title: H1-QKI KO-d15-4

first: Weinian

last: Shou

state: IN

department: Pediatrics

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC hg38
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

source_name: cardiomyocytes

growth_protocol: the hESCs were dissociated using Accutase  and were cultured on Matrigel-coated plates in mTesR medium.

extract_protocol:
Rneasy Plus Micro Kit
KAPA mRNA Hyperprep Kit (KK8581)

treatment_protocol: hESCs were differentiated into cardiomyocytes following published protocols. In brief,  Cardiomyocyte differentiation was initiated when cells were ~95% confluent by culturing cells in RPMI1640/B-27 minus insulin medium RPMI 1640 with B-27 supplement minus insulin supplemented with 6 μM CHIR-99021 for differentiation on days 0 and 1. For days 3 and 4, IWP-2 was added to the fresh medium. From day 5 onward, cells were cultured with fresh RPMI1640/B-27 medium every two days.

value: hESCs-derived cardiomyocytes

tag: differentiation day

value: QKI KO


title: Input for the EBF1-ChIP in dHet-B-ALL-760

status: Public on Oct 19 2020

type: SRA

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

library_source: genomic

data_processing:
Basecalling and fastq files generation was performed by using Illumina bcl2fastq 2.17.1.14 (pipeline version 0.2.1)
ChIPSeq: The reads were aligned to the mm9 genome assembly using bowtie2 with default configurations
ChIPSeq: Duplicated reads were filtered and blacklisted regions were removed using samtools and Picard.
ChIPSeq: Peaks were identified using MACS2 (v2.1.0.20150731) with q-value cutoff 0.01 and filtered for p-value cut-off 10e-10 (EBF1) or 10e-7 (Pax5). The peaks were further filtered with the fold change cut-off 4.
ATACSeq: The paried-end sequencing reads were trimmed using trim galore (0.4.0), which is a wrapper for the Cutadapt (1.8.1) tools. The trimmed reads were mapped to the mouse genome (mm9) using bowtie2 (2.2.8) with the default settings.
ATACSeq: The duplicated reads were removed using Picard tools (1.136). The reads mapping to blacklisted regions, mitochondrial genome and the reads with mapping quality below 30 were removed. The properly mapped reads were used for identifying peaks by MACS2 (2.1.1) with the BAMPE mode and q-value cut off 0.01. The differentially induced peaks were identified by comapring between the samples and further filtered for a p-value cutoff 10-10 and fold change 4.
The reads were normalized to 10 million mapped reads using Homer tools (v 4.1) in bedGraph format for visualization.
Genome_build: mm9
Supplementary_files_format_and_content: The reads normalized to 10 million in the bedGraph format were generated using Homer tools

molecule: genomic DNA

organism: Mus musculus

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 713)

growth_protocol: The normal pro-B cell lines were established by culturing c-Kit+ fetal liver cells of Ebf1+/+ or Ebf1+/-Pax5+/- cells with OP9 feeder cells in OptiMEM medium supplemented with 4%FCS, 50μM 2-ME, 1% Penicillin-Streptmycin-Glutamine, 10ng/ml Stem cell factor (SCF), 10ng/ml Flt3-L, and 5ng/ml IL-7. Leukemic Ebf1+/-Pax5+/- cell lines were established similarly using bone marrow CD19+AA4.1hi cells.

extract_protocol:
Cells were crosslinked  with formaldehyde, lysed and DNA was fragmented into pieces of average 300bp by sonication. Chromatin was precipitated with a specific antibody and protein A-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified via QIAquick PCR Purification Kit according to the manufacturer's manual.
Library preparation for ChIP analysis was performed with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Catalog #E7370) according to the manufacturer’s protocol. No size selection was used and amplification was performed using 10 PCR cycles. The ATAC-seq libraries were prepared using the NEB Nextera DNA sample preparation kit according to the manufacturer's instructions.

tag: cell type

value: Ebf1+/- Pax5+/- lymph node

tag: strain

tag: genotype

tag: chip antibody


title: H1-QKI KO-d15-3

city: Indianapolis

country: USA

institute: Indiana University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: Input for the EBF1-ChIP in dHet-B-ALL-713

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 760)


title: H1-QKI KO-d15-2


title: A499_WT_FrA_2

description: Library of 96 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right read (R2) of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read (R1) contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for quantification.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: bone marrow cells

growth_protocol: Hematopoietic stroma cells and hematopoietic progenitors were isolated from Ebf1+/+ Prx1-Cre and Ebf1 fl/fl Prx1-Cre

extract_protocol:
Intact bones (femora and tibia) were chopped into small fragments and crushed in FACS buffer (PBS-2% FCS) using pestle and mortar. Bone marrow cells were collected and RBC lysis was performed. Next, the cells were washed with FACS buffer and stained for analysis. For sorting of HSPCs the cells were enriched by magnetic depletion. Briefly, the BM cells were labeled with a cocktail of biotinylated antibodies (CD3, CD19, B220, CD11b, Gr1 and Ter119) and then with streptavidin-conjugated magnetic nanobeads (BioLegend). The Lineage- cells obtained were stained with following antibodies: anti-lineage (CD3, CD19, B220, CD11b, Gr1 and Ter119), anti-Sca1, anti-c-kit, anti-CD135, anti-CD48, anti-150, and then further purified by FACS sorting. The immunophenotypes of assayed hematopoietic cells were as follow: LSKs (Lin-Sca1+c-kit+), HSCs (CD135-CD48-CD150+LSK), MMP3 (CD135-CD48+CD150-LSK), MPP4 (CD135+ CD150-LSK), CLPs (Lin-Sca1loc-kitloIL-7Rα+CD135+), pro-B cells (B220+CD43+), pre-B cells (B220loCD43-), rec-B cells (B220hiCD43-), B cells (B220+CD19+), T cells (CD3+), myeloid cells (Mac1+Gr1+) and erythroid cells (Ter119+). For non-hematopoietic BM cell isolation, the bone chips were digested with 0.3% collagenase type II and 0.02% DNase I at 37°C for 45 min with gentle shaking. After enzymatic digestion, the cells were filtered, washed with FACS buffer, and stained accordingly. CAR cells were identified as CD45-CD31-Lin-PDGFRα+Sca1-, PαS cells were identified as CD45-CD31-Lin-PDGFRα+ Sca1+.
The aRNA was reversely transcribed in order to generate libraries for sequencing, as previously described18. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)

treatment_protocol: no treatment

tag: tissue

value: bone marrow

tag: sequencing runs

tag: illumina barcode

tag: barcode sequence

value: CGATGT

value: wild type

tag: celltype

value: B cells


title: H1-QKI KO-d15-1


title: Control83

type: genomic

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

description: Anonymized patient/sample code

hyb_protocol: According to Illumina's Instructions

scan_protocol: According to Illumina's Instructions

data_processing: Analyses were performed in RStudio version 1.0.136 using R v3.4.1. IDAT files were loaded into ChAMP version 2.10.2 and normalized using the BMIQ method. Positional batch effects were removed by using ComBat to correct for Sentrix_ID and Sentrix_Position. Leukocyte population heterogeneity was estimated and corrected for using the RefBase function.

label: Cy3, Cy5

source_name: DNA from EDTA-stored blood

label_protocol: According to Illumina's Instructions

extract_protocol: Zymo gDNA Extraction kit

treatment_protocol: Blood taken by venupuncture and stored in an EDTA tube

value: CTRL

tag: age

tag: Sex

value: Male

tag: codon129 genotype

value: MM

tag: mrc scale

value: blood


title: EBF1-ChIP_Rep2

source_name: Rag2(-/-) pro-B cells

value: pro-B cells

value: fetal liver


title: EBF1-ChIP_Rep1


title: meVSV iBMDM

city: beijing

first: fuping

last: you

address: xueyuan street

country: China

institute: Peking University Health Science Center

data_processing:
RNA sequencing libraries were generated using NEBNext Ultra-fast RNA Library Prep Kit for Illumina (NEB), and sequenced on an Illumina Hiseq platform.
The original image data obtained by high throughput sequencing was transformed into original sequence by base calling analysis, which is called raw data. The results were stored in fastq file format
Data were filtered using the following specifications by cutadapt software to obtain clean data: 1. The BWA algorithm is used to remove the low quality regions at both ends of the sequence, and the quality threshold is Q30; 2. Remove the joint sequence from it; 3. Removal of sequences containing fuzzy base N; 4. The sequences with length less than 60 bp were removed
Tophat2 software was used to compare the similarity between clean data and reference genome to obtain the position information of reads on the reference genome and the characteristic information of sequencing samples to generate BAM file
Gene expression was quantified as fragments per kilobase of transcript per million fragments mapped (FPKM) algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: immortalized bone marrow-derived macrophage

growth_protocol: Cells were cultured in DMEM containing 10% FBS, 1% glutamine and 1% streptomycin-penicillin in a 10 cm dish for further study

extract_protocol:
Supernatant was removed and cells were covered with 350ul Buffer RLT at the end of treatment. Total RNA was extracted following the strandard protocol of RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with VSV for 0 or 9 hours

tag: treatment

value: VSV

tag: cell line

value: Mettl3 knockdown


title: hPDLSCs_cultured_14day_rep2

type: RNA

city: Guangzhou

first: Zhao

last: Chen

state: Guangdong

address: Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China

department: Department of Stomatology

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Isolated hPDLSCs were cultured in Dulbecco α-modified Eagle medium (DMEM) (Hyclone, Los Angeles, CA) supplemented with 10% fetal bovine serum (FBS) (Gibco, Grand Island, NY, USA), 100 mmol/L ascorbic acid 2-phosphate, 2 mmol/L glutamine, 100 U/mL penicillin and 100 mg/mL streptomycinand (HyClone, NY, USA), and maintained at 37 °C in a humidified atmosphere with 95% air and 5% CO2. Single-cell suspensions were inoculated into six-well plates at a density of 1×104 cells/well. The limited dilution techniques are used to obtain colonies of single cell origin

extract_protocol: According to the manufacturer’s protocol, total RNA was isolated from cultured cells with Trizol reagent (Thermo Fisher Scientific, Waltham, MA). The quantity and quality of RNA are determined by nano dropper ND-1000 (Nano Dropper Technology Company, Wilmington, DE). The RNA Integrity and gDNA contamination are tested by Denaturing Agarose Gel Electrophoresis.

