patient234 N F Etrolizumab Screen Colon Active 1.97394113389663 Almac


title: SAM24358883 Patient205 Y M Etrolizumab Screen Colon Active 1.58182701054765 Almac


title: SAM24358944 Patient214 Y F Etrolizumab Week14 Ileum Active 1.78533896506747 Almac


title: SAM24359020 Patient195 Y M Etrolizumab Week14 Colon Active 1.68844583976897 Almac


title: SAM24359046 Patient199 N F Etrolizumab Screen Colon Active 1.19465435237613 Almac


title: SAM24358988 Patient194 Y F Etrolizumab Week14 Ileum Active 1.86035876962982 Almac


title: SAM24358969 Patient214 Y F Etrolizumab Screen Ileum Active 1.43112778220996 Almac


title: SAM24358885 Patient213 Y F Etrolizumab Screen Ileum Active 1.74480541926769 Almac


title: SAM24358888 Patient222 Y M Etrolizumab Screen Ileum Inactive 1.03326572585281 Almac


title: SAM24358978 Patient232 Y M Placebo Screen Colon Active 1.40443588393732 Almac


title: SAM24359474 Patient210 Y M Etrolizumab Screen Ileum Active 1.60866939347923 Almac


title: SAM24358928 Patient233 Y F Etrolizumab Screen Ileum Active 1.36658381483774 Almac


title: SAM24358896 Patient208 Y M Etrolizumab Screen Ileum Active 1.33202884175395 Almac


title: SAM24358890 Patient227 Y M Placebo Screen Colon Active 1.25945681592073 Almac


title: SAM24359099 Patient196 N M Etrolizumab Screen Colon Active 1.44850028195782 Almac


title: SAM24358930 Patient211 N M Etrolizumab Week14 NA NA 1.18536384960078 Almac


title: SAM24358895 Patient224 Y F Etrolizumab Screen Ileum Active 1.19024015771199 Almac


title: SAM24358900 Patient215 N F Etrolizumab Screen Colon Active 1.08696917088876 Almac


title: SAM24358868 Patient222 Y M Etrolizumab Week14 Colon Active 0.831263032701823 Almac


title: SAM24358878 Patient65 Y M Placebo Screen Ileum Active 1.24074715413724 Almac


title: SAM24358756 Patient202 N F Etrolizumab Week14 Ileum Active 1.66832736162325 Almac


title: SAM24358913 Patient193 Y F Placebo Screen Colon Active 1.21485273615673 Almac


title: SAM24358704 Patient200 Y M Placebo Week14 Colon Active 1.33834601809613 Almac


title: SAM24358918 Patient193 Y F Placebo Week14 Colon Active 1.43032101989769 Almac


title: SAM24359070 Patient190 N M Etrolizumab Week14 Colon Active 1.85834185693455 Almac


title: SAM24358961 Patient63 Y M Etrolizumab Screen Ileum Inactive 1.53471252028586 Almac


title: SAM24359061 Patient58 N F Etrolizumab Screen Colon Active 0.963447156655618 Almac


title: SAM24358953 Patient61 Y F Etrolizumab Screen Ileum Active 1.85476641292337 Almac


title: SAM24358810 Patient184 Y M Etrolizumab Screen Colon Inactive 1.40667857077306 Almac


title: SAM24358933 Patient187 Y F Etrolizumab Screen Ileum Active 1.46563241530222 Almac


title: SAM24358947 Patient63 Y M Etrolizumab Week14 Ileum Inactive 1.63264242435337 Almac


title: SAM24358903 Patient189 N F Etrolizumab Screen Colon Active 1.76596516836928 Almac


title: SAM24358951 Patient61 Y F Etrolizumab Week14 Ileum Active 1.3472879446523 Almac


title: SAM24358921 Patient187 Y F Etrolizumab Week14 Ileum Active 1.45553102598387 Almac


title: SAM24358919 Patient36 N M Placebo Screen Colon Inactive 1.3440393710668 Almac


title: SAM24358914 Patient52 Y F Etrolizumab Screen Ileum Active 1.49118367437446 Almac


title: SAM24358984 Patient21 Y F Etrolizumab Week14 Ileum Inactive 1.17300405235483 Almac


title: SAM24358927 Patient54 Y F Placebo Screen Ileum Active 1.41459211247667 Almac


title: SAM24358910 Patient28 Y F Etrolizumab Week14 Ileum Active 1.78531668311993 Almac


title: SAM24358882 Patient30 N M Etrolizumab Screen Ileum Active 1.66135561317039 Almac


title: SAM24358939 Patient28 Y F Etrolizumab Screen Ileum Active 1.58810014901479 Almac


