title: NMF426-mCherry_CenH3_ChIPseq

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

data_processing:
Paired-end reads were demultiplexed, trimmed to 50bp (if needed)
HiC contact maps were produced according to Imakaev et al. (Imakaev et al. 2012). Briefly, an attempt was made to uniquely map the first 15 base pairs (bp) of each read to the Neurospora genome. If a unique match was not found, the read was extended 5 bp and another attempt was made. This process continued until a unique match was found or the end of the read reached (50 bp).
Read pairs were then assessed using a number of quality control filters, typically removing reads that covered unligated products (Dangling Ends), products that were too close to the restriction site, Self-circles, and extremely large or small fragments.
Read pairs passing all filters (typically 10% of total read pairs) were used to build uncorrected contact maps (arrays) that were then corrected to account for the unequal representation of genomic loci in HiC datasets. Corrected maps were used in all subsequent analyses
To calculate the ratio of observed contacts to expected contacts, the median contact frequency was calculated at each genomic distance (up to a distance of ~3.5 Mb at which point contact frequency had reached background levels) and used as the expected contact frequency at each respective distance.
To directly compare datasets, a fixed number of reads (prior to filtering) were sampled with the program seqtk, such that the sampled number of raw reads from each dataset produced approximately equal numbers of reads that passed the filtering steps.
To make ChIP-seq enrichment files across 10kb bins to use for Circos plots, .bcf files were produced using samtools' mpileup function from ChIP-seq .bam files, the .bcf files were "fixed" to replace empty positions with zeros, and processed with a custom script to report the ChIP-seq enrichment over 10kb bins (the resulting seven files were catenated into one file).
Genome_build: Neurospora crassa assembly 12, but with the large inversion on LGVI (as evident from our data) corrected. (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf)
Supplementary_files_format_and_content: "...array.txt" files are the generated tab-delininated files with raw counts (on a log2 scale) for each bin (the entire genome is divided into 50kb or 10kb segments, and a bin indicates the intersection of two of these segments in an array format) across the genome. "...observed_expected.txt" is a file where the above array file containing observed interactions in our HiC dataset was normalized by the "expected" interaction if interactions were locally strong and stochastically decreased as genomic distance increased.

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: 2.5x10^8 conidia were grown in cultures of 50mL 1xVogels, 1.5% Sucrose medium for 3-4 hours at 30oC with shaking at 200rpm (At this time, >70% of the conidia for all strains had germination tubes >4x their original size, as roughly measured by light microscopy)

extract_protocol:
To determine the concentration of genomic DNA (gDNA) per aliquot of spheroplasts, 1 aliquot per replicate was resuspended in 200 μL decrosslinking buffer (50 mM Tris-HCl [pH 8], 5 mM Na Ethylenediaminetetraacetic acid (Na-EDTA), 0.5% (w/v) sodium dodecyl sulfate (SDS)) plus 100 mg proteinase K and incubated at 65 °C overnight. The next day, the volume was brought to 500 uL with TE buffer (10 mM Tris-HCl [pH 8], 1 mM Na-EDTA) plus 40 mg RNase A and aliquots were incubated at 37°C for 30 minutes. gDNA was then extracted twice with a 1:1 mixture of buffered phenol (pH 8) and chloroform, and once with chloroform. gDNA was precipitated by adding 1/10 volume of Na acetate (pH 5.2) and 1 volume of isopropanol. DNA pellets were washed 3x with 70% (v/v) ethanol, dried at RT for 10 minutes and resuspended in 50 μL TE. The DNA concentration was determined from the absorbance at 260 nm. Spheroplasts corresponding to 3.5 μg of gDNA were resuspended in 270 μL of HindIII buffer and 30 μL of 10% (w/v) SDS was added to a final concentration of 0.1% (w/v). Spheroplasts were then lightly decrosslinked by incubation at 65°C for 10 minutes and then placed immediately on ice. 33 μL of 10% (v/v) Triton X-100 and 8.3 μL of 10x HindIII buffer was added and gDNA digested with 400 U (20 μL of 20 U/μL from NEB) HindIII for 16 hours at 37 °C while nutating. The next day, samples were placed on ice and split into two aliquots. To construct HiC libraries, one aliquot of HindIII digested chromatin was labeled with biotin-14-dCTP in a 210 μL reaction consisting of 30 μM dATP, 30 μM dTTP, 30 μM dGTP, 30 μM biotin-14-dCTP and 25 U of Klenow (large fragment). This reaction was incubated at 37 °C for 45 minutes with nutating. Klenow (large fragment) and HindIII was then inactivated by the addition of SDS to 1.5% (w/v) and incubation at 65°C for 30 minutes. This chromatin was then used in a 3.5 mL ligation reaction consisting of 50 mM Tris-HCl [pH 7.5 @ 25 °C], 10 mM MgCl2, 0.9% (v/v) Triton X-100, 10 mM Dithiothrireitol (DTT), 100 μg/mL BSA, 1 mM adenosine triphosphate (ATP) and 1675 U T4 DNA ligase (4.2 μL of 400,000 U/mL T4 DNA ligase from NEB). This reaction was incubated at 16°C for 4 hours. At the end of the 4 hour 3C and HiC ligation reactions, 250 mg of proteinase K was added and all reactions were allowed to decrosslink at 65°C overnight. The next day, another 250 mg of proteinase K was added and samples were decrosslinked at 65°C for another 2 hours. Samples were cooled to ~25°C on ice, and extracted with 5 mL of phenol (pH 8) by vortexing for 2 minutes. After centrifugation (3500 RPM, 10 minutes), the aqueous phase was removed and extracted with 5 mL of phenol (pH 8):chloroform (1:1) by vortexing for 2 min. After centrifugation (3500 RPM, 10 minutes), the aqueous phase was removed and brought to a volume of 5 mL with TE. DNA was precipitated by the addition of 0.5 mL 3 M Na Acetate [pH 5.2], 50 mg glycogen, 12.5 mL 95% ethanol and incubation at -80°C for 1 hour. DNA was pelleted by centrifugation (20,000 g, 20 minutes, 4°C), the supernatant decanted and DNA resuspended in 450 μL TE by vortexing. DNA was again extracted with 1 volume of phenol (pH 8):chloroform (1:1) and then chloroform as before. DNA was then ethanol precipitated as before and resuspended in 25 μL of TE/10 buffer (10 mM Tris-HCl [pH 8 @ 25°C], 0.1 mM Na-EDTA). To remove biotin-dCTP from unligated ends, the HiC libraries were digested for 2 hours at 12°C in a 50 μL reaction consisting of 5 μL of NEB buffer 2, 100 μg/mL BSA, 100 μM dATP, 100 μM dGTP and 5 U of T4 DNA polymerase. These reactions were quenched by adding Na-EDTA to 10 mM and DNA extracted with 1 volume of phenol (pH 8):chloroform and then with 1 volume of chloroform. DNA was ethanol precipitated, resuspeneded in 500 μL of TE and sheared by sonication (duty cycle 80, power 1.2, 10 s, 5x with 1 minute rest on ice between pulses). Sheared, biotinylated DNA was captured by adding 25 μL of streptavidin beads (Invitrogen) that had been equilibrated in BW buffer (5 mM Tris-HCl [pH 8 @ 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% (v/v) Tween-20) and incubating for 30 minutes with shaking. Beads were washed 2x with BW buffer, 2x with TE/10 buffer and resuspended in 25 μL TE/10 buffer.
To prepare HiC libraries for Illumina sequencing, either Illumina TruSeq kits was used according to the manufacturers’ protocol, or essentially a “homemade version” of that protocol was used. In the homemade version, DNA ends were repaired in reactions consisting of 25 μL of HiC libraries on streptavidin beads, 5 μL of T4 DNA ligase buffer, 2 μL 10 mM (each) dNTPs, 0.5 μL end repair enzyme mix (0.5 U T4 DNA polymerase, 0.25 U Klenow Fragment, 2.25 U T4 DNA Polynucleotide Kinase) in a final volume of 50 μL and incubated at 20°C for 30 minutes. Beads were washes 2x with BW buffer and 2x with TE/10, resuspended in 16.5 μl TE/10. A-tailing was performed by adding 2 ul 10x NEB Buffer #2, 1 ul 4 mM dATP, 0.5 ul Klenow 3’ to 5’ exo minus (5 U/ul) and incubating at 37 C for 30 minutes, mixing every 10 minutes. Beads were again washed with BW and TE/10 buffers as above and resuspended in 20 ul TE/10. Indexed adaptors were ligated by adding 25 ul 2x ligase buffer (132 mM Tris-HCl [pH 7.6], 20 mM MgCl2, 2 mM DTT, 2 mM ATP, 15% (w/v) PEG 6000), 2.5 ul T4 DNA ligase (400 U/ul) and 2.5 ul Illumina TruSeq DNA adapters diluted 1:10 and incubating at RT for 20 minutes, mixing every 10 minutes. Ligation reactions were quenched with 5 ul of 0.5 M Na-EDTA [pH 8] and beads washed 3x with BW buffer and 2x with TE/10. Beads were then resuspended in 50 ul TE/10 and HiC libraries amplified in 50 ul PCR reactions using the Phusion polymerase and the following cycle: 45 s at 98°C; 18 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C; 1 minute at 72°C. The PCR product was separated from the beads, cleaned with Ampure XP beads, and resuspended in 25 ul TE/10. Library quality was assessed by gel electrophoresis before deeps sequencing.
Indexed paired-end HiC libraries were pooled and sequenced either on an Illumina HiSeq 2500 as either 100nt or 50nt paired end sequencing runs, or a NextSeq500 as a 75nt paired-end sequencing run at the University of Oregon Genomics Core Facility

treatment_protocol: 2.6 mL of methanol-free formaldehyde (20%) was added to a final concentration of 1%. After a 10 minute room temperature (RT) incubation with shaking at 100 RPM, crosslinking reactions were quenched by adding 3.4 mL of 2 M Tris-HCl [pH 8 @ 25 °C] to a final concentration of 125 mM and incubating at room temperature (RT) for another 10 minutes with shaking at 100 RPM. Conidia were harvested by centrifugation (3000 RPM, 5 minutes) and resuspended gently in 40 mL spheroplasting buffer (1 M sorbitol, 100 mM KPO4  [pH 7.5]) plus 30 mM β-mercaptoethanol, pelleted again (3000 RPM, 5 minutes) and resuspended in 40 mL spheroplasting buffer. 200 mg of VinoTaste Pro (Novozymes) was added and strains were spheroplasted for 60 minutes at 30°C with shaking at 100 RPM. Spheroplasts were harvested by centrifugation (2000 RPM, 5 minutes) and washed 3x with 20 mL HindIII buffer (50 mM NaCl, 10 mM Tris-HCl [pH 7.9 @ 25°C], 10 mM MgCl2, 100 μg/mL bovine serum albumin (BSA)). Washed pellets were resuspended in 6 mL HindIII buffer, split into 1 mL aliquots in 1.7 mL eppendorf tubes. Spheroplasts were pelleted (1500 g, 5 minutes) and the supernatant was aspirated away. Aliquots were frozen in liquid nitrogen and stored at -80°C.