treatment_protocol: hPDLSCs at differentiated group were cultured with an osteogenic differentiation medium containing 50 mg/mL ascorbic acid, 10 ng/mL dexamethasone, and 10 mmol/L β-glycerolphosphate (Sigma, St Louis, MO, USA) for 14 days in 6-well plates.  hPDLSCs at undifferentiated group were cultured in 10 % FBS in DMEM with no supplements.

value: human periodontal ligament stem cells (hPDLSCs)

tag: time point

value: after 14 days cultured


title: hPDLSCs_osteogenic differentiation_14day_rep2

institute: Nanfang Hospital, Southern Medical University

value: after 14 days odontogenic induction


title: H1-d15-4

value: hESCs-derived cardiomyocytes

tag: differentiation day

value: WT


title: hPDLSCs_cultured_14day_rep3

tag: cell type


title: Control81

description: Anonymized patient/sample code

value: Female

value: MV


title: meCON iBMDM

value: Mock

value: immortalized bone marrow-derived macrophage


title: Control92

description: Anonymized patient/sample code

value: CTRL


title: Control84

description: Anonymized patient/sample code

value: Male


title: Control79

description: Anonymized patient/sample code

value: MM


title: Control82

description: Anonymized patient/sample code

value: blood


title: hPDLSCs_cultured_14day_rep1


title: EBF1-ChIP in dHet-B-ALL-760

value: Ebf1+/- Pax5+/- lymph node

tag: strain


title: hPDLSCs_osteogenic differentiation_14day_rep1


title: H1-d15-3

tag: genotype


title: EBF1-ChIP in dHet-B-ALL-713

tag: chip antibody


title: H1-d15-2


title: WTVSV iBMDM

value: wild type


title: Control80

description: Anonymized patient/sample code

tag: tissue


title: mLANA_ChIP_3A_rep3

city: Hannover

first: Rishikesh

last: Lotke

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Institut für Virologie

institute: Medizinische Hochschule Hannover

data_processing:
Basecalling was performed using the built-in Real-Time Analysis (RTA) software version 2.4.11.
All FASTQ sequence files were checked for quality using the FastQC tool. Reads exceeding 51 bp were trimmed from the 3’ end down to 51 bp using the FASTQ/A trimmer tool from the FASTX-toolkit.
We used Bowtie for aligning reads to the mouse (mm9) genome for mouse datasets, and human (hg19) genome for human datasets, using the default options with the following exceptions: --best, --strata and -m 1. For data from cells containing the KSHV genome, reads were also aligned to the HQ404500 sequence to which two copies of TRs were appended. Alignment of the reads to the long unique region (LUR) was performed with the aforementioned settings. All resulting SAM files were sorted, duplicates were removed and finally converted to BAM format.
Peak calling was performed using MACS using the default options with the following exceptions: --nomodel and --shiftsize value was set to half the size of mean fragment length of the ChIP-Seq library as determined by Agilent 2100 Bioanalyzer. For KSHV LUR, peak calling was performed with the aforementioned settings but with the genome size set to 137706 bp and using an additional option --nolambda. For alignment to the terminal repeat (TR) regions of the KSHV genome, reads were aligned using Bowtie with the aforementioned options for read alignment, except -m 1 was changed to -M 1. The SAM files were sorted and converted to BAM without removal of duplicates. No peak calling was performed for alignments for the TR. Instead, the aligned reads were extended to match the library fragment size using the igvtools ‘Count’ command from the Integrative Genomics Viewer (v2.3) with default settings, the window size set to 10 and the extension factor set depending on the average fragment size of the library.
Genome_build: hg19 (GRCh37) for human genome, HQ404500 appended with two copies of TRs for KSHV genome and mm9 (MGSCv37) for mouse genome.
Supplementary_files_format_and_content: wig files were generated during peak calling step using the MACS peak caller.

source_name: BALB/c B cell lymphoma

growth_protocol: BCBL-1, BJAB-mCherry, BJAB-kLANA and BJAB-rKSHV.219 were cultured in RPMI 1640 (Gibco) with 20% (v/v) Foetal Calf Serum (FCS) (HyClone) whereas A20-GFP, A20-mLANA WT and A20-mLANA 3A mutant were cultured in RPMI 1640 with 10% (v/v) FCS. All cells were incubated in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
ChIP was performed as described in (Si, Verma, & Robertson, 2006; Günther & Grundhoff, 2010) with the following modifications. For kLANA and mLANA ChIP, the formaldehyde fixation time was 10 minutes, while for Brd2/4 it was 20 minutes. For the Brd2/4 ChIP experiments we used rabbit polyclonal antigen-affinity purified IgG antibodies (Bethyl laboratories, Inc. BRD2-A302-583A and BRD4-A301-958A100) at a concentration of 3 µg/mg of lysate. Antibodies were incubated with the lysates for 6 hours before adding protein G beads and then further incubated for 16 hours. For kLANA ChIP, we used an IgG2c rat monoclonal antibody (Advanced Biotechnologies Inc. 13-210-100) and prepared antibody-conjugated beads as previously described (Zhang et al., 2016), with the exception of the beads being washed and finally resuspended in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris HCl - pH 8.0, 167 mM NaCl). Rabbit IgG Cell Signaling Technology® and Rat IgG Abcam were used as isotype controls in, respectively, the Brd2/4 and kLANA ChIP experiments. For the mLANA experiments, we used 50 µl of EZview™ Red anti-FLAG® M2 Affinity Gel (Sigma-Aldrich) per lysate derived from ~3 x 10^7 nuclei.
Libraries were prepared using the NEXTflex™ ChIP-Seq and NEXTflex™ ChIP-Seq Barcodes - 12 kits from BIOO Scientific Corp. according to the manufacturer’s instructions (NEXTflex™ ChIP-Seq kit Manual 5143-02) to prepare single-end DNA libraries from ChIP DNA using the gel-free protocol and libraries were size selected to be between 300-400 bp.

treatment_protocol: BCBL-1, BJAB-mCherry, BJAB-kLANA and BJAB-rKSHV.219 cells were plated in T-75 flasks at a cell density of 0.5 x 10^6 cells/ml and in the absence or presence of I-BET151 at a final concentration of 0.5 µM for 48 hours. For induction of A20-GFP, A20-mLANA WT or A20-mLANA 3A, cells were cultured in a T-75 flask at a density of 0.2 x 10^6 cells/ml supplemented with doxycycline at a final concentration of 1 µg/ml.

value: A20-mLANA 3A

tag: modification to cells

value: A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct

value: Dox

value: EZview Red anti-FLAG M2 Affinity Gel (Sigma-Aldrich F2426)


title: Control73

description: Anonymized patient/sample code


title: WTCON iBMDM


title: mLANA_ChIP_WT_rep3

value: A20-mLANA WT

value: A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct


title: Control74

description: Anonymized patient/sample code


title: GU0744_P [VDJ sequencing]

city: Iowa City

first: Weizhou

last: Zhang

state: IA

address: 100 Medical Laboratories

department: Pathology

institute: The University of Iowa

data_processing:
10x Data was processed with the Cell Ranger pipeline, version 2.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Contains RNA sequencing of the T-cell receptor of individual cells

source_name: T cells from peripheral blood

extract_protocol:
Viable (Hoechst-), immune (CD45+) single-cell suspensions generated from three ccRCC tumor samples and peripheral blood were sorted on a FACS ARIA sorter (BD Biosciences) for lymphoid and myeloid lineages. The cells were sorted into ice-cold 1x PBS + 0.04% non-acetylated bovine-serum albumin (New England BioLabs). Sorted cells were counted and viability as assessed using the MoxiGoII counter (Orflo Technologies). Single cells were re-suspended at 1000 cells/ul with a viability > 90%. Libraries were generated using using the Chromium Single Cell V(D)J Enrichment Kit and sequenced on the Illumina HiSeq 4000
Libraries were generated using using the Chromium Single Cell V(D)J Enrichment Kit

tag: patient age

value: matched peripheral blood

tag: tumor stage

tag: histological grade


title: batch1_RiboSeq_ko

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

data_processing:
Library strategy: Ribo-seq
Adapters were removed with cutadapt v2.1
Ribo-Seq: cutadapt -a AGATCGGAAGAG -j 4 --minimum-length 20 -q 20 --trimmed-only
RNA-Seq: cutadapt -a AGATCGGAAGAG -j 4 --minimum-length 20 -q 20
Trimmed sequences were mapped to the mm10 genome assembly with GENCODE M22 genome annotation using STAR v2.7.1a with default parameters.
Read counts were extracted from STAR output.
Genome_build: mm10
Supplementary_files_format_and_content: tsv (tab-separated txt), gene-level read counts from STAR output

molecule: polyA RNA

source_name: Embryonic fibroblast

growth_protocol: Wild-type and eIF4G2(-/-) knock-out cells were grown in 150 mm plates (SPL Life Sciences) at 30-60% density in DMEM (PanEco, Moscow, Russia) supplemented with 10% FBS (HyClone). Cells were re-plated once in 3 days to obtain 12 plates per experiment.

extract_protocol:
Cells were put on ice, washed with ice-cold PBS supplemented with 100 ug/ml cycloheximide, lyzed in (20 mM Tris-HCl, pH 7.5 250 mM NaCl 1,5 mM MgCl2, 1mM DTT, 0,5% Triton X-100, 100 μg/ml cycloheximide and 20 U/ml TURBO DNAse). For total poly(A)-plus RNA sequencing, the lysates were deproteinized using Trizol-LS (Invitrogen) extraction, RNA was precipitated, purified via Oligotex resin (QIAGEN), and fragmented via mild alkaline hydrolysis. For ribosome footprints sequencing, the lysates were treated with RNase I (Ambion), the 80S monosomes were purified via 10-60% sucrose density gradient centrifugation, and deproteinized using acid phenol extraction. Both RNA_seq and ribo_seq RNA fragments were further purified via 15% PAGE and the RNA from 28 to 34 nt long was excised and extracted from gel slices.
RNA was dephosphorylated using T4 PNK, then preadenylated Universal miRNA cloning linker (NEB) was ligated to RNA fragments using truncated T4 RNA ligase 2 (NEB), excised from 15% PAG, and reverse transcribed with SuperScript III revertase (Invitrogen). The DNA was excised from 7.5% PAG and circularized using CircLigase II (Illumina). The resulting libraries were depleted of rRNA-derived products, amplified with NEB TrueSeq adapters and sequenced.

