title: Pho ChIP-seq in S2 cells

extract_protocol:
~2x107 cells were fixed for 10 min at room temperature by gently mixing in 10 mL crosslinking solution (1% formaldehyde, 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), crosslinking was quenched by adding 2M glycine to a final concentration of 240 mM. The cells were sequentially collected by centrifugation at 700 x g for 10 min and washed trice with 10 mL ice-cold PBS. These cell pellets were sonicated in parallel to obtain chromatin fragments of ~200 to 700 bp, each in 4 mL sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, Roche protease inhibitor cocktail) with a Sonic Dismembrator Model 500 (Fisher Scientific, 10 x 30 seconds on / 45 seconds off cycles, 50% power settings). After sonication, debris was removed by centrifugation at 4°C for 10 minutes at 13,000 rpm, and equal amount of 6M urea was added to the solution then incubated for 10 minutes at 4°C on a rotating wheel. The soluble chromatin was dialysed using a membrane with a molecular weight cut-off of 3.5 kDa, at 4°C against 2 L dialysis buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 4% glycerol) overnight. Insoluble debris was removed by quick centrifugation (7,500 rpm, 2 min). 120 Î¼g of extract were incubated in a final volume of 1 mL IP buffer (15 mM Hepes pH 7.9 / 200 mM KCl / 1.5 mM MgCl2 / 0.2 mM EDTA pH 8 / 0.25% NP-40 / 20% glycerol / 0.3 mM DTT / 1x "Complete" protease inhibitor cocktail / 1 mM PMSF) with 1:100 anti-Pho antibody (kindly provided by Judith Kassis1) for 12 hours at 4°C.  100 µL protein A/G agarose beads (Calbiochem), previously blocked with 1 mg/mL BSA, was added to each chromatin at 4°C overnight. The beads were sequentially washed trice with 5-10 volumes of 6 M urea/2 M thiourea/10 mM HEPES (pH 8.0), PBS, and 1% SDS/PBS. Centrifugation of the beads between washing steps was carried out (7,500 rpm, 2 min).
The libraries were prepared according to the manufacturer's instructions using the NEBNext kit (E6200). Briefly, DNA was fragmented by sonication to a maximum of 300 bp. Next the ends of the fragments were repaired with a combination of fill-in reactions and exonuclease activity to produce blunt ends that were then tailed with an A-base. Illumina-specific Adaptors were ligated followed by removal of unligated adaptors using AMpure XP beads (Beckman Coulter). Finally a PCR with 12-15 cycles for both kits was performed to enrich final adaptor-ligated fragments. Quality and quantity were assessed on an Agilent Bioanalyzer Chip DNA 7500 or High Sensitivity. For all libraries, sequencing was performed on the MiSeq platform, using v2, 300-cycle reagent kits (Illumina).

value: Pho antibody


title: E95repl_Mark3

status: Public on Jul 18 2017

type: SRA

city: Paris

first: Pascale

last: Gilardi-Hebenstreit

address: 46 Rue d'Ulm

department: IBENS - UMR ENS - CNRS 8197 - INSERM 1024

country: France

institute: Institut de Biologie de l'Ecole Normale Superieure

library_source: genomic

data_processing:
Library strategy: 4C-Seq
De-multiplexing, mapping and 4C-seq were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm9 (NCBIM37) Mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009 Genome Biology) with parameters -n 2 --best -strata -m 5.
Mapped reads were translated to restriction fragments using the HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
4C figures were made using a running mean algorithm with a window size of eleven fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Signal/restriction fragment (bedGraph) and locally normalized, smoothed (bedGraph), one per viewpoint, per cell type.

molecule: genomic DNA

organism: Mus musculus

source_name: E9.5 full embryo - replicate

extract_protocol:
Multiplexed samples were sequenced on the Illumina Genome HiSeq 2500 system using 100 bp single-end reads according to the manufacturer’s specifications. 4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline of the BBCF HTSstation (David et al. 2014, Plos ONE and available at http://htsstation.epfl.ch). Samples were mapped to the ENSEMBL Mouse assembly NCBIM37 (mm9).
Illumina adapters (single end reads) were included in the inverse 4C PCR primers used for 4C-seq library preparation
Cells were isolated in PBS supplemented with 10% Fetal Calf Serum. Tissue sample were further made single cell by collagenase treatment and applying a cell-strainer cap (BD Biosciences). Chromatin was crosslinked in the presence of 2% formaldehyde.
PCR amplification using primers with included adapter sequences (for Illumina HiSeq2500)

treatment_protocol:
4C–seq libraries were constructed as described before (Matelot and Noordermeer, Methods in Molecular Biology 2016). 4C-seq libraries were prepared from 35 E9.5 embryos. The primary restriction enzyme used was DpnII (New England Biolabs, R0125L) and the secondary restriction enzyme was NlaIII (New England Biolabs, R0543M). For each viewpoint 1000 ng of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences.
Circular Chromosome Conformation Capture (4C) technique was performed as described (Matelot and Noordermeer, Methods in Molecular Biology 2016). Cross-linked chromatin was digested with DpnII, ligated under diluted conditions, cross links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions.

tag: strain

tag: tissue

value: full embryo - replicate

tag: age

tag: genotype

value: WT


title: GlcNAc ChIP-seq on GalNAz fed S2 cells

city: Burnaby

first: David

last: Vocadlo

state: British Columbia

address: 8888 University Drive

department: Chemistry

country: Canada

institute: Simon Fraser University

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bwa-mem or bwa-bwasw algorithm version 0.7.5a-r405.
Bam-format alignment files were generated with Samtools version 0.1.19-96b5f2294a.
Multiple runs were merged with Samtools.
Duplicate read-pairs were removed with Samtools.
BDG files generated with macs version1.4
Genome_build: dm3

organism: Drosophila melanogaster

growth_protocol: Drosophila melanogaster Schneider S2 cells were cultured in Sf-900 II SFM medium (Invitrogen) supplemented 100 U/ml Penicillin and 100 mg/ml Streptomycin at 25°C. Cells were passaged at 1:4 ratio every two days to keep logarithmic growth.

extract_protocol:
~2x107 cells were fixed for 10 min at room temperature by gently mixing in 10 mL crosslinking solution (1% formaldehyde, 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), crosslinking was quenched by adding 2M glycine to a final concentration of 240 mM. The cells were sequentially collected by centrifugation at 700 x g for 10 min and washed trice with 10 mL ice-cold PBS. These cell pellets were sonicated in parallel to obtain chromatin fragments of ~200 to 700 bp, each in 4 mL sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, Roche protease inhibitor cocktail) with a Sonic Dismembrator Model 500 (Fisher Scientific, 10 x 30 seconds on / 45 seconds off cycles, 50% power settings). After sonication, debris was removed by centrifugation at 4°C for 10 minutes at 13,000 rpm, and equal amount of 6M urea was added to the solution then incubated for 10 minutes at 4°C on a rotating wheel. The soluble chromatin was dialysed using a membrane with a molecular weight cut-off of 3.5 kDa, at 4°C against 2 L dialysis buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 4% glycerol) overnight. Insoluble debris was removed by quick centrifugation (7,500 rpm, 2 min). Before each enrichment of O-GlcNAz modified nuclear proteins, 500 µL solution (1% SDS/PBS) consisting of 800-1,000 µg nuclear protein was mixed with 50 µL Streptavidin-agarose slurry (Sigma), incubated for 1 h at 4°C for preclearing. The supernatant was transferred to a new tube and reacted with 200 µM Biotin-azo-phosphine for overnight at room temperature. Unreacted probe was removed by chloroform/methanol precipitation. Air-dried protein pellets were resuspended in 6 M urea/2 M thiourea/10 mM HEPES (pH 8.0) and enriched by Streptavidin-agarose slurry (Sigma) for a couple of hours at 4 °C with gentle rocking. The beads were sequentially washed trice with 5-10 volumes of 6 M urea/2 M thiourea/10 mM HEPES (pH 8.0), PBS, and 1% SDS/PBS. Centrifugation of the beads between washing steps was carried out (7,500 rpm, 2 min). Bound proteins were cleaved from the beads by treating with one beads volume of elution buffer (100 mM Na2S2O4 in 1% SDS/PBS) for 30 min trice. Collect and combine the eluants. Removal of the majority of Na2S2O4 from the eluants was achieved by precipitating them with chloroform/methanol method; 10% of each eluted sample was analyzed by Immunoblot using Odyssey (LI-COR Biosciences).
The libraries were prepared according to the manufacturer's instructions using the NEBNext kit (E6200). Briefly, DNA was fragmented by sonication to a maximum of 300 bp. Next the ends of the fragments were repaired with a combination of fill-in reactions and exonuclease activity to produce blunt ends that were then tailed with an A-base. Illumina-specific Adaptors were ligated followed by removal of unligated adaptors using AMpure XP beads (Beckman Coulter). Finally a PCR with 12-15 cycles for both kits was performed to enrich final adaptor-ligated fragments. Quality and quantity were assessed on an Agilent Bioanalyzer Chip DNA 7500 or High Sensitivity. For all libraries, sequencing was performed on the MiSeq platform, using v2, 300-cycle reagent kits (Illumina).

treatment_protocol: For labeling, media was aspirated and the cells were washed with PBS. DMSO stocks of Ac4GlcNAz was added to achieve the final treatment conditions and incubated for 16-24 h, with vehicle-only controls always included. ~3.3x106 S2 cells were used as a unit of cells for each experiment. This amount of cells yeilded more that enough DNA and protein for downstream analysis and ensured a large biological sample size.

value: Schneider's Drosophila Line 2 (SL2) cells

tag: cell line

tag: passages

tag: chip antibody/selection

value: GalNAz feeding, Staudinger ligation, and streptavidin purification


title: I_input_rep_2_for_K4

city: Grenoble

first: Christel

last: Carles

state: Auvergne/Rhone Alpes

address: 17 rue des Martyrs, bât. C2

department: Laboratoire Physiologie Cellulaire Végétale (LPCV)

institute: University Grenoble Alpes

data_processing:
Base-calling performed with Casava 1.8.2
reads were aligned using bwa 0.6.2-r126
files were converted into bam formate using samtools 0.1.19+
duplicated reads were removed using Picard-tools 1.93
bed files were generated using bedtools v2.17.0-97-ge80528b
H3K27me3 and H3K4me3 positive islands were determined using SICER V1.1 with window size 200 bp, gap size 400 bp and effective genome size of 90 % , a FDR-cutt-off of 0.0001 was employed
Genome_build: TAIR10
Supplementary_files_format_and_content: Significantly enriched islands (determined with input as control), csv-files, containing Chr, start, stop, ChIP_island_read_count, CONTROL_island_read_count, p_value,  fold_change, FDR_threshold

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: All employed lines were in Landsberg errecta (Ler) ecotype background. ap1 and cal double mutants (ap1-1 cal-1) (Bowman et al., 1993) and 35S::AP1:GR ap1-1 cal-1 (Wellmer et al., 2006) were described previously. After 2-3 days of stratification at 4°C, seeds were germinated on Murashige and Skoog medium supplemented with 0.3 % sucrose, in growth cabinets (Percival) providing a controlled environment in long days (LD) of 16 hours light at 18°C and 8 hours darkness at 16°C. At about ten days after germination, plants were transferred to a 1:1 mixture of soil/vermiculite.

