title: TKO 0h A: RNA-seq in WT ESCs

value: KLF WT


title: TKO 0h B: RNA-seq in WT ESCs

status: Public on Sep 06 2019

type: SRA

city: New York

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

country: USA

institute: Weill Cornell Medicine

library_source: transcriptomic

data_processing:
Alignment of the RNAseq data was performed with tophat2 algorithm (--very-sensitive option) while gene expression quantification and differential expression was performed with the use of Htseq-count and DESeq algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts per transcript as generated from Htseq-countare submitted in the raw.csv file

molecule: total RNA

organism: Mus musculus

source_name: Embryonic Stem Cells (V 6.5)

growth_protocol: Mouse ES V6.5 were cultured on irradiated feeder cells in KO-DMEM media (Invitrogen) supplemented with 15% heat-inactivated fetal bovine serum, GlutaMAX, penicillin-streptomycin, non-essential amino acids, β-mercaptoethanol and 1000 U/ml LIF, with or without the presence of 2i (1uM MEKinhibitor (Stemgent 04-0006) and 3uM GSK3 inhibitor (Stemgent 04-0004)).

extract_protocol: RNA-seq: Total RNA was prepared with TRIZOL (Life technologies #15596018) following manufacturer’s instructions. Libraries were generated by the Weill Cornell Genomics core facility using the Illumina TruSeq stranded mRNA library preparation kit (#20020594) and sequenced on an Illumina HiSeq4000 platform on SE50 mode.

treatment_protocol: V6.5 cells were infected using lentiviruses harboring the c3GIC9 vector76  (TRE3G-Cas9-P2A-GFP-PGK-Puro-IRES-rtta) containing gRNA/s targeting either KLF4 only or KLF2, KLF4 and KLF5 in tandem. Following infection cells were selected using Puromycin (LifeTech K210015) and clonal populations were manually picked. Expression of CRISPR-Cas9 from these stable cell lines was induced by addition of Doxycycline for 24hrs (1:1000 dilution of 2mg/ml stock) and KO efficiency in each clonal population was verified by WB: KLF4 (R&D, AF3158) KLF5 (R&D AF3758) KLF2 (Novus biologicals, NBP6181) ESRRB (PPMX, PPH6705) NANOG (Bethyl laboratories, A300-397A) ACTIN (abcam, ab49900). Successful KO clones were then used for subsequent experiments (qPCR, ChIP-seq, RNA-seq, 3C and HiChIP) after induction with doxycycline for the indicated time points (ESC TKO 0 hours and ESC TKO 24 hours).

tag: cell type

value: Embryonic Stem Cells (V 6.5)

tag: genotype

tag: culture

value: cultured in 2i condition


title: EC-DG-3458-H3K27AC_MEF_1

library_source: genomic

data_processing:
Reads were trimmed for residual adapters (cutadapt version 1.8.1).
Alignment to the mouse reference genome version mm10 was performed using standard parameters, permitting maximum one mismatch in seed alignment (Bowtie version 2.2.5).
Reads marked as positional duplicates or falling into mouseENCODE blacklisted genomic regions (liftOver to mm10; Consortium, 2012) were filtered out.
Coverage tracks in RPKM were generated from alignments using bamCoverage (V2.3.6).
ChIP-seq peaks (enrichment of signals over background) were called at 10^-2 (MACS version 2.1.1), and peaks detected in more than half of biological replicates were retained for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files for coverage tracks; BED files for peak coordinates.

molecule: genomic DNA

source_name: MEF

growth_protocol: Mouse ES V6.5 were cultured on irradiated feeder cells in KO-DMEM media (Invitrogen) supplemented with 15% heat-inactivated fetal bovine serum, GlutaMAX, penicillin-streptomycin, non-essential amino acids, β-mercaptoethanol and 1000 U/ml LIF (ESC medium).  All V6.5 samples for HiCHIP and two replicates of ChIPseq were cultured in the presence of 2i  (1uM MEKinhibitor (Stemgent 04-0006) and 3uM GSK3 inhibitor (Stemgent 04-0004)). Mouse embryonic fibroblasts (MEFs) were isolated from a "reprogrammable" mouse harboring a polycystronic OKSM cassette in the Col1a1 locus and M2rtTA in the Rosa26 locus. Cells were reprogrammed in the presence of 1ug/ml doxycycline and 50ug/ml ascorbic acid and cultured in ES medium as described above.

extract_protocol:
Cells were crosslinked in 1% formaldehyde at RT for 10 minutes and quenched with 125mM glycine for 5 mins at RT. 50 million cells were used for KLF4 ChIPs and 10 million for H3K27acetylation ChIP. Cell pellets were washed twice in PBS and resuspended in 400ul lysis buffer (10mM Tris pH8, 1mM EDTA, 0.5% SDS) per 20 million cells. Cells were sonicated in a bioruptor device (30 cycles 30sec on/off, high setting) and spun down 10 minutes at 4°C at maximum speed. Supernatants were diluted 5 times with dilution buffer (0.01%SDS, 1.1% triton,1.2mM EDTA,16.7mM Tris pH8, 167mM NaCl) and incubated with the respective antibody (2-3ug/10M cells) (KLF4 R&D #3158, H3K27ac  ab4729) O/N with rotation at 4°C. Next day, protein G Dynabeads (ThermoScientific) preblocked with BSA protein (100ng per 10ul Dynabeads) were added (10ul blocked Dynabeads per 10 million cells) and incubated for 2-3 hours at 4°C. Beads were immobilized on a magnet and washed twice in low salt buffer (0.1% SDS,1% triton, 2mM EDTA, 150mM NaCl, 20mM Tris pH8), twice in high salt buffer (0.1% SDS,1% triton, 2mM EDTA, 500mM NaCl, 20mM Tris pH8), twice in LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris pH8) and once in TE. DNA was then eluted from the beads by incubating with 150ul elution buffer (1% SDS, 100mM NaHCO3) for 20 minutes at 65°C (vortexing every 10min). Supernatants were collected and reverse-crosslinked by incubation at 65°C O/N in presence of proteinase K. After RNase A treatment for 1hr at 37°C, DNA was purified using the minElute kit (Qiagen).
6-10ng of immunoprecipitated material was used for ChIP-seq library preparation using the KAPA Hyper prep kit (KAPA Biosystems). Libraries were sequenced on an Illumina HiSeq 2500 platform on SE50 mode.

tag: strain

value: OKSM Col1a1/M2rtTA ROSA26

tag: Stage

value: MEF

tag: medium

value: MEF medium without doxycyclin

tag: marker

value: unsorted

tag: antibody

tag: batch


title: ATAC-seq_ESC_2

data_processing:
Paired-end reads were aligned to mm10 (bowtie2 version 2.3.2, --no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail -I 10 -X 2000), and mitochondrial DNA alignments were excluded.
Reads marked as positional duplicates or falling into mouseENCODE blacklisted genomic regions (liftOver to mm10; Consortium, 2012) were filtered out.
Coverage tracks in FPKM were generated from alignments using bamCoverage (V2.3.6).
Read ends were adjusted for Tn5 transposase offsets. Peaks were called at p<10-5 (MACS version 2.1.1) per replicate, and only common peaks between two independent biological replicates were retained for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files for coverage tracks; BED files for peak coordinates.

source_name: ESC

extract_protocol:
50,000 cells were washed once with 50 μL of cold PBS and resuspended in 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). The suspension of nuclei was then centrifuged for 10 min at 800 g at 4°C, followed by the addition of 50 μL transposition reaction mix (25 μL TD buffer, 2.5 μL Tn5 transposase and 22.5 μL nuclease-free H2O) using reagents from the Nextera DNA library Preparation Kit (Illumina #FC-121-103). Samples were then incubated at 37°C for 30min. DNA was isolated using a ZYMO Kit (#D4014).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described in Buenrostro et al and the library was then PCR amplified for the appropriate number of cycles using Nextera primers. Samples were subject to a dual size selection (0.55x-1.5x) using SPRI beads (Beckman Coulter #B23317). Finally, the ATAC libraries were sequenced on a HiSeq 2500 platform on PE50 mode.

value: ESC

value: ESC medium


title: EC-DG-3458-H3K27AC_MEF_2


title: ATAC-seq_DAY9_2

value: ESC medium with 1ug/ml doxycycline and 50ug/ml ascorbic acid

value: sorted for SSEA+


title: ATAC-seq_DAY6_2


title: RNA-seq_ESC_2

data_processing:
Expression of genes was quantified in transcripts per kilobase million (TPM) using  quasi mapping (Salmon, version 0.8.2) to GENCODE (version M6, mm10) reference gene annotation. Salmon provides alignment-free transcript quantification information in a single step.
Genome_build: mm10
Supplementary_files_format_and_content: Plain tab-delimited text files with estimated TPM and read counts.

extract_protocol:
Total RNA was prepared with TRIZOL (Life technologies #15596018) following manufacturer’s instructions.
Libraries were generated by the Weill Cornell Genomics core facility using the Illumina TruSeq stranded mRNA library preparation kit (#20020594) and sequenced on an Illumina HiSeq4000 platform on SE50 mode.


title: RNA-seq_D9_1


title: ATAC-seq_DAY3_2


title: ATAC-seq_DAY6_1


title: RNA-seq_D6_1


title: ATAC-seq_MEF_2


title: RNA-seq_D3_2


title: ATAC-seq_MEF_1


title: ATAC-seq_DAY3_1


title: MEF-H3K27ac rep2

description:
MEF-H3K27ac_high-confidence_interactions.tsv
HiChIP

data_processing:
Read alignment: bowtie2 2.2.3. Paired-end reads were mapped against the mm10 reference sequence using bowtie2 (special paramters: --very-sensitive-local --local)
Filtering: GenomicTools "gtools-hic filter". Discards read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<10 kb)
Matrix generation: HicBench. For each replicate and each chromosome, a matrix with binned interactions (bin-size 10kb) was generated.
Normalization: custom script. Each loop with > 1 read across all replicates of the same condition was kept. We applied normalization by sequencing depth per replicate to raw read-counts (both Hi-C and HiChIP; leading to counts-per-million; CPM). Hi-C data only was additionally distance-normalized as recently described (Gong et al., 2018)
High-confidence interactions: custom script. We have applied an approach similar to mango, which employs a binomial test per diagnoal in the normalized counts-matrix. To define significant HiChIP loops, we have filtered all interactions for CPM>3 in all available replicates and p<0.1. For significant Hi-C loops, we have filtered more stringently using CPM>15 in all replicates and p<0.01.
Topologically associated domains (TADs): We called TADs from normalized corrected Hi-C matrices in PSCs processed at 10kb resolution using a recently published software (Ramirez et al., Nat Comm, 2018) with the use of the following parameters: --minDepth 120000 --maxDepth 420000 --thresholdComparison 0.001 --delta 0.01 --correctForMultipleTesting fdr
genome build: mm10
processed data files format and content: custom tsv: left anchor coordinates; right anchor coordiantes; raw read-counts per replicate; normalized read-counts (CPM) for all replicates; distance-normalized read-counts as described before (Gong et al., 2018).

source_name: Mouse embryonic fibroblasts

growth_protocol: MEF were grown in low oxygen incubator with DMEM media, V6.5 were grown in KO-DMEM media and 2i conditions (for HiChIP and ChIP-seq), MEF at different times of reprogramming were grown in the presence of dox and ascorbic acid

extract_protocol:
cells were collected with trypsin and fixed with 1% formaldehyde
Libraries were constructed according to the HiChIP protocol and sequenced on Illumina HiSeq2500.