tag: antibody used

value: RFP-trap_A, from Chromotek


title: E11.0_T2_2711

status: Public on May 19 2016

type: SRA

city: Beijing

first: Xianlong

last: Li

address: 5, Yiheyuan Rd., Haidian District

department: Biodynamic Optical Imaging Center, College of Life Sciences

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
remove Illumina adaptor sequences, primer UP1, primer UP2 and 3’ ployA sequences using cutadapt (ver 1.6)
sequence alignment to the mouse genome (mm9) and spiked-in sequences using tophat (v2.0.12)
Cufflinks (v2.2.1) was used to estimate the expression level of each detected gene as fragment per kilobase of transcript per million fragments mapped (FPKM) value
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_tracking (cufflinks output)

molecule: polyA RNA

organism: Mus musculus

source_name: AGM

extract_protocol:
E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T1 CD201-: CD31+CD45-CD41lowc-Kit+CD201low/-, T2 pre-HSCs: CD31+CD45+c-Kit+CD201high, T2 CD41low: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+; bonemarrow: Adult HSC: ESLAM(CD45+ EPCR+ CD48- CD150+).
FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol.

tag: cell type

value: Type2 pre-HSCs


title: N2108_dim-3_HiC

country: USA

description:
genomic DNA HiC libraires
2.5x10^8 conidia were grown in cultures of 50mL (1xVogels, 1.5% Sucrose) medium for 3-4 hours at 30oC with shaking at 200rpm (At this time, >70% of the conidia for all strains had germination tubes >4x their original size, as roughly measured by light microscopy) then crosslinked in 1% formaldehyde for 10 minutes at RT, quenched with 1M glycine for 15minutes at RT, the cells spheroplasted and the chromatin fragmented by MNase.  Antibody specific to mCherry (RFP-trap, Chromotek) prebound to agarose beads was applied to the cell lysate and allowed to bind overnight at 4oC.  Beads were washed, and samples were decrosslinked for 16 hours at 65oC.  ChIP libraries were prepared for sequencing with the eluted DNA with the TruSeq kit from Illumina.  Reads were aligned to the neurospora_crassa_or74a_12_genome_FIXED.fasta genome, duplicates were removed, and reads were sorted.

library_source: genomic

molecule: genomic DNA

source_name: germinated condia

tag: genotype


title: E11.0_T2_2417


title: E11.0_T2_2704


title: N5580_hpo_HiC

description: genomic DNA HiC libraires

value: N5580 hpo


title: N3944_dim-5_HiC

description: genomic DNA HiC libraires


title: E11.0_T2_2419


title: E11.0_T2_2701


title: E11.0_T2_2415


title: E11.0_T2_2416


title: NMF39_WildType_HiC

description: genomic DNA HiC libraires

value: NMF39 WildType


title: E11.0_T2_2412


title: E11.0_T2_2413


title: E11.0_T2_2418


title: E11.0_T2_2408


title: E11.0_T2_2407


title: E11.0_T2_2113


title: E11.0_T2_2103


title: E11.0_T2_2111


title: E11.0_T2_2102


title: E11.0_T1_3011

value: Type1 pre-HSCs


title: E11.0_T1_3014


title: E11.0_T1_3007


title: E11.0_T1_3009


title: E11.0_T1_3010


title: E11.0_T1_3006


title: E11.0_T2_2105


title: E11.0_T1_3001


title: E11.0_T1_2614


title: E11.0_T1_2613


title: E11.0_T1CD201neg_3613

molecule: total RNA


title: E11.0_T1_2610


title: E11.0_T1_3002


title: E11.0_T2_2401


title: E11.0_T1_2607


title: E11.0_T1_2604


title: E11.0_T1_2602


title: E11.0_T1_2605


title: E11.0_T1_2509


title: E11.0_T1_2510


title: E11.0_T1_2508


title: E11.0_T1_2612


title: E11.0_T1_2608


title: E11.0_T1_3004


title: E11.0_T1_2616


title: E11.0_T1_3005


title: E11.0_T1_2615


title: E11.0_T1_2501


title: E11.0_T1_2603


title: E11.0_T1_2504


title: E11.0_EC_3209

value: endothelial cells


title: E11.0_EC_3208


title: E11.0_EC_3205


title: E11.0_EC_3207


title: E11.0_EC_3211


title: E11.0_T2_2104


title: E12.5_FL_01M1

source_name: FL

extract_protocol:
E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+
FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol.

value: E12 HSCs


title: E11.0_T2_17M2


title: E11.0_T2_23M4


title: E11.0_T1_2606


title: E12.5_FL_01M3


title: ctrl-sham-01

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

data_processing:
Torrent_Suite 4.0.2 for basecalling with parameters: `BaseCaller --keypass-filter on --phasing-residual-filter=2.0 --trim-qual-cutoff 15 --trim-qual-window-size 30 --trim-adapter-cutoff 16 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual --max-phasing-levels 2`
Sequenced reads were aligned against mouse genome mm9 using Tmap version 3.0.1 with default RNA-Seq setting `map4`
Gene expression levels were measured by counting numbers of reads in all the exons using HTSeq version 0.5.4p3 with parameters: `htseq-count -m union -s yes -t exon -i gene_symbol`
Differential gene expression was measured using DESeq version 1.16.0
Genome_build: mm9
Supplementary_files_format_and_content: comma-separated values files for raw read counts; comma-separated value file with differentially expressed genes.

source_name: heart ventricles of Pitx2f/f control mouse at  5-day-post-sham

extract_protocol:
Total RNA was extracted form the ventricles using miRNeasy mini kit (Qiagen), and then mRNA was purified using Dynabeads mRNA DIRECT Micro Kit (Ambion, life technologies)
the libraries were prepared using Ion Total RNA-Seq Kit v2 for IonProton System (Ion Torrent, Life Technologies).

tag: tissue

value: heart

tag: tissue compartment

value: ventricles

tag: surgery

value: sham surgery at Postnatal day 2

tag: age

value: postnatal day 7

value: pitx2flox control


title: E11.0_T2_17M4


title: ctrl-sham-02

source_name: heart ventricles of Pitx2f/ control mouse at  5-day-post-sham


title: E11.0_EC_20M7

value: Endothelial Cells


title: CKO-5DPR-02

source_name: heart ventricles of pitx2CKO mouse at 5-day-post-resection

value: cardiac apex resection at Postnatal day 2

value: MCKcre;pitx2f/f (pitx2CKO)


title: E11.0_EC_20M6


title: E11.0_EC_20M5


title: E11.0_EC_20M4


title: CKO-5DPR-01


title: E11.0_T2_23M3


title: E11.0_T2_23M1


title: E11.0_EC_20M1


title: E11.0_EC_20M3


title: DL4312G_BR2_3

city: Edinburgh

first: Benura

last: Azeroglu

address: Alexander Crum Brown Road

country: United Kingdom

institute: University of Edinburgh

description: processed data file: DL4312G_BR2_processed.txt

data_processing:
Library strategy: DNA-seq
Paired-end raw datasets were mapped against the reference genomic sequence using BWA sequence aligner (version 0.7.11) and subsequently processed using SAMtools (version 1.2)
Replication profiles of exponentially growing cultures were calculated by normalizing to the number of uniquely mapped sequence reads and then to the normalised reads of a non-replicating stationary-phase wild-type culture.
An in-lab R-script has been used to calculate the enrichment (normalised read depth) in 1 kb non-overlapping windows across the genome.
A non-parametric smoothing method (LOESS, Local regression) has been applied to the data points of the replication profiles for each strain.
Supplementary_files_format_and_content: txt files including count data for the whole genome

organism: Escherichia coli

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25

extract_protocol:
To further eliminate potential RNA, 3 units of RiboshredderTM were added per sample. Samples were purified by phenol/chloroform extraction and ethanol precipitation.
Construction of libraries using the Illumina TruSeq DNA Sample Prep kit and DNA sequencing was carried out on an Illumina HiSeq 2000 platform by Edinburgh Genomics

treatment_protocol: DNA was isolated from cultures after 1 hour induction of sbcDC expression using the Promega Wizard® Genomic DNA purification kit.