extract_protocol:
Formaldehyde cross-linking and extraction of nuclei was performed as described in Carles and Fletcher (2009) with the following modifications: infiltration time was prolongated (6 min and 24 min), filtration of the extract after grinding was performed through 75 µm and 50 µm nylon meshes and sonication was done for 13x 30 sec on, 1 min off, position H (this longer sonication was only performed for biological replicate 2). Immunoprecipitation reactions were set up as described in Carles and Fletcher (2009) except that 15 µg of cauliflower and 10 µg of wild type chromatin was used and the chromatin was incubated with 5 µl of the antibody alone for 5 hours prior to addition of Protein A Agarose beads without salmon sperm DNA (Millipore). Washing of the ChIP reaction was performed using binding/wash buffer as described in Carles and Fletcher (2009) but for four times 10 min at 4°C and once 10 min at room temperature (RT).   Elution and reverse cross-linking was performed as described in Kaufmann et al. (2010) except that the elution was done by vortex mixing for 1 min at RT and input samples (1/3 of the chromatin used for one ChIP sample) were brought to the same volume by adding elution buffer and Tris pH9 in the same ratio as to the ChIP samples.  Reverse cross-linked samples were purified using the MinElute Reaction Cleanup Kit (Quiagen) and DNA was eluted in 30 µl Elution buffer.  For biological replicate 2, three technical replicates of ChIP on the same nuclear extract were performed and pooled on one MinElute column.
Libraries from ChIP samples of Replicate 1 were prepared and sequenced on a GAIIx (Illumina) sequencer as described previously (Yant et al., 2010; Immink et al., 2012). For biological replicate 2, ChIP-seq library preparation was performed using the Truseq ChIP sample preparation kit (Illumina, ref. IP-202-1012) according to the manufacturer's instructions except that PCR amplification was performed prior to size selection. Briefly, sonicated chromatin was repaired prior to 3' ends adenylation. Illumina's indexed adapters were ligated to the adenylated double-stranded DNA fragments. A 18-cycles PCR was performed on the ligated DNA using Illumina's PCR primers. The libraries were then size-selected between 300 and 700 bp on a 2% agarose gel. Each library was validated using high sensitivity chip (Agilent, ref. 5067-4626) on an Agilent Bioanalyzer and quantified using the Kapa library quantification kit (Clinisciences, ref. KK4824). Equimolar amounts of 4 libraries were pooled, diluted to 10 nM, denatured, and diluted again to 7 pM. 100 µl of the diluted pool were hybridized on one lane of an Illumina's Flow Cell. Clustering and 50 cycles sequencing were performed according to Illumina's instructions on a Hiseq2000. Libraries were multiplexed by three (H3K4me3 samples) or four and sequenced on a HiSeq2000 (Illumina) sequencer, yielding 50 bp single-end reads.
All inputs were sequenced with the HiSeq2000.

value: wild type (Ler)

value: inflorescences (whole main inflorescences of wild type plants were harvested. Flowers older than stage 12 were removed)

tag: developmental stage

value: I

tag: chip antibody


title: E95repl_Krox20DS


title: E95repl_Krox20


title: t2_input_rep_1

treatment_protocol: 2 days after dexamethason treatment : plants were treated with induction solution (10 µM Dexamethason, 0.015 % Silvet) by pipetting the solution directly onto the cauliflower structures. This process war repeated once after 30 min.

value: ap1 cal 35S::AP1-GR

value: apices (only the cauliflower structures of the main inflorescence were harvested. Leaf and pedicel tissue contamination was minimized by dissection)


title: I_input_rep_1


title: E95repl_ElemA


title: I_H3K27me3_rep_2

value: anti-H3K27me3 [Millipore, catalog# 17-622, lot# DAM1739345 (Repl. 1), lot#  2246083 (Repl.2)]


title: E95repl_ElemC


title: E95repl_ElemB


title: t2_H3K27me3_rep_2


title: L_H3K27me3_rep_2

source_name: rosette leaf

value: rosette leaves of flowering Arabidosis plants were harvested

value: L


title: E95_Nrbf2

source_name: E9.5 full embryo

value: full embryo


title: I_H3K4me3_rep_2

value: anti-H3K4me3 [Millipore, catalog# 17-614, lot# NG1794844 (Repl.1), lot#  2043923 (Repl.2)]


title: t0_H3K27me3_rep_2


title: E95repl_Elem2


title: GlcNAc ChIP-seq on S2 cells using WGA purification

extract_protocol:
~2x107 cells were fixed for 10 min at room temperature by gently mixing in 10 mL crosslinking solution (1% formaldehyde, 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), crosslinking was quenched by adding 2M glycine to a final concentration of 240 mM. The cells were sequentially collected by centrifugation at 700 x g for 10 min and washed trice with 10 mL ice-cold PBS. These cell pellets were sonicated in parallel to obtain chromatin fragments of ~200 to 700 bp, each in 4 mL sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, Roche protease inhibitor cocktail) with a Sonic Dismembrator Model 500 (Fisher Scientific, 10 x 30 seconds on / 45 seconds off cycles, 50% power settings). After sonication, debris was removed by centrifugation at 4°C for 10 minutes at 13,000 rpm, and equal amount of 6M urea was added to the solution then incubated for 10 minutes at 4°C on a rotating wheel. The soluble chromatin was dialysed using a membrane with a molecular weight cut-off of 3.5 kDa, at 4°C against 2 L dialysis buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 4% glycerol) overnight. Insoluble debris was removed by quick centrifugation (7,500 rpm, 2 min).20 Î¼g of extract were incubated in a final volume of 1 mL IP buffer (15 mM Hepes pH 7.9 / 200 mM KCl / 1.5 mM MgCl2 / 0.2 mM EDTA pH 8 / 0.25% NP-40 / 20% glycerol / 0.3 mM DTT / 1x "Complete" protease inhibitor cocktail / 1 mM PMSF) with 100 Î¼l of a 50% slurry of washed succinylated WGA-agarose resin (Vector Labs) for 12 hours at 4°C. Note: The length of these washes can range from 10 min to overnight. An overnight wash can significantly reduce background signal. The length of washing was optimized by examination of the background present in the control and optimizing washing times to reduce this background signal. Succinylated WGA has high affinity for GlcNAc, and a reduced affinity for sialic acids. Beads were washed with IP buffer containing 0.5 mM DTT and 0.4% NP-40, followed by a 1 hour incubation with 1 M GlcNAc (Galab) on ice to elute resin-bound proteins
The libraries were prepared according to the manufacturer's instructions using the NEBNext kit (E6200). Briefly, DNA was fragmented by sonication to a maximum of 300 bp. Next the ends of the fragments were repaired with a combination of fill-in reactions and exonuclease activity to produce blunt ends that were then tailed with an A-base. Illumina-specific Adaptors were ligated followed by removal of unligated adaptors using AMpure XP beads (Beckman Coulter). Finally a PCR with 12-15 cycles for both kits was performed to enrich final adaptor-ligated fragments. Quality and quantity were assessed on an Agilent Bioanalyzer Chip DNA 7500 or High Sensitivity. For all libraries, sequencing was performed on the MiSeq platform, using v2, 300-cycle reagent kits (Illumina).

treatment_protocol: Cells were not treated.

value: Purification with WGA resin


title: E95_Krox20DS


title: E95_Mark3


title: t2_H3K4me3_rep_2


title: E95_Krox20


title: E95repl_Krox20US


title: E95_Krox20US


title: t0_H3K4me3_rep_2


title: V59

city: New York

first: Spiro

last: Pantazatos

state: New York

address: 1051 Riverside Dr.

department: Psychiatry

country: USA

institute: Columbia University

library_source: transcriptomic

data_processing:
For each clinical sample, raw RNA-seq reads were aligned and mapped to the Ensembl GRCh37 human reference genome and assembled using Tophat v2.0.9 resulting in BAM files for each of 59 samples. Between 17,000,000 and 57,000,000 reads were obtained for each sample, and ~75–90% of reads were successfully mapped to the genome for each sample. Of these reads, ~10–15% aligned to multiple genomic loci.
For each BAM file resulting from Tophat2, read counts per gene were summarized using the ‘summarizeOverlaps’ (union mode) function in the GenomicAlignments R library and a transcript database derived from the GRCh37 human genome assembly.
Read counts per gene were normalized and written to csv file using the 'counts' function in DeSeq2 v1.6.3
For micro RNA samples, sequence adaptors were first trimmed i.e. using the command "cutadapt -b GATCGTCGGACTGTAGAACTCTGAAC -b TGGAATTCTCGGGTGCCAAGG", the resulting FastQ files were then converted to FASTA format and processed according to the Small RNA Analysis pipeline in CLC Genomics Workbench version 7.5 (http://www.clcbio.com/products/clc-genomics-workbench/ ) using default settings (i.e. mature length variants were allowed 2 additional or missing upstream and downstream base-pairs and 2 mismatched base-pairs, and alignment was strand-specific). Unique reads were extracted and counted and subsequently merged and annotated according to known miRNA species included in miRBase Release 21. Total counts for each miRNA (1,353 unique annotations with positive counts for one or more samples) were divided by the total library size to arrive at an expression value for each sample.
Genome_build: GRCh37 human genome assembly
Supplementary_files_format_and_content: counts_output.csv: Rows are gene ensemble IDs, columns are sample IDs

molecule: total RNA

organism: Homo sapiens

source_name: dorsal lateral prefrontal cortex (Brodmann Area 9)

extract_protocol:
RNA was extracted from dorsal prefrontal cortex (BA9) as previously described (Sibille E, Arango V, Galfalvy HC, Pavlidis P, Erraji-Benchekroun L, Ellis SP, et al. Gene expression profiling of depression and suicide in human prefrontal cortex. Neuropsychopharmacology. 2004;29(2):351–61) and according to the guidelines recommended by the NIH Roadmap Epigenomics Mapping Consortium (REMC). We used the Ambion’s mirVana miRNA isolation kit (#. AM1560, Life Technologies, Carlsbad, CA, USA) to isolate total RNA from postmortem brain tissue (Brodmann Area 9).
The coding RNA library was generated using the TruSeq Stranded Total RNA Sample Prep kit (Illumina, San Diego, CA, USA) which includes rRNA depletion and chemical fragmentation. Paired-end, strand specific sequencing for total RNA was performed on Illumina HiSeq 2500 with 100 bp read lengths.

tag: diagnosis

value: non-psychiatric controls (CON)

tag: age (yrs)

tag: Sex

value: Female

tag: rin

tag: pmi

tag: brain ph


title: E95_ElemB


title: V58

value: Male

value: dorsal lateral prefrontal cortex (Brodmann Area 9)


title: wild type retina sample 3 (WR3)

city: San Diego

first: Nadejda

last: Beliakova-bethell

state: CA

address: 9500 Gilman Dr, La Jolla

institute: University of California San Diego

data_processing:
Generating genome index using STAR-2.5.3a using the Danio_rerio.GRCz10.dna.toplevel.fa and Danio_rerio.GRCz10.89.gtf from ensemble ftp
Alignment using STAR-2.5.3a
Read counting using featureCounts v1.5.2
Generating normalized expression measurements
Quantifying differential expression
Genome_build: Danio_rerio.GRCz10.dna.toplevel.fa and Danio_rerio.GRCz10.89.gtf from ensemble ftp
For more analysis done, see https://gist.github.com/coralzhang/fc4e51609ff316486c1682feed6404a9/471afb15b7f7b230a38e4eedaadcf5f679412a07
Supplementary_files_format_and_content: text file with raw read counts or FPKM

organism: Danio rerio

source_name: retina

extract_protocol:
Total RNAs was extracted from the biological replicates by an optimized procedure that combined TRIzol (Life Technologies, Grand Island, NY) and RNeasy Micro kit (Qiagen, Valencia, CA). The quality of the extracted total RNAs were evaluated by Bioanalyzer electrophoresis (Agilent Technologies, Santa Clara, CA).
Libraries were prepared according to Illumina's instructions.