value: Reprogrammable mouse embryonic fibroblasts (MEFs) prepared from rtTA3-OKSM embryos (embryonic day-E13.5) that were heterozygous for the Oct4-GFP reporter, OKSM cassette and rtTA3.

tag: culture condition

value: collected at passage 3


title: MEF-H3K27ac rep1


title: RNA-seq_MEF_2


title: EC-DG-3458-H3K27AC_DAY3_1


title: ATAC-seq_DAY9_1


title: EC-EA-3702-H3K27AC_DAY3_1


title: RNA-seq_D3_1


title: ATAC-seq_ESC_1


title: d6-Klf4 rep2

description:
day6-Klf4_high-confidence_interactions.tsv
HiChIP

source_name: reprogramming - day 6

value: cultured with dox and ascorbic acid for the number of days indicated


title: d6-Klf4 rep1


title: ES-H3K27ac rep1

description:
ES-H3K27ac_high-confidence_interactions.tsv
HiChIP

source_name: Embryonic stem cells

value: V6.5 embryonic stem cells


title: RNA-seq_ESC_1


title: d3-Klf4 rep3

description:
day3-Klf4_high-confidence_interactions.tsv
HiChIP

source_name: reprogramming - day 3


title: d6-Klf4 rep3


title: ES-H3K27ac rep2


title: d3-Klf4 rep1


title: d3-Klf4 rep2


title: ES-Klf4 rep4

description:
ES-Klf4_high-confidence_interactions.tsv
HiChIP


title: RNA-seq_D9_2


title: RNA-seq_D6_2


title: RNA-seq_MEF_1


title: ES-Klf4 rep3


title: ES-Klf4 rep1

growth_protocol: MEF were grown in low oxygen incubator with DMEM media, V6.5 were grown in KO-DMEM media and 2i conditions (for HiChIP), MEF at different times of reprogramming were grown in the presence of dox and ascorbic acid

value: Klf4 R&D cat. numb.#F3158


title: 171120_314C

status: Public on Aug 26 2019

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

data_processing:
Demultiplexing, bcl2fastq v2.18.0.12 --no-lane-splitting --barcode-mismatches 1 -l INFO -r 4 -d 4 -p 4 -w 4
Alignment to GRCm38, Gencode annotation release M15 using STAR v2.5.3a --runMode alignReads --runThreadN 12 --genomeLoad NoSharedMemory --outSAMunmapped None --outSAMattributes Standard  --limitOutSAMoneReadBytes 1000000 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 25 --quantMode GeneCounts --outSAMprimaryFlag AllBestScore --outReadsUnmapped Fastx
Quality Control filter samples by: Minimum raw read counts in at least two biological samples = 30;
Genome_build: (GRCm38), version M16 (Ensembl 91) primary assembly annotation used for STAR alignment
Supplementary_files_format_and_content: Mouse count matrix (ASCII text) from running STAR alignment with --quantmode GeneCounts parameter for each sample

molecule: polyA RNA

growth_protocol: Florescent B16F10 cells infused into zebrafish which extravasated as clusters through Angiopellosis (termed B16Met cells) were isolated from zebrafish and cultured in vitro with IMDM 10% FBS

extract_protocol:
Total RNA was purified with miRNeasy extraction kit (Qiagen)
Libraries  were prepared using Illumina® TruSeq® stranded mRNA Library Prep Kit

value: B16-F10 melanoma cells

tag: media

value: IMDM 10% FBS

tag: extravasation

value: Y


title: 171120_324C

source_name: B16-F10_no extravasation

value: N


title: 171120_314_b


title: d6-Klf4 rep4


title: AP2-FG ChIP-seq experiment-2 IP

status: Public on May 05 2019

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

data_processing:
Reads were mapped on the P. berghei genome with allowing one mismatch within 60 bp sequence using Bowtie 2.0. Bedgraph files were ceated from the mapping data (IP).
The mapping data were analyzed with the MACS2 peak-calling algorithm using  approximately5.45 × 106  in the experiment-1 and 9.74 × 106 in the experiment-2, respectively.). Numbers of INPUT reads used for normalization were 138 × 107 in the experiment-1 and 1.62 × 107 in the experiment-2, respectively. Conditions for peak calling included an FDR < 0.01 in both experiments.
Genome_build: PlasmoDB, version 9.1
Supplementary_files_format_and_content: Mapping data, bedgraph; Peak-calling, text.

organism: Plasmodium berghei ANKA

source_name: AP2-FG ChIP-seq experiment-2 IP

growth_protocol: Balb/c mice were infected with P. berghei expressing GFP-fused AP2-FG.

extract_protocol:
The infected whole blood was fixed immediately with formalin (1% in final concentration), and erythrocytes were depleted by lysis in 0.85% NH4Cl with changing the solution several times. ChIP was performed according to the protocol in “Standard protocols on Next Generation Sequencing” (edited by Ai Nikaido, Yodosha Co., Ltd., 2014). Briefly, chromatin was sheared by sonication using Bioruptor. Chromatin was IPed with anti-GFP polyclonal antibodies (Abcam) conjugated to Dynabeads Protein A (Life Technologies, Gaithersburg, MD).  Obtained DNA fragments were sequenced by the illumina NextSeq sequencer.
Single read - illumina NextSeq 500

treatment_protocol: Six mice were infected with AP2-FG::GFP parasites and treated with sulfadiazine in drinking water (10 mg/ml) for depletion of asexual blood stages.

value: gametocyte

value: ANKA

value: GFP-fused AP2-FG expressing

value: anti-GFP polyclonal antibodies (Abcam)


title: AP2-FG ChIP-seq experiment-1 IP

source_name: AP2-FG ChIP-seq experiment-1 IP


title: Patient 2 (180510)

status: Public on Mar 19 2019

description:
180510_human_rc_matrix.txt
DC-002_S9

data_processing:
Demultiplexing, bcl2fastq v2.18.0.12 --no-lane-splitting --barcode-mismatches 1 -l INFO -r 4 -d 4 -p 4 -w 4
Technical replicates (named with 180508 or 180510 prefix) for each sample are processed separately prior to alignment to the SLIMM 13K index after which they are processed as a single pooled sample
Alignment to rRNA (all samples), STAR v2.5.2b --outSAMunmapped None --outSAMattributes Standard --outSAMtype BAM Unsorted --outSAMprimaryFlag AllBestScore --outReadsUnmapped Fastx
Alignment to hg38 (all samples), STAR v2.5.2b --outSAMunmapped None --outSAMattributes Standard  --limitOutSAMoneReadBytes 1000000 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 25 --quantMode GeneCounts --outSAMprimaryFlag AllBestScore --outReadsUnmapped Fastx
Alignment to SLIMM 13K index (all samples), Bowtie v2.3.4 -q --no-unal --mm -p 24 -k 60 --un-conc-gz
Taxonomic profiling (all samples), SLIMM v0.2.2
STI Gene Count Generation (CT, GC, MG) for STI positive swabs (DC-001, DC-004, DC-006, DC-008), HTSeq Count v0.9.1 -s no -t gene -a 0
STI Gene Count Generation (CT, GC, MG) for STI positive swabs (DC-001, DC-004, DC-006, DC-008), HTSeq Count v0.9.1 -s no -t gene -a 0 --nonunique all
Alignment to TV (all samples), Bowtie v2.3.4 -q --no-unal --mm -p 24 -k 60
Genome_build: Chlamydia trachomatis (CT) D/UW-3/CX (AE001273.1) used for HTSeq
Genome_build: Neisseria gonorrhoeae (GC) FA 1090 (AE004969.1) used for HTSeq
Genome_build: Mycoplasma genitalium (MG) G37 (L43967.2) used for HTSeq
Genome_build: Trichomonas vaginalis (TV) G3 (NZ_AAHC00000000.1) used for Bowtie2 alignment
Genome_build: hg38 with gencode v25 primary assembly annotation used for STAR alignment
Supplementary_files_format_and_content: human count matrix (ASCII text) by running STAR alignment with --quantmode GeneCounts parameter

organism: Homo sapiens

source_name: Cervical swab

extract_protocol:
Thawed samples were agitated vigorously using a FastPrep Beadbeater (MP Biomedicals, Santa Ana, CA) to release adherent material then DNA and total RNA was simultaneously extracted using a Quick DNA/RNA™ nucleic acid isolation kit (Zymo Research) with on-column DNAse I treatment of the RNA
Libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) (12 cycles PCR amplification) and dual indexed with a KAPA Dual-Indexed Adapter Kits (1.5µM final concentration)

tag: sexually transmitted pathogen

value: negative

tag: tissue

value: cervical swab


title: Patient 4 (180510)

description:
180510_human_rc_matrix.txt
DC-004_S3

value: GC, TV


title: Patient 6 (180510)

description:
180510_human_rc_matrix.txt
DC-006_S6

value: MG, TV


title: Patient 3 (180510)

description:
180510_human_rc_matrix.txt
DC-003_S8


title: Patient 9 (180510)

description:
180510_human_rc_matrix.txt
DC-009_S2


title: Patient 5 (180510)

description:
180510_human_rc_matrix.txt
DC-005_S7


title: Patient 8 (180510)

description:
180510_human_rc_matrix.txt
DC-008_S10

value: MG


title: Patient 10 (180510)

description:
180510_human_rc_matrix.txt
DC-010_S1


title: Patient 7 (180508)

description:
180508_human_rc_matrix.txt
DC-007_S5


title: Patient 10 (180508)

description:
180508_human_rc_matrix.txt
DC-010_S1


title: Patient 6 (180508)

description:
180508_human_rc_matrix.txt
DC-006_S6


title: Patient 5 (180508)

description:
180508_human_rc_matrix.txt
DC-005_S7


title: Patient 1 (180510)

description:
180510_human_rc_matrix.txt
DC-001_S4

value: CT, TV


title: Patient 9 (180508)

description:
180508_human_rc_matrix.txt
DC-009_S2


title: Patient 4 (180508)

description:
180508_human_rc_matrix.txt
DC-004_S3


title: Patient 7 (180510)

description:
180510_human_rc_matrix.txt
DC-007_S5


title: Patient 8 (180508)

description:
180508_human_rc_matrix.txt
DC-008_S10


title: Patient 1 (180508)

description:
180508_human_rc_matrix.txt
DC-001_S4


title: Patient 3 (180508)

description:
180508_human_rc_matrix.txt
DC-003_S8


title: Patient 2 (180508)

description:
180508_human_rc_matrix.txt
DC-002_S9


title: 171120_324_a


title: S6_tumor

status: Public on Feb 19 2019

city: Wuhan

first: Chunhua

last: Wei

address: 1277 JieFang Avenue

country: China

institute: Huazhong University of Science and Technology

data_processing:
100 bp stranded paired-end reads were mapped to the human reference ( GRCh38) using TopHat (version 2.0.11) and Bowtie2 (version 2.2.2). Cufflink was used to assemble mapped reads based on reference annotation file and FPKM (Fragments per kilobase of transcript per million mapped reads) value were calculated for annotated genes.
HTSeq-count was used to count reads of annotated genes for differential expression analysis.
Differentially expressed genes between lung tumor tissues with brain metastasis group (BM+) and lung tumor tissue without brain metastasis group (BM-) were identified by DESeq2 R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: [HTSeq_count.txt]  Counts.
Supplementary_files_format_and_content: [DESeq2_results.txt]  rlog transformed counts of differentially expressed genes analyzed by DESeq2 with log2Fold Change being more than 2 and P value of statistical test less than 0.05.