value: NIH 3T3

tag: rna population

value: cytoplasmic RNA


title: H1-d15-1

value: hESCs-derived cardiomyocytes

value: WT


title: Control75

description: Anonymized patient/sample code

value: CTRL

tag: age

tag: Sex

value: Female

value: MV


title: mLANA_ChIP_A20_rep3

value: A20 cells transduced with lentivirus containing IRES-EGFP expression construct


title: mLANA_ChIP_3A_rep2


title: Control77

description: Anonymized patient/sample code

value: Male

tag: codon129 genotype

value: VV

tag: mrc scale

value: blood


title: mLANA_ChIP_WT_rep2

tag: cell line

tag: treatment


title: GU0700_P [VDJ sequencing]


title: Control71

description: Anonymized patient/sample code

value: MM


title: GU0715_P [VDJ sequencing]


title: Control70

description: Anonymized patient/sample code


title: batch1_RNASeq_wt

data_processing:
Adapters were removed with cutadapt v2.1
Ribo-Seq: cutadapt -a AGATCGGAAGAG -j 4 --minimum-length 20 -q 20 --trimmed-only
RNA-Seq: cutadapt -a AGATCGGAAGAG -j 4 --minimum-length 20 -q 20
Trimmed sequences were mapped to the mm10 genome assembly with GENCODE M22 genome annotation using STAR v2.7.1a with default parameters.
Read counts were extracted from STAR output.
Genome_build: mm10
Supplementary_files_format_and_content: tsv (tab-separated txt), gene-level read counts from STAR output

value: wild-type

value: polyA RNA


title: batch1_RiboSeq_wt


title: Tcf7 and Lef1 Knockout RNASeq 3

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adapter sequence using cutadpt,then mapped to mm10 whole genome and Gencode vM12 annotation using STAR 2.7.0  with parameters --outSAMstrandField intronMotif   --outSAMunmapped Within      --outFilterMultimapNmax 3   --outFilterMismatchNmax 2
Raw read counts for each gene are generated using Subread
Differential expressed genes are identified using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file with raw reads count for GenCode genes

source_name: T follicular helper cells

growth_protocol: CD45.2+ WT or Tcf1/Lef1-deficient Smarta TCR transgenic CD4 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by footpad injection of GP61-KLH conjugates. On day 5 post-immunization, the draining inguinal lymph nodes were harvested, CD45.1+ cells were depleted, followed by cell sorting to collect CD45.2+ Tfh cells for downstream analysis.

extract_protocol:
Tfh cells were sort-purified from the lymph nodes and total RNA was extracted using standard Qiagen RNeasy columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: inguinal lymph nodes

tag: cell phenotypes

value: CD4+, CXCR5+, PD1+

tag: genotypes

value: Tcf7 and Lef1 Knockout


title: mLANA_ChIP_A20_rep2

value: Dox

value: EZview Red anti-FLAG M2 Affinity Gel (Sigma-Aldrich F2426)


title: Control72

description: Anonymized patient/sample code


title: mLANA_ChIP_WT_rep1

value: A20-mLANA WT

value: A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct


title: Tcf7 and Lef1 Knockout RNASeq 2

tag: strain


title: GU0700_T [VDJ sequencing]

source_name: T cells from renal tumor

value: renal cell carcinoma


title: mLANA_ChIP_A20_rep1


title: GU0744_T [VDJ sequencing]


title: GU0744_P

data_processing:
10x Data was processed with the Cell Ranger pipeline, version 2.2
Genome_build: GRCh38
Supplementary_files_format_and_content: filltered expression matrices with corresponding gene names (.tsv) and barcodes (.tsv)

source_name: CD45+ immune cells from peripheral blood

extract_protocol:
Viable (Hoechst-), immune (CD45+) single-cell suspensions generated from three ccRCC tumor samples and peripheral blood were sorted on a FACS ARIA sorter (BD Biosciences) for lymphoid and myeloid lineages. The cells were sorted into ice-cold 1x PBS + 0.04% non-acetylated bovine-serum albumin (New England BioLabs). Sorted cells were counted and viability as assessed using the MoxiGoII counter (Orflo Technologies). Single cells were re-suspended at 1000 cells/ul with a viability > 90%. Libraries were generated using using the Chromium Single Cell 5-prime Enrichment Kit and sequenced on the Illumina HiSeq 4000
Libraries were generated using using the Chromium Single Cell 5-prime Enrichment Ki


title: Tcf7 and Lef1 Knockout RNASeq 1


title: Control RNASeq 4

value: WT


title: GU0715_T [VDJ sequencing]


title: Control RNASeq 3


title: GU0700_P


title: hPDLSCs_osteogenic differentiation_14day_rep3

tag: cell type

value: human periodontal ligament stem cells (hPDLSCs)

tag: time point

value: after 14 days odontogenic induction


title: Control76

description: Anonymized patient/sample code

value: CTRL

value: Female

value: MV

tag: tissue


title: GU0715_P


title: Control67

description: Anonymized patient/sample code

value: Male

value: MM

value: blood


title: Control64

description: Anonymized patient/sample code


title: Control RNASeq 2

value: inguinal lymph nodes


title: A20-mLANA 3A 48h Dox 3

description:
M3905r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 2000 ng of each labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing:
Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file: GE2_107_Sep09.xml. Measurements of on-chip replicates were averaged using the geometric mean of ProcessedSignal (PS) values (for each channel independently) to retrieve one resulting value per probe, sample, and channel. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per feature that exceeded 0.5.
For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:
normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)
Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

label_protocol: Synthesis of Cy3- or Cy5-labeled cRNA was performed with the ‘Quick Amp Labeling kit, two color’ (#5190-0444, Agilent Technologies) according to the manufacturer’s recommendations, except for a two-fold downscaling of all reaction volumes.

growth_protocol: A20-GFP, A20-mLANA WT and A20-mLANA 3A mutant were cultured in RPMI 1640 with 10% (v/v) FCS. All cells were incubated in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA from A20-GFP, A20-mLANA WT and A20-mLANA 3A mutant cells in the absence and presence of 1 µg/ml doxycycline for 24 and 48 hours was isolated using the Qiagen RNeasy® Mini kit.

treatment_protocol: For induction of A20-GFP, A20-mLANA WT or A20-mLANA 3A, cells were cultured in a T-75 flask at a density of 0.2 x 10^6 cells/ml supplemented with doxycycline at a final concentration of 1 µg/ml.

value: A20-mLANA 3A

tag: modification to cells

value: 48 hours


title: A20-mLANA 3A 48h No Dox 3

description:
M3905g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.

value: No Dox


title: Control62

description: Anonymized patient/sample code


title: Control78

description: Anonymized patient/sample code


title: GU0715_T

source_name: CD45+ immune cells from renal tumor

tag: patient age


title: TCF1 CUTnRUN

data_processing:
Library strategy: CUTnRUN
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adapter seqeunce using cutadpt then mapped to mm10 whole genome using bwa mem v0.7.17
PCR duplicates are marked using PICARD MarkDuplicates
RPKM normalized big wiggle files are generated using bamCoverage from Deeptools v3.2.1 with parameters --normalizeUsing RPKM --ignoreDuplicates --minMappingQuality 20
Genome_build: mm10
Supplementary_files_format_and_content: Big wiggle files of bam coverage

extract_protocol:
Tfh cells were sort-purified from the lymph nodes, and nuclei extracted, treated with anti-Tcf1 antibody followed by protein-A-micrococcal nuclease, and DNA fragments collected.
The Tcf1 antibody-directed, Mnase-generated DNA fragments were collected, PCR-amplified to generate sequencing libraries.

value: CD4+, CXCR5+, PD1+


title: GU0700_T

tag: tumor stage


title: Control65

description: Anonymized patient/sample code


title: Control RNASeq 1


title: A20-mLANA 3A 24h Dox 3

description:
M3904r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.

value: Dox

value: 24 hours


title: A20-mLANA 3A 24h No Dox 3

description:
M3904g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.


title: BRD4_ChIP_I-BET

source_name: Pleural Effusion Lymphoma

value: I-BET

tag: chip antibody

value: IgG Rabbit Polyclonal anti-BRD4 (Bethyl laboratories, Inc. A301-958A100)


title: Tcf7 Lef1 KO rep2 [ATAC-Seq]

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adapter seqeunce using cutadpt then mapped to mm10 whole genome using bwa mem v0.7.17
PCR duplicates are marked using PICARD MarkDuplicates
RPKM normalized big wiggle files are generated using bamCoverage from Deeptools v3.2.1 with parameters --normalizeUsing RPKM --ignoreDuplicates --minMappingQuality 20
Genome_build: mm10
Supplementary_files_format_and_content: Big wiggle files of bam coverage

extract_protocol:
WT or WT or Tcf1/Lef1-deficient Tfh cells were sort-purified from the lymph nodes, treated with TN5 transposase to generate tagged DNA fragments.
TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries

tag: genotype

value: Tcf7 and Lef1 Knockout


title: Control61

description: Anonymized patient/sample code

tag: age


title: BRD2_ChIP_I-BET

value: IgG Rabbit Polyclonal anti-BRD2 (Bethyl laboratories, Inc. A302-583A)


title: A20-mLANA 3A 48h Dox 2

description:
M3903g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.