value: retina

value: wildtype

value: 5 dpf


title: E95_ElemC

value: WT


title: V57

value: DSM-IV major depressive disorder non-suicides (MDD)


title: wild type retina sample 2 (WR2)


title: L_H3K4me3_rep_2

value: wild type (Ler)


title: pde6c mutant retina sample 1 (PR1)

value: pde6c mutant


title: wild type retina sample 1 (WR1)

data_processing:
Generating genome index using STAR-2.5.3a using the Danio_rerio.GRCz10.dna.toplevel.fa and Danio_rerio.GRCz10.89.gtf from ensemble ftp
Alignment using STAR-2.5.3a
Read counting using featureCounts v1.5.2
Generating normalized expression measurements with cufflinks-2.2.1
Quantifying differential expression
Genome_build: Danio_rerio.GRCz10.dna.toplevel.fa and Danio_rerio.GRCz10.89.gtf from ensemble ftp
For more analysis done, see https://gist.github.com/coralzhang/fc4e51609ff316486c1682feed6404a9/471afb15b7f7b230a38e4eedaadcf5f679412a07
Supplementary_files_format_and_content: text file with raw read counts or FPKM


title: V86


title: V83

value: DSM-IV major depressive disorder suicides (MDD-S)


title: V85


title: V82


title: E95_ElemA


title: E95_DeltaC_H3K27ac_rep2

data_processing:
Chip-seq data were analysed using Eoulsan (Jourdren et al., Bioinformatics 2012) with extended support for ChIP-seq workflows (https://github.com/GenomicParisCentre/eoulsan/tree/branch-chip-seq).
First, reads were filtered out when they would not pass Illumina filters (module filterreads with option illuminaid). Files corresponding to technical replicates were merged (module technicalreplicatemerger, with option format=fastq), followed by trimming of the reads using Trim Galore ! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/; version 0.4.1 in module trimadapt, with cutadapt v1.8.1 and options: length=41, quality=20, error=0.1, stringency=8, and is.paired=yes for E8.5 data and is.paired=no for E9.5 data).
Mapping was performed using STAR (Dobin et al., Bioinformatics 2013) (version 2.4.0k in module mapreads with mapper.arguments=“--outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 1 --alignEndsType EndToEnd --alignMatesGapMax 2000 --outSAMunmapped Within”).
Further filters were applied to the mapped reads before conversion into BAM (module filtersam with removeunmapped=true; module sortsam; module rmdupgalax with is_sort=true; module sam2bam with compression.level=5).
BIGWIG files were created from the resulting BAM files using deepTools’ bamCoverage (Ramírez et al., Nucleic Acids Res. 2014) (version 1.6.0, with options: --binSize 1 --normalizeTo1x 200000000 --fragmentLength 200 --outFileFormat bigwig).
Genome_build: mm9
Supplementary_files_format_and_content: Normalized signal (bigwig), one per age per genotype per replicate.

extract_protocol:
Sequencing was performed on multiplexed samples using 50 bp single-end reads on an Illumina HiSeq system according to the manufacturer’s specifications.
The libraries were prepared with the NEXTflex ChIP-Seq Kit (Bioo Scientific).

treatment_protocol: ChIP experiments were performed as previously described (Vitobello et al.,Dev. Cell. 2011). Briefly, 10 embryos at E9.5 were dissected in cold PBS. Cell suspensions were obtained by passing them through a 21G needle fitted onto a 5ml syringe. The cells were cross-linked with 1% formaldehyde for 10 min and washed twice in PBS, 1 mM PMSF, 1 X PIC (Protease Inhibitor Cocktail). Sonication was performed on a Covaris S220 using the following programme: duty factor = 10, peak incident power = 140, cycles per burst = 200 during 600 seconds. 10 µg of chromatin was used for each IP using 3 µg of the following antibodies: anti H3K4me1 (C15410037, Diagenode) and anti H3K27ac (ab4729, Abcam) in RIPA buffer.

value: DeltaC


title: V56


title: V81


title: E95_DeltaC_H3K27ac_rep1


title: V55


title: V84


title: E95_DeltaC_H3K4me1_rep1


title: E95_DeltaC_H3K4me1_rep2


title: V53


title: V80


title: V52


title: pde6c mutant retina sample 3 (PR3)


title: pde6c mutant retina sample 2 (PR2)


title: V54


title: V79


title: E95_DeltaC_input_rep2


title: V76


title: V78


title: V77


title: E95_DeltaC_input_rep1


title: V74


title: V51


title: V73


title: E95_DeltaA_H3K27ac_rep2

value: DeltaA


title: V72


title: V49


title: V50


title: V70


title: V71


title: E95_DeltaA_H3K27ac_rep1

value: full embryo


title: V48


title: V67


title: E95_DeltaA_H3K4me1_rep2


title: V69


title: V68


title: V47


title: V64


title: V66


title: V65


title: V46


title: V45


title: E95_DeltaA_input_rep1


title: V75


title: V63


title: V62


title: V44


title: V61


title: E95_DeltaA_H3K4me1_rep1


title: V43


title: E95_WT_H3K27ac_rep1


title: V60


title: DHPM-thione inactive treatment rep1

city: Cambridge

first: Dan

last: Tardiff

state: Massachusetts

address: 790 Memorial Drive

institute: Yumanity Therapeutics

data_processing:
Sequenced reads were trimmed with "fastq_quality_trimmer -v -t 20 -l 25" to remove low quality bases.
Reads were mapped with  TopHat v2.1.1 with the following parameters: "tophat -p 8 --no-coverage-search --library-type=fr-secondstrand   --solexa1.3-quals  --segment-length 20 -I 2000   --no-novel-juncs    -G  Saccharomyces_cerevisiae.EF4.65.gtf ".  The GTF file used in th emapping was downloaded from ESEMBL: "ftp://ftp.ensembl.org/pub/release-65/gtf/saccharomyces_cerevisiae/"
We obtained reads counts per gene running htseq-count with the following parameters "--mode=intersection-strict --stranded=yes "
Gene count normalization and differential expression was performed with DEseq.
Genome_build: sacCer3, Apr2011
Supplementary_files_format_and_content: excel file with raws counts and DE-seq normalized counts.

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: Wild-type yeast (5 mL cultures) grown to log-phase in CSM-galactose were treated with 0.8 mM CQ, 20 mM 10{3,3,1}, 11, or a DMSO solvent control for 6 hours at 30°C. Cells were centrifuged, washed once with ice-cold water, and cell pellets flash frozen in liquid nitrogen prior to storage at -80°C.

extract_protocol:
RNA was extracted from yeast pellets using a hot acid phenol protocol
RNA-seq libraries from yeast total RNA (1 mg) were prepared for sequencing with the PrepX RNA-Seq Kit from IntegenX according to the standard protocol and sequenced on a HiSeq 2500.

tag: concentration

value: 20 uM

tag: rna type

value: total RNA

value: W303 with deletion of pdr1 and pdr3


title: DHPM-thione inactive treatment rep2

tag: strain


title: V42

value: non-psychiatric controls (CON)

value: Female

tag: tissue


title: E95_WT_H3K4me1_rep2

tag: age


title: V41

value: Male

value: dorsal lateral prefrontal cortex (Brodmann Area 9)


title: E95_WT_H3K4me1_rep1

tag: genotype


title: DHPM-thione active treatment rep1


title: known metal chelator treatment rep2


title: known metal chelator treatment rep1


title: V40


title: E95_WT_input_rep2


title: control treatment rep 2


title: control treatment rep 1


title: V39


title: E95_WT_H3K27ac_rep2


title: E95_WT_input_rep1


title: V38


title: ycs4S rec8 delta input rep3

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

data_processing:
Sequencing reads were mapped to SacCer3 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml). The one condition adjusted was to only collect information about reads that mapped to a single position in the genome.
Reads from two biological replicates were extended towards 3’ ends to a final length of 150 bp using MACS-2.1.0 (https://github.com/taoliu/MACS). MACS2 was also used to remove predicted PCR duplicates.
Bedgraph files from MACS2 were converted into variableStep wiggle files.
To create normalized wiggle files: Median coverage of all base positions in the ChIP sample was calculated. The coverage at each position was then divided by the calculated median. The same division was also performed for the input sample, followed by subtraction of the input from the ChIP sample at each position.
Genome_build: SacCer3
Supplementary_files_format_and_content: Wiggle file: ChIP enrichment at each base position

source_name: input for ycs4S rec8 delta mock rep1

growth_protocol: To induce synchronous meiosis, strains were inoculated at OD600 = 0.3 in BYTA medium for 16.5 hours at 30°C. Then cultures were washed twice with water and resuspended into SPO medium at OD600 = 1.9 at 30°C (details are described in (Blitzblau et al., 2012)).

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013).
Library preparation was performed using Illumina TruSeq DNA Sample Prep Kits v1 but adaptors were used at 1:20 dilution. Amplified ChIP DNA between 300 and 500bp was gel purified on 1.8% agarose and sequentially quantified using the Qubit assay HS kit as well as an Agilent 2100 Bioanalyzer. Fragments were sequenced on an Illumina HiSeq 2500 instrument using a 51-bp single-end sequencing protocol.

tag: meiotic time point

value: 3 hour


title: ycs4S rec8 delta mock rep1

source_name: ChIP for ycs4S rec8 delta input rep3

tag: antibody

value: Mock


title: E85_WT_H3K27ac_rep1

source_name: E8.5 full embryo

extract_protocol:
Sequencing was performed on multiplexed samples using 42 bp paired-end reads on an Illumina NextSeq according to the manufacturer’s specifications.
The libraries were prepared with the MicroPlex Library Preparation kit (Diagenode)

treatment_protocol: ChIP experiments were performed as previously described (Vitobello et al.,Dev. Cell. 2011). Briefly, 20 embryos at E8.5 were dissected in cold PBS. Cell suspensions were obtained by passing them through a 21G needle fitted onto a 5ml syringe. The cells were cross-linked with 1% formaldehyde for 10 min and washed twice in PBS, 1 mM PMSF, 1 X PIC (Protease Inhibitor Cocktail). Sonication was performed on a Covaris S220 using the following programme: duty factor = 5, peak incident power = 140, cycles per burst = 200 during 480 seconds. 5 µg of chromatin was used for each IP using 3 µg of the following antibodies: anti H3K4me1 (C15410037, Diagenode) and anti H3K27ac (ab4729, Abcam) in RIPA buffer.