tag: strain

value: delta_recG263::KanR lacZ::xxx mhpR::xxx proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZx-


title: ctrl-5DPR-02

source_name: heart ventricles of Pitx2f/f control mouse at 5-day-post-resection


title: ctrl-5DPR-01


title: DL4312G_BR2_2


title: DL4312G_BR1_3

description: processed data file: DL4312G_BR1_processed.txt


title: DL4312G_BR1_1


title: DL4311G_BR2_3

description: processed data file: DL4311G_BR2_processed.txt

value: delta_recG263::KanR lacZ::xxx mhpR::xxx proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZx-


title: DL4311G_BR2_2


title: DL4311G_BR2_1


title: DL4312G_BR1_2


title: DL4311G_BR1_3

description: processed data file: DL4311G_BR1_processed.txt


title: DL4311G_BR1_2


title: DL4201G_BR2_1

description: processed data file: DL4201G_BR2_processed.txt

value: lacZ::xxx mhpR::xxx proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZx-


title: DL4184G_BR2_2

description: processed data file: DL4184G_BR2_processed.txt

value: lacZ::xxx mhpR::xxx proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZx-


title: DL4184G_BR2_1


title: DL4201G_BR2_3


title: DL4201G_BR1_1

description: processed data file: DL4201G_BR1_processed.txt


title: DL4184G_BR1_3

description: processed data file: DL4184G_BR1_processed.txt


title: DL4184G_BR1_1


title: DL4311C_ChIP-seq

data_processing:
Adaptor Sequences were removed using fastx_clipper. (http://hannonlab.cshl.edu/fastx_toolkit/index.html) -  Example: fastx_clipper -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATG -i DL4900_raw.fasta  -o DL4900_clipped.fasta
Data collapsed using fastx collapser to remove identical sequencing reads (http://hannonlab.cshl.edu/fastx_toolkit/index.html) - Example: fastx_collapser -i DL4900_clipped.fasta -o DL4900_clip_clp.fasta
reads were mapped to the E. coli K12 MG1655 (NC000913.3) genome using Novoalign version 2.07  (www.novocraft.com) - Example: (novoalign -f DL4900_clip_clp.fasta -d NC000913.3.nix -r Random > DL4900.novo)
yPileup was used to generate count data for the whole genome - Example:  pyPileup.py --file_type=novo -f DL4184.novo --tab=NC000913.3.tab --chr=Wholechom.txt -- ignorestrand
Genome_build: Escherichia coli K12 MG1655 NC000913.3
Supplementary_files_format_and_content: txt files including count data for the whole genome

extract_protocol:
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1/100 anti-RecA antibody (Abcam, ab63797). IP samples were then incubated with Protein G Dynabeads® (Life Technologies) for 2 h at room temperature. All samples were washed 3 times with 1 X PBS + 0.02% Tween-20 before re-suspending the Protein G dynabeads in 200 μl of TE buffer (10 mM Tris (pH 7.4), 1 mM EDTA) + 1% SDS. 100 μl of TE buffer was added to the input samples and all samples were then incubated at 65°C for 10 h to reverse formaldehyde crosslinks. DNA was isolated using the MinElute PCR purification kit (Qiagen). DNA was eluted in 50 μl of TE buffer using a 2-step elution. Samples were stored at -20°C.
All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit.

treatment_protocol: Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M

value: delta_recG263::KanR lacZ::χχχ mhpR::χχχ proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZχ-


title: DL4184G_BR1_2


title: DL4312G_BR2_1


title: E11.0_EC_20M2


title: DL4201G_BR2_2


title: DL4201C_ChIP-seq

value: lacZ::χχχ mhpR::χχχ proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZχ-


title: Jurkat DMSO Ser2 ChIP

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 80
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

organism: Homo sapiens

source_name: T-ALL

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

treatment_protocol: Jurkat cells were treated with DMSO (0.1%) for 6 hrs prior to cross linking.

tag: cell line

value: Jurkat

tag: chip antibody

value: RNA Pol II (Ser2 phospho CTD)

tag: antibody manufacturer

value: Millipore

tag: antibody catalog

tag: system

value: Blood

tag: cell number

value: 200 million

tag: drug

value: DMSO

tag: concentration

tag: treatment duration


title: DL4184C_ChIP-seq

value: lacZ::χχχ mhpR::χχχ proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZχ-


title: Jurkat 50 nM THZ531 Ser2 ChIP

treatment_protocol: Jurkat cells were treated with THZ531 (50 nM) for 6 hrs prior to cross linking.


title: DL4201G_BR1_3


title: Jurkat 500 nM THZ531 Ser2 ChIP

treatment_protocol: Jurkat cells were treated with THZ531 (500 nM) for 6 hrs prior to cross linking.


title: Older_9

city: New Haven

first: Pasquale

last: Patrizio

state: CT

address: 150 Sargent drive

department: Ob/Gyn

institute: Yale University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg19 whole genome using bowtie v2-2.1.0 with parameters -p 8 -r 150  --library-type fr-firststrand --b2- 'very-sensitive'
Raw gene counts were estimated with HTSeq (Simon Anders, Bioinformatics, 2014)
Normalized gene expression levels, represented as counts per million (CPM), were obtained for transcripts from Ensembl database and were processed for statistical analysis with EdgeR (Robinson et al., Bioinformatics, 2010)
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated files (.csv) include normalized gene counts (counts per million) values for each Sample

source_name: cumulus oophorus cells_older

growth_protocol: Patients undergoing controlled ovarian stimulation for in vitro fertilization (IVF) procedures

extract_protocol:
Frozen samples were treated with Actarus pico pure kit for total RNA extraction, and genomic DNA was removed with DNAseI
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CCs were bipsied from cumulus-oocyte-complexes approximatey 2 hours post follicular aspiration. Samples were washed in PBS and centrifuged at 1500g. Dry pellets were snap frozen in liquid nitrogen

tag: donor patient status

value: male factor infertility/oocyte donation and oocyte freezing couples only

tag: age group

value: cumulus oophorus cells


title: Older_8

tag: cell type


title: Older_5


title: Older_7


title: Older_6


title: DL4311G_BR1_1

tag: genotype


title: DL4312C_ChIP-seq

value: delta_recG263::KanR lacZ::χχχ mhpR::χχχ proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZχ-


title: DL4201G_BR1_2


title: Scrambled control_2

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

description:
Lentivirally stable transduction
Scrambled control

data_processing:
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were  mapped to hg19 genome using TopHat v2 with default settings.
Read counts for each refseq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: hg19
Supplementary_files_format_and_content: Gene level read counts

source_name: AML cell line (MV4-11)_scrambled

growth_protocol: Cells were maintained in Iscove's Modified Dulbecco's Medium, Catalog No. 30-2005, supplemented with 10% final concentration of fetal bovine serum.

extract_protocol:
Total RNA were isolated using TriZol, Invitrogen.
poly(A) RNA-seq library was prepared following manufacturer's default

treatment_protocol: Cells were stably transduced using lentivirus with either shRNA against PRMT5 or scrambled vector control.


title: PRMT5/Knockdown_3

description:
Lentivirally stable transduction
PRMT5/Knockdown

source_name: AML cell line (MV4-11)_PMRT5/Knockdown


title: Older_3


title: Scrambled control_3


title: Older_2


title: WT3a_FLT3 2 WGBS

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

description: Biological replicate 2 of FLT3-ITD leukemia for WGBS. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation

data_processing:
Base quality- and adapter-trimmed Fastq files were aligned with bsmap 2.74 using the following parameters: -v 10 -g 2 -w 5 -p 8 -x 1000 -R -S 42; Duplicate reads were removed by picard tools. Cytosine methylation ratios were calculated with the bsmap utility script methratio.py using the following parameters: -z -g -m 5 --ct-snp=no-action. Note that when a sample was run on more than one lane of the same flow cell, the fastq files have been concatenated accordingly.
Genome_build: mm9
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context (2nt upstream to 2nt downstream in Watson strand direction), methylation ratio, number of effective total C+T counts on this locus (strands combined), number of total C counts on this locus (strands combined), number of total C+T counts on this locus (strands combined), number of total G counts on this locus of reverse strand (value is NA), number of total G+A counts on this locus of reverse strand (value is NA), lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

source_name: Thymus

growth_protocol: Sca1+ enriched Dnmt3a KO or WT murine bone marrow cells were transduced with retroviruses expressing MSCV-FLT3-ITD-IRES-GFP or MSCV-GFP transgenes and transplanted into lethally irradiated recipients by retro-orbital injections. Thymus or whole bone marrow cells from each genotype were collected from transplant recipients.

extract_protocol:
Extract DNA using Qiagen Allprep Mini kit.
Tru-Seq DNA sample prep kit

treatment_protocol: Adapter-ligated fragments were bisulfite converted with Qiagen Epitect kit.

value: Leukemic cells

tag: cell surface marker


title: E11.0_EC_3228

value: endothelial cells


title: Older_4


title: KO3a_FLT3 1 WGBS

description: Biological replicate 1 of Dnmt3aKO/FLT3-ITD leukemia for WGBS. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation

source_name: Bone marrow


title: Scrambled control_1


title: PRMT5/Knockdown_2


title: Jurkat 500 nM THZ531 Pol2

data_processing:
Aligned using bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extendedin the direction of alignment to be 200bp. Counts are normalized to reads-per-million unique mapped reads

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Jurkat cells were grown in RPMI medium supplemented with 1% glutamine and 10% FBS.  Cells were cultured at 37 degrees C in a humidified chamber in the presence of 5% CO2. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

treatment_protocol: Jurkat cells were grown as described above and treated with 500 nM THZ531 for 6 hrs prior to cross-linking.

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz

tag: antibody lot

value: 100 million


title: Older_1


title: Jurkat 50 nM THZ531 Pol2

treatment_protocol: Jurkat cells were grown as described above and treated with 50 nM THZ531 for 6 hrs.


title: Younger_10

source_name: cumulus oophorus cells_younger


title: Older_0


title: E11.0_EC_3226


title: Younger_9


title: Jurkat DMSO CDK12 ChIP

treatment_protocol: Jurkat cells were treated with DMSO for 6 hrs before cross linking with formaldehyde.

value: Greenleaf Lab

value: 300 million


title: PRMT5/Knockdown_1


title: Jurkat DMSO Pol2

treatment_protocol: Jurkat cells were grown as described above and treated with 0.1% DMSO for 6 hrs prior to cross-linking.

value: Jurkat


title: E11.0_EC_3222


title: Younger_7


title: Apothecium formation (stipe)

city: Wuhan

first: Xueliang

last: Lyu

state: Hubei

address: Shizishan street NO.1

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

description: replicate 1

data_processing:
1. 3' adaptor sequence removal: since tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences;
2. Empty reads removal (reads with only 3' adaptor sequences but no tags);
3. Low quality tags removal (tags with unknown sequences ‘N');
4. Removal of tags which are too long or too short, leaving tags of 21nt long;
5. Removal of tags with a copy number of 1 (probably be sequencing error);
6. Generate clean tags.
Genome_build: S. sclerotiorum transcript database in the Broad Institute
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

organism: Sclerotinia sclerotiorum

source_name: Ascogonidium

growth_protocol: (i) Vegetative stage: activating hyphal agar discs of the Ep-1PNA367 stain were placed on a cellophane membrane overlaid onto PDA medium at 20°C; subsequently, the mycelia were collected at 12, 24, 36, 48 and 60 h; (ii) Sclerotial formation stage: the colonies growing on the cellophane membrane overlaid onto PDA medium were further incubated under the same conditions and then the cultures were collected at 84, 96, 108, 120 and 132 h; (iii) Early stages of infection: fresh hyphal fragments of the Ep-1PNA367 strain were overlaid onto sterilized cheese cloth, which was overlaid onto the leaves of the A. thaliana ecotype Columbia-0, followed by inoculation at 20°C with 100% relative humility; the cheese cloth with hyphae was then rolled up from the leaves at 9 h and 12 h; (iv) Sclerotial myceliogenic germination stage: sclerotia were surface sterilized with sodium hypochlorite and were sowed on a PDA plate at 20°C to induce myceliogenic germination, and when approximately 50% of sclerotia had germinated, the sclerotia were harvested; (v) Sclerotial carpogenic germination stage: sclerotia were dried at room temperature and were pretreated in a freezer (4-6°C) for up to one month and then were surface sterilized and sowed on wet sterilized sands in a plate at 15°C to induce carpogenic germination; when approximately 50% of the sclerotia germinated (stipes having only emerged from sclerotia), the sclerotia were harvested; and (vi) Early apothecial formation stage: sclerotia were allowed to grow in the same incubator, and the stipes were cut and collected immediately before apothecium formation for RNA extraction.