title: Control63

description: Anonymized patient/sample code

value: CTRL

tag: Sex


title: batch1_RNASeq_ko

value: NIH 3T3

tag: rna population

value: polyA RNA


title: Control60

description: Anonymized patient/sample code

value: Male

tag: codon129 genotype

tag: mrc scale


title: BRD2-4_Input_I-BET

tag: cell line

tag: treatment


title: Control66

description: Anonymized patient/sample code

value: MM


title: Control58

description: Anonymized patient/sample code

value: Female

value: MV

value: blood


title: A20-mLANA 3A 24h Dox 2

description:
M3902g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.

value: A20-mLANA 3A


title: A20-mLANA 3A 48h No Dox 2

description:
M3903r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.

value: No Dox

value: 48 hours


title: Control59

description: Anonymized patient/sample code


title: WT rep2 [ATAC-Seq]

value: inguinal lymph nodes

tag: cell phenotypes

value: CD4+, CXCR5+, PD1+

value: WT


title: WT rep1 [ATAC-Seq]

tag: strain


title: A20-mLANA 3A 48h Dox 1

description:
M3901r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.

value: Dox


title: Control68

description: Anonymized patient/sample code


title: BRD4_ChIP_No_I-BET

value: No I-BET

value: IgG Rabbit Polyclonal anti-BRD4 (Bethyl laboratories, Inc. A301-958A100)


title: SIDT1 KO

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

description: Profiling of known plant microRNAs of Arabidopsis thaliana; Glycine max; Hordeum vulgare; Oryza sativa; Triticum aestivum; Glycine max; Zea mays

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 aligned to pre-miRNA sequence in miRBase_v16
Sequenced reads with no more than 2 mismatches and 2 shifts were identified as one miRNA and formed the final miRNA expression profile.
Genome_build: miRBase 16.0
Supplementary_files_format_and_content: tab-delimited text files include Count values for each Sample

source_name: Liver

extract_protocol:
Small RNAs were extracted from the mice liver using miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. A 100 μl mixture consisting of 20 μg of small RNA and 10 mM NaIO4 was incubated at 0°C for 40 min in the dark. The oxidized RNA was precipitated with ethanol, rinsed once with 75% ethanol, air dried, and dissolved in 50 μl of DEPC water. An equal volume of 2 M Lys-HCl was added, and the solution was incubated at 45°C for 90 min for β-elimination. The solution was then precipitated twice with ethanol, rinsed once with 75% ethanol, air dried, dissolved in DEPC water. The samples from three different individuals with the same genotype were mixed and subjected to deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: 3 month old


title: Control55

description: Anonymized patient/sample code

value: CTRL

value: VV


title: A20-mLANA 3A 24h No Dox 2

description:
M3902r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.

value: 24 hours


title: Control56

description: Anonymized patient/sample code

value: Female


title: A20-mLANA 3A 48h No Dox 1

description:
M3901g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.


title: BRD2_ChIP_No_I-BET

value: IgG Rabbit Polyclonal anti-BRD2 (Bethyl laboratories, Inc. A302-583A)


title: SIDT1 WT


title: JKR491-163/BA_Normal_Normal_410

city: New York

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
RNA-seq sample quality was assessed using FastQC and MultiQC.
Samples were aligned to human reference genome based on STAR RNA-sequencing aligner and sequencing reads were assigned to genomic features by featureCounts.
Genomic features with 0 counts in more than 20% of the samples were filtered out.
Data was then transfromed to log2-counts per million by voom-transform.
Fold changes (FCHs) vs. normals were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Genome_build: GRCh38

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted from skin biopsy samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 240ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragemented mRNA by revervse transcription, second strand synthesis and ligation of specific adapters.
Next generation sequencing was performed on Illumina Hiseq 4000 with single-ended 100 red cycles. Image analysis and bases calling was conducted in real-time by the Illumina analysis pipeline.

tag: ptid

tag: lesion

value: Normal

tag: gender

value: F

tag: race

value: African-American


title: BRD2-4_Input_No_I-BET

tag: modification to cells


title: A20-mLANA 3A 24h Dox 1

description:
M3900r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.

value: A20-mLANA 3A

tag: time point


title: Control54

description: Anonymized patient/sample code

value: Male

value: MM

tag: tissue

value: blood


title: Control57

description: Anonymized patient/sample code


title: kLANA_ChIP_I-BET_rep2

value: I-BET

tag: chip antibody

value: IgG2c rat anti-KSHV LANA monoclonal (Advanced Biotechnologies Inc. 13-210-100)


title: Control53

description: Anonymized patient/sample code

tag: age


title: JKR782-001_Keloid_NL_K1

value: NL


title: GU0744_T

tag: patient age

tag: tumor stage

tag: histological grade


title: kLANA_Input_I-BET_rep2


title: kLANA_ChIP_No_I-BET_rep2

value: No I-BET


title: kLANA_Input_No_I-BET_rep2


title: N1_Normal_Normal_N1

value: M


title: A20-mLANA 3A 24h No Dox 1

description:
M3900g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA 3A IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.

value: No Dox


title: Control69

description: Anonymized patient/sample code

value: CTRL

tag: Sex

tag: codon129 genotype

value: MV

tag: mrc scale


title: Control51

description: Anonymized patient/sample code

value: Female

value: VV


title: kLANA_ChIP_I-BET_rep1

tag: cell line

tag: treatment


title: A20-GFP 48h Dox 4

description:
M3899r
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.

value: IRES-EGFP expression construct

value: Dox

value: 48 hours


title: N3_Normal_Normal_N3

tag: ptid

value: Normal

value: F

value: African-American


title: A20-GFP 24h Dox 4

description:
M3898r
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.

value: 24 hours


title: kLANA_IgG_I-BET_rep1

value: I-BET

value: Rat IgG Isotype Control (Abcam ab37361)


title: A20-GFP 48h No Dox 4

description:
M3899g
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.


title: Control50

description: Anonymized patient/sample code

value: blood


title: N20_Normal_Normal_N20

tag: lesion


title: kLANA_ChIP_No_I-BET_rep1

value: No I-BET

value: IgG2c rat anti-KSHV LANA monoclonal (Advanced Biotechnologies Inc. 13-210-100)


title: Control49

description: Anonymized patient/sample code

value: Male


title: A20-mLANA WT 48h Dox 3

description:
M3853g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.

value: A20-mLANA WT


title: A20-GFP 24h No Dox 4

description:
M3898g
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.

value: No Dox


title: JKR782-003_Keloid_NL_K3

value: NL

tag: gender


title: A20-mLANA WT 48h No Dox 3

description:
M3853r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.


title: Control48

description: Anonymized patient/sample code

value: CTRL

value: Female

value: VV


title: N19_Normal_Normal_N19

value: M

tag: race


title: kLANA_IgG_No_I-BET_rep1

tag: modification to cells


title: N2_Normal_Normal_N2

value: Normal


title: 2iP_D

city: Madrid

first: Cian

last: Lynch

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: Cell culture in 2i +p38i +JNKi conditions, with 3 rounds of FACS selection (see: Methods)

data_processing:
RNA-seq processing:
The analysis was performed using Nextpresso (Graña O et al. 2017). Read files were quality-checked with FastQC.
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Homo sapiens GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used
Genome_build: Homo sapiens GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used
Supplementary_files_format_and_content: table generated with Cufflinks and contain transcripts abundance measured in FPKM values for each gene and sample replicate

source_name: RNA-seq human PSC cells replicate D in 2iP conditions

growth_protocol: Cells were maintained in mTeSR1 medium (which contains FGF2 and TGFb1) for Primed state as the control condition (see: Methods)

extract_protocol:
Total RNA was isolated on columns, including a DNase1-treatement, using the RNAeasy kit (Qiagen #74104) according to manufacturer's instructions.
10 ng of total RNA samples were processed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) by following manufacturer instructions. Resulting cDNA was sheared on a S220 Focused-ultrasonicator (Covaris) and subsequently processed with the ""NEBNext Ultra II DNA Library Prep Kit for Illumina"" (NEB #E7645). Briefly, oligo(dT)-primed reverse transcription was performed in presence of a template switching oligonucleotide, double stranded cDNA was produced by 11 cycles of PCR and submitted to acoustic shearing. Fragments were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to Illumina adapters. Adapter-ligated libraries were completed by limited-cycle PCR (8 cycles).

treatment_protocol: For inhibitor-treated cultures, cells were given rhLIF at 10 ng/mL plus treated with small molecule inhibitors as detailed in the Methods section (MEKi: PD at 0,5 micro-molar; GSK3i: CHIR99021 at 1 micro-molar; CDK8/19i: ETP-47709 at 1,1 micro-molar.

tag: cell type

value: pluripotent stem cells (PSCs)

value: Cell culture in 2i +p38i +JNKi conditions, with 3 rounds of FACS selection (see:Methods)


title: Control46

description: Anonymized patient/sample code

value: MV

tag: tissue


title: 2iP_C3

source_name: RNA-seq human PSC cells replicate C3 in 2iP conditions (merge: C1+C2+C3)


title: A20-mLANA WT 24h Dox 3

description:
M3852g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.

value: Dox

tag: time point

value: 24 hours


title: JKR782-001_Keloid_LS_K2

value: LS

value: F

tag: age

value: African-American


title: Control47

description: Anonymized patient/sample code

value: blood


title: JKR782-003_Keloid_LS_K4


title: Control45

description: Anonymized patient/sample code

value: Male


title: 2iP_C1

source_name: RNA-seq human PSC cells replicate C1 in 2iP conditions (merge: C1+C2+C3)


title: 2iP_C2

source_name: RNA-seq human PSC cells replicate C2 in 2iP conditions (merge: C1+C2+C3)


title: Control43

description: Anonymized patient/sample code

source_name: DNA from EDTA-stored blood

value: MM


title: Control44

description: Anonymized patient/sample code


title: JKR782-003_Keloid_LS_K5


title: A20-GFP 24h Dox 3

description:
M3850g
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.

value: IRES-EGFP expression construct


title: A20-mLANA WT 24h No Dox 3

description:
M3852r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.

value: A20-mLANA WT

value: No Dox


title: Tcf7 Lef1 KO rep1 [ATAC-Seq]

tag: strain

value: inguinal lymph nodes

tag: cell phenotypes

value: CD4+, CXCR5+, PD1+

tag: genotype

value: Tcf7 and Lef1 Knockout


title: A20-GFP 48h Dox 3

description:
M3851g
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.