value: WT


title: V37

value: DSM-IV major depressive disorder non-suicides (MDD)


title: E85_WT_H3K27ac_rep2


title: ycs4S rec8 delta anti-Red1 rep2

source_name: ChIP for ycs4S rec8 delta input rep2


title: ycs4S rec8 delta anti-Hop1 rep2


title: ycs4S rec8 delta anti-Hop1 rep1

source_name: ChIP for ycs4S rec8 delta input rep1


title: DHPM-thione active treatment rep2


title: ycs4S rec8 delta anti-Red1 rep1


title: V35


title: ycs4S rec8 delta input rep1

description:
H7661_Red1_ChIP_reps.wig
H7661_Hop1_ChIP_reps.wig

source_name: input for ycs4S rec8 delta anti-Red1 rep1 and ycs4S rec8 delta anti-Hop1 rep1


title: E85_WT_H3K4me1_rep2


title: V36


title: E85_WT_H3K4me1_rep1


title: V34


title: ycs4S anti-Hop1 rep2

source_name: ChIP for ycs4S input rep2


title: E95_DeltaA_input_rep2


title: ycs4S anti-Hop1 rep1

source_name: ChIP for ycs4S input rep1


title: ycs4S anti-Red1 rep2


title: V33


title: ycs4S anti-Red1 rep1


title: E85_WT_input_rep2


title: V31


title: ycs4S rec8 delta input rep2

source_name: input for ycs4S rec8 delta anti-Red1 rep2 and ycs4S rec8 delta anti-Hop1 rep2


title: 14055-MM_146_8h

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
base calling: Casava1.8
read alignment, RNA-seq data: TopHat 1.4.1
bedgraph track generation: custom-written python script
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)

molecule: polyA RNA

extract_protocol:
Mice were sacrificed via CO2 euthanasia. Femur and tibia bones were harvested and bone marrow flushed with DMEM. Collected cells pelleted and resuspended in 10mL of 1X Red blood Cell (RBC) Lysis buffer for 5min. Cells were resuspended in 20mL of fresh DMEM. 2.5e6 bone-marrow cells plated in a 15-cm TC dish in 20mL of BMDM Media (DMEM, 20% FBS, 30% L929 condition media, and 1% Pen/Strep) and grown at 5% CO2 and 37°C. BMDM media was completely replaced on day 3. On Day 6, BMDMs were replated at a concentration of 1e6 cells per well in a 6 well plate and incubated for 16hr. Stimulations and treatments began at day 7. Stimulated cells were lysed using an RNAeasy kit (Qiagen) with DNAseI digestion (Qiagen) as per manufacturer’s protocol. RNA-seq libraries were prepared from polyA+ selected RNA using the TruSeq RNA Sample Preparation kit at the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech. Libraries were sequenced on the Illumina HiSeq 2500 generating single-end 50 bp reads.
TruSeq RNA Sample Preparation Kit

value: bone marrow

tag: cell type

value: macrophage

value: miRNA-146 KO

tag: lps stimulation


title: rec8 delta anti-Red1 rep1

description:
reanalysis of: GSM1695731
H7660_H7772_Red1_ChIP_reps.wig

source_name: ChIP for rec8 delta input rep1


title: Wild type anti-Hop1 rep1

source_name: ChIP for Wild type input rep3


title: Wild type anti-Red1 rep2

description:
reanalysis of: GSM1695719
H119_Red1_ChIP_reps.wig

source_name: ChIP for Wild type input rep2


title: V27


title: Wild type anti-Red1 rep1

description:
reanalysis of: GSM1695718
H119_Red1_ChIP_reps.wig

source_name: ChIP for Wild type input rep1


title: 14053-MM_155_8h

value: miRNA-155 KO


title: E85_WT_input_rep1


title: ycs4S input rep1

description:
H7011_Red1_ChIP_reps.wig
H7011_Hop1_ChIP_reps.wig

source_name: input for ycs4S anti-Red1 rep1 and ycs4S anti-Hop1 rep1


title: V32

source_name: dorsal lateral prefrontal cortex (Brodmann Area 9)


title: Wild type input rep3

source_name: input for Wild type anti-Hop1 rep1


title: rec8 delta anti-Hop1 rep2

source_name: ChIP for rec8 delta input rep2


title: 14057-MM_dko_8h

value: miRNA-155/miRNA 146 KO


title: 14051-MM_WT_8h

value: wildtype


title: V25


title: rec8 delta anti-Hop1 rep1


title: V24

value: DSM-IV major depressive disorder suicides (MDD-S)


title: V30


title: rec8 delta input rep1

description:
reanalysis of: GSM1695729
H7660_H7772_Red1_ChIP_reps.wig
H7660_H7772_Hop1_ChIP_reps.wig

source_name: input for rec8 delta anti-Red1 rep1 and rec8 delta anti-Hop1 rep1


title: 14054-MM_146_0h


title: V28


title: V23


title: Hey RAB25 RFP14 exp2

city: Houston

first: Funda

last: Meric-Bernstam

state: TX

address: 1400 Pressler St.

department: Invest. Cancer Therapeutics

institute: The University of Texas MD Anderson Cancer Center

data_processing:
STAR 2.5.2b for reads alignment
cufflinks 2.2.1 for reads quantification
Genome_build: hg19
Supplementary_files_format_and_content: fpkm produced by cufflinks

source_name: ovarian cancer cells

growth_protocol: Hey human ovarian cancer cell lines were obtained originally from ATCC and maintained  in RPMI-1640  media  supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Samples were snap frozen in liquid nitrogen at the time of harvest and total RNA was isolated from each condition by Norgen Total RNA Purification Kit (Norgen Biotek Corp, ON Canada), quantified by Picogreen (Invitrogen), and quality was assessed using a 2200 Tapestation (Agilent). RNA from each biological replicate (500 ng) was converted to double-stranded cDNA using Ovation RNA-Seq System V2 kit (Nugen), and cDNA was sheared by sonication with the following conditions: Peak Incident Power = 175, Duty Cycle = 20%, Intensity = 5, Cycles per burst = 200, for a time = 120 seconds using Covaris E220 sonicator (Covaris). To ensure the proper fragment size, samples were checked on a TapeStation using the DNA High Sensitivity kit (Agilent).
The sheared DNA proceeded to library preparation using KAPA library prep hyper kit (KAPA) following the “with beads” manufacturer protocol. Briefly, this protocol consists of 3 enzymatic reactions for end repair, A-tailing and adaptor ligation, followed by barcode insertion by PCR using KAPA HiFi polymerase (6 cycles). PCR primers were removed by using 1.8x volume of Agencourt AMPure PCR Purification kit (Agencourt Bioscience Corporation). At the end of library preparation, samples were analyzed by TapeStation to verify correct fragment size and the absence of extra bands. Samples were quantified using KAPA qPCR quantification kit.
Equimolar amounts of DNA were pooled for capture (2-6 samples per pool). Whole exome biotin labeled probes from Roche Nimblegen (V3) were used following manufacture’s protocol for the capture step. Briefly, DNA was pooled (2-6 samples), dried, resuspended with capture reagents and probes, and incubated at 47°C on a thermocycler with a heated lid (57°C) for 64-74 hours. Targeted regions were recovered using streptavidin beads, streptavidin-biotin-probe-target complexes were washed, and another round of PCR amplification was performed according to manufacturer’s protocol. The quality of each captured sample was analyzed by TapeStation using the DNA High Sensitivity kit, and the enrichment was accessed by qPCR using specific primers designed by Roche Nimblegen. The minimum cutoff for the enrichment was 50-fold.The captured libraries were sequenced on a HiSeq 2000 (Illumina Inc., San Diego, CA, USA) on a version 3 TruSeq paired-end flowcell at a cluster density between 700 – 1000 K clusters/mm2 according to manufacturer’s instructions. Sequencing was performed on a HiSeq 2000 for 2 × 100 paired end reads with a 7 nt read for indexes using Cycle Sequencing v3 reagents (Illumina).

treatment_protocol: Hey ovarian cancer cells with stable overexpression of RAB25 (10 cm plate, 70-80% confluent) were treated with stapled peptide RFP14 (10 μM) or the equivalent amount of DMSO in serum free media  (RPMI) overnight, followed by stimulation with 5% FBS for 8 hours. pcDNA3 mock vector expressing HEY ovarian cancer cells labelled as HeyCont were similarly treated with DMSO overnight and stimulated with 5% FBS for 8 hours in parallel.

tag: treatment

tag: replicate


title: V21

tag: diagnosis

tag: age (yrs)


title: Hey RAB25 DMSO exp1


title: 14052-MM_155_0h


title: Hey RAB25 RFP14 exp1


title: Hey RAB25 DMSO exp2


title: Hey Cont DMSO exp2

value: DMSO


title: Wild type anti-Hop1 rep2

description:
reanalysis of: GSM1695721
H119_H6408_Hop1_ChIP_reps.wig

source_name: ChIP for Wild type input rep4


title: ycs4S input rep2

source_name: input for ycs4S anti-Red1 rep2 and ycs4S anti-Hop1 rep2


title: Wild type input rep4

description:
reanalysis of: GSM1695720
H119_H6408_Hop1_ChIP_reps.wig

source_name: input for Wild type anti-Hop1 rep2


title: V26

tag: Sex

tag: rin


title: V15

tag: pmi

tag: brain ph


title: 14056-MM_dko_0h


title: V29


title: R1881_mTOR_ChIP-seq.bam.bigwig

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

institute: Université Laval

description: genomic DNA enriched following mTOR chromatin immunoprecipitation

data_processing:
Sequences were aligned to the human genome database (Hg19) using BWA v0.5.9 (Li and Durbin, 2009)
Significant DNA binding (peak) was determined using MACS v1.4.1 software (Zhang et al., 2008).
Peak annotation, tag directory, bed file generation, and de novo motif discovery were performed with the Homer package v3.18.
Genome_build: hg19
Supplementary_files_format_and_content: data are presented as BedGraph and annotated peak lists in excel from the merged of two samples for control condition and two samples for R1881-treated cells.

source_name: LNCaP human prostate cancer cell line treated with R1881 for 48h

growth_protocol: LNCaP cells were seeded in RPMI media with no phenol red and with charcoal-stripped serum (no steroids) . 48h later, cell were treated with 10nM R1881 or vehicle (EtOH) for 48h before crosslink.

extract_protocol:
After 48h treatment with vehicle or R1881 nuclei were isolated and subjected to chromatin immunoprecipitation. Following mTOR ChIP, genomic DNA was purified with QIAGEN DNA extraction kit.
Libraries were performed at the Génome Québec Innovation Centre (McGill University) using standard protocol for HiSeq - Illumina Single reads 50bp sequencing lane

treatment_protocol: Cells were treated for 48h with R1881 (10nM) or vehicle (EtOH).