source_name: primary lung tumors

extract_protocol:
Tissue specimens were dissected and preserved immediately in liquid nitrogen after surgery or biopsy. RNA was harvested using Trizol reagent. Truseq Stranded mRNA Sample Pre Kit (Illumina, San Diego, California, USA) was used with 1 ug of total RNA to construct the stranded libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: NSCLC

value: lung tumors

tag: brain metastasis

value: YES

tag: time point

value: pre-treatment


title: S4_tumor


title: S7_tumor


title: S8_tumor

value: NO


title: S5_tumor


title: S1_tumor


title: ES-Klf4 rep2

tag: cell type

value: V6.5 embryonic stem cells

value: cultured in 2i condition


title: SP_FPL [CytoScanHD_Array]

status: Public on Jan 03 2019

type: genomic

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing:
Data were analyzed using the Chromosome Analysis Suite (ChAS, Affymetrix). Alterations were retrieved using the Chromosome Analysis Suite (ChAS, Affymetrix), NetAffx Build na33.1 (hg19) considering 25 altered markers in 150 kbp for gains, 35 markers in 75 kbp for losses and 50 markers in 5 Mbp for LOH as filters. Alterations found in his peripheral blood sample were considered to be constitutional and were discarded.
CEL files and CYCHP files obtanied with ChAS version na33.1
Command Console CHP file version 1
Data Type: affymetrix-multi-data-type-analysis
affymetrix-array-type = CytoScanHD_Array
affymetrix-algorithm-param-ArraySet = CytoScanHD_Array
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 2.2.0

label: biotin

source_name: Human peripheral blood sample

label_protocol: 500ng starting genomic DNA were processed using the Affymetrix® Cytogenetics Copy Number Assay User Guide (P/N 702607 Rev. 2)

extract_protocol: DNA was extracted with QIAamp DNA Mini Kit (Qiagen)

tag: subject id

tag: subject status

value: immunocompetent patient

tag: gender

value: female

tag: age

value: 95 years old

value: peripheral blood


title: SP24 [CytoScanHD_Array]

value: male

value: 76 years old


title: SP11.1 [CytoScanHD_Array]

value: 86 years old


title: R78_CEC_1 [CytoScanHD_Array]

source_name: Human skin biopsy from cutaneous invasive squamous cell carcinoma

value: 81 years old

tag: condition

value: cSCC

value: invasive squamous cell carcinoma of the face


title: SP10 [CytoScanHD_Array]

value: 85 years old


title: R126_QA_2 [CytoScanHD_Array]

source_name: Human skin biopsy from actinic keratosis

value: 80 years old

value: AK

value: actinic keratosis of the face


title: R146_Elas_1 [CytoScanHD_Array]

source_name: Human skin biopsy from healthy sun-exposed skin

value: SES

value: healthy sun-exposed skin of the scalp


title: R145_CEC_1 [CytoScanHD_Array]

value: invasive squamous cell carcinoma of the scalp


title: R190_QA_3 [CytoScanHD_Array]

value: immunocompetent patient


title: R181_CEC_2 [CytoScanHD_Array]

value: 79 years old


title: SP5_SVA [CytoScanHD_Array]

value: female


title: R79_PS_1 [CytoScanHD_Array]

value: healthy sun-exposed skin of the face


title: SP18 [CytoScanHD_Array]

value: peripheral blood


title: R163_QA_1 [CytoScanHD_Array]

value: male

value: 87 years old

value: actinic keratosis of the scalp (adjacent to the squamous cell carcinoma)


title: R149_CEC_3 [CytoScanHD_Array]

value: 96 years old

value: cSCC


title: R191_Elas_3 [CytoScanHD_Array]

value: 95 years old

value: apparently healthy sun-exposed skin of the face


title: R99_CEC_2 [CytoScanHD_Array]

value: 85 years old


title: SP15 [CytoScanHD_Array]

value: 83 years old


title: R182_Elas_2 [CytoScanHD_Array]

value: SES


title: R161_CEC_1 [CytoScanHD_Array]


title: SP25 [CytoScanHD_Array]


title: R183_QA_2 [CytoScanHD_Array]

value: AK

value: actinic keratosis of the face


title: SP27 [CytoScanHD_Array]

value: immunocompetent patient


title: R189_CEC_3 [CytoScanHD_Array]

value: invasive squamous cell carcinoma of the face


title: R148_QA_1 [CytoScanHD_Array]

value: 76 years old

value: actinic keratosis of the scalp


title: SP_FDV [CytoScanHD_Array]

value: 79 years old

value: peripheral blood


title: R162_Elas_1 [CytoScanHD_Array]

value: male

value: 87 years old

value: healthy sun-exposed skin of the scalp


title: R191_Elas_3

type: RNA

data_processing: Data were analyzed using the RMA algorithm and then corrected with ComBat. LIMMA was applied to calculate significant differential expression between samples. This was performed in R (v 3.1.1) with aroma.affymetrix and bioconductor packages

label_protocol: 200ng of total RNA from each sample was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay

extract_protocol: RNA was extracted with a mirVanaTM miRNA Isolation Kit

value: female

value: sun-exposed skin (SES)


title: R78_CEC_1

value: 81 years old

value: cutaneous squamous cell carcinomas (cSCC)


title: R79_PS_1

value: healthy sun-exposed skin of the face


title: R99_CEC_2

value: 85 years old

value: invasive squamous cell carcinoma of the scalp


title: R81_QA_1 [CytoScanHD_Array]

value: AK

value: actinic keratosis of the face


title: R150_Elas_3 [CytoScanHD_Array]

value: immunocompetent patient

value: 96 years old

value: SES


title: R190_QA_3

value: 95 years old

value: actinic keratosun-exposed skin (SES) (AK)


title: R183_QA_2

value: male

value: 79 years old


title: R182_Elas_2


title: R181_CEC_2

value: invasive squamous cell carcinoma of the face


title: R151_QA_3 [CytoScanHD_Array]


title: R151_QA_3


title: R149_CEC_3


title: R162_Elas_1

value: 87 years old

value: healthy sun-exposed skin of the scalp


title: R150_Elas_3

value: sun-exposed skin (SES)


title: R146_Elas_1

value: 76 years old


title: R81_QA_1

value: female

value: 81 years old


title: R161_CEC_1

value: cutaneous squamous cell carcinomas (cSCC)

value: invasive squamous cell carcinoma of the scalp


title: R126_QA_2

value: 80 years old

value: actinic keratosis of the face


title: R163_QA_1

value: immunocompetent patient

value: actinic keratosis of the scalp (adjacent to the squamous cell carcinoma)


title: R145_CEC_1


title: R148_QA_1

value: actinic keratosis of the scalp


title: R115_Elas_2

value: 83 years old


title: R101_QA_2

value: male

value: 85 years old

value: actinic keratosun-exposed skin (SES) (AK)


title: R116_QA_2


title: R107_QA_1

value: 86 years old

value: actinic keratosis of the face (preauricular  adjacent to the squamous cell carcinoma)


title: R106_PS_1

value: sun-exposed skin (SES)

value: healthy sun-exposed skin of the face (preauricular)


title: R105_CEC_1

value: female

value: invasive squamous cell carcinoma of the face (preauricular)


title: R114_CEC_2

value: cutaneous squamous cell carcinomas (cSCC)


title: R124_CEC_2

value: invasive squamous cell carcinoma of the face


title: ED_6

status: Public on Dec 31 2018

description: Human primary basophils from D3 stimulated with anti-IgE and anti-IgD

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Human primary basophils_stimulated with anti-IgE and anti-IgD

label_protocol: 2ng of total RNA from each sample was processed and labelled according to manuals GeneChip WT Pico Reagent Kit (P/N 703262, Rev.1 2015) and Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)

extract_protocol: RNA was extracted following the RNeasy Micro kit protocol by Qiagen

tag: donor id

value: donor 3

value: peripheral blood

value: FACSorted human primary basophils

tag: treated with

value: both anti-IgE and anti-IgD


title: R100_PS_2

value: immunocompetent patient

value: healthy sun-exposed skin of the scalp


title: R125_Elas_2

value: 80 years old

value: healthy sun-exposed skin of the face


title: Neg_5

description: Human primary basophils from D2 unstimulated

source_name: Human primary basophils_unstimulated

value: donor 2


title: E_6

description: Human primary basophils from D3 stimulated with anti-IgE

source_name: Human primary basophils_stimulated with anti-IgE

value: anti-IgE


title: E_5

description: Human primary basophils from D2 stimulated with anti-IgE


title: ED_5

description: Human primary basophils from D2 stimulated with anti-IgE and anti-IgD


title: R189_CEC_3

value: 95 years old


title: ED_4

description: Human primary basophils from D1 stimulated with anti-IgE and anti-IgD

value: donor 1


title: LymeDisease Pt34 Visit1

status: Public on Dec 21 2018

city: Stanford

first: Lisa

middle: K

last: Blum

state: CA

address: 269 Campus Drive

institute: Stanford University

description: Single-cell barcoded amplicon mixture

data_processing:
Data processing pipeline has been described in greater detail in previous publications (e.g., Blum 2018, DOI: 10.1002/eji.201747460)
After adapter trimming (Trimmomatic 0.33) and stitching of paired-end reads (FLASH 1.2.11),  sequences from each index (representing one 96-well plate of sorted cells) were binned into separate fastq files based on their well-specific barcode oligo sequences
Within each plate+well combination, sequences were clustered into operational taxonomic units (OTUs) with usearch (v8.1.1756_i86linux32), and heavy- and light-chain consensus sequences selected for each OTU.
Consensus OTU sequences were analyzed with version 1.3.1 of IMGT HighV-QUEST, and the productive OTU sequence with the greatest number of contributing reads was selected for the heavy and light chain from each cell.
Processed fasta files of heavy- and light-chain sequences from each cell were produced from the gapped nucleotide sequences from IMGT, spanning FR1-FR4.
Supplementary_files_format_and_content: fasta files of stitched consensus reads from the heavy- and light-chain genes of each single B cell. Heavy- and light-chain sequences can be paired based on matching record IDs in the heavy and light fasta files.