value: 48 hours


title: 2iP_B2

source_name: RNA-seq human PSC cells replicate B2 in 2iP conditions (merge: B1+B2+B3)

value: pluripotent stem cells (PSCs)

value: Cell culture in 2i +p38i +JNKi conditions, with 3 rounds of FACS selection (see:Methods)


title: A20-GFP 24h No Dox 3

description:
M3850r
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.


title: A20-GFP 48h No Dox 3

description:
M3851r
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.


title: Control41

description: Anonymized patient/sample code

value: CTRL

tag: Sex

value: Female

value: MV


title: Control42

description: Anonymized patient/sample code

tag: codon129 genotype


title: 2iP_B3

source_name: RNA-seq human PSC cells replicate B3 in 2iP conditions (merge: B1+B2+B3)


title: JKR782-004_Keloid_NL_K6

value: NL

value: F


title: S159_TCR Sample 14

city: Shanghai

first: zheyi

last: chen

address: 1665 Kong Jiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The 10x Genomics Cell Ranger (3.0.1 version) pipeline was used to demultiplex raw files into FASTQ files, extract barcodes and UMI, filter, and map reads to the hg38 reference genome, and generate a matrix containing UMI counts.
A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings, according to the manufacturer’s recommendations. TCR reads were aligned to theGRCh38 reference genome, and consensus TCR annotation was performed using cell ranger vdj. Only in-frame TCR alpha-beta pairs were considered to define the dominant TCR of a single-cell. Each unique dominant alpha-beta pair was defined as a clonotype. For two cells to be assigned tothe same clonotype, both alpha and beta sequences had to be shared. If one clonotype was present in at least two cells, cells harboring this clonotype would be considered clonal, and the number of cells with such dominant alpha-beta pair indicated the degree of clonality of the clonotype.
Genome_build: hg38
Supplementary_files_format_and_content: filtered_feature_bc_matrix.tar contains counts matrix (stored in the Market Exchange Format for sparse matrices). It also contains gzipped TSV files with genes and barcode sequences corresponding to row and column indices respectively.  filtered_contig_annotations.csv contains high-level annotations of each high-confidence, cellular contig. The main information includes cell-barcode, unique contig_id, raw_clonotype_id and annotated VDJ segments, etc.

source_name: ESCC_adjacent normal tissue

extract_protocol:
Tissues-infiltrating immune cells from the paired fresh ESCC tumors and adjacent normal esophagus tissues were isolated by mincing the freshly obtained surgical specimens into 1-mm cubic pieces, followed by enzymatic digestion using 0.1% collagenase IV, 0.002% DNAse I, and 0.01% hyaluronidase, and were incubated on a rocker for 20–40 min at 37°C. The digested tissues were then passed through a 40 µm cell strainer and washed twice with PBS prior to surface staining with antibodies (CD45-APC, CD235-FITC) for 30 min at 4°C, and then washed and resuspended in 200 µL FACS buffer. PI was added 5 min before flow cytometry sorting for dead cell discrimination. CD45+ CD235- PI- cells were sorted with FACS Aria II Cell Sorter (BD Biosciences), post-sort purity was routinely > 95% for the sorted populations.
Single-cell library preparation was carried out according to the manual of the Chromium Single-cell V (D) J Reagent Kits. Briefly, cell suspensions were first loaded on the Single-cell A Chip for gel bead-in-emulsion (GEM) generation and barcoding, aiming for a recovery of 10,000 cells per sample. Next, reverse transcription, RT cleanup cDNA amplification and quantification were performed to build a 5’ gene library. In addition, a human T Cell V(D)J Enrichment Kit was used to isolate and enrich for the V(D)J sequence before TCR library construction. Finally, libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit (300 cycles).

tag: subject status

value: esophagus squamous cell carcinoma patient

tag: pathological stage

value: IIIB

tag: tissue type

value: adjacent normal tissue


title: 2iP_B1

source_name: RNA-seq human PSC cells replicate B1 in 2iP conditions (merge: B1+B2+B3)

tag: treatment


title: S158_TCR Sample 13

value: Male

value: IIB


title: 2iP_A

source_name: RNA-seq human PSC cells replicate A in 2iP conditions


title: A20-mLANA WT 48h No Dox 2

description:
M3829g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.

source_name: BALB/c B cell lymphoma

tag: cell line

value: A20-mLANA WT

value: No Dox


title: Control40

description: Anonymized patient/sample code

value: MM

tag: mrc scale

value: blood


title: Control39

description: Anonymized patient/sample code


title: Male_Week_12_Testis

city: Los Angeles

first: Tsotne

last: Chitiashvili

state: CA

address: 615 Charles E Young Dr S

institute: University of California - Los Angeles

description:
10X Genomics
scRNA-seq

data_processing:
scRNA-seq reads were aligned to human hg38 genome assembly using 10X Genomics Cell ranger v2.2. Expression matrixes generated by Cell Ranger were imported to Scanpy for downstream analysis. First, all the libraries were merged using Scanpy and cells were subject to the same filtration. All gene that were expressed in less than 5 cells were discarded and cells with less than 250 detected genes were filtered out. Data was scaled by detected number of UMIs and mitochondrial gene percentage. Cells were clustered by Louvain algorithm and UMAP package was used to visualize cells in 2D plot.
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Prenatal Gonads

extract_protocol: scRNA-seq libraries were generated immediately after tissue dissociation using 10X Genomics Chromium instrument and Chromium single cell 3’ reagent kit V2. Each individual run was designed to target 6000 cells per library. Libraries were generated according to manufacturer’s instructions and library fragment size distribution was determined by BioAnalyzer instrument. Afterwards libraries were pulled together and sequenced on Illumina Novaseq 6000 platform, at average depth of 400-420 million reads per sample.

treatment_protocol: Fetal tissues were processed 24-48 hours after the termination. Upon arrival, tissues were gently washed with PBS and placed in dissociation buffer. Dissociation buffer consisted of Collagenase IV 10mg/ml (Life Technologies #17104-019), Dispase II 250 ug/ml (Life Technologies #17105041), DNAseI 1:1000 (Sigma 4716728001), 10% FBS (Life technologies 10099141) diluted in PBS. Tissues were dissociated for 15 minutes at 370C. After every 5 minutes tissues were pipetted against the bottom of Eppendorf tube. Cells were centrifuged for 5 minutes at 500g and resuspended in PBS+0.04% BSA. Cells were strained through 40mincron strainer and counted using automated cell counter (Thermo Fisher, Countess II). Cell concentration was adjusted to 800-1200 cells per microliter and immediately used for scRNA seq

value: male

tag: developmental timepoint

value: Week 12 post-fertilization

value: prenatal testis


title: S150_TCR Sample 12


title: A20-mLANA WT 48h Dox 2

description:
M3829r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.

tag: modification to cells

value: Dox

value: 48 hours


title: Control38

description: Anonymized patient/sample code

data_processing: Analyses were performed in RStudio version 1.0.136 using R v3.4.1. IDAT files were loaded into ChAMP version 2.10.2 and normalized using the BMIQ method. Positional batch effects were removed by using ComBat to correct for Sentrix_ID and Sentrix_Position. Leukocyte population heterogeneity was estimated and corrected for using the RefBase function.

value: CTRL

value: Female

value: MV


title: S149_TCR Sample 11

value: esophagus squamous cell carcinoma patient

value: IIA


title: 8iONLY_C

description: Cell culture in CDK8/19i only conditions

source_name: RNA-seq human PSC cells replicate C in 8iONLY conditions

tag: cell type

value: pluripotent stem cells (PSCs)


title: A20-mLANA WT 24h Dox 2

description:
M3828r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.

value: 24 hours


title: 8iONLY_B

source_name: RNA-seq human PSC cells replicate B in 8iONLY conditions

value: Cell culture in CDK8/19i only conditions


title: S135_TCR Sample 10

value: Male

value: adjacent normal tissue


title: Control37

description: Anonymized patient/sample code

value: MM

tag: tissue


title: Control36

description: Anonymized patient/sample code

value: blood


title: A20-GFP 48h Dox 2

description:
M3827r
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.

value: IRES-EGFP expression construct

tag: time point


title: 8iP_D

description: Cell culture in CDK8/19i +p38i +JNKi conditions

source_name: RNA-seq human PSC cells replicate D in 8iP conditions


title: Control35

description: Anonymized patient/sample code

tag: age

value: VV


title: JKR782-004_Keloid_LS_K7

tag: ptid

tag: lesion

value: LS

tag: gender

value: F

tag: race

value: African-American


title: A20-mLANA WT 24h No Dox 2

description:
M3828g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.

value: A20-mLANA WT

value: No Dox


title: A20-GFP 24h Dox 2

description:
M3826r
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.

value: Dox


title: A20-GFP 48h No Dox 2

description:
M3827g
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.

value: 48 hours


title: 8iONLY_A

source_name: RNA-seq human PSC cells replicate A in 8iONLY conditions


title: 8iP_C

source_name: RNA-seq human PSC cells replicate C in 8iP conditions

value: Cell culture in CDK8/19i +p38i +JNKi conditions


title: S133_TCR Sample 8

value: esophagus squamous cell carcinoma patient

tag: Sex

value: IIIB


title: Control34

description: Anonymized patient/sample code

value: CTRL

value: Female

tag: codon129 genotype


title: S134_TCR Sample 9

tag: subject status

tag: pathological stage

value: IIIA

value: adjacent normal tissue


title: 8iP_B

source_name: RNA-seq human PSC cells replicate B in 8iP conditions

value: pluripotent stem cells (PSCs)

tag: treatment


title: 8iP_A

source_name: RNA-seq human PSC cells replicate A in 8iP conditions


title: A20-GFP 24h No Dox 2

description:
M3826g
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.

tag: cell line

value: IRES-EGFP expression construct

value: 24 hours


title: S159_TCR Sample 7

value: Male

tag: tissue type

value: tumors


title: A20-GFP 48h Dox 1

description:
M3741r
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.