tag: cell line

value: LNCaP prostate tumor cell line

tag: chip antibody

value: mTOR


title: Wild type input rep2

description:
reanalysis of: GSM1695717
H119_Red1_ChIP_reps.wig

source_name: input for Wild type anti-Red1 rep2

tag: strain


title: Wild type input rep1

description:
reanalysis of: GSM1695716
H119_Red1_ChIP_reps.wig

source_name: input for Wild type anti-Red1 rep1


title: 14050-MM_WT_0h

tag: tissue


title: V22

value: Female


title: THP-1, VDR 24 h 1,25(OH)2D3 replicate 2

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: Chromatin IP against VDR

data_processing:
Alignment to hg19 using Bowtie v1.0 parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best
Peak discovery using MACS2 parameters: -m 5 50 –bw 150
Genome_build: hg19
Supplementary_files_format_and_content: tdf

source_name: human monocytic cell line THP-1

growth_protocol: THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
proteins were crosslinked with formaldehyde to DNA, then VDR-bound fragments were pulled down by chromatin immunoprecipitation
ChIP-seq library was prepared from 5-10 ng ChIP DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) per manufacturer's protocol

treatment_protocol: Treated with EtOH or 24 h 100 nM 1,25(OH)2D3

value: monocytic cell line THP-1

tag: time

value: VDR (Cell Signaling Technologies CST 12550)


title: THP-1, VDR 24 h 1,25(OH)2D3 replicate 3

description: Chromatin IP against VDR


title: V20

value: Male

value: dorsal lateral prefrontal cortex (Brodmann Area 9)


title: H3K27me3_WT_r2

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description:
ChIP-Seq
GA6866-GCCAAT-ChIP-seq-mouse-WT-H3K27me3.sam_noDup-GA6872-CTTGTA-ChIP-seq-mouse-MLL4-KO-H3K27me3.sam_noDup-W200-G400-E10.scoreisland.sicerdiff.gz

data_processing:
Basecalls performed using CASAVA 1.0
Short reads were mapped to the mouse genome by using Bowtie2 with default parameters (PMID: 22388286 ). Later analysis excluded short reads mapped to multiple genomic positions and kept only one read for each genomic site when it received multiple reads.
ChIP-Seq read enriched regions were identified with SICER (PMID: 19505939) with a window size of 200 bps and a gap size of 400 bps27. A conservative set of MLL4 binding sites were identified with stringent parameters and input control: E value = 1,000 and FDR = 0.001. To have a conservative prediction on genomic regions that were not bound by MLL4, we increased the E-value for MLL4 peak call until the ChIP-Seq signal of the additionally called peaks was indistinguishable from the input signal; for this purpose, non-stringent parameters were set: E value = 100,000 and FDR = 0.05. ChIP-Seq peaks for histone modifications H3K4me1, H3K27me3 and H3K27ac without inputs were called with an E-value of 10. Differential H3K4me1 peaks between Mll4 deletion and control cells were predicted by EdgerR (FDR < 0.001; FC > 2) (PMID: 19910308).
The mRNA expression level of a gene is quantified by RPKM (reads per kilo-base of exon model per million reads; PMID 18516045) with in-house script.
For Hi-C data analysis, in-house scripts were used to exclude pair-end tags/reads (PETs) with each end mapped to different chromosomes or showing low mapping quality (MAPQ < 10). For PETs mapped to exactly the same positions, only one PET was kept. To speed up calculation, we divided the genome into r = 1K bps bins to generate an interaction matrix to record the number of PETs linking any two genomic bins for each sample where HiC data was generated; PETs spanning below 1K bps and over 2M bps were excluded from the counting.
Genome_build: mm9
Supplementary_files_format_and_content: *rpkm.gz: zipped text file for gene expression. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
Supplementary_files_format_and_content: *.sicerdiff.gz: zipped peak file reacording differential peak call from SICER. Columns from left to right denonte: chrom, start, end,  Readcount_A,  Normalized_Readcount_A, ReadcountB, Normalized_Readcount_B, Fc_A_vs_B, pvalue_A_vs_B, FDR_A_vs_B, Fc_B_vs_A, pvalue_B_vs_A, FDR_B_vs_A.
Supplementary_files_format_and_content: *FDR0.05.gz or *FDR0.001.gz: zipped peak file recording peak call from SICER with input control. Columns from left to right denote: chrom, start, end, chipseq_island_read_count, control_island_read_count, p-value, fold-change, and FDR.
Supplementary_files_format_and_content: *.scoreisland.gz: zipped peak file recoding peak call from SICER without control. Columns from left to right denote: chrom, start, end, score.
Supplementary_files_format_and_content: *.III.gz: zipped txt file recording # of Hi-C PETs linking two 1K-bp regions. Column from left to right: chrom, start of one region, start of the other region, number of PETs.
Supplementary_files_format_and_content: *.edger3.gz prediction from edger3. Columns from left to right: peak region, logFC, logCPM, Pvalue and FDR

source_name: Naive CD4 T cells

extract_protocol:
For RNA-Seq: the total RNAs were purified using Qiagen's miRNeasy micro kit (Qiagen cat# 217084) plus Qiagen’s DNase set (Qiagen cat# 79254) for on-column DNase digestion option. PolyA-tailed RNAs were purified from pure total RNA using Dynabeads® mRNA DIRECT™ Kit (ambion life technologies cat# 61012). ChIP and Hi-C follow the protocols described previously in (PMID: 17512414) and (PMID: 25497547 ) with minor modifications.
Library constructions for ChIP-Seq, RNA-Seq and Hi-C follow the protocols described previously in (PMID: 17512414), (PMID: 19528076) and (PMID: 25497547 ) with minor modifications.

value: lymph nodes

value: wild type

value: H3K27me3 (07-449, Millipore)


title: THP-1, VDR 24 h 1,25(OH)2D3 replicate 1

description: Chromatin IP against VDR


title: V18


title: Input_mTOR_ChIP-seq.bam.bigwig

description: input genomic DNA from LNCaP cells

source_name: Input DNA from LNCaP prostate cancer cell line


title: V16


title: THP-1, VDR 24 h EtOH replicate 1

description: Chromatin IP against VDR

value: EtOH


title: Control_mTOR_ChIP-seq.bam.bigwig

source_name: LNCaP human prostate cancer cell line treated with vehicle for 48h

value: control


title: H3K27ac_WT

description:
ChIP-Seq
GA4747-1-ATCACG-naivd-CD4-MLL4flflCreNeg-H3K27ac-m1_0_0_noDup-GA4748-2-CGATGT-naive-CD4-MLL4flflCrePos-H3K27ac-m1_0_0_noDup-W200-G400-E10.scoreisland.sicerdiff.gz

value: H3K27ac (ab4729, Abcam)


title: V13

value: non-psychiatric controls (CON)


title: V9


title: V17


title: Hey Cont DMSO exp1


title: Dnase_WT

description:
Dnase-Seq
GA5725


title: V14


title: V8


title: THP-1, VDR 24 h EtOH replicate 3

description: Chromatin IP against VDR


title: V19


title: V12


title: THP-1, VDR 24 h EtOH replicate 2

description: Chromatin IP against VDR


title: H3K4me1_crispr_r2

description:
ChIP-Seq
GA7832-GCCAAT-ChIPseq-mouse-8725-H3K4me1-2.sam_noDup-GA7828-CGATGT-ChIPseq-mouse-8723-H3K4me1-2.sam_noDup-W200-G400-E10.scoreisland.sicerdiff.gz

value: lymph nodes + spleen

value: KO a MLL4 binding site

value: H3K4me1 (ab8895, Abcam)


title: THP-1, VDR 2 h EtOH replicate 3

description: Chromatin IP against VDR

value: 2 h


title: H3K4me1_crispr_ctrl_r2

value: Control for KO MLL4 binding site


title: H3K27me3_KO_r2

value: Mll4 KO


title: V11


title: H3K4me1_KO_r2

description:
ChIP-Seq
GA7201-ATCACG-ChIP-seq-mouse-Naïve-WT-H3K4me1_noDup-GA7202-CGATGT-ChIP-seq-mouse-Naïve-MLL4-KO-H3K4me1_noDup-W200-G400-E10.scoreisland.sicerdiff.gz


title: V10

value: DSM-IV major depressive disorder suicides (MDD-S)

value: Female


title: H3K27ac_KO


title: H3K27me3_KO_r1

description:
ChIP-Seq
GA7211-GGCTAC-ChIP-seq-mouse-Naïve-WT-H3K27me3_noDup-GA7212-CTTGTA-ChIP-seq-mouse-Naïve-MLL4-KO-H3K27me3_noDup-W200-G400-E10.scoreisland.sicerdiff.gz


title: H3K27me3_WT_r1


title: H3K4me1_WT_r1

description:
ChIP-Seq
GA6861-ATCACG-ChIP-seq-mouse-WT-H3K4me1.sam_noDup-GA6867-CAGATC-ChIP-seq-mouse-MLL4-KO-H3K4me1.sam_noDup-W200-G400-E10.scoreisland.sicerdiff.gz


title: THP-1, VDR 2 h 1,25(OH)2D3 replicate 3

description: Chromatin IP against VDR

value: monocytic cell line THP-1

value: VDR (Cell Signaling Technologies CST 12550)


title: HiC_KO_r2

description:
Hi-C
GA7715_r799l6_HiC.bin1Kmin5Kmax2M.III.gz

value: lymph nodes


title: H3K4me1_crispr_r1

description:
ChIP-Seq
GA7831-ACAGTG-ChIPseq-mouse-8725-H3K4me1-1.sam_noDup-GA7827-ATCACG-ChIPseq-mouse-8723-H3K4me1-1.sam_noDup-W200-G400-E10.scoreisland.sicerdiff.gz


title: V5

value: Male

value: dorsal lateral prefrontal cortex (Brodmann Area 9)


title: H3K4me1_crispr_ctrl_r1

value: Control for KO a MLL4 binding site


title: V4


title: THP-1, VDR 2 h 1,25(OH)2D3 replicate 1

description: Chromatin IP against VDR


title: V7


title: H3K4me1_WT_r2

value: wild type


title: THP-1, VDR 2 h 1,25(OH)2D3 replicate 2

description: Chromatin IP against VDR


title: HiC_WT_r1

description:
Hi-C
GA6875_CD4T_HiC.bin1Kmin1Kmax2M.III.gz


title: THP-1, VDR 2 h EtOH replicate 2

description: Chromatin IP against VDR

value: EtOH


title: HiC_WT_r2

description:
Hi-C
GA7713_r799l6_HiC.bin1Kmin5Kmax2M.III.gz


title: RNA-seq.shTRIM28_rep1

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0, with "-k 10 --non-deterministic", RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MCAS 1.3.7; Scores represent the ChIP-seq tag numbers, RNA-seq reads count were calculated using HTSeq 0.6.1p1

source_name: MCF7 cells

growth_protocol: The breast cancer cell line MCF7 was obtained from the American Type Culture Collection (ATCC) and grown in suggested media conditions. EZH2 and TRIM28 knockdown was achieved by using stable pGIPZ short-hairpin interfering RNA in lentivirus (clone: V2LHS_17507, Open Biosystems). A lentiviral scrambled plasmid was used as control for transfection and virus packaging. The stable EZH2 and TRIM28 depleted clones were maintained with Puromycin (Sigma).