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Well-specific barcode oligos were added to the cDNA of each cell by template switching during reverse transcription. The wells of each plate were pooled together, and cDNA purified using Ampure RNAClean SPRI beads.
Plate-specific index sequences and Illumina sequencing adaptors were added by PCR with primers specific for immunoglobulin constant regions, and up to 48 plates were pooled for each MiSeq run.
MiSeq 2x330 paired-end sequencing

treatment_protocol: PBMCs were stained with markers to identify B cell populations, and plasmablasts (CD19+CD20-CD27+CD38hi) were single cell sorted into 96-well plates.

value: Peripheral Blood Mononuclear Cells

tag: timepoint

value: Untreated

value: Lyme disease

tag: treatment response

value: Responder


title: D_6

description: Human primary basophils from D3 stimulated with anti-IgD

source_name: Human primary basophils_stimulated with anti-IgD

value: anti-IgD


title: LymeDisease Pt31 Visit1

description: Single-cell barcoded amplicon mixture


title: Neg_4

description: Human primary basophils from D1 unstimulated


title: LymeDisease Pt33 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt25 Visit7

description: Single-cell barcoded amplicon mixture

value: 2 years post-treatment


title: D_5

description: Human primary basophils from D2 stimulated with anti-IgD

value: peripheral blood


title: LymeDisease Pt27 Visit7

description: Single-cell barcoded amplicon mixture


title: D_4

description: Human primary basophils from D1 stimulated with anti-IgD

value: FACSorted human primary basophils


title: LymeDisease Pt25 Visit3

description: Single-cell barcoded amplicon mixture

value: 1 month post-treatment


title: E_4

description: Human primary basophils from D1 stimulated with anti-IgE


title: LymeDisease Pt25 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt24 Visit7

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt27 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt23 Visit5

description: Single-cell barcoded amplicon mixture

value: 6 months post-treatment


title: LymeDisease Pt24 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt22 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt23 Visit3

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt21 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt21 Visit7

description: Single-cell barcoded amplicon mixture


title: Neg_6

description: Human primary basophils from D3 unstimulated

value: donor 3


title: LymeDisease Pt21 Visit5

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt23 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt20 Visit7

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt20 Visit3

description: Single-cell barcoded amplicon mixture


title: R114_CEC_2 [CytoScanHD_Array]

value: immunocompetent patient

value: male

value: 83 years old

value: cSCC

value: invasive squamous cell carcinoma of the scalp


title: LymeDisease Pt20 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt18 Visit1

description: Single-cell barcoded amplicon mixture


title: R115_Elas_2 [CytoScanHD_Array]

value: SES

value: healthy sun-exposed skin of the scalp


title: LymeDisease Pt17 Visit5

description: Single-cell barcoded amplicon mixture

value: Peripheral Blood Mononuclear Cells

value: Non-responder


title: LymeDisease Pt17 Visit7

description: Single-cell barcoded amplicon mixture

value: Lyme disease


title: LymeDisease Pt32 Visit1

description: Single-cell barcoded amplicon mixture

value: Untreated


title: LymeDisease Pt16 Visit5

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt17 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt17 Visit3

description: Single-cell barcoded amplicon mixture


title: R125_Elas_2 [CytoScanHD_Array]

value: female

value: 80 years old

value: healthy sun-exposed skin of the face


title: R100_PS_2 [CytoScanHD_Array]

value: 85 years old


title: LymeDisease Pt16 Visit7

description: Single-cell barcoded amplicon mixture

value: 2 years post-treatment


title: LymeDisease Pt15 Visit7

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt25 Visit5

description: Single-cell barcoded amplicon mixture

value: 6 months post-treatment

value: Responder


title: LymeDisease Pt14 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt14 Visit3

description: Single-cell barcoded amplicon mixture

value: 1 month post-treatment


title: LymeDisease Pt13 Visit5

description: Single-cell barcoded amplicon mixture


title: R124_CEC_2 [CytoScanHD_Array]

value: immunocompetent patient

value: invasive squamous cell carcinoma of the face


title: LymeDisease Pt14 Visit5

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt13 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt13 Visit3

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt15 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt13 Visit7

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt11 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt10 Visit5

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt10 Visit7

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt6 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt10 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt11 Visit3

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt4 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt11 Visit5

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt9 Visit1

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt11 Visit7

description: Single-cell barcoded amplicon mixture


title: R116_QA_2 [CytoScanHD_Array]

value: male

value: 83 years old

value: AK

value: actinic keratosis of the face


title: LymeDisease Pt2 Visit1

description: Single-cell barcoded amplicon mixture

value: Peripheral Blood Mononuclear Cells


title: LymeDisease Pt3 Visit1

description: Single-cell barcoded amplicon mixture

value: Lyme disease


title: R101_QA_2 [CytoScanHD_Array]


title: LymeDisease Pt10 Visit3

description: Single-cell barcoded amplicon mixture

value: Non-responder


title: R106_PS_1 [CytoScanHD_Array]

value: female

value: 86 years old

value: SES

value: healthy sun-exposed skin of the face (preauricular)


title: R105_CEC_1 [CytoScanHD_Array]

value: cSCC

value: invasive squamous cell carcinoma of the face (preauricular)


title: LymeDisease Pt1 Visit1

description: Single-cell barcoded amplicon mixture

value: Untreated

value: Responder


title: R107_QA_1 [CytoScanHD_Array]

value: immunocompetent patient

value: actinic keratosis of the face (preauricular,  adjacent to the squamous cell carcinoma)


title: Healthy14 Visit H3

description: Single-cell barcoded amplicon mixture

value: 1 year after initial visit

value: Healthy control


title: Healthy15 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy18 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy17 Visit H2

description: Single-cell barcoded amplicon mixture

value: 6 months after initial visit


title: Healthy13 Visit H2

description: Single-cell barcoded amplicon mixture


title: Healthy17 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy12 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy13 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy11 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy9 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy6 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy8 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy10 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy4 Visit H2

description: Single-cell barcoded amplicon mixture


title: Healthy6 Visit H2

description: Single-cell barcoded amplicon mixture


title: Healthy3 Visit H1

description: Single-cell barcoded amplicon mixture

value: Initial Visit


title: Healthy5 Visit H3

description: Single-cell barcoded amplicon mixture

value: Peripheral Blood Mononuclear Cells


title: Healthy2 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy3 Visit H3

description: Single-cell barcoded amplicon mixture


title: Healthy2 Visit H2

description: Single-cell barcoded amplicon mixture


title: Healthy1 Visit H2

description: Single-cell barcoded amplicon mixture


title: LymeDisease Pt16 Visit1

description: Single-cell barcoded amplicon mixture

value: Lyme disease


title: LymeDisease Pt20 Visit5

description: Single-cell barcoded amplicon mixture

value: 6 months post-treatment


title: ventral AFG ctrl rep 3

status: Public on Jul 01 2018

city: Cincinnati

first: James

last: Wells

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

description:
TPM_matrix_AFG.xlsx
Counts_matrix_AFG.xlsx

data_processing:
Quality check and trimming of raw reads was performed using CSBB [https://sourceforge.net/projects/csbb-v2-1/], respectively at default parameters. Quality trimmed Reads were mapped to the Homo sapien genome build hg19 [ucsc - https://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19] and quantified using CSBB [uses RSEM at default parameters].
Genome_build: hg19
Supplementary_files_format_and_content: Matrix with genes and samples providing expression of genes in each sample in TPM(Transcripts per Million) and Read Counts. File is in .xlsx format

source_name: ventral anterior foregut culture

extract_protocol:
Total RNA was extracted from three independent biological replicates using the Nucleo-spin RNA kit (Machery-Nagel).
Libraries were constructed with TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: For day 9 anterior foregut (AFG) cultures, they were treated with Noggin (200ng/mL) or BMP4 (100ng/mL) from day 6-9 to dorsalize or ventralize the AFG cultures, respectively. To knockdown SOX2, AFG cultures were treated with doxycycline (1µg/mL) from day 3-9.

tag: Stage

value: day 9

tag: treatment

value: CHIR + BMP4


title: ventral AFG SOX2-KD rep 2

value: CHIR + BMP4 + DOX(SOX2-KD)


title: ventral AFG SOX2-KD rep 3


title: HEO 2mo rep 3

description:
TPM_matrix_HEO.xlsx
Counts_matrix_HEO.xlsx

source_name: Human esophageal organoids

value: 2 month organoid culture

value: ctrl


title: dorsal AFG ctrl rep 3

source_name: dorsal anterior foregut culture

value: CHIR + NOG


title: HEO 2mo rep 1


title: Healthy4 Visit H3

description: Single-cell barcoded amplicon mixture


title: dorsal AFG SOX2-KD rep 2

value: CHIR + NOG + DOX(SOX2-KD)


title: HEO 2mo rep 2


title: dorsal AFG ctrl rep 2


title: ventral AFG ctrl rep 2


title: ventral AFG ctrl rep 1


title: HEO 1mo rep 2

value: 1 month organoid culture


title: HEO 1mo rep 1


title: HEO 1mo rep 3


title: dorsal AFG SOX2-KD rep 3


title: ventral AFG SOX2-KD rep 1


title: dorsal AFG SOX2-KD rep 1


title: dorsal AFG ctrl rep 1


title: COS-7_CGG_siTRA3

status: Public on Jun 19 2018

description: CGG_siTRA3_(Clariom_D_Human).sst-rma-gene-full.chp Signal

hyb_protocol: Sample was hybridized to Affymetrix Human Clariom D array using a Affymetrix GeneChip Hybridization Oven 645

data_processing:
The data were normalized using the SST-RMA algorithm and analyzed in the Transcriptome Analysis Console (TAC, Affymetrix)
The 'RMA_SST_ExonNormalization.txt' contains  Exon log2 SST-RMA data

organism: Chlorocebus sabaeus

label_protocol: 100ng of total RNA from each sample, isolated from COS-7 cells under different experimental conditions was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Plus protocol

extract_protocol: RNA was extracted following Qiagen protocol including DNAse treatment

tag: tissue source

value: kidney

tag: cell line

value: transfected with CGG expansion at the 5'UTR FMR1 (60X) and with knockdown for TRA2A (cond4)


title: COS-7_CGG_siTRA1

description: CGG_siTRA1_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: COS-7_CGG_siTRA2

description: CGG_siTRA2_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: COS-7_siTRA1

description: siTRA1_(Clariom_D_Human).sst-rma-gene-full.chp Signal

value: knockdown for TRA2A (cond3)


title: COS-7_siTRA2

description: siTRA2_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: COS-7_CGG_TRA1

description: CGG_TRA1_(Clariom_D_Human).sst-rma-gene-full.chp Signal

value: transfected with CGG expansion at the 5'UTR FMR1 (60X) and with overexpression of TRA2A (cond5)


title: COS-7_CGG1_rehyb

description: CGG1_rehyb_(Clariom_D_Human).sst-rma-gene-full.chp Signal

value: transfected with CGG expansion at the 5'UTR FMR1 (60X) (cond1)


title: COS-7_GFP_TRA3

description: GFP_TRA3_(Clariom_D_Human).sst-rma-gene-full.chp Signal

value: overexpressing TRA2A (cond2)


title: COS-7_CGG2

description: CGG2_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: COS-7_GFP_TRA2

description: GFP_TRA2_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: COS-7_CTL3

description: CTL3_(Clariom_D_Human).sst-rma-gene-full.chp Signal

value: Control COS-5


title: COS-7_CGG3

description: CGG3_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: COS-7_GFP_TRA1

description: GFP_TRA1_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: SCC13_Gi_2

status: Public on Jun 04 2018

description: Gene expression data from SCC13 cell line

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST array with WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev.1)  in a Affymetrix GeneChip Hybridization Oven 645

data_processing: The data was analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Total RNA from SCC13 cell line

label_protocol: Total RNA from each sample was processed and labelled according to manuals Ambion® WT Expression (P/N 4425209 Rev.B 05/2009) (Ambion/Applied Biosystems, Foster City, CA, USA) and WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev.1) (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: RNA was extracted following Quiagen protocol

tag: tissue

value: human skin squamous cell carcinoma

tag: shRNA

value: short hairpin GFP


title: SCC13_Bi_2

value: short hairpin BMI1


title: SCCL3_EZH2I_1

value: short hairpin EZH2


title: SCC13_Ri_2

value: short hairpin RING1B


title: shBAF8h1

status: Public on Apr 11 2018

description:
TB9
Gene expression data from EphA2 shRNA transfected TC252 cells

data_processing: Data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples. This was performed in R (v 3.1.1) with aroma.affymetrix and bioconductor packages

source_name: EphA2 shRNA transfected TC252 cells

label_protocol: 100ng of total RNA from each sample was processed, labelled according to the Affymetrix GeneChip® WT Plus Reagent kit

extract_protocol: Total RNA was extracted using the NucleoSpin miRNA kit from Macherey-Nagel

value: Ewing sarcoma cell line

tag: transfected with


title: SCCL3_EZH2I_2


title: COS-7_CTL2

description: CTL2_(Clariom_D_Human).sst-rma-gene-full.chp Signal

value: Control COS-6


title: shBAF24h2

description:
TB35
Gene expression data from EphA2 shRNA transfected TC252 cells

tag: cell type


title: SCC13_Gi_1


title: shCT0h1

description:
TC2
Gene expression data from control shRNA transfected TC252 cells

source_name: control shRNA transfected TC252 cells

value: shCtrl


title: COS-7_siTRA3_rehyb

description: siTRA3_rehyb_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: COS-7_CTL1