title: SAM24358902 Patient60 Y F Etrolizumab Week14 Ileum Active 1.13101143637218 Almac


title: SAM24359044 Patient51 N M Etrolizumab Screen Ileum Active 1.62857341622343 Almac


title: SAM24358974 Patient46 Y M Etrolizumab Screen NA NA 1.48063763253517 Almac


title: SAM24358881 Patient44 N M Etrolizumab Screen Ileum Active 1.96543485506124 Almac


title: SAM24358985 Patient38 N F Etrolizumab Week14 Ileum Active 1.82587169886012 Almac


title: SAM24358889 Patient2 Y M Etrolizumab Screen Ileum Active 1.38690696598979 Almac


title: SAM24358999 Patient48 Y M Etrolizumab Week14 Colon Active 1.44163331137064 Almac


title: SAM24358905 Patient32 Y F Etrolizumab Screen Ileum Active 1.67069508573148 Almac


title: SAM24359104 Patient79 Y F Etrolizumab Screen Ileum Inactive 0.663774407580972 GNE

value: GNE


title: SAM24359095 Patient37 N F Etrolizumab Week14 Ileum Active 0.573036454270569 GNE


title: SAM24359089 Patient192 Y F Etrolizumab Week14 Colon Active 0.442140060737685 GNE


title: SAM24359088 Patient144 Y F Etrolizumab Week14 Colon Active 0.677648410796768 GNE


title: SAM24359087 Patient89 N M Etrolizumab Week14 Ileum Active 0.452482406134555 GNE


title: SAM24359103 Patient17 Y M Etrolizumab Screen Colon Active 0.476778847213831 GNE


title: SAM24359083 Patient192 Y F Etrolizumab Screen Colon Active 0.423906539371962 GNE


title: SAM24359079 Patient150 N F Etrolizumab Week14 Colon Active 0.403677317009702 GNE


title: SAM24359013 Patient48 Y M Etrolizumab Screen Colon Active 1.69090059624309 Almac


title: SAM24359072 Patient71 Y F Etrolizumab Week14 Colon Inactive 0.450736180193313 GNE


title: SAM24359093 Patient58 N F Etrolizumab Week14 Colon Active 0.737283015506073 GNE


title: SAM24359037 Patient6 N M Etrolizumab Screen Colon Active 0.514036348423806 GNE


title: SAM24359102 Patient166 Y F Etrolizumab Screen Ileum Active 0.579198225624011 GNE


title: SAM24359032 Patient199 N F Etrolizumab Week14 Ileum Active 0.408572234595874 GNE


title: SAM24359034 Patient6 N M Etrolizumab Week14 Colon Active 0.369355433198945 GNE


title: SAM24359082 Patient66 Y M Placebo Screen Colon Active 0.562531991083448 GNE


title: SAM24359080 Patient103 Y F Etrolizumab Week14 Ileum Inactive 0.557124083450933 GNE


title: SAM24359056 Patient102 Y F Etrolizumab Screen Ileum Inactive 0.519889558161615 GNE


title: SAM24359060 Patient135 Y F Etrolizumab Week14 Ileum Active 0.695200181455644 GNE


title: SAM24359051 Patient177 Y F Etrolizumab Screen Ileum Active 0.392603965684564 GNE


title: SAM24359050 Patient93 N F Placebo Screen NA NA 0.413979950056635 GNE


title: SAM24359048 Patient47 Y M Placebo Screen Ileum NA 0.527131525628113 GNE


title: SAM24359040 Patient26 Y F Etrolizumab Screen NA NA 0.549584721111796 GNE


title: SAM24359028 Patient177 Y F Etrolizumab Week14 Ileum Active 0.51420102206451 GNE


title: SAM24359031 Patient148 Y M Placebo Week14 Colon Active 0.401187574973767 GNE


title: SAM24359027 Patient68 Y M Etrolizumab Week14 Ileum Inactive 0.471838856255114 GNE


title: SAM24359025 Patient178 N M Etrolizumab Week14 Colon Active 0.674191751986521 GNE


title: SAM24359030 Patient47 Y M Placebo Week14 Colon Active 0.402852382353691 GNE


title: SAM24359096 Patient166 Y F Etrolizumab Week14 Colon Active 0.769365490671485 GNE


title: SAM24359100 Patient111 Y M Etrolizumab Screen Ileum Active 0.556432021706481 GNE


title: SAM24359023 Patient241 Y M Etrolizumab Week14 Ileum Active 0.718232323512686 GNE


title: SAM24359002 Patient188 N M Placebo Screen Colon Active 0.712207022649384 GNE


title: SAM24359011 Patient248 Y M Etrolizumab Screen Colon Active 0.650620849001612 GNE