extract_protocol:
For ChIP-seq, MCF7 lysates with were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-seq, RNA was harvested using Trizol reagent from control, EZH2, and TRIM28 depleted MCF7 cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TRIM28 Knock Down


title: HiC_WT_r3

description:
Hi-C
GA7714_r799l6_HiC.bin1Kmin5Kmax2M.III.gz


title: V3

value: non-psychiatric controls (CON)


title: THP-1, VDR 2 h EtOH replicate 1

description: Chromatin IP against VDR


title: V1


title: V2


title: RNA-seq.shTRIM28_rep2


title: 400-2

city: Austin

first: Ningling

last: Kang

state: MN

address: 801 16th AVE NE

department: Hormel Institute

institute: University of Minnesota

data_processing:
Illumina Real time Analysis and  CASAVA software 1.8.2 were used for basecalling.
Raw reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.  Quality control checks on raw sequence data for each sample were performed with FastQC.  Read mapping was performed via Bowtie (v2.2.4.0) using the Human genome (hg19) as reference
Raw reads for each gene generated from the HiSeq2500 sequencer were subjected to statistical analysis using the edgeR package and cuffdiff2 package based on two selection criteria (fold change ≥ 2 & FDR < 0.05, and fold change ≥ 1.5 & FDR < 0.01).  The overlap of these four criteria was used to identify a list of 1196 genes.  This list was then subjected to Ingenuity Pathway Analysis.  Heatmaps were generated by the DeSeq2 package utilizing raw read counts as input.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for all samples

source_name: Liver hepatic stellate cells

growth_protocol: To prepare polyacrylamide hydrogels with stiffness of 400 Pa and 25600 Pa, acrylamide/bisacrylamide with variable ratios were mixed with TEMED, APS and SBS for polymerization. Each gel mixture was then immediately pipetted on the center of a coverslip that was previously washed with 0.4% MPS solution for salinization.  Another coverslip, previously treated with SurfafSil to form hydrophobic surface, was placed on top of the gel solution.  2 minutes later, the top coverslip was removed and the gel was treated with dopamine hydrochloride solution (1 mg/ml in 50 mM HEPES, pH 8.5) for 20 mins followed by incubation with collagen I solution (0.05 mg/ml in PBS, pH 7.4) for 30 mins.  After rinsing with PBS and sterilization by microwave heating, the polyacrylamide gels were then placed in a 6-well cell culture plate for HSCseeding.  Cells were cultured in DMEM medium supplemented with 10% FBS and antibiotics and they were harvested 2 days later for RNA isolation.

extract_protocol:
RNA samples were isolated from HSCs using a RNeasy Micro Kit (Qiagen, 74004) and RNase-free DNase 1 was used to treat the sample to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stiffness stimulation

value: 400 Pa polyacrylamide hydrogel

value: liver

value: stellate cells


title: HiC_KO_r1

description:
Hi-C
GA6876_CD4T_HiC.bin1Kmin1Kmax2M.III.gz


title: V6

source_name: dorsal lateral prefrontal cortex (Brodmann Area 9)


title: RNA-seq.shCtrl_TRIM28_rep2

value: Control


title: MLL4_r2

description:
ChIP-Seq
GA6843-TTAGGC-ChIPSeq-mouse-WT-MLL4-1-kz775kz746_noDup-W200-G400-E10.scoreisland.gz

value: MLL4 (PMCID:PMC3869375)


title: RNA-seq.shEZH2_rep2

value: EZH2 Knock Down


title: RNA-seq.shEZH2_rep1


title: H3K4me1_KO_r1

value: Mll4 KO

value: H3K4me1 (ab8895, Abcam)


title: RRBS_mESC_RA_WT_2

city: Rehovot

first: Moshe

last: Oren

address: 234 Herzl St.

country: Israel

institute: The Weizmann Institute of Science

description: processed data file: SingleCpG_mESC_RRBS_oxRRBS.txt.gz

data_processing:
The final RRBS and OX-RRBS libraries were sequenced using the Illumina Hiseq2500 to obtain 100 bp paired-end sequencing reads. Adapter trimming and quality filtering was performed with the trim_galore software using default parameters for RRBS analysis. BSMAP was used for read alignment (using genome build mm9) and extraction of single base-resolution methylation levels. Integration of biological replicates, 200 bp tiles and DMRs were calculated with the MethylKit package using a minimum coverage of 10, methylation difference of 30%, and q-value <= 0.01. Total methylation levels (5mC+5hmC) of single CpGs and 200bp tiles were obtained from the RRBS data. 5mC levels were obtained accordingly from the OX-RRBS data, and 5hmC levels were calculated as (Total - 5mC) levels. Only CpGs that were covered by all biological replicates and that had 5hmC>=0 values were used for the analysis
Genome_build: mm9
Supplementary_files_format_and_content:
'200bpTiles_Unified.txt.gz' containing genomic location tile, Total, 5hmc, 5hmc values of all conditions
'SingleCpG_mESC_RRBS_oxRRBS.txt.gz' containing genomic location CpG, Total and 5mc values of all mESC conditions

extract_protocol:
129s-Trp53tm2Tyj/J p53+/- (Jackson Laboratory, Mt Desert Is., ME, USA) heterozygous p53+/- male and female mice were time mated. E2.5 morulas were isolated from the uteri of female mice and allowed to attach to irradiated MEF feeder layers in 2i medium. Subsequently, 2i medium was changed daily. For differentiation experiments, feeders were depleted by 30–45 minutes of incubation on 0.1% gelatin, followed by gentle aspiration of purified mESCs. For RA-induced differentiation, feeder-depleted cells were seeded on gelatin and transferred to differentiation medium containing for 16 hours followed 1μM retinoic acid (RA). RA was replenished daily for 4 days.
Reduced representation bisulfite sequencing (RRBS) was performed according to a previously published protocol  (Boyle, P. et al. 2012).
Briefly, genomic DNA was isolated using the PureLink genomic DNA kit (Invitrogen) according to the manufacturer’s instructions and subjected to enzymatic digestion by MSPI (New England Biolabs) for 16 hours. Klenow polymerase (New England Biolabs) was then added to each sample for end filling and poly-A tailing, followed by Truseq adapter ligation (Illumina). The library was then pooled and subjected to either bisulfite treatment as in the RRBS protocol or to an OX-RRBS protocol using the CEGX kit (Cambridge Epigentix). Validation of oxidation efficiency was done with the provided DNA sequences that were also A tailed and adapter ligated.

tag: age

tag: genotype/variation

value: WT

tag: tissue/cell type

value: mouse embryonic stem cells (mESC)

tag: cell state

value: induced to differentiate by RA


title: RRBS_mESC_RA_WT_3


title: RRBS_mESC_RA_WT_5


title: RRBS_mESC_RA_WT_4


title: 25600-1

value: 25600 Pa polyacrylamide hydrogel

tag: cell type


title: 25600-3


title: 400-1


title: oxRRBS_mESC_RA_WT_2


title: RRBS_mESC_NT_WT_4

value: naïve state


title: oxRRBS_mESC_RA_WT_4


title: RNA-seq.shCtrl_TRIM28_rep1

tag: treatment


title: oxRRBS_mESC_RA_WT_1


title: RRBS_mESC_NT_WT_5


title: RNA-seq.shCtrl_EZH2_rep2


title: 25600-2


title: RRBS_mESC_NT_WT_2


title: RNA-seq.shCtrl_EZH2_rep1


title: oxRRBS_mESC_RA_WT_3


title: oxRRBS_mESC_NT_WT_4


title: oxRRBS_mESC_NT_WT_5


title: RRBS_mESC_RA_WT_1


title: HeLaS3_STAP-processed_TFF2

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

description:
polyA+ RNA
PCR amplified cDNA (STAP-seq transcript)

data_processing:
In short, STARR-seq single- and paired-end Illumina sequencing reads were mapped in fasta format to the human genome (hg19), only considering the regular chromosomes 1-22, and X using bowtie version 0.12.9 using bowtie options -v 3 -m 1 --best --strata (Langmead et al. 2009). Only uniquely mapped reads with up to 3 mismatches and a maximal insert size of 2 kb for paired-end datasets were considered. Genome coverage bigwig files were generated using all reads with bedtools genomecov version 2.19.1 (Quinlan and Hall 2010) and normalized to reads per million (r.p.m.). For both genome-wide STARR-seq and input libraries, reads from two biological replicates were combined. For more specific details, please see our methods section.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized coverage tracks (reads per million) are in bigWig foramat. All supplemental tables are in tab separated value format.
Supplementary_files_format_and_content: The differential_peaks_inhibitor_vs_no-inhibitor_supp.table3.tsv contains combined (see methods) peak locations, log2 fold changes (with-inhibitor over without-inhibitor), FDR adjusted enriched p-values, FDR adjusted depleted p-values, nearest TSS Ensembl ID (version 75) from peak edges, nearestTSS common name, with-inhibitor peak ranks, and without-inhibitor peak ranks (na means that this peak is specific to the other condition.
Supplementary_files_format_and_content: The peaks_inhibitor_correctedEnrichment4_supp.table3.tsv contains genome wide STARR-seq with inhibitor treatment peak locations, peak ranks, corrected enrichments, p-values, summit chromHMM annotation, peak summit genomic annotation, nearest TSS Ensembl ID (version 75) from peak edges, nearestTSS common name, flag columns for peaks with a DHS binomial p-values < 0.05 for HeLaS3 and other cell lines (see methods), and a flag column for closed peaks in HeLaS3 and other cell lines that contains a transposable element of enriched families.
Supplementary_files_format_and_content: The shortlisted_regions_inhibitor_supp.table3.tsv file contains genome wide STARR-seq with inhibitor treatment short listed region locations, enrichments, p-values, summit chromHMM annotation, peak summit genomic annotation, nearest TSS Ensembl ID (version 75) from peak edges, nearestTSS common name.
Supplementary_files_format_and_content: The peaks_no-inhibitor_correctedEnrichment4_supp.table3.tsv contains genome wide STARR-seq without inhibitor treatment peak the locations, peak rank, corrected enrichment, p-value, summit chromHMM annotation, peak summit genomic annotation, nearest TSS Ensembl ID (version 75) from peak edges, nearestTSS common names.

growth_protocol: Cells were cultured in DMEM (Gibco; cat. no. 52100-047), supplemented with 10% heat-inactivated FBS (Sigma; cat. no. F7524) and 2 mM L-glutamine (Sigma; cat. no. G7513) at 37°C in a carbon dioxide (CO2) enriched atmosphere (95% air and 5% CO2). Cells were harvested at 80% confluency by removing the growth medium, washing with 1x PBS, treating with 0.25% Trypsin-EDTA (Gibco; cat. no. 25200-056) until dispersion of the cell layer and resuspension in complete medium.

extract_protocol: 6h after electroporation, total RNA was extracted using the RNeasy Maxi kit (Qiagen; cat. no. 75162), followed by polyA+ RNA isolation using Invitrogen Dynabeads Oligo(dT)25 (scaling up the manufacturer’s protocol accordingly; cat. no. 61005) and DNase treatment with Ambion Turbo DNase (cat. no. AM2239) at a concentration of at most 200 ng/µl for 30 minutes (min) at 37°C. The reactions were then subjected to Qiagen RNeasy MinElute reaction clean-up (cat. no. 74204), for Turbo DNase inactivation and RNA concentration.

treatment_protocol: For STARR-seq screens with inhibitor treatment, the PKR (C16, Sigma; cat. no. I9785-5MG) and TBK1/IKK inhibitors (BX-795 hydrochloride, Sigma; cat. no. SML0694-5MG) were added to the electroporated cells directly after resuspension in complete growth medium at a final concentration of 1 µM per inhibitor. Note: Both inhibitors are kept at -20ºC as 10 mM stocks in DMSO.