extract_protocol:
Different time-point samples from the vegetative stage, sclerotial formation stage and infection stage were pooled together respectively according to equal quantities for RNA extraction. The six RNA libraries were incubated for 30 min at 37°C with 10 units of DNase I (Roche Applied Science) to remove residual genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The six RNA libraries were incubated for 30 min at 37°C with 10 units of DNase I (Roche Applied Science) to remove residual genomic DNA. Tag-based transcriptome sequencing methods were used to perform the DGE (Solexa/Illumina, Shenzhen, China) analysis.

tag: tissue

value: Ascogonidium


title: E11.0_EC_3224


title: E11.0_EC_3223


title: Myceliogenic germination

description: replicate 1

source_name: Sclerotia of myceliogenic germination

tag: strain

value: Sclerotia of myceliogenic germination


title: Infection

description: pooled sample, replicate 1

source_name: Hyphae, 9 h and 12 hpi

value: Hyphae, 9 h and 12 hpi


title: E11.0_EC_3219

source_name: AGM


title: Younger_5


title: Younger_8


title: Carpogenic germination

description: replicate 1

source_name: Sclerotia of carpogenic germination

value: Sclerotia of carpogenic germination


title: Younger_6


title: Younger_4


title: E11.0_EC_3221


title: E11.0_EC_3216


title: Younger_3


title: E11.0_EC_3214


title: E11.0_EC_3227


title: E11.0_EC_3213


title: Younger_2


title: Sclerotial development

description: pooled sample, replicate 1


title: E14.5_FL_15M8

source_name: FL

value: E14 HSCs


title: E14.5_FL_15M7


title: Vegetative growth

description: pooled sample, replicate 1


title: E14.5_FL_15M6


title: double thymidine block at 25.5h

city: Shanghai

first: Zefeng

last: Wang

address: 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

data_processing:
RNA-Seq reads were mapped to the human genome (build hg19) using the MapSplice informatics tool with default parameters
The mapped reads were further analyzed with Cufflinks to calculate the level of gene expression with FPKM
The levels of alternatively spliced isoforms were quantified with MISO (Mixture-of-Isoforms) probabilistic framework (Katz et al., 2010) using the annotated AS events for human hg19version 2.
The levels of alternatively spliced isoforms were also quantified with VAST-TOOLS using the event annotation as previously described
Genome_build: hg19

growth_protocol: Cells were cultured in humidified incubators with 5% CO2. Cell cycle synchronization was adapted from the protocol of Whitfield et al. (Whitfield et al., 2002); ~ 750,000 log phase HeLa cells were plated in 15 cm dishes in complete media and allowed to attach for 16 hrs, reaching < 30% confluence.

extract_protocol:
For RNA-Seq, cells (both adherent and detached) were harvested every 1.5 hrs for 30 hrs and frozen immediately for purification of total RNA.
RNA from synchronized cells was extracted with TRIZOL (Invitrogen), treated with DNAse I (Qiagen), and purified on RNAeasy columns. (Qiagen) according to the manufacturer’s protocol. RNA-seq libraries were robotically prepared with Illumina TruSeq Total RNA Sample Prep kits according to the manufacturer’s protocol

treatment_protocol: Cells were subsequently treated with 2 mM thymidine (Sigma) for a total of 18 hrs, washed 2 times with 1xPBS, and supplemented with fresh complete media for 10 hrs. 2 mM thymidine was subsequently added for a second block of 18 hrs and washed as described previously. Mitotic block was performed by double thymidine arrest (as above) and release in fresh media for 3.5 hrs followed by addition of nocodazole 100 μM (Sigma) for 10 hrs. G1 block was performed by serum starvation for 72 hrs in DMEM containing 0.05% FBS.

tag: cell cycle

tag: cell line

value: HeLa cells

tag: sample type

value: double thymidine block at 25.5h


title: E14.5_FL_15M4


title: double thymidine block at 30h

value: double thymidine block at 30h


title: E14.5_FL_15M3


title: Younger_1

value: male factor infertility/oocyte donation and oocyte freezing couples only

value: cumulus oophorus cells


title: double thymidine block at 21h

value: double thymidine block at 21h


title: E11.0_EC_3217

value: endothelial cells


title: E14.5_FL_15M1


title: double thymidine block at 22.5h

value: double thymidine block at 22.5h


title: E14.5_FL_15M2


title: E12.5_FL_13M6

value: E12 HSCs


title: double thymidine block at 19.5h

value: double thymidine block at 19.5h


title: double thymidine block at 18h

value: double thymidine block at 18h


title: E12.5_FL_13M7


title: E12.5_FL_13M4


title: double thymidine block at 4.5h

value: double thymidine block at 4.5h


title: double thymidine block at 6h

value: double thymidine block at 6h


title: double thymidine block at 12h

value: double thymidine block at 12h


title: double thymidine block at 9h

value: double thymidine block at 9h


title: double thymidine block at 3h

source_name: S

value: S

value: double thymidine block at 3h


title: E12.5_FL_13M3


title: double thymidine block at 15h

value: HeLa cells

value: double thymidine block at 15h


title: E12.5_FL_13M8


title: double thymidine block at 10.5h

value: double thymidine block at 10.5h


title: E12.5_FL_13M2


title: double thymidine block at 0h

value: double thymidine block at 0h


title: E12.5_FL_13M1


title: E11.0_T1_14M4

value: Type1 pre-HSCs


title: E12.5_FL_13M5


title: E11.0_T1_14M5


title: E11.0_T1_14M2


title: E11.0_T1_14M3


title: E11.0_T1_12M1


title: KO3a_FLT3_2 RNA-seq

description: Biological replicate 2 of Dnmt3aKO/FLT3-ITD leukemia. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation

data_processing:
Reads were aligned with Tophat 2.0.10 to both refseq transcriptome and mm9 genome using parameters: -p 12 --library-type fr-unstranded --read-realign-edit-dist 0 --min-anchor-length 6 --microexon-search --transcriptome-index=mm9_refseq. The refseq transcriptome gtf file was obtained from the Illumina iGenomes collection as recommended by the software developers
Refseq reference-based transcript assembly and transcript quantification were performed by Cufflinks 2.1.1 using parameters: --max-bundle-frags 500000 -p 16 -u -A 0.16 -b -M -g
Differential expression of Refseq genes was assessed by Cuffdiff 2.1.1 using parameters: -b -M -p 12 --min-reps-for-js-test 2 -u
Genome_build: mm9
Supplementary_files_format_and_content: gene_exp.diff is a tab separated text file of the Cuffdiff output for differential gene expression analysis of the following groups: WT double positive T cells (WT_GFP biological replicates 1, 2), FLT3-ITD leukemia (WT_FLT3 biological replicates 1, 2), and Dnmt3a knockout FLT3-ITD eluekmia (KO3a_FLT3 biological replicates 1 and 2). The remaining files are tab separated text files of the Cufflinks output for gene level expression abundance measurements produced by Cufflinks for each sample.

source_name: Bone Marrow

growth_protocol: Sca1+ enriched Dnmt3a KO or WT murine bone marrow cells were transduced with retroviruses expressing MSCV-FLT3-ITD-IRES-GFP or MSCV-GFP transgenes and transplanted into lethally irradiated recipients by retro-orbital injections. Freshly sorted donor-derived mouse thymus and bone marrow cells (CD4+CD8+)  from each genotype were collected from transplant recipients.

extract_protocol:
Extract RNA using Qiagen Allprep DNA/RNA mini kit.
Tru-Seq RNA sample prep kit

treatment_protocol: PolyA selection

value: Bone marrow

value: Leukemic cells


title: WT3a_FLT3_3 RNA-seq

description: Biological replicate 3 of FLT3-ITD leukemia. Donor whole bone marrow cells were subjected to to retroviral transduction and transplantation

value: thymus


title: KO3a_FLT3_RRBS_2 RRBS

description: Biological replicate 2 of Dnmt3aKO/FLT3-ITD leukemia. Donor whole bone marrow cells were subjected to retroviral transduction and transplantation

data_processing:
Base quality- and adapter-trimmed Fastq files were aligned with bsmap 2.73 in RRBS mode using the following parameters: -g 1 -w 5 -D C-CGG -p 8 -R -s 12 -S 42 -u; methylation ratios were calculated with the bsmap utility script methratio.py using the following parameters: -z --ct-snp=no-action
Genome_build: mm9
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context (2nt upstream to 2nt downstream in Watson strand direction), methylation ratio, number of effective total C+T counts on this locus, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

growth_protocol: Bulk or Sca1+ enriched Dnmt3a KO or WT murine bone marrow cells were transduced with retroviruses expressing MSCV-FLT3-ITD-IRES-GFP or MSCV-GFP transgenes and transplanted into lethally irradiated recipients by retro-orbital injections. Whole bone marrow cells from each genotype were collected from transplant recipients.