title: SAM24359024 Patient123 N M Placebo Week14 Ileum Active 0.372138000921967 GNE


title: SAM24358990 Patient107 Y F Etrolizumab Week14 Colon Active 0.584782208685013 GNE


title: SAM24359022 Patient228 N F Etrolizumab Week14 Colon Active 0.368310942072465 GNE


title: SAM24358983 Patient223 Y F Placebo Screen Ileum Active 0.642624021738392 GNE


title: SAM24358970 Patient147 Y M Etrolizumab Screen Ileum Active 0.839764829044132 GNE


title: SAM24358979 Patient38 N F Etrolizumab Screen Ileum Active 0.768932813439224 GNE


title: SAM24358952 Patient27 Y F Etrolizumab Screen Ileum Active 0.63839571913048 GNE


title: SAM24358962 Patient4 Y M Placebo Screen Colon Active 0.607763115388128 GNE


title: SAM24358960 Patient165 N F Etrolizumab Screen Ileum Active 1.00596448161558 GNE


title: SAM24358949 Patient219 Y M Etrolizumab Week14 Ileum Active 0.779581215679047 GNE


title: SAM24358968 Patient163 N F Etrolizumab Screen Ileum Active 0.649727582222595 GNE


title: SAM24358959 Patient77 N M Etrolizumab Screen Ileum Active 0.575749570021822 GNE


title: SAM24358946 Patient133 Y M Etrolizumab Week14 Colon Active 0.61568492932463 GNE


title: SAM24358948 Patient212 N M Etrolizumab Week14 Ileum Active 0.800167812464321 GNE


title: SAM24358942 Patient165 N F Etrolizumab Week14 Ileum Active 0.539482783734792 GNE


title: SAM24358940 Patient145 Y F Etrolizumab Screen Colon Active 3.10956682882786 GNE


title: SAM24358852 Patient185 N F Etrolizumab Screen Ileum Inactive 1.7011028611082 GNE


title: SAM24358853 Patient1 Y M Etrolizumab Screen NA NA 0.903326893806885 GNE


title: SAM24358941 Patient163 N F Etrolizumab Week14 Ileum Active 1.01799213515747 GNE


title: SAM24359000 Patient164 Y M Etrolizumab Week14 Colon Active 0.567581499283838 GNE


title: SAM24359085 Patient144 Y F Etrolizumab Screen NA NA 0.468141685000887 GNE


title: SAM24359092 Patient37 N F Etrolizumab Screen Ileum Active 0.542749117105395 GNE


title: SAM24359086 Patient235 Y F Placebo Screen Colon Active 0.481967793611142 GNE


title: SAM24359101 Patient249 Y M Etrolizumab Screen Colon Active 0.521276707082835 GNE


title: SAM24359008 Patient197 Y F Etrolizumab Screen Colon Active 0.90468489830581 GNE


title: SAM24359010 Patient134 Y F Placebo Screen Ileum NA 1.2759919019223 GNE


title: SAM24359077 Patient103 Y F Etrolizumab Screen Colon Active 0.462848161896727 GNE


title: SAM24359053 Patient178 N M Etrolizumab Screen Ileum Active 0.436817280144217 GNE


title: SAM24358997 Patient110 N M Etrolizumab Screen Ileum Active 0.673544433356474 GNE


title: SAM24358996 Patient107 Y F Etrolizumab Screen Colon Active 0.732452348586439 GNE


title: SAM24358995 Patient164 Y M Etrolizumab Screen Colon Active 0.840745473932825 GNE


title: SAM24358993 Patient188 N M Placebo Week14 Colon Active 0.570048699560185 GNE


title: SAM24359004 Patient139 N F Etrolizumab Week14 Colon Active 0.520719352453665 GNE


title: SAM24358956 Patient212 N M Etrolizumab Screen NA NA 0.537487462021725 GNE


title: SAM24358976 Patient59 N F Etrolizumab Screen Colon Active 0.459441444844913 GNE


title: SAM24358982 Patient62 Y M Etrolizumab Screen Ileum Active 0.680614152961684 GNE


title: SAM24358991 Patient45 Y F Etrolizumab Week14 Ileum Active 0.55440681523115 GNE


title: SAM24358980 Patient21 Y F Etrolizumab Screen Ileum Inactive 0.824379066340912 GNE


title: SAM24358989 Patient110 N M Etrolizumab Week14 Ileum Active 0.621921174731079 GNE


title: SAM24358950 Patient116 N M Etrolizumab Week14 Ileum Inactive 0.440977000634017 GNE


title: SAM24358876 Patient24 Y M Etrolizumab Screen Colon Active 0.449390838550654 GNE