value: cervical adenocarcinoma cell line

tag: drug treatment

value: no drug

tag: experimental procedure

value: STAP-seq


title: HeLaS3_STAP-processed_mCP


title: RRBS_mESC_RA_p53_KO_4


title: RRBS_mESC_NT_WT_1


title: oxRRBS_mESC_NT_WT_1


title: ChIP-seq.Input


title: ChIP-seq.TRIM28

tag: antibody


title: oxRRBS_mESC_NT_WT_2


title: HeLaS3_STAP-processed_SULT1C2


title: oxRRBS_mESC_NT_WT_3


title: I_H3K27me3_rep_1

source_name: inflorescence

extract_protocol:
Formaldehyde cross-linking and extraction of nuclei was performed as described in Carles and Fletcher (2009) with the following modifications: infiltration time was prolongated (6 min and 24 min), filtration of the extract after grinding was performed through 75 µm and 50 µm nylon meshes and sonication was done for 13x 30 sec on, 1 min off, position H (this longer sonication was only performed for biological replicate 2). Immunoprecipitation reactions were set up as described in Carles and Fletcher (2009) except that 15 µg of cauliflower and 10 µg of wild type chromatin was used and the chromatin was incubated with 5 µl of the antibody alone for 5 hours prior to addition of Protein A Agarose beads without salmon sperm DNA (Millipore). Washing of the ChIP reaction was performed using binding/wash buffer as described in Carles and Fletcher (2009) but for four times 10 min at 4°C and once 10 min at room temperature (RT).   Elution and reverse cross-linking was performed as described in Kaufmann et al. (2010) except that the elution was done by vortex mixing for 1 min at RT and input samples (1/3 of the chromatin used for one ChIP sample) were brought to the same volume by adding elution buffer and Tris pH9 in the same ratio as to the ChIP samples.  Reverse cross-linked samples were purified using the MinElute Reaction Cleanup Kit (Quiagen) and DNA was eluted in 30 µl Elution buffer.  For biological replicate 2, three technical replicates of ChIP on the same nuclear extract were performed and pooled on one MinElute column.
Libraries from ChIP samples of Replicate 1 were prepared and sequenced on a GAIIx (Illumina) sequencer as described previously (Yant et al., 2010; Immink et al., 2012). For biological replicate 2, ChIP-seq library preparation was performed using the Truseq ChIP sample preparation kit (Illumina, ref. IP-202-1012) according to the manufacturer's instructions except that PCR amplification was performed prior to size selection. Briefly, sonicated chromatin was repaired prior to 3' ends adenylation. Illumina's indexed adapters were ligated to the adenylated double-stranded DNA fragments. A 18-cycles PCR was performed on the ligated DNA using Illumina's PCR primers. The libraries were then size-selected between 300 and 700 bp on a 2% agarose gel. Each library was validated using high sensitivity chip (Agilent, ref. 5067-4626) on an Agilent Bioanalyzer and quantified using the Kapa library quantification kit (Clinisciences, ref. KK4824). Equimolar amounts of 4 libraries were pooled, diluted to 10 nM, denatured, and diluted again to 7 pM. 100 µl of the diluted pool were hybridized on one lane of an Illumina's Flow Cell. Clustering and 50 cycles sequencing were performed according to Illumina's instructions on a Hiseq2000. Libraries were multiplexed by three (H3K4me3 samples) or four and sequenced on a HiSeq2000 (Illumina) sequencer, yielding 50 bp single-end reads.
All inputs were sequenced with the HiSeq2000.

tag: genotype

value: wild type (Ler)

value: inflorescences (whole main inflorescences of wild type plants were harvested. Flowers older than stage 12 were removed)

tag: developmental stage

value: I

value: anti-H3K27me3 [Millipore, catalog# 17-622, lot# DAM1739345 (Repl. 1), lot#  2246083 (Repl.2)]


title: HeLaS3_STAP-processed_OCT4

tag: cell line


title: HeLaS3_STAP-processed_SCP1


title: RRBS_mESC_NT_WT_3


title: RRBS_mESC_RA_p53_KO_2


title: t2_H3K27me3_rep_1

value: ap1 cal 35S::AP1-GR

value: apices (only the cauliflower structures of the main inflorescence were harvested. Leaf and pedicel tissue contamination was minimized by dissection)

tag: chip antibody


title: oxRRBS_mESC_RA_p53_KO_2


title: RRBS_mESC_RA_p53_KO_1


title: I_H3K4me3_rep_1

value: anti-H3K4me3 [Millipore, catalog# 17-614, lot# NG1794844 (Repl.1), lot#  2043923 (Repl.2)]


title: L_H3K27me3_rep_1

source_name: rosette leaf

value: rosette leaves of flowering Arabidosis plants were harvested

value: L


title: HeLaS3_OCT4_cp-compare_bac

description:
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)

value: STARR-seq


title: oxRRBS_mESC_RA_p53_KO_4

value: mouse embryonic stem cells (mESC)


title: oxRRBS_mESC_RA_p53_KO_3

value: induced to differentiate by RA


title: RRBS_mESC_RA_p53_KO_3


title: HeLaS3_SULT1C2_cp-compare_bac


title: t2_H3K4me3_rep_1


title: oxRRBS_mESC_RA_p53_KO_1


title: RRBS_mESC_NT_p53_KO_1


title: HeLaS3_TFF2_cp-compare_bac


title: HeLaS3_mCP_cp-compare_bac


title: RRBS_mESC_NT_p53_KO_2


title: RRBS_mESC_NT_p53_KO_3


title: t0_H3K4me3_rep_1


title: oxRRBS_mESC_NT_p53_KO_3


title: oxRRBS_mESC_NT_p53_KO_2


title: oxRRBS_mESC_NT_p53_KO_1


title: RRBS_Liver_p53_KO_2

description: processed data file: 200bpTiles_Unified.txt.gz

extract_protocol:
p53 heterozygous male and female mice were bred to produce p53 wild type (WT) and p53-null offspring. Mouse tail genotyping was performed by PCR. Animals were sacrificed at the age of 16 weeks and liver samples were collected.
Reduced representation bisulfite sequencing (RRBS) was performed according to a previously published protocol  (Boyle, P. et al. 2012).
Briefly, genomic DNA was isolated using the PureLink genomic DNA kit (Invitrogen) according to the manufacturer’s instructions and subjected to enzymatic digestion by MSPI (New England Biolabs) for 16 hours. Klenow polymerase (New England Biolabs) was then added to each sample for end filling and poly-A tailing, followed by Truseq adapter ligation (Illumina). The library was then pooled and subjected to either bisulfite treatment as in the RRBS protocol or to an OX-RRBS protocol using the CEGX kit (Cambridge Epigentix). Validation of oxidation efficiency was done with the provided DNA sequences that were also A tailed and adapter ligated.

tag: gender

value: male

value: liver


title: HeLaS3_SCP1_blocking-3_bac

value: cervical adenocarcinoma cell line


title: t0_H3K27me3_rep_1

tag: tissue


title: RRBS_Liver_p53_KO_3


title: HeLaS3_SCP1_blocking-4_bac

value: no drug


title: RRBS_Liver_p53_KO_1


title: HeLaS3_SCP1_cp-compare_bac


title: HeLaS3_SCP1_blocking-1_bac


title: L_H3K4me3_rep_1


title: HeLaS3_SCP1_blocking-control_bac


title: ORI_bac_input

description:
plasmid DNA (containing genomic DNA fragments)
PCR amplified Plasmid library


title: RRBS_Liver_WT_2

value: WT


title: HeLaS3_SCP1_noinh_bac


title: SCP1_bac_input

source_name: plasmid DNA (containing genomic DNA fragments)


title: HeLaS3_ORI_inh_bac

value: TBK1(BX-795 hydrochloride, Sigma; cat. no. SML0694-5MG) + IKK/PKR(C16, Sigma; cat. no. I9785-5MG)


title: HeLaS3_ORI_noinh_bac


title: HCT116_ORI_inh_bac

value: colorectal cancer cell line


title: HCT116_ORI_noinh_bac


title: HCT116_SCP1_noinh_bac


title: HeLaS3_ORI_noinh_genomewide_rep1

description:
plasmid DNA (containing genomic DNA fragments)
PCR amplified Plasmid library
differential_peaks_inhibitor_vs_no-inhibitor_supp.table3.tsv
peaks_no-inhibitor_correctedEnrichment4_supp.table3.tsv


title: HeLaS3_ORI_noinh_genomewide_rep2

description:
plasmid DNA (containing genomic DNA fragments)
PCR amplified Plasmid library
HeLaS3_ORI_noinh_genomewide.combined.bw
differential_peaks_inhibitor_vs_no-inhibitor_supp.table3.tsv
peaks_no-inhibitor_correctedEnrichment4_supp.table3.tsv


title: ORI_geomewide_input_lib1


title: Diet 3

city: University Park

middle: Asher

last: Galbraith

state: Pennsylvania

address: 19a Chemical Ecology Lab

institute: Penn State University

data_processing:
Raw data were processed with Trimmomatic v0.32 to remove low quality reads, adaptor sequences, and reads with more than 5% unknown bases
A set of non-redundant transcripts was generated from the trimmed reads de novo using Trinity v2.1.0 using the default parameters.
The processed reads were aligned to this reference transcriptome using Tophat v2.0.10.
Read counts for each transcript were imported into R v3.0.2 for further analyses. Transcripts with low read counts (<10 across all samples) were removed from further analyses. The data was normalized using a trimmed mean of M-values (TMM) method and tested for differential expression using  a generalized linear model in EdgeR v3.4.2.
Genome_build: de novo transcriptome generated using Trinity v2.1.0

organism: Trichoplusia ni

source_name: Salivary glands

growth_protocol: Insects were reared on tomato, cabbage, and pinto bean artificial diet

extract_protocol:
Salivary glands from fifth instar larvae were dissected, flash frozen and RNA was extracted using Qiagen Rneasy protocol
library was constructed using Illumina protocols

value: Labial glands

tag: instar

value: Fifth

tag: diet

value: pinto bean artificial diet


title: Cabbage 2

value: Cabbage


title: Cabbage 3


title: HeLaS3_ORI_inh_genomewide_rep1

description:
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)
differential_peaks_inhibitor_vs_no-inhibitor_supp.table3.tsv
peaks_inhibitor_correctedEnrichment4_supp.table3.tsv
shortlisted_regions_inhibitor_supp.table3.tsv


title: Cabbage 1


title: Tomato 3

value: Tomato


title: RRBS_Liver_WT_3

tag: age


title: HeLaS3_SCP1_blocking-2_bac


title: Tomato 2


title: ORI_geomewide_input_lib2

description:
plasmid DNA (containing genomic DNA fragments)
PCR amplified Plasmid library
ORI_genomewide_input.combined.bw


title: Tomato 4

value: tomato


title: Diet 4


title: Diet 2


title: RRBS_Liver_WT_1

tag: genotype/variation


title: Run-75_H05_CD8_YFV_short_paired-end

status: Public on Jul 17 2017

city: Berkeley

first: Shaked

last: Afik

address: Stanley Hall

department: Computational Biology Graduate Group

institute: UC Berkeley

description:
CD8+ YFV-specific T cell donor 2
NA
NA

data_processing:
Low quality bases were trimmed with trimmomatic using the following parameters: LEADING:15, TRAILING:15, SLIDINGWINDOW:4:15, MINLEN:16.
Trimmed reads were then aligned to the genome (hg38 or mm10 for human or mouse samples, respectively) with TopHat2 for TCR reconstruction, and aligned to the transcriptome with RSEM for transcriptome quantification.
For transcriptome analysis of the human CMV and YFV donors (donors 1 and 2), low quality cells were filtered out prior to normalization. Cells were filtered out if their read depth was less than 1 million pairs or if the cell expressed less than 20% of all expressed transcript, where a transcript was considered expressed if it had a TPM value of >10 in at least 10% of cells, leaving 353 out of 378 cells for further analysis.
Normalization of TPM values was done with our newly developed normalization framework SCONE. In our study, the chosen normalization first scaled each sample with the DEseq scaling factor to account for differences in sequencing depth. Then, we ran RUVg with k=1.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Normalized TPM expression matrix of high quality cells from donors 1 and 2.