value: bone marrow


title: WT3a_FLT3_RRBS_2 RRBS

description: Biological replicate 2 of FLT3-ITD leukemia RRBS. Donor whole bone marrow cells were subjected to to retroviral transduction and transplantation


title: KO3a_FLT3_RRBS_1 RRBS

description: Biological replicate 1 of Dnmt3aKO/FLT3-ITD leukemia. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation


title: KO3a_FLT3_1 RNA-seq


title: WT3a_FLT3_2 RNA-seq

description: Biological replicate 2 of FLT3-ITD leukemia. Donor bone marrow cells were enriched for ckit prior to retroviral transduction and transplantation


title: KO3a_GFP_2 RNA-seq

description: Biological replicate 2 of CD4/CD8 double positive thymocytes from Dnmt3aKO;GFP control. Donor bone marrow cells were enriched for ckit prior to retroviral transduction and transplantation

value: Murine thymus derived CD4/CD8 double positive T cells


title: WT3a_FLT3_RRBS_1 RRBS

description: Biological replicate 1 of FLT3-ITD leukemia RRBS. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation


title: WT3a_FLT3_1 RNA-seq

description: Biological replicate 1 of FLT3-ITD leukemia. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation


title: WT_GFP_1 RNA-seq_T2

description:
Technical replicate 2 of biological replicate 1 of CD4/CD8 double positive thymocytes from WT GFP control
Processed data for GSM1517787 is available on the GSM1517786 record.


title: WT_GFP_2 RNA-seq_T2

description:
Technical replicate 2 of biological replicate 2 of CD4/CD8 double positive thymocytes from WT GFP control
Processed data for GSM1517789 is available on the GSM1517788 record.


title: WT_GFP_2 RNA-seq_T1

description: Technical replicate 1 of biological replicate 2 of CD4/CD8 double positive thymocytes from WT GFP control


title: WT_GFP_1 RNA-seq_T1

description: Technical replicate 1 of biological replicate 1 of CD4/CD8 double positive thymocytes from WT GFP control


title: PC15_MYS

city: Pamplona

first: Raul

last: Castanera

address: Campus Arrosadia, DPTO Producción Agraria

country: Spain

institute: Public University of Navarre

data_processing:
csfasta and qual files converted to fastq
Mapping performed with Bowtie
Transcript quantifcation performed with RSEM
Genome_build: GCA_000697685.1
Supplementary_files_format_and_content: PC15_TE_annotation_v1.5.gff: Annotation of transposable elements (TE) in PC15 strain, in gff format. PC9_TE_annotation_v1.5.gff: Annotation of transposable elements  (TE)  in PC15 strain, in gff format. PC15_TEs.genes.results: Expression of each TE in PC15 (standard output of RSEM).  PC9_Tes.genes.results: Expression of each TE in PC9 (standard output of RSEM)

organism: Pleurotus ostreatus

source_name: P. ostreatus mycelia

growth_protocol: Submerged fermentation, orbital shaking

extract_protocol:
Rneasy columns
Libraries were constructed from polyA fragments using the Whole transcriptome analysis kit, according to manufacturer's reccomendations.

tag: medium

value: Malt Yeast Sucrose

tag: developmental stage

value: Mycelium in exponential growth phase


title: PC9_MYS


title: C_difficile_Plate_1

status: Public on May 18 2016

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Reads were aligned to the reference genome using Bowtie2 v. 2.1.0
The resulting sorted aligned reads were analyzed with Cufflinks to measure the relative abundance.The expression of each transcript was quantified as FPKM.  Data normalization and differential expression (DE) analysis were done using the DESeq package from Bioconductor. A cutoff false discovery rate adjusted p-value (or q-value) of less than 0.05 was used to select significant DE genes
Genome_build: NC_013316.1

organism: Clostridioides difficile R20291

source_name: Clostridium difficile cells

growth_protocol: For planktonic samples, overnight culture in brain heart infusion media supplemented with 0.5% yeast extract and 0.1% L-cysteine (BHIS) was mixed 1:10 with fresh BHIS and grown with shaking for 6 h before mixing 1:1 with RNAProtect™ (Qiagen). Biofilm samples were grown for 1 week in glass jars containing 8 mm glass beads. The glass beads were added in order to increase surface area and maximize RNA yields. BHIS medium was changed daily and 6 h prior to cell harvest. To harvest adherent cells (biofilm), media was removed and the beads rinsed with fresh media before covering with RNAProtect™ and subjecting to vigorous shaking for 2 min. For plate growth samples, overnight culture was streaked onto Columbia blood agar plates (BD Biosciences) and kept in the anaerobic chamber for 24 hours prior to a three-day room temperature growth in an anaerobic GasPak container (BD Biosciences). Plates were returned to the anaerobic chamber for cell harvesting and placement into RNAprotect™. All samples were stored at -80°C until used for RNA-sequencing.

extract_protocol:
The RNeasy™ RNA purification kit (Qiagen) was used per the manufacturer’s instructions. Total RNA samples were treated with DNase I (Invitrogen). The level of ribosomal RNA present in total RNA samples was reduced prior to library construction using the Ribo-Zero™ Gram Positive Bacteria rRNA Removal Kit (Epicentre Technologies, Madison, WI).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth

value: plate


title: C_difficile_Planktonic_2

value: planktonic


title: C_difficile_Biofilm_3

value: biofilm


title: KO3a_GFP_1 RNA-seq

description: Biological replicate 1 of CD4/CD8 double positive thymocytes from Dnmt3a KO;GFP control. Donor bone marrow cells were enriched for ckit prior to retroviral transduction and transplantation


title: C_difficile_Planktonic_1


title: E11.0_T1_14M1


title: C_difficile_Plate_2


title: C_difficile_Biofilm_1


title: C_difficile_Biofilm_2


title: C_difficile_Plate_3


title: S_aureus_16h

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

description:
Bacterial cells, pelleted
rRNA-depleted
Processed data file: S_aureus_3h_vs_16h.xlsx

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis.
Reads corresponding to ribosomal RNA were filtered out and removed.
Expression values for coding genes as well as sRNA track were calculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench.
Samples were compared using "Set Up Experiment" tool for transcriptomic analysis and standardized via quantile normalization using CLC Genomics Workbench.
Expression values were exported into Excel files.
Genome_build: The S. aureus USA300 genome file was accessed from: https://dx.doi.org/10.6084/m9.figshare.2061132.v1
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in Excel format.

organism: Staphylococcus aureus

source_name: Bacterial cells, stationary growth phase

growth_protocol: Strains were grown in TSB medium at 37°C with shaking for 3h or 16h.

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit, and contaminating DNA was removed by treatment with Ambion DNA-free.
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies.

treatment_protocol: Samples were stored at -80°C prior to RNA extraction.

tag: strain/background

value: USA300 Houston

tag: genotype/variation

value: wild-type

tag: growth medium

value: TSB

tag: growth conditions (time/temp/shaking)

tag: growth phase

value: stationary


title: S_aureus_3h

source_name: Bacterial cells, exponential growth phase

value: exponential


title: Mouse CHi-C Biological Replicate 1

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

description:
CHiC
processed data file: mESC_merge_final_seqmonk.txt.gz, mESC_merge_final_washU_text.txt.gz

data_processing:
Library strategy: CHi-C
Standard Illumina base-calling pipeline.
HiCUP v0.5.3  (using Bowtie v1.1.0) mapped sequence reads to the relevant genome assembly and removed common Hi-C artefacts.
Filtered reads-pairs so that at least one member of the pair mapped to a bait fragment.
CHiCAGO v1.0.0 identifies significant fragment-fragment CHi-C interactions
Genome_build: Mouse (mm9)
Supplementary_files_format_and_content: Text files listing statistically significant CHi-C interactions. For the SeqMonk format files, interacting fragments are referenced on adjacent lines. The columns refer to: chromosome, start, end, name, number of reads, interaction score. For the WashU Format files, interacting fragments are referenced on the same line. The columns refer to: chromosome, start, end, chromosome, start, end, interaction score.

source_name: Mouse Embryonic Stem Cells

growth_protocol: GM12878 cell culture conditions  GM12878 cells were obtained from the Coriell Cell Repositories and grown in suspension in RPMI-1640 medium supplemented with 2 mM glutamine, 15% FBS and 1% penicillin-streptomycin under standard culture conditions.    Mouse ESC culture conditions  J1 (129S4/SvJae) murine ESCs were expanded on irradiated primary embryonic fibroblasts under standard pluripotent conditions (15% FBS) on tissue culture plates coated with 0.1% gelatin. To harvest the cells and remove contaminating feeder cells, ESCs were trypsinized and passaged twice for 30 min each.