title: SAM24358879 Patient115 N M Etrolizumab Screen Ileum Active 0.772609367867899 GNE


title: SAM24358877 Patient198 N F Placebo Screen Ileum Active 0.521440132942372 GNE


title: SAM24358869 Patient146 N M Placebo Week14 Ileum Active 0.85959564650208 GNE


title: SAM24358867 Patient213 Y F Etrolizumab Week14 Ileum Active 0.954990902665667 GNE


title: SAM24358871 Patient40 N M Etrolizumab Screen Ileum Active 0.895218932042548 GNE


title: SAM24358872 Patient3 Y F Etrolizumab Screen Colon Active 1.46287650938188 GNE


title: SAM24358870 Patient122 Y M Etrolizumab Screen Ileum Active 0.874514058415886 GNE


title: SAM24358874 Patient125 Y M Etrolizumab Screen NA NA 0.507068020496903 GNE


title: SAM24359007 Patient248 Y M Etrolizumab Week14 Ileum Active 0.522168655282719 GNE


title: SAM24358866 Patient65 Y M Placebo Week14 Ileum Active 0.822664307308962 GNE


title: SAM24358864 Patient3 Y F Etrolizumab Week14 Ileum Active 1.12367660466996 GNE


title: SAM24358862 Patient44 N M Etrolizumab Week14 Ileum Active 0.783686857846115 GNE


title: SAM24358858 Patient198 N F Placebo Week14 Ileum Active 0.88573787619345 GNE


title: SAM24358863 Patient246 Y M Etrolizumab Week14 Ileum Active 0.419127385628177 GNE


title: SAM24358857 Patient19 Y F Etrolizumab Week14 Ileum Active 1.31005212551282 GNE


title: SAM24359076 Patient190 N M Etrolizumab Screen Ileum Active 0.408883290668201 GNE


title: SAM24359105 Patient104 N M Etrolizumab Week14 Ileum Active 0.115880288490518 GNE


title: SAM24358945 Patient243 N F Etrolizumab Week14 NA NA 0.0215080599738704 GNE


title: SAM24358884 Patient41 N M Etrolizumab Screen Ileum Active 0.39876141846235 GNE


title: SAM24359067 Patient71 Y F Etrolizumab Screen Ileum Active 0.259445859478652 GNE


title: SAM24359069 Patient137 N M Etrolizumab Week14 Ileum Inactive 0.633923042899757 GNE


title: SAM24359071 Patient216 Y F Placebo Week14 Ileum Active 0.838011222907924 GNE


title: SAM24359068 Patient113 Y F Etrolizumab Week14 Colon Inactive 0.999246912569148 GNE


title: SAM24359075 Patient5 Y M Placebo Screen Ileum Active 0.163178394592882 GNE


title: SAM24359094 Patient14 N M Etrolizumab Week14 Ileum Active 1.28949142760047 GNE


title: SAM24359058 Patient68 Y M Etrolizumab Screen Ileum Inactive 0.559697287740751 GNE


title: SAM24358856 Patient24 Y M Etrolizumab Week14 Colon Active 0.837046578269241 GNE


title: SAM24359047 Patient90 Y F Etrolizumab Screen Ileum Active 0.902909857669553 GNE


title: SAM24359045 Patient85 Y F Etrolizumab Screen Ileum Active 1.0221655746593 GNE


title: SAM24359059 Patient12 N F Etrolizumab Screen Colon Active 1.08523012049247 GNE


title: SAM24359057 Patient14 N M Etrolizumab Screen Colon Active 0.616717314345941 GNE


title: SAM24359043 Patient70 Y M Etrolizumab Screen Colon Active 0.600439156410614 GNE


title: SAM24359062 Patient137 N M Etrolizumab Screen Colon Active 0.998164425577036 GNE


title: SAM24358873 Patient88 N F Etrolizumab Screen Ileum Active 0.704498285422863 GNE


title: SAM24359041 Patient226 N F Placebo Screen Ileum Active 0.887321943476807 GNE


title: SAM24359035 Patient93 N F Placebo Week14 NA NA 0.700390171170594 GNE


title: SAM24359055 Patient148 Y M Placebo Screen Ileum Active 0.863001052996154 GNE


title: SAM24359036 Patient98 Y F Etrolizumab Week14 NA NA 0.656637242016896 GNE


title: SAM24359005 Patient203 Y M Placebo Screen Ileum Active 1.34036273665687 GNE


title: SAM24359039 Patient174 N M Etrolizumab Screen NA NA 0.546397597766511 GNE


title: SAM24359012 Patient169 Y F Etrolizumab Screen Colon Active 1.56999552253821 GNE