title: Control31

description: Anonymized patient/sample code

value: MV

tag: mrc scale

value: blood


title: Control33

description: Anonymized patient/sample code


title: S158_TCR Sample 6

value: IIB


title: Primed_C

description: Cell culture in Primed conditions

source_name: RNA-seq human PSC cells replicate C in Primed conditions

value: Cell culture in Primed conditions


title: S150_TCR Sample 5


title: Primed_B

description: Cell culture in Primed conditions

source_name: RNA-seq human PSC cells replicate B in Primed conditions


title: Primed_A

description: Cell culture in Primed conditions

source_name: RNA-seq human PSC cells replicate A in Primed conditions


title: S149_TCR Sample 4

value: IIA


title: S135_TCR Sample 3


title: Control32

description: Anonymized patient/sample code

source_name: DNA from EDTA-stored blood

value: MM


title: Control29

description: Anonymized patient/sample code


title: mLung2918 [d3CovCtrl2918]

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

description:
081820_CoVmLung_totalRNAseq
d3Ctrl3_Tr_S4

data_processing:
Pre-processing with Trim-Galore-0.6.5 followed by UCSC sluganalytics platform
Genome_build: mm10
Supplementary_files_format_and_content: txt count data

growth_protocol: 6-8 week male C57Bl/6 mice were used for the experiment.

extract_protocol:
Total RNA was extracted from lung tissue according to Quick-RNA MiniPrep kit protocol from Zymo Research
Total RNAseq library construction was performed according to SMART-Seq Stranded Kit protocol

treatment_protocol: The mice were inoculated 1.5x10^9 pfu Ad5-hACE2 or Ad5-empty in 75uL DMEM and infected SARS-CoV2 at each time point.

tag: strain background

tag: genotype/variation

tag: treatment/time point

value: SARA-CoV2_2X10^5, 3 dpi

value: lung


title: S133_TCR Sample 1

value: esophagus squamous cell carcinoma patient

value: IIIB


title: A20-GFP 24h Dox 1

description:
M3740r
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.

tag: modification to cells

value: Dox

tag: time point


title: S134_TCR Sample 2

value: Female

tag: age

value: IIIA


title: mLung2917 [d3CovCtrl2917]

description:
081820_CoVmLung_totalRNAseq
d3Ctrl2_Tr_S1

tag: tissue


title: A20-mLANA WT 48h No Dox 1

description:
M3739g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.

value: A20-mLANA WT

value: No Dox

value: 48 hours


title: Control28

description: Anonymized patient/sample code

extract_protocol: Zymo gDNA Extraction kit

value: CTRL


title: Control27

description: Anonymized patient/sample code


title: mLung2693 [7CoVmLung]

description:
060520_CoVmLung_totalRNAseq_8x
mLung2693_L3d3Trt_S1

value: SARA-CoV2_1X10^5, 3 dpi


title: mLung2696 [13CoVmLung]

description:
060520_CoVmLung_totalRNAseq_8x
mLung2696_L4d3Trt_S7


title: S158_mRNA Sample 13

value: Male

value: adjacent normal tissue


title: S159_mRNA Sample 14


title: 8i3i-rep3

description: Cell culture in serum/LIF +CDK8/19i +GSK3i (CHIR99021) wt mES cells replicate3

data_processing:
RNA-seq processing:
The analysis was performed using Nextpresso (Graña O et al. 2017). Read files were quality-checked with FastQC.
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Mus musculus GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used
Genome_build: mm10 (Genome Reference Consortium Mouse Build 38)
Supplementary_files_format_and_content: tables were generated with Cufflinks 2.2.1 and contain transcripts abundance measured in FPKM values

growth_protocol: Cells were maintained in Serum/LIF or KSR/LIF (serum-free) as indicated in the sample names, and detailed in the Methods section.

extract_protocol:
For RNA-seq Total RNA was extracted using the RNeasy kit (Qiagen)
For RNA-seq 1 µg of total RNA sample was used . PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: Cells were treated with small molecule inhibitors as detailed in the Methods section (MEKi: PD at 1 micro-molar; GSK3i: CHIR99021 at 3 micro-molar; CDK8/19i: ETP-47709 at 1,1 micro-molar; Flavopiridol at 60 nano-molar;

tag: sample type

value: Cell culture


title: 8i3i-rep2

description: Cell culture in serum/LIF +CDK8/19i +GSK3i (CHIR99021) wt mES cells replicate2


title: S150_mRNA Sample 12


title: mLung2692 [5CoVmLung]

description:
060520_CoVmLung_totalRNAseq_8x
mLung2692_L2d3Trt_V2_S4

value: SARA-CoV2_5X10^4, 3 dpi


title: 8i3i-rep1

description: Cell culture in serum/LIF +CDK8/19i +GSK3i (CHIR99021) wt mES cells replicate1


title: mLung2690 [3CoVmLung]

description:
060520_CoVmLung_totalRNAseq_8x
mLung2690_L1d3Ctrl_V2_S3


title: 8i-rep3

description: Cell culture in serum/LIF +CDK8/19i wt mES cells replicate3

value: serum/LIF +CDK8/19i wt mES cells


title: Only Plant-N – R-2 (Mock)

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

description:
RNA_Seq_HS_FPKM.xlsx
HS_vs_NHS.xlsx, NHS+SA187_vs_NHS.xlsx,  and ACC_vs_NHS.xlsx

data_processing:
Sequenced reads were checked for quality using FASTQC v0.11.5 .
Adapters and low-quality reads or bps were filtered using Trimmomatic 0.36 , retaining first 100 bps and by using the default settings available for paired-end reads in Trimmomatic.
The trimmed reads were then cross-checked for quality and were aligned to the Arabidopsis thaliana reference genome (TAIR10) using Tophat v2.1.1Trapnell, Pachter, and & Salzberg 2009) with 2bp mismatches reporting one maximum hit.
Summary of read counts per gene was calculated using feature Counts v1.5.1 (Liao, Smyth, and & Shi 2014).
FPKM for individual replicates was calculated using Cufflinks v.2.2.1 (Trapnell et al. 2012). Differentially expressed genes between two conditions were identified using CuffDiff tool from Cufflinks package v2.2.1
Genome_build: TAIR 10
Supplementary_files_format_and_content: FPKM  values in MS excel files

organism: Arabidopsis thaliana

source_name: total plants

growth_protocol: Arabidopsis thaliana plants were grown at 22⁰C under 16 h light and 8 h dark period

extract_protocol:
Total RNA was extracted using Nucleospin RNA plant kit (Macherey-Nagel), we further followed with DNaseI treatment to remove gemomic DNA as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Ribo-zero Illumina protocol
RNA-seq was carried out on three independent biological replicates

treatment_protocol:
Two different heat stress regimes (37⁰+44⁰C and 44⁰C) ) were implemented on SA187 colonized plants
5 days seedling growing in 1/2 MS media with and without SA187 transferred to new 1/2 MS plates and given two different heat stress: acclimation on day 9 and day 11(37⁰+44⁰C) and direct heat stress on day 11 (44⁰C)

value: 15 days old seedling

tag: ecotype

tag: inoculation

value: non-inoculated

tag: temperature

value: 22⁰C (NHS)


title: Control25

description: Anonymized patient/sample code

tag: Sex

tag: codon129 genotype

value: blood


title: 8i-rep2

description: Cell culture in serum/LIF +CDK8/19i wt mES cells replicate2

tag: treatment


title: Only Plant-37+44⁰C - R-3

description:
RNA_Seq_HS_FPKM.xlsx
ACC_vs_NHS.xlsx and ACC_vs_HS.xlsx


title: S149_mRNA Sample 11

source_name: ESCC_adjacent normal tissue

tag: subject status

value: esophagus squamous cell carcinoma patient

tag: pathological stage

value: IIA


title: 8i-rep1

description: Cell culture in serum/LIF +CDK8/19i wt mES cells replicate1


title: Plant+SA-187-37+44⁰C -R-2

description:
RNA_Seq_HS_FPKM.xlsx
ACC+SA187_vs_ACC.xlsx, ACC+SA187_vs_HS+SA187.xlsx and ACC+SA187_vs_NHS+SA187.xlsx

value: Inoculated with SA187


title: 2i-rep3

description: Cell culture in serum/LIF +2i wt mES cells replicate3

source_name: serum/LIF +2i wt mES cells replicate3

value: serum/LIF +2i wt mES cells


title: A20-mLANA WT 48h Dox 1

description:
M3739r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 48 hours after Dox treatment.

tag: cell line

value: A20-mLANA WT

value: Dox


title: Plant+SA  187-N – R-3 (Mock)

description:
RNA_Seq_HS_FPKM.xlsx
HS+SA187_vs_NHS+SA187.xlsx, ACC+SA187_vs_NHS+SA187.xlsx and ACC+SA187_vs_NHS+SA187.xlsx


title: 2i-rep2

description: Cell culture in serum/LIF +2i wt mES cells replicate2

source_name: serum/LIF +2i wt mES cells replicate2


title: Control30

description: Anonymized patient/sample code

value: CTRL

value: Female

value: MV

tag: mrc scale


title: Plant+SA  187-N – R-2 (Mock)


title: A20-mLANA WT 24h No Dox 1

description:
M3738g
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.

source_name: BALB/c B cell lymphoma

value: No Dox

value: 24 hours


title: Control24

description: Anonymized patient/sample code


title: Control23

description: Anonymized patient/sample code


title: Control22

description: Anonymized patient/sample code

value: Male


title: A20-mLANA WT 24h Dox 1

description:
M3738r
A20 cells transduced with lentivirus containing FLAG-tagged mLANA WT IRES-EGFP expression construct.
Gene expression 24 hours after Dox treatment.


title: 2i-rep1

description: Cell culture in serum/LIF +2i wt mES cells replicate1

source_name: serum/LIF +2i wt mES cells replicate1

value: Cell culture


title: S159_mRNA Sample 7

value: IIIB

tag: tissue type

value: tumors


title: S133_mRNA Sample 8

value: adjacent normal tissue


title: S158_mRNA Sample 6

value: IIB


title: S135_mRNA Sample 10

value: esophagus squamous cell carcinoma patient


title: S150_mRNA Sample 5


title: S149_mRNA Sample 4

value: IIA


title: A20-GFP 48h No Dox 1

description:
M3741g
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 48 hours after no Dox treatment.