extract_protocol:
Cell pellets were incubated in 50 ml ice-cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal CA-630, protease inhibitor cocktail (Roche)) for 30 minutes on ice, followed by a centrifugation to pellet the cell nuclei (650 x g for 5 minutes). Nuclei were resuspended in 1.25 x NEBuffer 2, SDS was added (0.3% final concentration) and the nuclei were incubated at 37˚C with agitation (950 rpm) for one hour. Triton X-100 was added at a final concentration of 1.7 % and the nuclei were incubated at 37˚C with agitation (950 rpm) for one hour. Restriction digest was performed overnight at 37˚C with agitation (950 rpm) with HindIII (NEB; 1500 units per 5 million cells). The restriction sites were then filled in with Klenow (NEB) using biotin-14-dATP (Life Technologies), dCTP, dGTP and dTTP (all at a final concentration of 30 µM) for 60 minutes at 37˚C. After addition of SDS (1.42 % final concentration) and incubation at 65˚C with agitation (950 rpm) for 25 minutes, ligation was performed for four hours at 16˚C (50 units T4 DNA ligase (Life Technologies) per 5 million cells starting material) in a total volume of 8.2 ml ligation buffer (50 mM Tris-HCl, 10 mM MgCl2, 1 mM ATP, 10 mM DTT, 100 µg/ml BSA, 0.9 % Triton X-100) per 5 million cells starting material. Reverse crosslinking (65˚C overnight in the presence of Proteinase K (Roche)) was followed by RNase A (Roche) treatment and two sequential phenol/chloroform extractions. The DNA was precipitated in the presence of sodium acetate 3 M pH 5.2 (1/10 volume) and ethanol (2.5 x volumes) overnight at -20˚C. After three consecutive washes with 70% ethanol, the DNA concentration was determined using Quant-iT Pico Green (Life Technologies). 40 µg of Hi-C library DNA were incubated with T4 DNA polymerase (NEB) for 4 hours at 20˚C to remove of biotin from non-ligated fragment ends, followed by phenol/chloroform purification and DNA precipitation overnight at -20˚C, followed by a 70% ethanol wash.
Sonication was performed to obtain DNA fragments with a size peak around 400 bp (Covaris E220 settings: duty factor: 10%; peak incident power: 140W; cycles per burst: 200; time: 55 seconds). The sonicated DNA was end-repaired (T4 DNA polymerase, T4 DNA polynucleotide kinase, Klenow (all NEB)) for 30 minutes at room temperature, followed by DNA purification (Qiagen PCR purification kit). dATP was added with Klenow exo- (NEB) for 30 minutes at 37˚C, and the enzyme was heat-inactivated (20 minutes at 65˚C). A double size selection using AMPure XP beads (Beckman Coulter) was performed: first, the ratio of AMPure XP beads solution volume to DNA sample volume was adjusted to 0.6:1. After incubation for 10 minutes at room temperature, the sample was transferred to a magnetic separator (DynaMag-2 magnet; Life Technologies), and the supernatant was transferred to a new eppendorf tube. The ratio of AMPure XP beads solution volume to DNA sample volume was then adjusted to 0.9:1 final. After incubation for 10 minutes at room temperature, the sample was transferred to a magnet (DynaMag-2 magnet; Life Technologies). Following two washes with 70% ethanol, the DNA was eluted in 100 µl of TLE (10 mM Tris-HCl pH 8.0; 0.1 mM EDTA). Biotin-marked ligation products were isolated using MyOne Streptavidin C1 Dynabeads (Life Technologies) on a DynaMag-2 magnet (Life Technologies) in binding buffer (5 mM Tris pH8, 0.5 mM EDTA, 1 M NaCl) for 30 minutes at room temperature, followed by two washes in binding buffer, and one wash in ligation buffer (NEB). PE adapters (Illumina) were ligated onto Hi-C ligation products bound to streptavidin beads for 2 hours at room temperature (T4 DNA ligase NEB, in ligation buffer, slowly rotating). After washes in wash buffer (5 mM Tris, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) and binding buffer, the DNA-bound beads were resuspended in a final volume of 30 µl NEBuffer 2. Bead-bound Hi-C DNA was amplified with 7 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). The concentration and size distribution of Hi-C library DNA after PCR amplification was determined by Bioanalyzer profiles (Agilent Technologies). To capture ligation products containing promoter sequences, 500 ng of Hi-C library DNA was lyophilized using a vacuum concentrator (Savant SPD 2010) at 45˚C. The DNA pellet was resuspended in 3.4 µl H2O, and custom hybridization blockers (Agilent Technologies) were added to the Hi-C DNA. Hybridization buffers and the custom-made RNA capture bait system (Agilent Technologies: biotinylated RNAs targeting the HindIII restriction fragment ends of 22,225 mouse gene promoters, and of 21,841 human gene promoters, respectively) were prepared according to the manufacturer’s instructions (SureSelect Target Enrichment, Agilent Technologies). The Hi-C library DNA was mixed with hybridization buffer, denatured for 5 minutes at 95˚C, and then incubated with the capture bait system at 65˚C. After 24 hours, biotin pulldown (MyOne Streptavidin T1 Dynabeads; Life Technologies) and washes were performed following the SureSelect Target enrichment protocol (Agilent Technologies). After the final wash, the beads were resuspended in 30 µl NEBuffer 2, without prior DNA elution. A post-capture PCR (four amplification cycles using Illumina PE PCR 1.0 and PE PCR 2.0 primers) was performed and the Capture Hi-C libraries were paired-end sequenced (HiSeq 1000, Illumina).

treatment_protocol: 30 to 40 million cells were fixed in 2 % formaldehyde (Agar Scientific) for 10 minutes, and the reaction was quenched by the addition of ice-cold glycine (0.125 M final concentration). Cells were collected (centrifugation 400 x g for 10 minutes), washed with PBS, and collected again (400 x g for 10 minutes). The supernatant was removed and the cell pellet was immediately frozen in liquid nitrogen and stored at -80˚C.

tag: cell type

value: Embryonic Stem Cells


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 5 of differentiation transduced with shRNA Nonsilencing rep 1

city: Royal Parade

last: Keniry

state: Victoria

department: Molecular Medicine

country: Australia

institute: The Waler and Eliza Hall Institute of Medical Research

data_processing:
Instrument control: HiSeq control software v2.0.12.0
Base calling and quality scoring:Illumina RTA 1.13.48
fastq.gz file generation and de-multiplexing: CASAVA pipeline version 1.8.2
Sequenced reads were mapped using the align function in the Rsubread package (version 1.10.5, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Allele-specific counts were obtained using samtools pileup for SNPs between the Mus musculus castaneus and Mus musculus domesticus strains on the X chromosome listed in the Mouse Genomes Project vcf file
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file contains read counts for each SNP position on the X chromosome split into reads that map to the 129 strain (ref) or the CAST strain (alt).
Supplementary_files_format_and_content: Read counts for each SNP position on the X chromosome split into reads that map to the 129 strain (ref) or the CAST strain (alt).

source_name: differentiated mouse embryonic stem cell

growth_protocol: ES cells were cultured on gelatin-coated tissue culture ware at 37°C in a humidified atmosphere with 5% (v/v) carbon dioxide and 5% (v/v) oxygen in 2i+LIF medium. ES cells were differentiated by seeding into 75% 2i+LIF medium 25% ES cell DMEM+FBS. After 24 hours, the medium was changed to 50% 2i+LIF medium 50% ES cell DMEM+FBS. After 48 hours, the medium was changed to 25% 2i+LIF medium 75% ES cell DMEM+FBS. After 72 hours, the cells were split and seeded at 10^4 cells per cm2 in 100% ES cell DMEM+FBS.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit.
RNA libraries were created with TruSeq RNA library preparation v2 kits.

treatment_protocol: ES cells were transduced with retrovirus on day 2 of differentiation, when in 50% 2i plus LIF, 50% serum containing DME media containing 4 μg/mL polybrene and cells were selected with 3 µg/mL puromycin after 24 hours.

value: 129/C57 dams x CAST sires

value: E3.5 mouse embryo derived ES cell

tag: genotype

value: Setdb1+/+ Xist-deltaA/+

tag: shRNA

value: Nonsilencing

tag: sequencing protocol

value: single-end


title: Mouse CHi-C Biological Replicate 2

data_processing:
Library strategy: CHi-C
Standard Illumina base-calling pipeline.
HiCUP v0.5.3  (using Bowtie v1.1.0) mapped sequence reads to the relevant genome assembly and removed common Hi-C artefacts.
Filtered reads-pairs so that at least one member of the pair mapped to a bait fragment.
CHiCAGO v1.0.0 identifies significant fragment-fragment CHi-C interactions
Genome_build: Mouse (mm9)Supplementary_files_format_and_content: Text files listing statistically significant CHi-C interactions. For the SeqMonk format files, interacting fragments are referenced on adjacent lines. The columns refer to: chromosome, start, end, name, number of reads, interaction score. For the WashU Format files, interacting fragments are referenced on the same line. The columns refer to: chromosome, start, end, chromosome, start, end, interaction score.


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 5 of differentiation transduced with shRNA Setdb1.4 rep 2

tag: tissue


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 5 of differentiation transduced with shRNA Setdb1.6 rep 2

tag: strain


title: RRBS in female Setdb1+/+ Xist∆A/+  MEFs replicate 1

description: bisulfite treated DNA

data_processing:
Basecalls performed using CASAVA version 1.4
Adapter trimming was performed with TrimGalore
Sequencing reads were mapped to a bisulfite-converted mm10 genome with n-masked SNPs using Bismark
Reads were split into either to the 129 or CAST genomes using SNPsplit where C/T SNPs are excluded
Methylation calls were made using the Bismark Methylation Extractor
Genome_build: mm10
Supplementary_files_format_and_content: Allele specific methylation calls in text format

source_name: mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were obtained from E13.5 embryos. Cells were cultured in DMEM with 10% (v/v) FBS at 37°C and 10% (v/v) CO2.

extract_protocol:
DNA was extracted using the Qiagen DNeasy kit.
eRRBS libraries were created as previously published (Akalin et al. 2012)

treatment_protocol: MEFs were transduced with retrovirus in medium containing 4 μg/mL polybrene and cells were selected with 3–5 µg/mL puromycin after 24 hours.

value: E13.5 mouse embryo derived fibroblasts

value: single-end with dark cycle


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 3 of differentiation transduced with shRNA Setdb1.6 rep 2


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 5 of differentiation transduced with shRNA Nonsilencing rep 2


title: RRBS in female Setdb1+/+ Xist∆A/+  MEFs replicate 2

description: bisulfite treated DNA


title: RRBS in female Setdb1+/gt Xist∆A/+ MEFs replicate 1

description: bisulfite treated DNA

value: Setdb1+/gt Xist-deltaA/+


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 3 of differentiation transduced with shRNA Setdb1.6 rep 1


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 5 of differentiation transduced with shRNA Setdb1.6 rep 1


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 5 of differentiation transduced with shRNA Setdb1.4 rep 1


title: RRBS in female Setdb1+/+ Xist∆A/+  MEFs replicate 3

description: bisulfite treated DNA


title: Mouse Hi-C

description:
Hi-C
processed data file: significantInteractions_1Mb.txt.gz, significantInteractions_25kb_upto1Mb.txt.gz

data_processing:
Library strategy: Hi-C
Standard Illumina base-calling pipeline.
HiCUP v0.5.3  (using Bowtie v1.1.0) mapped sequence reads to the relevant genome assembly and removed common Hi-C artefacts.
Homer v4.7 used to identify statistically significant interactions in Hi-C data