title: SAM24359065 Patient151 Y F Placebo Screen NA NA 0.107386227430314 GNE


title: SAM24359054 Patient238 Y M Etrolizumab Screen Ileum Active 0.939832437536524 GNE


title: SAM24358865 Patient88 N F Etrolizumab Week14 Colon Active 1.05484599779268 GNE


title: SAM24359014 Patient195 Y M Etrolizumab Screen Ileum Inactive 0.930973338816562 GNE


title: SAM24358954 Patient13 Y M Placebo Screen Colon Active 0.714025329924482 GNE


title: SAM24358957 Patient140 N M Etrolizumab Screen Colon Active 0.919037702795766 GNE


title: SAM24358972 Patient49 Y F Etrolizumab Screen Colon Active 0.921670240852045 GNE


title: SAM24358943 Patient147 Y M Etrolizumab Week14 Ileum Active 0.713970069666852 GNE


title: SAM24358925 Patient157 N F Placebo Screen Colon Active 0.622391528836999 GNE


title: SAM24358963 Patient116 N M Etrolizumab Screen Ileum Inactive 1.21952003848992 GNE


title: SAM24358975 Patient219 Y M Etrolizumab Screen Ileum Active 0.843013689303291 GNE


title: SAM24358994 Patient153 Y M Etrolizumab Week14 Ileum Active 1.03181140817958 GNE


title: SAM24358922 Patient143 Y F Etrolizumab Week14 Colon Active 0.469022973478368 GNE


title: SAM24358901 Patient32 Y F Etrolizumab Week14 Colon Inactive 0.200172081126897 GNE


title: SAM24358899 Patient138 Y F Etrolizumab Screen Ileum Active 0.546876219765805 GNE


title: SAM24358855 Patient173 Y F Etrolizumab Screen Colon Active 4.69782598505944 GNE


title: SAM24358860 Patient242 N M Etrolizumab Week14 Colon Active 0.710685203694578 GNE


title: SAM24358849 Patient20 N M Etrolizumab Screen Colon Active 1.64567192365636 GNE


title: SAM24358850 Patient180 N F Placebo Screen Ileum Active 1.25728034498004 GNE


title: SAM24358854 Patient206 N F Placebo Screen Ileum Active 0.252133994682536 GNE


title: SAM24358848 Patient10 Y M Etrolizumab Screen Ileum Active 0.147376745476419 GNE


title: SAM24358847 Patient57 Y F Etrolizumab Screen Ileum Active 1.61019803284863 GNE


title: SAM24358839 Patient105 Y F Etrolizumab Screen Colon Active 2.06154765543013 GNE


title: SAM24358840 Patient171 Y F Etrolizumab Week14 Colon Active 1.37010263214681 GNE


title: SAM24358846 Patient7 N F Etrolizumab Screen Ileum Active 0.798657343181959 GNE


title: SAM24358837 Patient43 Y F Placebo Screen NA NA 1.27632623447686 GNE


title: SAM24358844 Patient127 Y F Etrolizumab Screen Colon Active 0.981178830101958 GNE


title: SAM24358845 Patient35 Y M Etrolizumab Screen Ileum Active 1.60993030252513 GNE


title: SAM24358986 Patient234 N F Etrolizumab Week14 Colon Active 0.775903281765532 GNE


title: SAM24358841 Patient206 N F Placebo Week14 Ileum Active 0.957347297828332 GNE


title: SAM24358838 Patient186 N F Etrolizumab Screen Ileum Active 1.83683086674201 GNE


title: SAM24358833 Patient80 Y M Etrolizumab Week14 Ileum Active 1.08770220650441 GNE


title: SAM24358836 Patient119 Y F Placebo Week14 Colon Active 1.48472017820998 GNE


title: SAM24358835 Patient158 N F Placebo Week14 Ileum Active 1.26759627504365 GNE


title: SAM24358829 Patient158 N F Placebo Screen Ileum Active 1.45328815457731 GNE


title: SAM24358831 Patient117 Y M Etrolizumab Week14 Colon Inactive 1.28275037039521 GNE


title: SAM24358830 Patient239 N M Etrolizumab Screen Ileum Active 0.560036126077686 GNE


title: SAM24358826 Patient31 N M Placebo Screen Ileum Active 1.33588001662256 GNE


title: SAM24358823 Patient119 Y F Placebo Screen Ileum Inactive 1.2283698159254 GNE


title: SAM24358825 Patient87 Y M Etrolizumab Screen Colon Active 1.7814727703493 GNE


title: SAM24358824 Patient80 Y M Etrolizumab Screen Ileum Active 1.1987553984833 GNE


title: SAM24358821 Patient105 Y F Etrolizumab Week14 Colon Active 0.952077474869441 GNE