value: IRES-EGFP expression construct

value: 48 hours


title: S134_mRNA Sample 9

value: IIIA


title: Plant+SA-187-37+44⁰C -R-3

description:
RNA_Seq_HS_FPKM.xlsx
HS+SA187_vs_NHS+SA187.xlsx, NHS+SA187_vs_NHS.xlsx, ACC+SA187_vs_NHS+SA187.xlsx and ACC+SA187_vs_NHS+SA187.xlsx

value: 15 days old seedling

value: Inoculated with SA187


title: Ctrl-rep2

description: Cell culture in serum/LIF wt mES cells replicate2 (for comparison versus other serum/LIF conditions)

value: serum/LIF wt mES cells (for comparison versus other serum/LIF conditions)


title: A20-GFP 24h No Dox 1

description:
M3740g
A20 cells transduced with lentivirus containing IRES-EGFP expression construct.
Gene expression 24 hours after no Dox treatment.


title: Control19

description: Anonymized patient/sample code

value: CTRL

value: blood


title: S135_mRNA Sample 3


title: Ctrl-rep1

description: Cell culture in serum/LIF wt mES cells replicate1 (for comparison versus other serum/LIF conditions)


title: Control13

description: Anonymized patient/sample code

value: Female


title: Plant+SA-187-37+44⁰C -R-1


title: Control26

description: Anonymized patient/sample code


title: Serum_C1

description: Cell culture in serum/LIF wt mES cells replicate3 (for comparison versus KSR/LIF serum-free)

value: serum/LIF wt mES cells (for comparison versus KSR/LIF serum-free)


title: Only Plant-N – R-1 (Mock)

description:
RNA_Seq_HS_FPKM.xlsx
HS_vs_NHS.xlsx, NHS+SA187_vs_NHS.xlsx,  and ACC_vs_NHS.xlsx

value: non-inoculated

value: 22⁰C (NHS)


title: Control12

description: Anonymized patient/sample code

value: Male


title: Only Plant-37+44⁰C - R-2

description:
RNA_Seq_HS_FPKM.xlsx
ACC_vs_NHS.xlsx and ACC_vs_HS.xlsx


title: Control21

description: Anonymized patient/sample code


title: S133_mRNA Sample 1

value: IIIB

value: tumors


title: H1-QKI KO-d6

data_processing:
CellRanger 2.1.0 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat 2.3 was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfificationa.
The CCA function from Seurat 2.3 was used for integrative analysis of the WT and KO samples.
Genome_build: hg38
Supplementary_files_format_and_content: gz file of filtered gene-barcode matrices

source_name: cardiomyocytes

extract_protocol: CollagenaseI with DNAse for 1h, 0.05% Trypsin-EDTA with DNAse for 15 mins, DMEM +10% FBS to stop digestion and wash three times. And the cells were suspensed DMEM+10%FBS.

tag: cell type

value: hESCs-derived cardiomyocytes

tag: differentiation day

tag: genotype

value: QKI KO


title: Only Plant-N – R-3 (Mock)

tag: age


title: Plant+SA-187-44⁰C -R-3

description:
RNA_Seq_HS_FPKM.xlsx
HS+SA187_vs_NHS+SA187.xlsx and HS+SA187_vs_HS.xlsx

value: 44⁰C (HS)


title: Control18

description: Anonymized patient/sample code

tag: tissue


title: Serum_B1

description: Cell culture in serum/LIF wt mES cells replicate2 (for comparison versus KSR/LIF serum-free)

tag: sample type

value: Cell culture


title: H1-d6

value: WT


title: Control15

description: Anonymized patient/sample code


title: Control14

description: Anonymized patient/sample code


title: Plant+SA-187-44⁰C -R-1

value: 15 days old seedling

tag: ecotype


title: Control17

description: Anonymized patient/sample code


title: H1-QKI KO-d15


title: Serum_A1

description: Cell culture in serum/LIF wt mES cells replicate1 (for comparison versus KSR/LIF serum-free)


title: Control20

description: Anonymized patient/sample code


title: Control16

description: Anonymized patient/sample code


title: Control9

description: Anonymized patient/sample code


title: Control10

description: Anonymized patient/sample code


title: Control11

description: Anonymized patient/sample code


title: H1-d15


title: S134_mRNA Sample 2

value: esophagus squamous cell carcinoma patient

value: IIIA


title: Only Plant-44⁰C - R-3

description:
RNA_Seq_HS_FPKM.xlsx
HS_vs_NHS.xlsx and HS+SA187_vs_HS.xlsx

tag: inoculation


title: KSR_A1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate1 control

value: KSR/LIF (serum-free) wt mES cells control


title: Plant+SA  187-N – R-1 (Mock)

value: Inoculated with SA187

tag: temperature


title: KSR_C1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate3 control


title: KSR_B1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate2 control


title: Female_Week_13 ovary

source_name: Prenatal Gonads

tag: Sex

value: female

tag: developmental timepoint

value: Week 13 post-fertilization

value: prenatal ovaries


title: Only Plant-37+44⁰C - R-1

value: non-inoculated


title: Flavo_B1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate2 in Flavopiridol

tag: treatment

value: KSR/LIF (serum-free) wt mES cells in Flavopiridol


title: Ctrl-rep3

description: Cell culture in serum/LIF wt mES cells replicate3 (for comparison versus other serum/LIF conditions)

value: serum/LIF wt mES cells (for comparison versus other serum/LIF conditions)


title: Female_Week_10 ovary

value: Week 10 post-fertilization


title: Female_Week_16 ovary

value: Week 16 post-fertilization


title: Only Plant-44⁰C - R-1


title: Only Plant-44⁰C - R-2


title: Control7

description: Anonymized patient/sample code

value: CTRL

value: Female

tag: codon129 genotype

value: blood


title: Female_Week_9 ovary

value: Week 9 post-fertilization


title: Plant+SA-187-44⁰C -R-2

value: 15 days old seedling

value: 44⁰C (HS)


title: ETP_B1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate 2 in CDK8/19i

value: Cell culture


title: Flavo_A1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate1 in Flavopiridol


title: ETP_A1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate1 in CDK8/19i

value: KSR/LIF (serum-free) wt mES cells in CDK8/19i


title: Female_Week_7 ovary

value: Week 7 post-fertilization


title: hPDLSCs_cultured_14day_rep3 [miRNA]

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

label_protocol: RNA labeling and array hybridization was according to Exiqon's manual. After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C. c, Terminated by incubation for 15 min at 65°C.

growth_protocol: Isolated hPDLSCs were cultured in Dulbecco α-modified Eagle medium (DMEM) (Hyclone, Los Angeles, CA) supplemented with 10% fetal calf serum, 2 mmol/L glutamine, and 2% penicillin/streptomycin (HyClone, NY, USA), and maintained at 37 °C in a humidified atmosphere with 95% air and 5% CO2. Single-cell suspensions were inoculated into six-well plates at a density of 3×104 cells/well. The limited dilution techniques are used to obtain colonies of single cell origin

extract_protocol: According to the manufacturer’s protocol, total RNA was isolated from cultured cells with Trizol reagent (Thermo Fisher Scientific, Waltham, MA). The quantity and quality of RNA are determined by nano dropper ND-1000 (Nano Dropper Technology Company, Wilmington, DE). The RNA Integrity is determined by gel electrophoresis

treatment_protocol: hPDLSCs at differentiated group were cultured with an osteogenic differentiation medium containing 100 nM dexamethasone, 10 mmol/L β-glycerophosphate, and 50 mg/mL ascorbic acid (Sigma, St Louis, MO, USA) for 14 days in 6-well plates.  hPDLSCs at undifferentiated group were cultured in 10 % FBS in DMEM with no supplements.

value: human periodontal ligament stem cells (hPDLSCs)

tag: time point

value: after 14 days cultured


title: ETP_C1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate3 in CDK8/19i


title: Male_Week_16_Testis

value: male

value: prenatal testis


title: Male_Week_15_Testis

value: Week 15 post-fertilization


title: Male_Week_8_Testis

value: Week 8 post-fertilization


title: 2i_C1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate3 in 2i

value: KSR/LIF (serum-free) wt mES cells in 2i


title: hPDLSCs_cultured_14day_rep2 [miRNA]


title: 2i_A1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate2 in 2i


title: hPDLSCs_cultured_14day_rep1 [miRNA]


title: hPDLSCs_osteogenic differentiation_14day_rep2 [miRNA]

value: after 14 days odontogenic induction


title: hPDLSCs_osteogenic differentiation_14day_rep3 [miRNA]


title: Control8

description: Anonymized patient/sample code

value: CTRL


title: Control6

description: Anonymized patient/sample code

value: Male


title: Male_Week_7_Testis


title: 2i_B1

source_name: KSR/LIF (serum-free) wt mES cells replicate2 in 2i


title: Male_Week_6_Testis

value: Week 6 post-fertilization


title: wt-proB-Rep2 (array)

description:
Gene expression in wt proB cells
wt-proB-R2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: wt proB cells, Replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling Kit (One-Color) and RNA Spike-In Kit, according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: dHet leukemic cells were derived from the lymph node of Ebf1+/-Pax5+/- leukemic mice. dHet proB cells were derived by culturing the single-cell suspensions of freshly isolated c-Kit positive fetal liver cells were plated on OP9 feeder cells in OptiMEM medium, supplemented with 4% FCS, 1% PSG, 50 μM β-mercaptoethanol, 5 ng/ml interleukin 7 (IL-7), 10 ng/ml Flt3 ligand (Flt3L) and 10 ng/ml stem cell factor (SCF). wt proB (FrBC) cells were sorted from the control mice.

extract_protocol: The total RNA was prepared with the RNeasy Mini Kit following the manufacturer's recommendations.