description: CTL1_(Clariom_D_Human).sst-rma-gene-full.chp Signal

value: Control COS-7


title: SCC13_Ri_1


title: shBAF8h2

description:
TC1
Gene expression data from TC252 parental cells

source_name: TC252 parental cells


title: COS-7_CGG_TRA2

description: CGG_TRA2_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: COS-7_CGG_TRA3

description: CGG_TRA3_(Clariom_D_Human).sst-rma-gene-full.chp Signal


title: SCC13_Bi_1


title: shBAF1h2

description:
AC2
Gene expression data from control shRNA transfected A673 cells

source_name: control shRNA transfected A673 cells


title: shBAF24h1

description:
TB26
Gene expression data from EphA2 shRNA transfected TC252 cells


title: PAAD14

status: Public on Feb 22 2018

city: Shanghai

first: Shengli

last: Li

address: 270 Dong An Road

institute: Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences

description: Pancreatic carcinoma sample14

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat
mRNA and lncRNA annotated in GENCODEv25 were quantified using featureCounts, and circular RNA were identified and quantified by ACFS (https://github.com/arthuryxt/acfs).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Pancreatic carcinoma sample_blood exosome

extract_protocol:
4 ml plasma were used to extract exosomal RNAs by exoRNeasy Serum/Plasma Maxi kit (Qiagen). The exosomal RNAs were further treated with DNAse I and subjected to ribosome minus low-input RNAseq library preparation.
RNA libraries were prepared for sequencing using ribosome minus RNAseq protocols

value: patients with pancreatic carcinoma

value: Blood exosome


title: PAAD13

description: Pancreatic carcinoma sample13


title: PAAD10

description: Pancreatic carcinoma sample10


title: PAAD8

description: Pancreatic carcinoma sample8


title: PAAD12

description: Pancreatic carcinoma sample12


title: PAAD11

description: Pancreatic carcinoma sample11


title: PAAD6

description: Pancreatic carcinoma sample6


title: PAAD2

description: Pancreatic carcinoma sample2


title: PAAD1

description: Pancreatic carcinoma sample1


title: PAAD7

description: Pancreatic carcinoma sample7


title: PAAD5

description: Pancreatic carcinoma sample5


title: PAAD3

description: Pancreatic carcinoma sample3


title: HCC12

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat
mRNA and lncRNA annotated in GENCODEv25 were quantified using featureCounts, and circular RNA were identified and quantified by ACFS (https://github.com/arthuryxt/acfs).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPM or FPKM values for each sample

source_name: Blood exosome

tag: disease state

value: hepatocellular carcinoma

value: Blood

tag: tissue compartment

value: exosome


title: HCC20


title: HCC18


title: HCC16


title: HCC15


title: HCC21


title: shBAF0h1

description:
AB15
Gene expression data from EphA2 shRNA transfected A673 cells

source_name: EphA2 shRNA transfected A673 cells


title: shBAF0h2

description:
AB6
Gene expression data from EphA2 shRNA transfected A673 cells


title: HCC14


title: HCC13


title: PAAD9

description: Pancreatic carcinoma sample9

tag: subject status


title: HCC10


title: HCC11


title: HCC9


title: PAAD4

description: Pancreatic carcinoma sample4


title: HCC19


title: HCC8


title: HCC5


title: HCC4


title: shBAF1h1

description:
AC1
Gene expression data from A673 parental cells

source_name: A673 parental cells


title: HCC17


title: CRC11

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat
mRNA and lncRNA annotated in GENCODEv25 were quantified using featureCounts, and circular RNA were identified and quantified by ACFS (https://github.com/arthuryxt/acfs).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Colorectal Cancer sample_blood exosome

value: patients with colorectal carcinoma


title: CRC12


title: HCC2


title: HCC1


title: CRC8


title: CRC2


title: CRC4


title: CRC5


title: CRC6


title: CRC1


title: CRC7


title: CRC3


title: HCC6


title: HCC7


title: HCC3


title: CRC9


title: CRC10


title: Splenic Naive B cells (Replicate 4)

status: Public on Jul 27 2017

description:
Gene expression data from Splenic Naive B cells
Sample name: S4A

source_name: total RNA from sorted cells from spleen

label_protocol: 30ng of total RNA from each sample was processed and labelled according to manuals NuGEN Ovation® Pico WTA  System V2 (M01224 v2) and Encore™ Biotin Module (M01111 v6) (NuGEN, San Carlos, CA,  USA)

extract_protocol: RNeasy Micro kit (Qiagen)

value: spleen

value: Naive B cells

tag: cell markers


title: Splenic MZ (Replicate 4)

description:
Gene expression data from Splenic MZ
Sample name: S4D

value: MZ B cells


title: Splenic ME-SW (Replicate 1)

description:
Gene expression data from Splenic ME-SW
Sample name: S1C

value: ME-SW B cells


title: Splenic MZ (Replicate 2)

description:
Gene expression data from Splenic MZ
Sample name: S2D


title: Splenic ME-SW (Replicate 4)

description:
Gene expression data from Splenic ME-SW
Sample name: S4C


title: Intestinal ME-SW (Replicate 4)

description:
Gene expression data from Intestinal ME-SW B cells
Sample name: G5C

source_name: total RNA from sorted cells from terminal ileum

value: terminal ileum


title: Intestinal ME-M (Replicate 4)

description:
Gene expression data from Intestinal ME-M B cells
Sample name: G5B

value: ME-M B cells


title: Splenic ME-SW (Replicate 3)

description:
Gene expression data from Splenic ME-SW
Sample name: S3C


title: Intestinal ME-SW (Replicate 2)

description:
Gene expression data from Intestinal ME-SW B cells
Sample name: G2C


title: Intestinal Naive B cells (Replicate 3)

description:
Gene expression data from Intestinal N B cells
Sample name: G3A


title: Splenic Naive B cells (Replicate 2)

description:
Gene expression data from Splenic Naive B cells
Sample name: S2A


title: Splenic Naive B cells (Replicate 3)

description:
Gene expression data from Splenic Naive B cells
Sample name: S3A


title: Intestinal Naive B cells (Replicate 2)

description:
Gene expression data from Intestinal N B cells
Sample name: G2A


title: Intestinal ME-SW (Replicate 3)

description:
Gene expression data from Intestinal ME-SW B cells
Sample name: G3C


title: Splenic MZ (Replicate 1)

description:
Gene expression data from Splenic MZ
Sample name: S1D


title: Intestinal ME-SW (Replicate 1)

description:
Gene expression data from Intestinal ME-SW B cells
Sample name: G1C


title: Intestinal ME-M (Replicate 3)

description:
Gene expression data from Intestinal ME-M B cells
Sample name: G3B


title: Intestinal Naive B cells (Replicate 4)

description:
Gene expression data from Intestinal N B cells
Sample name: G5A


title: Splenic ME-SW (Replicate 2)

description:
Gene expression data from Splenic ME-SW
Sample name: S2C


title: Intestinal ME-M (Replicate 1)

description:
Gene expression data from Intestinal ME-M B cells
Sample name: G1B


title: Splenic MZ (Replicate 3)

description:
Gene expression data from Splenic MZ
Sample name: S3D


title: Intestinal N B cells (Replicate1)

description:
Gene expression data from Intestinal N B cells
Sample name: G1A


title: Splenic Naive B cells (Replicate 1)

description:
Gene expression data from Splenic Naive B cells
Sample name: S1A


title: WH8

status: Public on Jun 20 2017

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

description: Gene Expression

hyb_protocol: Hybridization and washing procedures strictly followed the manufacturer’s protocol (One Color Quick Amp Labeling Kit, Agilent Technologies)

scan_protocol: Microarrays were scanned using the SureScan Microarray Scanner (Agilent Technologies) using default parameters for Agilent microarrays, and images were processed using the Feature Extraction Software v12 (Agilent Technologies) for quality control, determination of feature intensities, and for background correction.

data_processing: The scanned images were analyzed with Feature Extraction Software v 12 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: whole blood

label_protocol: Expression levels were evaluated using the SurePrint G3 8x60K Mouse Gene Expression v2 Microarray (design ID G4858A-074809) and the Low Input Quick Amp Labeling kit, following a one-color labeling protocol (Agilent Technologies, USA).

extract_protocol: Blood from 8 CRAMP-deficient mice and 8 WT mice was collected by cardiac puncture and stored in RNAlater (Ambion, USA), 8 hours after CLP. Total RNA was isolated using Mouse RiboPure-Blood kit following the manufacturer’s protocol (Ambion, Thermofisher, USA). RNA integrity and concentration were assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit (Agilent Technologies, USA).

treatment_protocol: We used CRAMP–/– mice in a C57Bl/6 genetic background and their matched wild type (WT) controls. We induced peritonitis in mice using the model of cecal ligation and puncture (CLP) as previously described. The CLP model consists of the perforation of the cecum allowing the release of fecal material into the peritoneal cavity eventually leading to systemic infection. Briefly, animals were anesthetized and the cecum was ligated and punctured twice with a 21G needle. To obtain a mortality curve, 12 mice from each group were submitted to CLP. We observed all mice every 12 h until they die during 5 days, when the survivors were euthanized.

tag: strain

tag: genotype/variation

value: Wild-type

tag: health status

value: Healthy


title: KS8

description: Gene Expression

value: CRAMP Knock out

value: Sepsis


title: Intestinal ME-M (Replicate 2)

description:
Gene expression data from Intestinal ME-M B cells
Sample name: G2B


title: KH8

description: Gene Expression


title: WS8

description: Gene Expression


title: KS7

description: Gene Expression


title: KH7

description: Gene Expression


title: WS7

description: Gene Expression


title: WH7

description: Gene Expression


title: WS6

description: Gene Expression


title: KH6

description: Gene Expression


title: KS6

description: Gene Expression


title: KS5

description: Gene Expression


title: KH4

description: Gene Expression


title: WH6

description: Gene Expression


title: WH5

description: Gene Expression


title: N32

status: Public on Jun 19 2017

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat
mRNA and lncRNA annotated in GENCODEv25 were quantified using featureCounts, and circular RNA were identified and quantified by ACFS (https://github.com/arthuryxt/acfs).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.


title: N31


title: WH3

description: Gene Expression


title: N30


title: WH2

description: Gene Expression


title: KS1

description: Gene Expression


title: KH3

description: Gene Expression


title: N27


title: N28


title: KH2

description: Gene Expression


title: KH1

description: Gene Expression


title: WS1

description: Gene Expression


title: N29


title: WH1

description: Gene Expression


title: KH5

description: Gene Expression


title: WS5

description: Gene Expression


title: N26


title: WS4

description: Gene Expression


title: KS4

description: Gene Expression


title: WH4

description: Gene Expression


title: KS2

description: Gene Expression


title: KS3

description: Gene Expression


title: WS2

description: Gene Expression


title: WS3

description: Gene Expression


title: N25


title: N24


title: N22


title: N23


title: N21


title: N19


title: N18


title: N16


title: N15


title: N14


title: N13


title: N12


title: N9


title: N8


title: N10


title: N7


title: N5


title: N4


title: N6


title: N11


title: N1

tag: patient status

value: Normal


title: N3


title: N2


title: N20


title: N17


title: LN12_DNC_INF-gamma (50ng/mL)

status: Public on Jun 12 2017

description: Gene Expression

scan_protocol: The arrays were scanned using a SureScan Microarray Scanner (Agilent Technologies, USA) using default parameters for Agilent microarrays.