title: SAM24358819 Patient172 N F Etrolizumab Screen Ileum Active 1.89151271173826 GNE


title: SAM24358820 Patient186 N F Etrolizumab Week14 Colon Inactive 1.29508829327198 GNE


title: SAM24358842 Patient35 Y M Etrolizumab Week14 Ileum Active 1.71606572533799 GNE


title: SAM24358817 Patient185 N F Etrolizumab Week14 Colon Active 1.07094145565268 GNE


title: SAM24358827 Patient179 Y F Placebo Screen Colon Active 0.891062618509088 GNE


title: SAM24358818 Patient118 Y M Etrolizumab Screen Colon Inactive 1.01166769408775 GNE


title: SAM24358816 Patient57 Y F Etrolizumab Week14 Ileum Active 0.55009735382859 GNE


title: SAM24358815 Patient160 N F Placebo Week14 Colon Active 1.56044768447512 GNE


title: SAM24358813 Patient1 Y M Etrolizumab Week14 Ileum Active 0.995455522467749 GNE


title: SAM24358809 Patient121 Y F Placebo Screen Colon Active 1.6460691519858 GNE


title: SAM24358806 Patient160 N F Placebo Screen Colon Active 2.81191374694972 GNE


title: SAM24358808 Patient8 N M Etrolizumab Screen Colon Active 1.41751174364739 GNE


title: SAM24358811 Patient7 N F Etrolizumab Week14 NA NA 1.10490895678645 GNE


title: SAM24358834 Patient239 N M Etrolizumab Week14 Ileum Active 0.937363660022008 GNE


title: SAM24358802 Patient171 Y F Etrolizumab Screen NA NA 0.902213730726194 GNE


title: SAM24358801 Patient253 Y M Placebo Screen Colon Active 1.81626833127885 GNE


title: SAM24358799 Patient251 Y M Etrolizumab Screen Ileum Active 1.24681439227554 GNE


title: SAM24358800 Patient72 Y F Etrolizumab Screen Colon Active 1.14645182451815 GNE


title: SAM24358798 Patient244 Y F Etrolizumab Screen Ileum Active 1.09189353640894 GNE


title: SAM24358805 Patient129 Y M Etrolizumab Screen Colon Active 1.41710835659413 GNE


title: SAM24358792 Patient18 N M Etrolizumab Screen Ileum Active 1.3606914289133 GNE


title: SAM24358791 Patient162 N M Etrolizumab Screen Ileum Inactive 1.10077658450083 GNE


title: SAM24358796 Patient56 Y M Etrolizumab Screen Colon Active 1.27806879177466 GNE


title: SAM24358790 Patient109 N F Etrolizumab Screen Ileum Inactive 0.804275932175204 GNE


title: SAM24358794 Patient207 Y F Etrolizumab Screen Ileum Active 0.632472751375342 GNE


title: SAM24358797 Patient95 N F Etrolizumab Screen Ileum Active 1.00616209709079 GNE


title: SAM24358793 Patient220 N M Etrolizumab Screen Ileum Inactive 1.80070049258098 GNE


title: SAM24358787 Patient78 N M Etrolizumab Screen Ileum Inactive 1.07595177049108 GNE


title: SAM24358788 Patient183 Y F Etrolizumab Screen Ileum Active 1.21415577864524 GNE


title: SAM24358785 Patient29 Y M Etrolizumab Screen Colon Inactive 1.102474362338 GNE


title: SAM24358786 Patient120 N F Placebo Screen Colon Active 1.14241894501942 GNE


title: SAM24358775 Patient244 Y F Etrolizumab Week14 Ileum Active 1.06284797684247 GNE


title: SAM24358783 Patient75 Y F Etrolizumab Screen Colon Active 1.72918326371658 GNE


title: SAM24358779 Patient230 Y F Etrolizumab Week14 Colon Active 1.37601246905443 GNE


title: SAM24358776 Patient78 N M Etrolizumab Week14 Ileum Inactive 1.29344433990829 GNE


title: SAM24358781 Patient29 Y M Etrolizumab Week14 Colon Inactive 1.03688891621581 GNE


title: SAM24358778 Patient56 Y M Etrolizumab Week14 Colon Active 1.1073892515788 GNE


title: SAM24358784 Patient176 Y F Placebo Screen Ileum Active 1.58874763543892 GNE


title: SAM24358777 Patient220 N M Etrolizumab Week14 Colon Active 1.09651970171937 GNE


title: SAM24358774 Patient22 Y M Placebo Week14 Colon Active 1.46994155572711 GNE


title: SAM24358771 Patient128 Y M Etrolizumab Week14 Ileum Active 1.69198192546614 GNE