source_name: CD8+ YFV-specific T cell donor 2

growth_protocol: Mouse LCMV: Female C57BL/6 mice (The Jackson Laboratory), aged 7 weeks, were infected with 2x105 plaque forming units (PFU) LCMV Armstrong intraperitoneally i.p. or 4x106 PFU LCMV Clone 13 i.v. Human Donor 2: A healthy volunteer was vaccinated with a single dose (0.5 ml containing at least 105 PFU) of 17D live-attenuated yellow fever vaccine strain administered subcutaneously. Seroconversion after vaccination was confirmed by assaying the neutralizing antibody titers for YF-17D. Human Donor 3: Patient 355 (59yr old Male, infected with genotype 1a HCV, baseline viral load 467,000 IU/ml) received a prime vaccination of ChAd3-NSmut (2.5x1010 viral particles) and an MVA-NSmut (2x108 plaque forming units) boost vaccination 8 weeks later.

extract_protocol:
Mouse LCMV: Peripheral blood was obtained from the mice at day 7 post infection (p.i.) and lymphocytes were enriched using LSM density centrifugation. Cells were prestained with a near-IR fixable live/dead marker (Life Technologies, cat# L34976) and an APC- conjugated dextramer reagent for gp33 (Immudex, cat# A2160-APC) according to manufacturer recommendations. The cells were then stained with the following antibodies: FITC 2B4 (BioLegend, cat# 133504), PerCP-Cy5.5 CD44 (BioLegend, cat# 103032), PE KLRG1 (BioLegend, cat# 138408), PE-Cy7 PD1 (BioLegend, cat# 135215), BV421 CD127 (BioLegend, cat# 135024), BV510 CD8A (BioLegend, cat# 100752). Human Donor 1: Blood samples were obtained from a donor with detectable NLV-specific CD8+ T cell response. Lymphocytes were enriched via Ficoll gradient and prestained with a near-IR fixable live/dead marker (Life Technologies, cat# L34976) and an APC-conjugated dextramer reagent (Immudex, cat# WB2132-APC). The cells were then stained with the following antibodies: FITC CD8A (BioLegend, cat# 300906), PerCP-Cy5.5 CCR7 (BioLegend, cat# 353220), PE CD3 (BioLegend, cat# 317308), BV605 CD45RA (BioLegend, cat# 304133). Human Donor 2: A whole blood sample was obtained 9 months post-vaccination and lymphocytes were enriched from whole blood via Ficoll gradient centrifugation and a CD8 negative selection magnetic bead kit (Miltenyi Biotec). Cells were prestained with a live/dead marker (Life Technologies, cat# L34976) and an APC-labeled tetramer reagent (NS4B 214–222 LLWNGPMAV, kindly provided by Dr. Rafi Ahmed). The cells were then stained with the following antibodies: FITC CD8A (BioLegend, cat# 300906), PE CXCR3 (BioLegend, cat# 353705), PE-Cy7 CCR7 (BioLegend, cat# 353226), BV421 IL2Rb (BioLegend, cat# 339009), BV510 CD3 (BioLegend, cat# 317332), BV605 CD95 (BioLegend, cat# 305627), BV780 CD45RA (BioLegend, cat# 304140). Human Donor 3: PBMC were collected 14 weeks post-boost vaccination. PBMC were thawed and prestained with a live/dead marker (Life Technologies, cat# L34976) and a PE-conjugated pentamer reagent (PE-labeled HCV NS31406–1415 (KLSALGINAV; HLA-A*0201)). The cells were then stained with the following antibodies: FITC 2B4 (BioLegend, cat# 329505), PerCP-eFluor 710 LAG3 (eBioscience, cat# 46-2239), PE-Cy7 CCR7 (BioLegend, cat# 329919), APC CD39 (BioLegend, cat# 328209), BV421 PD1 (BioLegend, cat# 329919), BV510 CD3 (BioLegend, cat# 317332), BV605 CD8A (BioLegend, cat# 301040), BV780 CD45RA (BioLegend, cat# 304140).
Single cell lysates were converted to cDNA following capture with Agencourt RNA Clean beads using the SmartSeq2 protocol. The cDNA was amplified using 22-24 PCR enrichment cycles prior to quantification and dual-index barcoding with the Illumina Nextera XT kit. The libraries were enriched with 12 cycles of PCR, then combined in equal volumes prior to final bead cleanup and sequencing.

value: CD8+ YFV-specific T cell

tag: donor

value: Donor 2

tag: number of cells in sample


title: Run-75_H11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H11_S95_comb


title: Run-75_H10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H10_S94_comb


title: Run-75_H12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H12_S96_comb


title: Run-75_H04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H04_S88_comb

source_name: CD8+ Effector Memory T cell donor 2

value: CD8+ Effector Memory T cell


title: Run-75_H09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H09_S93_comb


title: Run-75_H08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H08_S92_comb


title: Run-75_H07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H07_S91_comb


title: HeLaS3_ORI_inh_genomewide_rep2

description:
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)
HeLaS3_ORI_inh_genomewide.combined.bw
differential_peaks_inhibitor_vs_no-inhibitor_supp.table3.tsv
peaks_inhibitor_correctedEnrichment4_supp.table3.tsv
shortlisted_regions_inhibitor_supp.table3.tsv

value: STARR-seq


title: Run-75_H03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H03_S87_comb


title: Run-75_H02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
NA
NA

source_name: CD8+ Naive T cell donor 2

value: CD8+ Naive T cell


title: Run-75_H01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H01_S85_comb


title: Run-75_G11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G11_S83_comb


title: Run-75_G10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G10_S82_comb


title: Run-75_G12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G12_S84_comb


title: Run-75_G07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G07_S79_comb


title: Run-75_G08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G08_S80_comb


title: Run-75_G03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G03_S75_comb


title: Run-75_G05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G05_S77_comb


title: Run-75_G06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G06_S78_comb


title: Run-75_G01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G01_S73_comb


title: Run-75_G02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
NA
NA


title: Run-75_G04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G04_S76_comb


title: Run-75_F12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F12_S72_comb


title: Run-75_F11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F11_S71_comb


title: Run-75_F10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F10_S70_comb


title: Run-75_F08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F08_S68_comb


title: Run-75_H06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-H06_S90_comb


title: Run-75_F09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F09_S69_comb


title: Run-75_F05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F05_S65_comb


title: Run-75_F07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F07_S67_comb


title: Run-75_F06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F06_S66_comb


title: Run-75_G09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-G09_S81_comb


title: Run-75_F01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
NA
NA


title: Run-75_F02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F02_S62_comb


title: Run-75_E12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E12_S60_comb


title: Run-75_F03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F03_S63_comb


title: Run-75_F04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-F04_S64_comb


title: Run-75_E09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E09_S57_comb


title: Run-75_E10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E10_S58_comb


title: Run-75_E07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E07_S55_comb


title: Run-75_E06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E06_S54_comb


title: Run-75_E05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E05_S53_comb


title: Run-75_E11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E11_S59_comb


title: Run-75_E08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E08_S56_comb


title: Run-75_E04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E04_S52_comb


title: Run-75_E03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E03_S51_comb


title: Run-75_E02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E02_S50_comb


title: Run-75_D10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D10_S46_comb


title: Run-75_D05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D05_S41_comb


title: Run-75_D07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D07_S43_comb


title: Run-75_D08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D08_S44_comb


title: Run-75_E01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-E01_S49_comb


title: Run-75_D12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D12_S48_comb


title: Run-75_D11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D11_S47_comb


title: Run-75_D06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D06_S42_comb


title: Run-75_D04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D04_S40_comb


title: Run-75_D03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D03_S39_comb


title: Run-75_D01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D01_S37_comb


title: Run-75_D02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D02_S38_comb


title: Run-75_C12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C12_S36_comb


title: Run-75_D09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-D09_S45_comb


title: Run-75_C11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C11_S35_comb


title: Run-75_C09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C09_S33_comb


title: Run-75_C10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C10_S34_comb


title: Run-75_C02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C02_S26_comb


title: Run-75_B12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B12_S24_comb


title: Run-75_B11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B11_S23_comb


title: Run-75_C03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C03_S27_comb


title: Run-75_C05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C05_S29_comb


title: Run-75_C07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C07_S31_comb


title: Run-75_C04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C04_S28_comb


title: Run-75_B10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B10_S22_comb


title: Run-75_C01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C01_S25_comb


title: Run-75_B08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B08_S20_comb


title: Run-75_B09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B09_S21_comb


title: Run-75_B06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B06_S18_comb


title: Run-75_B05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B05_S17_comb


title: Run-75_B04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B04_S16_comb


title: Run-75_B03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B03_S15_comb


title: Run-75_B07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B07_S19_comb


title: Run-75_B01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B01_S13_comb


title: Run-75_B02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-B02_S14_comb


title: Run-75_A12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
NA
NA


title: Run-75_A09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-A09_S9_comb


title: Run-75_A10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-A10_S10_comb


title: Run-75_A11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-A11_S11_comb


title: Run-75_A07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-A07_S7_comb


title: Run-75_A08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-A08_S8_comb


title: Run-75_C06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C06_S30_comb


title: Run-75_C08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-C08_S32_comb


title: Run-75_A06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-A06_S6_comb


title: Run-75_A04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-A04_S4_comb


title: Run-75_A05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-A05_S5_comb


title: Run-74_H12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H12_S96_comb


title: Run-75_A02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-75-samplesheetv3-A02_S2_comb


title: Run-75_A01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
NA
NA


title: Run-75_A03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
NA
NA


title: Run-74_H11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
NA
NA


title: Run-74_H08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H08_S92_comb


title: Run-74_H06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H06_S90_comb


title: Run-74_H05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H05_S89_comb


title: Run-74_H10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H10_S94_comb


title: Run-74_H07_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H07_S91_comb


title: Run-74_H04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H04_S88_comb


title: Run-74_G11_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G11_S83_comb


title: Run-74_H01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H01_S85_comb


title: Run-74_H02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H02_S86_comb


title: Run-74_H03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-H03_S87_comb


title: Run-74_G09_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G09_S81_comb


title: Run-74_G10_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G10_S82_comb


title: Run-74_G08_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
NA
NA


title: Run-74_G12_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G12_S84_comb


title: Run-74_G05_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G05_S77_comb


title: Run-74_G04_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G04_S76_comb


title: Run-74_G06_CD8_YFV_short_paired-end

description:
CD8+ YFV-specific T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G06_S78_comb


title: Run-74_G01_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G01_S73_comb


title: Run-74_G03_CD8_EffectorMemory_short_paired-end

description:
CD8+ Effector Memory T cell donor 2
NA
NA


title: Run-74_G02_CD8_Naive_short_paired-end

description:
CD8+ Naive T cell donor 2
Norm.TPM.cmv.yfv.xlsx
Run-74-samplesheetv3-G02_S74_comb