data_processing: The scanned images were analyzed with Feature Extraction Software v 10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: lymph node-derived stromal cells

label_protocol: In total 4 LNs were used for gene expression analysis, 2 LNs isolated from cancer patients (LN04 and LN15), 1 from a diverticulitis patient (LN12) and 1 isolated from a healthy liver donor (LN16). We compared treated and control FRCs and DNCs: cells were treated or not with INF-γ (50ng/mL) or TNFα (25ng/mL) in combination with IL-1β (5ng/mL). Expression levels of protein coding genes were evaluated by DNA microarrays using the SurePrint G3 Human Gene Expression 8x60K v2 Microarray Kit (Agilent Technologies, USA). Labeling of probes with cyanine 3 dye (Cy3), hybridization and washing procedures strictly followed the manufacturer’s protocol (One Color Quick Amp Labeling Kit, Agilent Technologies).

extract_protocol: RNA extraction was carried out using RNAeasy Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. The RNA quantification and quality analysis were carried out using the NanoVue spectrophotometer (GE Healthcare Life Sciences, Little Chalfont, United Kingdom).

treatment_protocol: This study evaluates gene expression and secretion of cytokines and chemokines in human-derived FRCs and DNCs during homeostasis and following inflammatory stimuli.

value: lymph node

tag: organ origin

value: intestine

tag: diagnosis

value: diverticulitis

value: Double Negative Cell

value: INF-gamma (50ng/mL)


title: LN04_FRC_INF-gamma (50ng/mL)

description: Gene Expression

value: Larynx

value: Cancer

value: Fibroblastic Reticular Cell

tag: treatment


title: LN04_DNC_TNFalpha (25ng/mL)+IL1 (5ng/mL)

description: Gene Expression

value: TNFalpha (25ng/mL)+IL1 (5ng/mL)


title: LN04_DNC_Control

description: Gene Expression

value: Control


title: LN12_FRC_INF-gamma (50ng/mL)

description: Gene Expression


title: LN15_DNC_Control

description: Gene Expression

value: Breast


title: LN12_DNC_Control

description: Gene Expression


title: LN04_DNC_INF-gamma (50ng/mL)

description: Gene Expression


title: LN16_DNC_Control

description: Gene Expression

value: liver

value: healthy


title: LN12_FRC_TNFalpha (25ng/mL)+IL1 (5ng/mL)

description: Gene Expression


title: LN15_FRC_INF-gamma (50ng/mL)

description: Gene Expression


title: LN16_DNC_INF-gamma (50ng/mL)

description: Gene Expression


title: LN16_FRC_TNFalpha (25ng/mL)+IL1 (5ng/mL)

description: Gene Expression


title: LN04_FRC_Control

description: Gene Expression


title: LN15_DNC_TNFalpha (25ng/mL)+IL1 (5ng/mL)

description: Gene Expression


title: LN15_FRC_TNFalpha (25ng/mL)+IL1 (5ng/mL)

description: Gene Expression


title: LN15_FRC_Control

description: Gene Expression


title: LN15_DNC_INF-gamma (50ng/mL)

description: Gene Expression


title: A47

description: Gene expression data from total RNA

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST and Affymetrix Almac Xcel array using a Affymetrix GeneChip Hybridization Oven 645

data_processing: Data were analyzed using the RMA algorithm in the Affymetrix Expression Console. Batch effect was corrected using COMBAT and then LIMMA was applied to calculate significant differential expression between samples. This was performed in R (v 3.1.1) with aroma.affymetrix and bioconductor packages

source_name: Gastric mucosa of Healthy Control

label_protocol: 100ng of total RNA from each sample was processed, labelled according to the Affymetrix SensationPlus FFPE 3'IVT protocol

extract_protocol: RNA was extracted following the Recover All Nucleic Acid for FFPE kit (Ambion, USA)

tag: localization

value: Antrum

tag: status

value: Healthy Control

tag: age

tag: Sex

value: Woman

value: Gastric mucosa of Healthy Control


title: LN16_DNC_TNFalpha (25ng/mL)+IL1 (5ng/mL)

description: Gene Expression

tag: tissue

value: lymph node


title: LN12_DNC_TNFalpha (25ng/mL)+IL1 (5ng/mL)

description: Gene Expression

value: intestine

tag: cell type


title: A43

description: Gene expression data from total RNA


title: A50

description: Gene expression data from total RNA


title: A46

description: Gene expression data from total RNA


title: A44

description: Gene expression data from total RNA

value: Body

value: Man


title: LN04_FRC_TNFalpha (25ng/mL)+IL1 (5ng/mL)

description: Gene Expression


title: LN16_FRC_Control

description: Gene Expression


title: LN16_FRC_INF-gamma (50ng/mL)

description: Gene Expression

value: INF-gamma (50ng/mL)


title: A45

description: Gene expression data from total RNA


title: LN12_FRC_Control

description: Gene Expression

value: diverticulitis


title: A23

description: Gene expression data from total RNA

source_name: Gastric mucosa of CIM-GC

value: CIM-GC

value: Gastric mucosa of CIM-GC


title: A27

description: Gene expression data from total RNA


title: A26

description: Gene expression data from total RNA


title: A24

description: Gene expression data from total RNA


title: A25

description: Gene expression data from total RNA


title: A20

description: Gene expression data from total RNA


title: A32

description: Gene expression data from total RNA

source_name: Gastric mucosa of CIM Control

value: CIM Control

value: Gastric mucosa of CIM Control


title: A34

description: Gene expression data from total RNA


title: A28

description: Gene expression data from total RNA

value: Transitional


title: A33

description: Gene expression data from total RNA


title: A22

description: Gene expression data from total RNA


title: A11

description: Gene expression data from total RNA

source_name: Gastric mucosa of IIM-GC

value: IIM-GC

value: Gastric mucosa of IIM-GC


title: A35

description: Gene expression data from total RNA

value: Antrum


title: A21

description: Gene expression data from total RNA


title: A30

description: Gene expression data from total RNA


title: A13

description: Gene expression data from total RNA

source_name: Gastric mucosa of IIM Control

value: IIM Control

value: Gastric mucosa of IIM Control


title: A31

description: Gene expression data from total RNA


title: A29

description: Gene expression data from total RNA


title: A38

description: Gene expression data from total RNA

value: Healthy Control

value: Gastric mucosa of Healthy Control


title: A8

description: Gene expression data from total RNA


title: A36

description: Gene expression data from total RNA


title: A9

description: Gene expression data from total RNA


title: A19

description: Gene expression data from total RNA


title: A15

description: Gene expression data from total RNA

value: Woman


title: A18

description: Gene expression data from total RNA


title: A42

description: Gene expression data from total RNA


title: A16

description: Gene expression data from total RNA


title: A41

description: Gene expression data from total RNA


title: A17

description: Gene expression data from total RNA


title: A10

description: Gene expression data from total RNA


title: A12

description: Gene expression data from total RNA


title: A39

description: Gene expression data from total RNA


title: A49

description: Gene expression data from total RNA

value: Body


title: A14

description: Gene expression data from total RNA

value: Man


title: A48

description: Gene expression data from total RNA


title: A40

description: Gene expression data from total RNA


title: A7

description: Gene expression data from total RNA


title: A51

description: Gene expression data from total RNA


title: 485

description:
Total RNA from leukocytes (whole Blood). The LeukoLock System
Gene expression data from colorectal cancer patients peripheral leukocytes

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 1.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

extract_protocol: RNA was extracted following Leukolock Total RNA Isolation System

tag: disease state

value: colorectal cancer

tag: condition

value: Control

tag: sample id

tag: paired sample

value: peripheral leukocytes


title: 482


title: 470

value: Infected


title: 475


title: 467


title: 466


title: 483


title: 469


title: 476


title: 462


title: 474


title: 473


title: 468


title: 456


title: 465


title: 460


title: 461


title: 457


title: 453


title: 463


title: 464


title: 458


title: A37

description: Gene expression data from total RNA


title: 471


title: 454


title: 448


title: 450


title: 449


title: 425


title: 452


title: 426


title: 407


title: 415


title: 442


title: 327


title: 352


title: 446


title: 333


title: 304


title: 322


title: 351


title: 399


title: 421


title: 298


title: 402


title: 432


title: 302


title: 447


title: 343


title: 330


title: 400


title: 266


title: 259


title: 301


title: 274


title: 250


title: 230


title: 245


title: 236


title: 222


title: 155


title: 437


title: EC-EA-3702-INPUT_ASYN_1

status: Public on May 16 2017

data_processing:
Reads were trimmed for residual adapters (cutadapt version 1.8.1).
Alignment to the mouse reference genome version mm10 was performed using standard parameters, permitting maximum one mismatch in seed alignment (Bowtie version 2.2.5).
Reads marked as positional duplicates or falling into mouseENCODE blacklisted genomic regions (liftOver to mm10; Dunham et al. 2012) were filtered out.
Coverage tracks in RPKM were generated from alignments using bamCoverage (V2.3.6) at the bin size of 10.
ChIP-seq peaks (enrichment of signals over background) were called at 10-5 (MACS version 2.1.1), and peaks detected in more than half of biological replicates were retained for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files for coverage tracks; narrowPeak files for peak coordinates.

source_name: embryonic stem cells

growth_protocol: V6.5 ESCs were cultured on irradiated feeder cells in KO-DMEM (Invitrogen) supplemented with L-Glutamine, penicillin-streptomycin, nonessential amino acids, β-mercaptoethanol, 1000 U/ml LIF and 15% heat-inactivated fetal bovine serum (FBS). Prior to synchronization, cells were expanded on gelatinized plates in the presence of 2i, MEK1 inhibitor (PD98059) and Gsk3 inhibitor (Chir99021) for at least 2 passages.

extract_protocol:
Asynchronous or mitotic ESCs were crosslinked in 1% formaldehyde at room temperature (RT) for 10 minutes and quenched with 125mM glycine 5 mins at RT. 25-50M ESCs were used for the TF ChIPs and 10M for the H3K27acetylation ChIP. Cell pellets were washed twice in PBS and resuspended in 400ul lysis buffer per 20 million cells  (10mM Tris pH8, 1mM EDTA, 0.5% SDS). Cells were sonicated in a bioruptor device (30 cycles 30sec on/off, high setting) and spin down 10 minutes at 4 degrees at maximum speed. Supernatants were diluted 5 times with dilution buffer (0.01%SDS, 1.1% triton,1.2mM EDTA,16.7mM Tris pH8, 167mM NaCl) and incubated with the respective antibody (2-3ug/10M cells) O/N with rotation at 4oC. Next day, protein G Dynabeads (ThermoScientific) preblocked with BSA protein (100ng per 10ul Dynabeads) were added (10ul blocked Dynabeads per 10 million cells) and incubated for 2-3 hours at 4oC. Beads were immobilized on magnet and washed twice in low salt buffer (0.1% SDS,1% triton, 2mM EDTA, 150mM NaCl, 20mM Tris pH8), twice in high salt buffer (0.1% SDS,1% triton, 2mM EDTA, 500mM NaCl, 20mM Tris pH8), twice in LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris pH8) and once in TE. DNA was then eluted from the beads by incubating with 150ul elution buffer (1% SDS, 100mM NaHCO3) for 20 minutes at 65 degrees (vortex every 10min). Supernatants were collected and reverse-crosslinked by incubation at 65 degrees O/N in presence of proteinase K. After Rnase A treatment for 1hr at 37oC, DNA was purified using the Qiagen minElute kit. 6-10ng of immunoprecipitated material was used for ChIP-seq.
ChIP-seq library preparation using the KAPA Hyper prep kit from KAPA Biosystems. Libraries were sequenced on an Illumina HiSeq 5000 platform on the SE50 mode.