title: SAM24358795 Patient221 Y F Etrolizumab Screen Colon Active 1.42009699767984 GNE


title: SAM24358772 Patient183 Y F Etrolizumab Week14 Ileum Active 1.41927277905051 GNE


title: SAM24358769 Patient69 Y F Etrolizumab Screen Ileum Active 0.959320868356826 GNE


title: SAM24358770 Patient50 Y F Etrolizumab Screen Ileum Active 0.14508990648393 GNE


title: SAM24358789 Patient128 Y M Etrolizumab Screen Ileum Active 1.09553142488326 GNE


title: SAM24358767 Patient15 Y F Etrolizumab Screen Colon Active 2.15999884496987 GNE


title: SAM24358766 Patient42 Y M Etrolizumab Screen Colon Active 1.18625906176042 GNE


title: SAM24358765 Patient167 Y M Etrolizumab Screen Colon Active 1.7096936823572 GNE


title: SAM24358764 Patient112 Y F Etrolizumab Screen Ileum Active 1.79779032615631 GNE


title: SAM24358762 Patient33 Y F Etrolizumab Screen Colon Active 1.47360660302414 GNE


title: SAM24358761 Patient168 Y M Etrolizumab Screen Colon Active 1.59035690565814 GNE


title: SAM24358760 Patient114 Y F Etrolizumab Screen Colon Active 1.65074374247202 GNE


title: SAM24358780 Patient221 Y F Etrolizumab Week14 Colon Active 0.982450774774243 GNE


title: SAM24358759 Patient202 N F Etrolizumab Screen Ileum Active 1.3317042920343 GNE


title: SAM24358757 Patient240 Y F Etrolizumab Screen Ileum Active 1.40608883782343 GNE


title: SAM24358755 Patient132 Y M Etrolizumab Week14 Colon Active 1.18080919196752 GNE


title: SAM24358754 Patient231 Y F Placebo Screen Ileum Inactive 1.40657059380287 GNE


title: SAM24358750 Patient131 N M Placebo Week14 Ileum Inactive 1.96802007161464 GNE


title: SAM24358753 Patient132 Y M Etrolizumab Screen Ileum Active 1.23821116284531 GNE


title: SAM24358749 Patient42 Y M Etrolizumab Week14 Colon Active 1.34307919912855 GNE


title: SAM24358748 Patient114 Y F Etrolizumab Week14 Colon Active 0.520506198814762 GNE


title: SAM24358747 Patient156 N M Etrolizumab Screen Colon Active 1.2504468014813 GNE


title: SAM24358746 Patient191 Y F Placebo Week14 Ileum Active 1.10320239642938 GNE


title: SAM24358745 Patient91 Y M Etrolizumab Week14 Colon Active 1.2275752987296 GNE


title: SAM24358768 Patient131 N M Placebo Screen Colon Active 2.10463303065343 GNE


title: SAM24358744 Patient11 N M Etrolizumab Week14 NA NA 1.318964258843 GNE


title: SAM24358742 Patient201 Y M Etrolizumab Screen Ileum Active 1.59389706982623 GNE


title: SAM24358763 Patient34 N M Placebo Screen Ileum Active 1.67178806231455 GNE


title: SAM24358741 Patient159 Y M Placebo Screen Colon Active 1.33367183913073 GNE


title: SAM24358738 Patient11 N M Etrolizumab Screen Colon Active 0.891510476634029 GNE


title: SAM24358740 Patient191 Y F Placebo Screen Ileum Active 1.32043271519625 GNE


title: SAM24358758 Patient15 Y F Etrolizumab Week14 Ileum Inactive 0.266735918363797 GNE


title: SAM24359475 Patient209 Y M Etrolizumab Screen Ileum Active 1.25086336281175 GNE


title: SAM24358736 Patient94 Y F Etrolizumab Screen Ileum Active 1.2171113676937 GNE


title: SAM24358751 Patient69 Y F Etrolizumab Week14 Colon Inactive 1.46849411896776 GNE


title: SAM24358735 Patient25 N F Etrolizumab Screen Colon Active 1.4875461389804 GNE


title: prime/boost challengeFluB attd14 dpc [SAMPLE 143]