value: wt proB (Fraction BC) bone marrow

value: wt proB cells


title: dHet-proB-Rep1 (array)

description:
Gene expression in dHet proB cells
dHet-proB-R1

source_name: Ebf1+/− Pax5+/- dHet fetal liver proB cells,Replicate1

value: Ebf1+/− Pax5+/- Rag2-/- proB fetal liver

value: dHet proB cells


title: Control4

description: Anonymized patient/sample code

value: Female

value: blood


title: 6TotmIFNbMD55A_S15_R1_001

status: Public on Oct 18 2020

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

description:
total RNA
RNA-seq_NormalizedReadCount.txt

data_processing:
RNA-seq: Data, as FASTQ file, were aligned to human hg19 genome using TopHat. HTSEQ was used to count reads at exons of genes. Normalization of read counts was done using DESEQ.
Ribo-seq: Preprocessing of fastq files consisted of adapter removal using cutadapt with the parameters (--quality-base=33  -O 7 -e 0.15 -m 20 -q 5) and removal of rRNA and tRNA contaminants by means of alignment against a reference using bowtie2with parameters (--seed 42 -p1 –local). The actual alignment of pre-processed fastq files was done with tophat2  and bowtie2  against GRCh37/hg19  using parameters ( --seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25). In a subsequent step the primary aligned reads filtered for a minimum mapping quality of 10.  HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt file containing normalized read counts (DESEQ) for all comparisons

source_name: MD55A3 cells

growth_protocol: 12T, 108T, MD55A3 Cell lines were derived from pathology-confirmed metastatic melanoma tumor resections. Cells were authenticated by Finger printing with STR profiling. 12T, 108T, MD55A3, 888-Mel and D10 cells were cultured in RPMI 1640 medium supplemented with heat-inactivated 10% fetal bovine serum 25 mM HEPES and 100 U/mL penicillin/streptomycin.

extract_protocol:
For the generation of total RNA libraries, total RNA was extracted using TRI Reagent (SIGMA), and mRNA was purified using Dynabeads mRNA DIRECT Purification Kit (Invitrogen), according to the manufactures’ protocol. For ribosome profiling in melanoma cell lines, cells were treated with Cycloheximide for 1 min (100ug/ml), lysed in lysis buffer (20mM Tris 7.5, 150mM NaCl, 15mM MgCl2, 1mM dithiothreitol) supplemented with 0.5% triton, 30 U/ml Turbo DNase (Ambion) and 100μg/ml cycloheximide. Cell lysates were loaded on sucrose cushion, followed by ultracentrifugation, and RNA was extracted from pelletsd using TRI reagent following manufacture protocol.
The construction of ribosome protected fragments (RPF) libraries were done as previously described in Ingolia NT et al, doi:10.1038/nprot.2012.086 (2012). Total RNA libraries were constructed using SENSE Total RNA-Seq Library Prep Kit for Illunima (LEXOGEN).

treatment_protocol: cell where cultured with Tryptophan-free RPMI 1640 media (custom purchased from Biological Industries)/ Tyrosine-free medium (custom purchased from Cell Culture Technologies) for 48h, IFNγ (PeproTech) was used at 250 U/mL for the indicated durations of time. IDO inhibitor, 1-Methyl-L-Tryptophan (SIGMA) was dissolved in 0.1N NaOH at a 20mM concentration, adjusted to PH=7.5, filter sterilized and used at a final concentration of 300µM for 48h.

value: Melanoma  cancer cells

value: Control


title: 3TotIFNa108T_S12_R1_001

source_name: 108T cells

value: IFNg


title: Control5

description: Anonymized patient/sample code


title: 7TotIFNaMD55A_S16_R1_001


title: 8TotIFNbMD55A_S17_R1_001


title: 4TotIFNb108T_S13_R1_001


title: hPDLSCs_osteogenic differentiation_14day_rep1 [miRNA]

value: human periodontal ligament stem cells (hPDLSCs)


title: 2TotmIFNb108T_S11_R1_001


title: dHet-B-ALL-713-Rep2 (array)

description:
Gene expression in dHet B-ALL (713) cells
dHet-B-ALL-713-R2

source_name: Ebf1+/− Pax5+/- dHet leukemic cells derived from lymph node (mouse 713),Replicate2

value: Ebf1+/− Pax5+/- lymph node

value: dHet B-ALL (713) cells

value: Ebf1+/− Pax5+/-


title: dHet-B-ALL-713-Rep1 (array)

description:
Gene expression in dHet B-ALL (713) cells
dHet-B-ALL-713-R1

source_name: Ebf1+/− Pax5+/- dHet leukemic cells derived from lymph node (mouse 713),Replicate1


title: dHet-B-ALL-760-Rep1 (array)

description:
Gene expression in dHet B-ALL (760) cells
dHet-B-ALL-760-R1

source_name: Ebf1+/− Pax5+/- dHet leukemic cells derived from lymph node (mouse 760),Replicate1

value: dHet B-ALL (760) cells


title: dHet-B-ALL-760-Rep2 (array)

description:
Gene expression in dHet B-ALL (760) cells
dHet-B-ALL-760-R2

source_name: Ebf1+/− Pax5+/- dHet leukemic cells derived from lymph node (mouse 760),Replicate2


title: rnaseq_3_mIFN_R1_001

source_name: 12T cells


title: 1TotmIFNa108T_S10_R1_001


title: dHet-B-ALL-686-Rep2 (array)

description:
Gene expression in dHet B-ALL (686) cells
dHet-B-ALL-686-R2

source_name: Ebf1+/− Pax5+/- dHet leukemic cells derived from lymph node (mouse 686),Replicate2

value: dHet B-ALL (686) cells


title: rnaseq_5_IFN_R1_001


title: wt-proB-Rep1 (array)

description:
Gene expression in wt proB cells
wt-proB-R1

source_name: wt proB cells, Replicate1


title: rnaseq_2_mIFN_R1_001


title: dHet-B-ALL-686-Rep1 (array)

description:
Gene expression in dHet B-ALL (686) cells
dHet-B-ALL-686-R1

source_name: Ebf1+/− Pax5+/- dHet leukemic cells derived from lymph node (mouse 686),Replicate1


title: Control3

description: Anonymized patient/sample code

source_name: DNA from EDTA-stored blood

value: CTRL


title: 5TotmIFNaMD55A_S14_R1_001


title: Control2

description: Anonymized patient/sample code

value: Male


title: rnaseq_4_IFN_R1_001


title: Flavo_C1

description: Cell culture in KSR/LIF (serum-free) wt mES cells replicate3 in Flavopiridol

value: Cell culture

value: KSR/LIF (serum-free) wt mES cells in Flavopiridol


title: merged_MD55A_mTyr

description:
Ribosomal RPF
Riboseq_set3_NormalizedReadCount.txt

data_processing:
Library strategy: Ribo-seq
RNA-seq: Data, as FASTQ file, were aligned to human hg19 genome using TopHat. HTSEQ was used to count reads at exons of genes. Normalization of read counts was done using DESEQ.
Ribo-seq: Preprocessing of fastq files consisted of adapter removal using cutadapt with the parameters (--quality-base=33  -O 7 -e 0.15 -m 20 -q 5) and removal of rRNA and tRNA contaminants by means of alignment against a reference using bowtie2with parameters (--seed 42 -p1 –local). The actual alignment of pre-processed fastq files was done with tophat2  and bowtie2  against GRCh37/hg19  using parameters ( --seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25). In a subsequent step the primary aligned reads filtered for a minimum mapping quality of 10.  HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt file containing normalized read counts (DESEQ) for all comparisons

value: starvation media, Tyrosine depletion


title: rnaseq_1_mIFN_R1_001


title: merged_MD55A_Full_Tyr

value: starvation media + Tyrosine addition


title: 5RFPFullaMD55A_R1


title: 108T_48-Trp_S9_R1_001

value: starvation media, Tryptophan depletion for 48h


title: 108T_48_full_S6_R1_001

value: starvation media + Tryptophan addition for 48h


title: 7aRFPmTyr48hMD55A_R1

value: Melanoma  cancer cells


title: 108T_48-Trp2_S10_R1_001


title: 6RFPFullbMD55A_R1


title: 108T_48-Trp_merged


title: Control1

description: Anonymized patient/sample code

value: blood


title: 108T_24-Trp_merged

value: starvation media, Tryptophan depletion for 24h


title: 108T_24_full_S5_R1_001

value: starvation media + Tryptophan addition for 24h


title: 8bRFPmTyr48hMD55A_R1


title: merged_mIFN

description:
Ribosomal RPF
Riboseq_set2_NormalizedReadCount.txt

value: Control


title: 108T_24-Trp2_S8_R1_001


title: merged_IFN

value: IFNg


title: merged_IDO_IFN

value: IDO + IFNg


title: merged_IDO_mIFN

value: IDO


title: 8RFPIFN1MTb_S8_R1_001


title: 7RFPIFN1MTa_S7_R1_001


title: 108T_24-Trp_S7_R1_001


title: 6RFP1MTb_S6_R1_001


title: shUSP7, bio. replicate 2

city: Baltimore

first: Jiou

state: MD

address: 615 N. Wolfe Street

department: Biochemistry and Molecular Biology

institute: The Johns Hopkins University

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

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

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.na32.hg19.transcript.csv

label: biotin

source_name: HEK293 shUSP7-2

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: HEK293 cells grown in DMEM, 10%FBS, 37˚C, 5% CO2

extract_protocol: Cells were lysed using RNAeasy mini kit (Qiagen), according to manufacturer's instructions. Genomic DNA was first removed by DNAse treatment on the column, and then, additionally, after total RNA was isolated, using DNase Turbo kit (Ambion), followed by additional round of cleaning through RNAeasy columns.

treatment_protocol: Cells were transfected in 60mm dishes using 4µg DNA, 10µl Lipofectamine 2000, in total 4.5ml  Optimem-MEM1. Origene's pRS-RFP-C plasmids encoding shRNAs against USP7, or non-targeting control (CTRL) were used for knockdown. Cells were knocked down for 78h before lysis.

tag: cell line

tag: knockdown


title: shUSP7, bio. replicate 1

source_name: HEK293 shUSP7-1


title: shUSP7, bio. replicate 3

source_name: HEK293 shUSP7-3


title: 5RFP1MTa_S5_R1_001