treatment_protocol: Mitotic arrest was done as follows: 80-90% confluent mouse ESCs were split 1:3 on gelatinized plates the day before synchronization. Nocodazole at 100ug/ml was added in the medium for 7hr prior to collection by mitotic shake-off.

tag: strain

tag: cell cycle

value: asynchronous

tag: chip antibody


title: EC-DG-3514-H3K27AC_MIT_1

value: mitotic

value: H3K27ac (ABCAM ab4729)


title: EC-EA-2697-INPUT_ASYN_1


title: EC-DG-3458-INPUT_ASYN_1


title: EC-DG-3514-H3K27AC_MIT_2


title: EC-DG-3458-H3K27AC_ASYN_2


title: EC-EA-2643-INPUT_ASYN_1


title: EC-DG-3514-INPUT_MIT_1


title: EC-DG-4040-INPUT_PCT10_1

source_name: embryonic stem cells mixed with neural progenitor cells in a ratio of 10:90


title: EC-EA-3702-INPUT_MIT_1


title: EC-DG-3458-H3K27AC_ASYN_1


title: EC-EA-3702-SOX2_MIT_2


title: EC-EA-3702-SOX2_ASYN_1


title: EC-EA-3702-SOX2_MIT_1


title: EC-EA-3702-OCT4_MIT_2

value: Oct4 (Santa Cruz SC-8628)


title: EC-EA-3702-KLF4_MIT_1


title: EC-EA-3702-OCT4_MIT_1


title: EC-DG-4040-KLF4_PCT10_1


title: EC-EA-3702-OCT4_ASYN_1


title: EC-DG-3514-KLF4_MIT_1


title: EC-EA-3702-KLF4_ASYN_1


title: EC-EA-2643-KLF4_ASYN_1


title: 455


title: EC-EA-2697-KLF4_ASYN_1


title: EC-DG-3514-KLF4_MIT_2


title: A16R [blood]

status: Public on Apr 19 2017

description: Gene expression from total RNA.

hyb_protocol: Samples were hybridized to Agilent-039494 Whole Human Genome Oligo Microarrays 8x60K v2, according to the Agilent 60-mer oligo microarray processing protocol and using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: Data were analyzed in two sets, blood and tissue. For each data set, it was background corrected and quantile normalized. Then LIMMA was applied to calculate significant differential expression between samples. This was performed in R (v 3.1.1) with Bioconductor packages.

source_name: Patient blood

label_protocol: 100ng of total RNA from each sample was amplified by linear T7 method, and the cRNA labeled with Cy3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol.

extract_protocol: RNA was extracted using standard RNA extraction protocols (Trizol).

tag: disease status

value: chronic spontaneous urticaria (CSU)/chronic idiopathic urticaria (CIU)

value: blood

tag: individual id


title: B7 [blood]

description: Gene expression from total RNA.

source_name: Healthy control blood

value: healthy


title: A17 [blood]

description: Gene expression from total RNA.


title: XX [blood]

description: Gene expression from total RNA.

value: XX


title: A14 [blood]

description: Gene expression from total RNA.


title: A21 [blood]

description: Gene expression from total RNA.


title: A13 [blood]

description: Gene expression from total RNA.


title: A12 [blood]

description: Gene expression from total RNA.


title: B10 [blood]

description: Gene expression from total RNA.


title: A8 [blood]

description: Gene expression from total RNA.


title: A15 [blood]

description: Gene expression from total RNA.


title: A20 [blood]

description: Gene expression from total RNA.


title: A22 [blood]

description: Gene expression from total RNA.


title: A5 [blood]

description: Gene expression from total RNA.


title: B5 [blood]

description: Gene expression from total RNA.


title: B9 [blood]

description: Gene expression from total RNA.


title: A10 [blood]

description: Gene expression from total RNA.


title: B2 [blood]

description: Gene expression from total RNA.


title: A7 [blood]

description: Gene expression from total RNA.


title: B4 [blood]

description: Gene expression from total RNA.


title: A19 [blood]

description: Gene expression from total RNA.


title: A4 [blood]

description: Gene expression from total RNA.


title: A18 [blood]

description: Gene expression from total RNA.


title: B3 [blood]

description: Gene expression from total RNA.


title: A2 [blood]

description: Gene expression from total RNA.


title: A3 [blood]

description: Gene expression from total RNA.


title: B8 [blood]

description: Gene expression from total RNA.


title: B6 [blood]

description: Gene expression from total RNA.


title: B1 [blood]

description: Gene expression from total RNA.


title: A19-W [tissue]

description: Gene expression from total RNA.

source_name: Patient wheal

value: wheal


title: A1 [blood]

description: Gene expression from total RNA.


title: A20-S [tissue]

description: Gene expression from total RNA.

source_name: Patient non-lesional skin

value: non-lesional skin


title: A22-S [tissue]

description: Gene expression from total RNA.


title: A22-W [tissue]

description: Gene expression from total RNA.


title: A13-S [tissue]

description: Gene expression from total RNA.


title: XX-S [tissue]

description: Gene expression from total RNA.


title: A17-W [tissue]

description: Gene expression from total RNA.


title: XX-W [tissue]

description: Gene expression from total RNA.


title: A16-W [tissue]

description: Gene expression from total RNA.


title: B10 [tissue]

description: Gene expression from total RNA.

source_name: Healthy control skin

value: skin


title: A17-S [tissue]

description: Gene expression from total RNA.


title: B7 [tissue]

description: Gene expression from total RNA.


title: A18-W [tissue]

description: Gene expression from total RNA.


title: A8-S [tissue]

description: Gene expression from total RNA.


title: A15-S [tissue]

description: Gene expression from total RNA.


title: A8-W [tissue]

description: Gene expression from total RNA.


title: A19-S [tissue]

description: Gene expression from total RNA.


title: A12-S [tissue]

description: Gene expression from total RNA.


title: A18-S [tissue]

description: Gene expression from total RNA.


title: B9 [tissue]

description: Gene expression from total RNA.


title: B2 [tissue]

description: Gene expression from total RNA.


title: B6 [tissue]

description: Gene expression from total RNA.


title: A14-S [tissue]

description: Gene expression from total RNA.


title: B8 [tissue]

description: Gene expression from total RNA.


title: A15-W [tissue]

description: Gene expression from total RNA.


title: A20-W [tissue]

description: Gene expression from total RNA.


title: A3-S [tissue]

description: Gene expression from total RNA.


title: A7-S [tissue]

description: Gene expression from total RNA.


title: A7-W [tissue]

description: Gene expression from total RNA.


title: A4-S [tissue]

description: Gene expression from total RNA.


title: siMIR204_1

status: Public on Dec 31 2016

description: Gene expression data from HaCaT transduced with shRNA against miR-204

source_name: Immortalized  Human Keratinocyte Cell Line

extract_protocol: RNA was extracted with Genelute Total Mammalian RNA Kit (Sigma)

tag: cell line

value: HaCaT


title: G2_CONTROL

description: Gene expression data from HaCaT transduced with control shRNA

value: HaCaT tansduced with control shRNA


title: G1_CONTROL


title: B1 [tissue]

description: Gene expression from total RNA.


title: MSC_Snail1_KO

status: Public on Dec 22 2016

description: Gene expression data from Snail1-KO MSCs

hyb_protocol: Sample was hybridized to Affymetrix Mouse Gene 2.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

data_processing: Data were analyzed using the RMA algorithm and then substaction was applied to calculate significant differential expression between samples. This was performed in R (v 3.1.1) with aroma.affymetrix and bioconductor packages

source_name: Snail1-KO MSCs

label_protocol: 100ng of total RNA from each sample was processed, labelled according to the Affymetrix GeneChip® WT PLUS Reagent Kit

extract_protocol: RNA was extracted following the GenElute Mammalian Total RNA miniprep Kit (Sigma-Aldrich) protocol

value: Mesenchymal Stem Cells (MSCs)

value: Derived from bone marrow

tag: genotype/variation


title: MSC_Ct_TGF_2h

description: Gene expression data from Snail1-WT MSCs treated with TGF-b1 2h

source_name: Snail1-WT MSCs treated with TGF-b1


title: MSC_Snail1_KO_TGF_2h

description: Gene expression data from Snail1-KO MSCs treated with TGF-b1 2h

source_name: Snail1-KO MSCs treated with TGF-b1


title: H9 hESCs infected with shRUNX1 and differentiated for 8hrs, rep1

status: Public on Oct 06 2016

city: New Haven

first: Jennifer

last: VanOudenhove

state: CT

address: 300 George St RM 786

department: Internal Medicine - Section of Hematology

institute: Yale University

hyb_protocol: The cDNA was hybridized to the Affymetrix GeneChip Human Transcriptome Array 2.0 for 16.5 hours overnight.

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

data_processing:
Due to evident fold change compression, Affymetrix was engaged to employ a GC content leveling and signal space transformation to reduce background levels. After this, the transformed CEL files were imported into Affymetrix Expression Console Build 1.3.1.187 where the data was normalized using the default RMA algorithm. Further analysis was performed using the Gene Level Differential Expression Analysis function available in the Affymetrix Transcriptome Analysis Console Version 1.0.0.234.
*pre.CEL: CEL files before Affymetrix adjustment
*cel: Affymetrix-adjusted CEL files

label_protocol: 50ng of RNA was used to synthesize cDNA using the GeneChip® WT PLUS Reagent Kit.

growth_protocol: H9 human embryonic stem cells were maintained using WiCell SOP-Sh-002 for Feeder Independent Growth using mTeSR1.

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

treatment_protocol: hESCs were infected with lentivirus carrying shRNA designed to knockdown RUNX1 (clone V2LHS_150257) or be non-silencing (Cat No. RHS4346) using the GIPZ Lentiviral RNAi System. hESCs were differentiated in media containing KNOCKOUT™ Dulbecco's modified Eagle's medium (DMEM), 20% heat-inactivated Defined Fetal Bovine Serum (FBS) [HyClone], 1mM L-glutamine with 1% v/v 2-mercaptoethanol, and 0.1 mM nonessential amino acids for times indicated before being scraped into Trizol.