city: Athens

first: Daniel

middle: Roberto

last: Perez

state: GA

address: 953 College Station Road

institute: University of Georgia

description: Fig. 7 and 8

hyb_protocol: Serum and NW samples were diluted 1:100 in a protein array blocking buffer (GVS, Sanford,  ME, USA), supplemented with E. coli lysate (GenScript, Piscataway, NJ, USA) to a final  concentration of 10 mg/mL, and preincubated at room temperature (RT) for 30 min. Concurrently,  arrays were rehydrated in blocking buffer (without lysate) for 30 min. Blocking  buffer was removed, and arrays were probed with preincubated serum samples using  sealed chambers to prevent cross-contamination of samples between the pads. Arrays were  incubated overnight at 4  C with gentle agitation. They were then washed at RT three  times with Tris-buffered saline (TBS) containing 0.05% Tween 20 (T-TBS), biotin-conjugated  goat anti-mouse IgA and Biotin-conjugated anti-mouse IgG (Jackson Immuno Research  Laboratories, Inc., West Grove, PA, USA) were diluted 1:400 in blocking buffer and applied  to separate arrays for 1 h, RT with gentle agitation. Arrays were washed three times  with T-TBS, followed by incubation with streptavidin-conjugated Qdot655 (Thermo Fisher  Scientific, Waltham, MA, USA) diluted 1:200 in blocking buffer for 1 h, RT. Arrays were  washed three times with T-TBS and once with water. Arrays were air dried by centrifugation  at 500 g for 5 min. Images were acquired using the ArrayCAM imaging system from  Grace Bio-Labs (Bend, OR, USA). Spot and background intensities were measured using  an annotated grid (.gal) file. Mean fluorescence across antigens grouped by isotypes were  used for subsequent analysis. The different antigens were acquired from Sino biological  (Wayne, PA, USA).

scan_protocol: Images were acquired using the ArrayCAM imaging system from Grace Bio-Labs (Bend, OR) with gain and exposure times of 50 and 400-1000ms, respectively.

data_processing: Spot and background intensities were measured using an annotated grid (.gal) file.  Signal intensities (SI) for each antigen on the array were first background corrected by subtracting sample-specific T-PBS buffer signals from purified protein spot signals. For statistical analysis,   A two-way ANOVA was performed. A P value below 0.05 was considered significan. All data analyses and graphs were performed using GraphPad Prism software version 9 (GraphPad Software Inc., San Diego, CA, USA). We utilized the raw data for our analyses without any further corrections.

source_name: Nasal wash

tag: tissue

value: Nasal wash

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

value: FluB att

tag: time point

value: d14 dpc

tag: mouse id


title: prime/boost challengeFluB attd14 dpc [SAMPLE 141]

description: Fig. 7 and 8

tag: strain


title: SAM24358732 Patient53 N F Placebo Screen Ileum Active 1.09575217982229 GNE


title: prime/boost challengeFluB attd14 dpc [SAMPLE 142]

description: Fig. 7 and 8


title: prime/boost challengeFluB attd14 dpc [SAMPLE 139]

description: Fig. 7 and 8


title: SAM24358730 Patient182 N M Etrolizumab Screen Ileum Inactive 1.01038809560226 GNE

value: M


title: prime/boost challengeFluB attd14 dpc [SAMPLE 140]

description: Fig. 7 and 8


title: SAM24358728 Patient250 Y M Etrolizumab Screen Colon Active 1.42198824549324 GNE

value: Y

value: Etrolizumab


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 136]

description: Fig. 7 and 8

value: FluB-RANS


title: SAM24358727 Patient39 N F Etrolizumab Screen Ileum Active 0.428534465969921 GNE

value: Ileum

value: Active


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 138]

description: Fig. 7 and 8


title: SAM24358726 Patient101 Y M Etrolizumab Screen Ileum Active 1.51720999330845 GNE

value: Screen


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 137]

description: Fig. 7 and 8


title: SAM24358737 Patient91 Y M Etrolizumab Screen Colon Active 1.52447225002971 GNE

value: Colon


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 134]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 135]

description: Fig. 7 and 8


title: SAM24358723 Patient218 Y F Etrolizumab Screen Ileum Active 1.37423174454998 GNE

value: F


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 131]

description: Fig. 7 and 8

value: FluB-RAM


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 133]

description: Fig. 7 and 8


title: prime/boost challengeFluB attd14 dpc [SAMPLE 144]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RANSd14 dpc [SAMPLE 132]

description: Fig. 7 and 8


title: SAM24358722 Patient181 N F Etrolizumab Screen Colon Active 1.09241709431078 GNE

value: N


title: SAM24358721 Patient217 Y M Etrolizumab Screen Colon Active 1.83989648497145 GNE


title: SAM24358734 Patient100 Y M Etrolizumab Screen Ileum Active 1.21246241077586 GNE


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 130]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 129]

description: Fig. 7 and 8


title: prime/boost challengeFluB-RAMd14 dpc [SAMPLE 128]

description: Fig. 7 and 8


title: SAM24358720 Patient130 Y F Placebo Screen NA NA 0.207107331729449 GNE

value: Placebo