extract_protocol:
Cell pellets were incubated in 50 ml ice-cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal CA-630, protease inhibitor cocktail (Roche)) for 30 minutes on ice, followed by a centrifugation to pellet the cell nuclei (650 x g for 5 minutes). Nuclei were resuspended in 1.25 x NEBuffer 2, SDS was added (0.3% final concentration) and the nuclei were incubated at 37˚C with agitation (950 rpm) for one hour. Triton X-100 was added at a final concentration of 1.7 % and the nuclei were incubated at 37˚C with agitation (950 rpm) for one hour. Restriction digest was performed overnight at 37˚C with agitation (950 rpm) with HindIII (NEB; 1500 units per 5 million cells). The restriction sites were then filled in with Klenow (NEB) using biotin-14-dATP (Life Technologies), dCTP, dGTP and dTTP (all at a final concentration of 30 µM) for 60 minutes at 37˚C. After addition of SDS (1.42 % final concentration) and incubation at 65˚C with agitation (950 rpm) for 25 minutes, ligation was performed for four hours at 16˚C (50 units T4 DNA ligase (Life Technologies) per 5 million cells starting material) in a total volume of 8.2 ml ligation buffer (50 mM Tris-HCl, 10 mM MgCl2, 1 mM ATP, 10 mM DTT, 100 µg/ml BSA, 0.9 % Triton X-100) per 5 million cells starting material. Reverse crosslinking (65˚C overnight in the presence of Proteinase K (Roche)) was followed by RNase A (Roche) treatment and two sequential phenol/chloroform extractions. The DNA was precipitated in the presence of sodium acetate 3 M pH 5.2 (1/10 volume) and ethanol (2.5 x volumes) overnight at -20˚C. After three consecutive washes with 70% ethanol, the DNA concentration was determined using Quant-iT Pico Green (Life Technologies). 40 µg of Hi-C library DNA were incubated with T4 DNA polymerase (NEB) for 4 hours at 20˚C to remove of biotin from non-ligated fragment ends, followed by phenol/chloroform purification and DNA precipitation overnight at -20˚C, followed by a 70% ethanol wash.
Sonication was performed to obtain DNA fragments with a size peak around 400 bp (Covaris E220 settings: duty factor: 10%; peak incident power: 140W; cycles per burst: 200; time: 55 seconds). The sonicated DNA was end-repaired (T4 DNA polymerase, T4 DNA polynucleotide kinase, Klenow (all NEB)) for 30 minutes at room temperature, followed by DNA purification (Qiagen PCR purification kit). dATP was added with Klenow exo- (NEB) for 30 minutes at 37˚C, and the enzyme was heat-inactivated (20 minutes at 65˚C). A double size selection using AMPure XP beads (Beckman Coulter) was performed: first, the ratio of AMPure XP beads solution volume to DNA sample volume was adjusted to 0.6:1. After incubation for 10 minutes at room temperature, the sample was transferred to a magnetic separator (DynaMag-2 magnet; Life Technologies), and the supernatant was transferred to a new eppendorf tube. The ratio of AMPure XP beads solution volume to DNA sample volume was then adjusted to 0.9:1 final. After incubation for 10 minutes at room temperature, the sample was transferred to a magnet (DynaMag-2 magnet; Life Technologies). Following two washes with 70% ethanol, the DNA was eluted in 100 µl of TLE (10 mM Tris-HCl pH 8.0; 0.1 mM EDTA). Biotin-marked ligation products were isolated using MyOne Streptavidin C1 Dynabeads (Life Technologies) on a DynaMag-2 magnet (Life Technologies) in binding buffer (5 mM Tris pH8, 0.5 mM EDTA, 1 M NaCl) for 30 minutes at room temperature, followed by two washes in binding buffer, and one wash in ligation buffer (NEB). PE adapters (Illumina) were ligated onto Hi-C ligation products bound to streptavidin beads for 2 hours at room temperature (T4 DNA ligase NEB, in ligation buffer, slowly rotating). After washes in wash buffer (5 mM Tris, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) and binding buffer, the DNA-bound beads were resuspended in a final volume of 30 µl NEBuffer 2. Bead-bound Hi-C DNA was amplified with 7 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). The concentration and size distribution of Hi-C library DNA after PCR amplification was determined by Bioanalyzer profiles (Agilent Technologies). The Hi-C library were paired-end sequenced (HiSeq 1000, Illumina).  Please note: this is a regular Hi-C library, not a CHi-C library.


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 3 of differentiation transduced with shRNA Nonsilencing rep 2


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 3 of differentiation transduced with shRNA Setdb1.4 rep 1


title: C_difficile_Planktonic_3


title: RRBS in female Setdb1+/gt Xist∆A/+ MEFs replicate 2

description: bisulfite treated DNA


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 0 of differentiation rep 1

source_name: mouse embryonic stem cell


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 0 of differentiation rep 2


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 3 of differentiation transduced with shRNA Setdb1.4 rep 2


title: WCE in female Setdb1+/gt Xist∆A/+ MEFs replicate 2

description:
sonicated genomic DNA
Used as a control for Setdb1 peak calling

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seqreads were aligned to the mm10 genome assembly using bowtie2
Setdb1 peaks were called using MACS version 2 with the following setting: callpeak (call peaks from alignment), pvalue(0.001) using the WCE data as control
Histone peaks were called using the in built MACS style peak caller within the Seqmonk software package with the folllowing settings: fragment length (10000), pvalue(0.00001), using H3 data as a control.
Aligned reads were split into allele specific files using SNPsplit
Genome_build: mm10
Supplementary_files_format_and_content: Setdb1 peak locations produced by MACS2 (.xls) and histone peak locations called by Seqmonk (.txt)

extract_protocol:
For ChIP-seq, nuclei were isolated from formaldehyde crosslinked NSCs and chromatin was fragmented by sonication. Chromatin immunoprecipitation was performed with corresponding antibodies. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking.
Sequencing libraries was generated with Illumina's TruSeq DNA Sample Preparation Kit according to manufacturer's instruction.

tag: chip antibody


title: RNAseq in female Setdb1+/+ Xist∆A/+ ES cells on day 3 of differentiation transduced with shRNA Nonsilencing rep 1


title: H3 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 2

description:
Immunoprecipitated DNA
Used as a control for histone ChIP peak calling


title: WCE in female Setdb1+/+ Xist∆A/+  MEFs replicate 1


title: WCE in Male Setdb1+/+ X/Y MEFs replicate 1

value: Setdb1+/+ X/Y


title: H3 ChIP in Male Setdb1+/+ X/Y MEFs replicate 2


title: H3 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 1


title: H3K27me3 ChIP in Male Setdb1+/+ X/Y MEFs replicate 3

description:
Immunoprecipitated DNA
Male_K27.txt


title: H3K27me3 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 2

description:
Immunoprecipitated DNA
GT_K27.txt


title: H3 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 2


title: H3K27me3 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 1

description:
Immunoprecipitated DNA
GT_K27.txt


title: H3 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 3


title: H3K27me3 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 1

description:
Immunoprecipitated DNA
Female_K27.txt


title: H3K9me3 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 2

description:
Immunoprecipitated DNA
GT_K9me3.txt


title: H3K27me3 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 3

description:
Immunoprecipitated DNA
Female_K27.txt


title: H3 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 1


title: H3K27me3 ChIP in Male Setdb1+/+ X/Y MEFs replicate 1

description:
Immunoprecipitated DNA
Male_K27.txt


title: H3K27me3 ChIP in Male Setdb1+/+ X/Y MEFs replicate 2

description:
Immunoprecipitated DNA
Male_K27.txt


title: H3K9me3 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 3

description:
Immunoprecipitated DNA
Female_K9me3.txt


title: H3K27me3 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 2

description:
Immunoprecipitated DNA
Female_K27.txt


title: H3K9me3 ChIP in Male Setdb1+/+ X/Y MEFs replicate 3

description:
Immunoprecipitated DNA
Male_K9me3.txt


title: H3K9me3 ChIP in Male Setdb1+/+ X/Y MEFs replicate 1

description:
Immunoprecipitated DNA
Male_K9me3.txt


title: H3K9me3 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 2

description:
Immunoprecipitated DNA
Female_K9me3.txt


title: H3K9me2 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 1

description:
Immunoprecipitated DNA
GT_K9me2.txt


title: H3K9me3 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 1

description:
Immunoprecipitated DNA
Female_K9me3.txt


title: H3K9me2 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 2

description:
Immunoprecipitated DNA
GT_K9me2.txt


title: H3K9me2 ChIP in Male Setdb1+/+ X/Y MEFs replicate 3

description:
Immunoprecipitated DNA
Male_K9me2.txt


title: H3K9me2 ChIP in Male Setdb1+/+ X/Y MEFs replicate 2

description:
Immunoprecipitated DNA
Male_K9me2.txt


title: H3K9me3 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 1

description:
Immunoprecipitated DNA
GT_K9me3.txt


title: H3K9me2 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 3

description:
Immunoprecipitated DNA
Female_K9me2.txt


title: H3 ChIP in Male Setdb1+/+ X/Y MEFs replicate 3


title: H3K9me2 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 2

description:
Immunoprecipitated DNA
Female_K9me2.txt


title: H3K9me2 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 1

description:
Immunoprecipitated DNA
Female_K9me2.txt


title: H3 ChIP in Male Setdb1+/+ X/Y MEFs replicate 1


title: H3K9me3 ChIP in Male Setdb1+/+ X/Y MEFs replicate 2

description:
Immunoprecipitated DNA
Male_K9me3.txt


title: Setdb1 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 2

description:
Immunoprecipitated DNA
GeneTrapAll_p0.001_downsample_peaks.xls

value: Setdb1 (Santa Cruz Biotechnology, sc-66884, lot L1812)


title: Setdb1 ChIP in Male Setdb1+/+ X/Y MEFs replicate 2

description:
Immunoprecipitated DNA
MaleAll_p0.001_downsample_peaks.xls


title: Setdb1 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 2

description:
Immunoprecipitated DNA
FemaleAll_p0.001_downsample_peaks.xls


title: TCR47B.BC4

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description:
TCR-beta RNA
H15.1-Blood-TCRB