value: female human embryonic stem cell (hESC) line

tag: differentiation state

value: 8 hrs FBS differentiated

tag: shRNA


title: Undifferentiated H9 hESCs infected with shRUNX1, rep2

source_name: undifferentiated H9 hESCs infected with shRUNX1

value: undifferentiated


title: H9 hESCs infected with shRUNX1 and differentiated for 72hrs, rep2

value: 72 hrs FBS differentiated


title: H9 hESCs infected with shRUNX1 and differentiated for 24hrs, rep1

value: 24 hrs FBS differentiated


title: H9 hESCs infected with shRUNX1 and differentiated for 24hrs, rep2


title: H9 hESCs infected with shRUNX1 and differentiated for 8hrs, rep2


title: Undifferentiated H9 hESCs infected with shRUNX1, rep1


title: H9 hESCs infected with non-silencing shRNA and differentiated for 8hrs, rep3

value: non-silencing


title: Undifferentiated H9 hESCs infected with shRUNX1, rep3


title: H9 hESCs infected with shRUNX1 and differentiated for 8hrs, rep3


title: H9 hESCs infected with non-silencing shRNA and differentiated for 72hrs, rep1


title: HT29_M6_Ct

description: Gene expression data from HT-29M6 control cells

source_name: HT-29M6 (HT-29 cells resistant to 1uM methotrexate) (untreated control)

value: Isolated from colorectal adenocarcinoma


title: H9 hESCs infected with shRUNX1 and differentiated for 72hrs, rep1


title: H9 hESCs infected with non-silencing shRNA and differentiated for 24hrs, rep1


title: H9 hESCs infected with non-silencing shRNA and differentiated for 24hrs, rep2


title: MSC_Ct

description: Gene expression data from Snail1-WT MSCs

source_name: Snail1-WT MSCs


title: H9 hESCs infected with shRUNX1 and differentiated for 72hrs, rep3


title: H9 hESCs infected with non-silencing shRNA and differentiated for 72hrs, rep3


title: H9 hESCs infected with shRUNX1 and differentiated for 24hrs, rep3


title: H9 hESCs infected with non-silencing shRNA and differentiated for 24hrs, rep3


title: H9 hESCs infected with non-silencing shRNA and differentiated for 72hrs, rep2


title: H9 hESCs infected with non-silencing shRNA and differentiated for 8hrs, rep2


title: Undifferentiated H9 hESCs infected with non-silencing shRNA, rep3

source_name: undifferentiated H9 hESCs infected with non-silencing shRNA


title: H9 hESCs infected with non-silencing shRNA and differentiated for 8hrs, rep1


title: Undifferentiated H9 hESCs infected with non-silencing shRNA, rep2


title: HT29_M6_Ct_TGF_2h

description: Gene expression data from HT-29M6 treated with PGE2 16h

source_name: HT-29M6 (HT-29 cells resistant to 1uM methotrexate) (treated with PGE2 16h)


title: Undifferentiated H9 hESCs infected with non-silencing shRNA, rep1


title: SK-ES-1  shMock

status: Public on Jun 30 2016

description: Gene expression data from control shRNA-transduced SK-ES-1 cells

source_name: Human Ewing sarcoma cancer cell line

label_protocol: 100ng of total RNA from each sample was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay

value: ES1 Cell Line

value: shMock


title: TC71  shBMI1

description: Gene expression data from shBMI1-transduced TC71 cells

value: TC71 Cell Line


title: A4573 shRING1B

description: Gene expression data from shRING1B-transduced A4573 cells

value: A4573 Cell Line


title: TC71 shRING1B

description: Gene expression data from shRING1B-transduced TC71 cells


title: A4573 shMock

description: Gene expression data from control shRNA-transduced A4573 cells


title: SK-ES-1  shRING1B

description: Gene expression data from shRING1B-transduced SK-ES-1 cells


title: A673 shBMI1

description: Gene expression data from shBMI1-transduced A673 cells

value: A673 Cell Line


title: 2b

status: Public on Dec 21 2015

description: Primary osteoblasts isolated from bone tissue

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th gen (Exiqon, Denmark). The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction  manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Primary human osteoblasts

label_protocol: 750 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer

extract_protocol: Total RNA was extracted using High Pure RNA Isolation kit (Roche Diagnostics, Indianapolis, USA)

tag: cy3 data file

tag: cy5 data file

value: Primary bone cells

value: Osteoarthritis


title: A673 shMock

description: Gene expression data from control shRNA-transduced A673 cells


title: A673 shRING1B

description: Gene expression data from shRING1B-transduced A673 cells


title: 1

tag: tissue


title: H9 hESCs differentiated for 72hrs, biological rep2

status: Public on Mar 22 2016

hyb_protocol: The cDNA was hybridized to the GeneChip Human Transcriptome Array 2.0 for 16.5 hours overnight

data_processing: Due to evident fold change compression, Affymetrix was engaged to employ a GC content leveling and signal space transformation to reduce background levels. After this the transformed CEL files [*_(HTA-2_0).cel or _(HTA-2_0)_2.cel files] were imported into Affymetrix Expression Console Build 1.3.1.187 where the data was normalized using the default RMA algorithm. Further analysis was performed using the Gene Level Differential Expression Analysis function available in the Affymetrix Transcriptome Analysis Console Version 1.0.0.234.

source_name: H9 hESCs differentiated for 72hrs

label_protocol: [cDNA protocol] 50ng of RNA was used to synthesize cDNA using the GeneChip® WT PLUS Reagent Kit.

treatment_protocol: hESCs were differentiated in media containing KNOCKOUT™ Dulbecco’s modified Eagle’s medium (DMEM), 20% heat inactivated Defined FBS [Hyclone], 1mM L-glutamine with 1% v/v 2-mercaptoethanol, and 0.1 mM nonessential amino acids for times indicated before being scraped into Trizol.

tag: gender

value: female

value: H9 ESC

tag: protocol

value: differentiated

tag: time

value: 72 hrs


title: H9 hESCs differentiated for 8hrs, biological rep2

source_name: H9 hESCs differentiated for 8hrs


title: H9 hESCs differentiated for 24hrs, biological rep1

source_name: H9 hESCs differentiated for 24hrs


title: undifferentiated H9 hESCs, biological rep2

source_name: undifferentiated H9 hESCs

value: control


title: undifferentiated H9 hESCs, biological rep1

value: undifferentiated


title: TC71 shMock

description: Gene expression data from control shRNA-transduced TC71 cells

tag: condition


title: H9 hESCs differentiated for 8hrs, biological rep3


title: H9 hESCs differentiated for 72hrs, biological rep1


title: H9 hESCs differentiated for 72hrs, biological rep3


title: undifferentiated H9 hESCs, biological rep3


title: H9 hESCs differentiated for 24hrs, biological rep2


title: H9 hESCs differentiated for 8hrs, biological rep1


title: 414


title: O-398

description: Bony fragments were extracted from the transcervical region of the femoral neck for both osteoporotic fracture (OP) and control samples

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th gen (Exiqon, Denmark). The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

source_name: Fresh femoral neck trabecular bone

label_protocol: 250 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer

extract_protocol: RNA was extracted following the miRNeasy Mini kit (Qiagen) protocol.

value: Bone tissue

value: Healthy


title: O-429


title: 132


title: O-495


title: O-455

value: Osteoporotic


title: O-470


title: O-461


title: O-369


title: O-449


title: O-500


title: O-467


title: O-422


title: shLOXL2_0d_R2

description: Gene expression data from LOXL2 sh-RNA-transduced mES cells

source_name: E14 mouse embryonic stem cell line_shLOXL2

extract_protocol: RNA was extracted using Trizol reagent

tag: cell type

value: mES cell line

tag: transduction construct

tag: ra treatment

value: no


title: shLOXL2_1d_R1

description: Gene expression data from LOXL2 sh-RNA transduced and RA-treated mES cells

source_name: E14 mouse embryonic stem cell line_shLOXL2_RA

value: yes


title: shLOXL2_0d_R1


title: shLOXL2_1d_R3


title: shCT_0d_R3

description: Gene expression data from control sh-RNA transduced mES cells

source_name: E14 mouse embryonic stem cell line_shCT

value: shCT


title: shCT_1d_R1

description: Gene expression data from control sh-RNA transduced and RA-treated mES cells

source_name: E14 mouse embryonic stem cell line_shCT_RA


title: shCT_1d_R3


title: shCT_1d_R2


title: shCT_0d_R1


title: shCT_0d_R2


title: shLOXL2_0d_R3


title: shLOXL2_1d_R2


title: H9 hESCs differentiated for 24hrs, biological rep3


title: O-352


title: HT29_BRAF_INH_3

status: Public on May 08 2015

description:
CRC cell lines
Gene expression data from AZ628-treated HT29 cells

hyb_protocol: Sample was hybridized to Affymetrix PrimeView array using a Affymetrix GeneChip Hybridization Oven 645

data_processing: Data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples. This was performed in R (v 3.0.2) with aroma.affymetrix and bioconductor packages

source_name: HT29 human colorectal cancer cell line

extract_protocol: RNA was extracted following the RNA-easy Quiagen protocol.


title: HT29_BRAF_INH_2


title: mm4271.I

status: Public on Mar 28 2015

description: Gene expression data from rag2ko mouse intestinal epithelial cells at 2 days after T. spiralis infection

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChip 3000-7G

source_name: day 2 post-T. spiralis infection rag2ko intestinal epithelial cells

label_protocol: MessageAmp Premier RNA Amplification and Biotin Labelling kit

extract_protocol: Trizol/Chloroform Extraction

value: intestinal epithelial cells

tag: genotype

tag: strain

value: C57Bl/6 background

tag: treatment

value: T. spiralis oral infection


title: mm4269.U

description: Gene expression data from rag2ko mouse intestinal epithelial cells

source_name: uninfected rag2ko intestinal epithelial cells


title: mm4249.I


title: WiDr_shC_1

description:
CRC cell lines
Gene expression data from control sh-RNA-transduced WiDr cells

source_name: WiDr human colorectal cancer cell line

tag: cell line

value: WiDr

value: shC


title: WiDr_shC_3


title: HT29_C_1

description:
CRC cell lines
Gene expression data from vehicle-treated HT29 cells

value: CTRL


title: WiDr_shIKKa_3

description:
CRC cell lines
Gene expression data from control sh-IKKalpha-transduced WiDr cells

value: shIKKa


title: WiDr_C_1

description:
CRC cell lines
Gene expression data from vehicle-treated WiDr cells


title: HT29_BRAF_INH_1


title: WiDr_shIKKa_1


title: WiDr_BRAF_INH_2

description:
CRC cell lines
Gene expression data from AZ628-treated WiDr cells


title: WiDr_shC_2


title: HT29_C_3


title: HT29_C_2


title: WiDr_BRAF_INH_3


title: mm4239.U


title: WiDr_shIKKa_2


title: WiDr_C_2


title: mm4241.U


title: WiDr_BRAF_INH_1


title: WiDr_C_3


title: 7_POST [miRNA]

status: Public on Dec 31 2014

description: Gene expression data from human adipose tissue.

hyb_protocol: Sample was hybridized to Affymetrix miRNA 3.0 array using an Affymetrix GeneChip Hybridization Oven 645.

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm (R version 3.0.2) and then LIMMA was applied to calculate significant differential expression between samples.

source_name: human adipose tissue, post surgery-induced weight loss

label_protocol: 350 ng of total RNA from each sample, isolated from human adipose tissue, was processed, labelled according to the Affymetrix GeneChip® WT Terminal Labeling Kit.

extract_protocol: RNA was extracted following Qiagen protocol.

value: subcutaneous adipose

value: female

value: POST surgery-induced weight loss

tag: individual


title: 36_PRE [miRNA]

source_name: human adipose tissue, pre surgery-induced weight loss

value: PRE surgery-induced weight loss


title: 34_POST [miRNA]


title: 36_POST [miRNA]


title: 31_POST [miRNA]


title: 33_POST [miRNA]


title: 7_PRE [miRNA]


title: 31_PRE [miRNA]


title: 33_PRE [miRNA]


title: mm4247.I


title: 29_POST [miRNA]


title: 2_PRE [miRNA]


title: 24_PRE [miRNA]


title: siMIR204_2

description: Gene expression data from HaCaT transduced with shRNA against miR-204

source_name: Immortalized  Human Keratinocyte Cell Line

label_protocol: 200ng of total RNA from each sample was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay

value: HaCaT


title: 15_PRE [miRNA]


title: 25_POST [miRNA]


title: 26_PRE [miRNA]


title: 26_POST [miRNA]


title: 29_PRE [miRNA]


title: 25_PRE [miRNA]


title: 21_PRE [miRNA]


title: 24_POST [miRNA]


title: 2_POST [miRNA]


title: 20_PRE [miRNA]


title: 22_PRE [miRNA]


title: 22_POST [miRNA]


title: 20_POST [miRNA]


title: 15_POST [miRNA]


title: 12_PRE [miRNA]


title: 34_PRE [miRNA]