data_processing:
Library strategy: TCR-seq
TCRseq libraries, error correction:  Raw paired-end data (FASTQ output option on MiSeq) was processed for sequencing error correction using a custom software pipeline.  Each mate-pair was first validated using the Burrows-Wheeler Aligner local alignment algorithm, then fully aligned (Smith-Waterman) for site-by-site comparison. Overlapping regions were individually scanned for nucleotide consistency at every position. Mismatches were resolved as follows:  1) If the mismatch occurred at a mapped position, the reference allele was selected. 2) If the location was unmapped or varied from the reference, the nucleotide identity was selected from the mate-paired stands by base quality, if the difference in quality differed by an order of magnitude. 3) If the quality score of the site on both paired reads was similar (<10x difference), the nucleotide identity from R1 was used by default. The output reads were constructed by merging the mate-pair overlapping, corrected regions, and appending the 3’ and 5’ overhangs.
TCRseq libraries, demultiplexing:  Internal 6mer barcode sequences (available through the support documents at [http://media.wix.com/ugd/c9f231_5f7f780864ec41f8a5cc57ffcb2a3277.pdf] were identified within the merged, error-corrected reads using string-search algorithm with linear average search time, whereby a 14-nt sliding window scanned the read from the end proximal to the barcode location (J cassette), the first eight nucleotides corresponding to the end of the conserved constant region of either alpha –chain or beta –chain, and the remaining six nucleotides constituting the manufacturer barcode. Every possible combination of 14-nucleotides was searched for simultaneously using a preprocessed hash table, with a single nucleotide mismatch allowed in each of the constant region and the barcode region, resulting in the assignment of each read to a barcode, or flagging it as “unmatched.”  All reads and their assigned barcode ID proceeded to CDR3 motif filtering.
TCRseq libraries, in silico translation and filtering:  Error corrected output files were in silico translated as previously described, using a custom pipeline writen in Perl, then filtered for sequences encoding an in-frame C/FXFG motif with no intervening stop codons, and thus a productive CDR3.  This output was tabulated by V-J cassette combination, aaCDR3, and combined VJ+aaCDR3 clonotype identifier, totCDR3 (Supplementary Table S2), in which a single count represents an error corrected R1-R2 mate pair of reads.
TCRseq libraries, V and J cassette mapping:  The presence of V or J cassettes was initially identified based on the coordinates to which the read was mapped in a GRCh37.p8 human reference, in which the Beta-chain on Chr. 7 had been masked (location 7q34 91557-667340) and replaced by a patch from Genbank (GRCh37.p9), which offered more up-to-date sequence data on this locus. Our cassette reference contained the entire set of amino acid sequences and CDR3 associated motifs, including pseudogenes, provided by the ImMunoGeneTics (IMGT) information system, for a comprehensive analysis. Sequences were translated into all three reference frames, and the correct CDR3 sequence identified based on the conserved cysteine in the V cassette and the conserved four residue motif in the J cassette.  In order to define the interval on which the TRAV and TRBV cassette family members might be resolved, we used the TCRseq data from all subjects to find the most uptream nucleotide position for each V in the reference sequence included in ≥95% of its mapped reads (for V).  Within this interval and exclusive of the final 5nt, the hamming distances between members of the same family were calculated.  All cases in which two or more validated cassettes were found to have a hamming distance of 0 within the shorter of the two nt intervals were annotated as indistinguishable (e.g. TRBV6-2/3).  Non-validated (pseudogene and ORF) V and J cassettes to which < 100 reads per library were mapped (across all libraries in this study) were considered spurious and discarded, while non-validated but productive, sequence-resolvable cassettes to which > 100 reads per library were mapped were included in the final data set despite their lack of previous validation (TRBV12-2, TRBV26, and TRBV7-1).
RNAseq libraries were mapped to the GRCh37 genome and Illumina iGenomes transcriptome using Tophat 2 and uniquely mapped read counts were computed using HTSeq. The resulting read counts were then normalized using the 'estimateSizeFactors' function in DESeq2.
Genome_build: GRCh37.p8, with TCRb locus (7q34 91557-667340) masked and replaced by a patch from Genbank (GRCh37.p9); V and J cassette sequences for reference mapping imported from IMGT
Supplementary_files_format_and_content: [TCRseq]  text files in tsv format that contain the VJ cassette combination, number of reads, VJ cassette gene names, amino acid CDR3 sequence, nucleotide CDR3 sequence, and insertion length for each observed clone.
Supplementary_files_format_and_content: [RNAseq] Excel spreadhseet containing the number of uniquely mapped reads associated with each gene calculated using HTSeq.

source_name: subject 15 (healthy), TCR-beta repertoire of peripheral blood, aliquot 1

extract_protocol:
Total RNA was isolated from cryofrozen human samples using the TissueLyzer system with Qiazol and steel beads (Qiagen).  RNAseq was performed on total RNA through the Columbia Genome Center, and concentration and RIN score obtained by BioAnalyzer.  For TCR library preparation, mRNA was isolated using magnetic oligo-dT Dynabeads (Life Technologies), according to manufacturer protocol, and final concentration determined by Qubit (Life Technologies).  Total RNA was obtained from 2.5x10^6 PBMCs using the Qiagen RNeasy system according to manufacturer instructions.
We utilized the commercially available iRepertoire primer set for nested amplicon rescued multiplex PCR (arm-PCR) of the complementarity-determining region 3 (CDR3) of the human TCR and TCR chains and addition of adaptors for Illumina platform sequencing.  ~400ng of mRNA or total RNA was included for tumor libraries or PBMC libraries respectively.  In our modification of the manufacturer’s protocol, reverse transcription was conducted with a one-step reverse transcription and amplification kit (Qiagen) at 50°C for 40min, 95°C for 15min, seventeen non-exponential thermocycles (94°C/30s, 60°C/2min, 72°C/30s) and ten exponential thermocycles (94°C/30s, 72°C/2min).  PCR1 product was purified using AmpureX-100 magnetic beads (Agencourt).  Secondary amplification of 40% of the resulting product was performed by multiplex PCR (Qiagen), allowing addition of Illumina adapter sequences, with 34 thermocycles (94°C/30s, 55°C/30s, 72°C/30s).  Libraries were purified by agarose gel electrophoresis, cutting between 200-400bp (predicted amplicon size 210-310bp), gel extracted (Qiagen), and sequenced on an Illumina MiSeq, obtaining paired-end reads 220-250nt as described below.

tag: individual

value: subject 15 (healthy)

value: peripheral blood

tag: tcr repertoire

value: TCR-beta


title: TCR3518A.BC5

description:
TCR-alpha RNA
H15.2-Blood-TCRA

source_name: subject 15 (healthy), TCR-alpha repertoire of peripheral blood, aliquot 2

value: TCR-alpha


title: TCR3518B.BC6

description:
TCR-beta RNA
H15.2-Blood-TCRB

source_name: subject 15 (healthy), TCR-beta repertoire of peripheral blood, aliquot 2


title: TCR62B.BC8

description:
TCR-beta RNA
G14-Blood-TCRB

source_name: patient 14 (glioblastoma), TCR-beta repertoire of peripheral blood

value: patient 14 (glioblastoma)


title: Setdb1 ChIP in Male Setdb1+/+ X/Y MEFs replicate 1


title: TCR77B.BC2

description:
TCR-beta RNA
L06-Brain-TCRB

source_name: patient 6 (low-grade glioma), TCR-beta repertoire of brain tumor tissue, seq run 2

value: patient 6 (low-grade glioma)

value: brain


title: TCR62A.BC2

description:
TCR-alpha RNA
G14-Blood-TCRA

source_name: patient 14 (glioblastoma), TCR-alpha repertoire of peripheral blood


title: TCR62B.BC4

description:
TCR-beta RNA
G14-Brain-TCRB

source_name: patient 14 (glioblastoma), TCR-beta repertoire of brain tumor tissue


title: H3K9me2 ChIP in Male Setdb1+/+ X/Y MEFs replicate 1

description:
Immunoprecipitated DNA
Male_K9me2.txt

value: 129/C57 dams x CAST sires


title: TCR106B.BC2

description:
TCR-beta RNA
G13-Blood-TCRB

source_name: patient 13 (glioblastoma), TCR-beta repertoire of peripheral blood

value: patient 13 (glioblastoma)


title: TCR62A.BC3

description:
TCR-alpha RNA
G14-Brain-TCRA

source_name: patient 14 (glioblastoma), TCR-alpha repertoire of brain tumor tissue


title: TCR111A.BC1

description:
TCR-alpha RNA
G13-Blood-TCRA

source_name: patient 13 (glioblastoma), TCR-alpha repertoire of peripheral blood


title: TCR106A.BC1

description:
TCR-alpha RNA
G13-Brain-TCRA

source_name: patient 13 (glioblastoma), TCR-alpha repertoire of brain tumor tissue


title: TCR95B.BC6

description:
TCR-beta RNA
G12-Blood-TCRB

source_name: patient 12 (glioblastoma), TCR-beta repertoire of peripheral blood

value: patient 12 (glioblastoma)


title: TCR105B.BC2

description:
TCR-beta RNA
G13-Brain-TCRB

source_name: patient 13 (glioblastoma), TCR-beta repertoire of brain tumor tissue


title: TCR95A.BC5

description:
TCR-alpha RNA
G12-Blood-TCRA

source_name: patient 12 (glioblastoma), TCR-alpha repertoire of peripheral blood


title: TCR94B.BC8

description:
TCR-beta RNA
G12-Brain-TCRB

source_name: patient 12 (glioblastoma), TCR-beta repertoire of brain tumor tissue


title: TCR95A.BC7

description:
TCR-alpha RNA
G12-Brain-TCRA

source_name: patient 12 (glioblastoma), TCR-alpha repertoire of brain tumor tissue


title: TCR46A.BC3

description:
TCR-alpha RNA
H15.1-Blood-TCRA

source_name: subject 15 (healthy), TCR-alpha repertoire of peripheral blood, aliquot 1


title: Setdb1 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 3

source_name: mouse embryonic fibroblasts

value: Setdb1+/+ Xist-deltaA/+

value: Nonsilencing


title: Setdb1 ChIP in female Setdb1+/+ Xist∆A/+  MEFs replicate 1

value: E13.5 mouse embryo derived fibroblasts

value: single-end


title: TCR59B.BC8

description:
TCR-beta RNA
G11-Blood-TCRB

source_name: patient 11 (glioblastoma), TCR-beta repertoire of peripheral blood

value: patient 11 (glioblastoma)


title: Human CHi-C Biological Replicate 2

description:
CHiC
processed data file: GM_merge_final_seqmonk.txt.gz, GM_merge_final_washU_text.txt.gz

data_processing:
Library strategy: CHi-C
Standard Illumina base-calling pipeline.
HiCUP v0.5.3  (using Bowtie v1.1.0) mapped sequence reads to the relevant genome assembly and removed common Hi-C artefacts.
Filtered reads-pairs so that at least one member of the pair mapped to a bait fragment.
CHiCAGO v1.0.0 identifies significant fragment-fragment CHi-C interactions
Genome_build: Human (hg19)
Supplementary_files_format_and_content: Text files listing statistically significant CHi-C interactions. For the SeqMonk format files, interacting fragments are referenced on adjacent lines. The columns refer to: chromosome, start, end, name, number of reads, interaction score. For the WashU Format files, interacting fragments are referenced on the same line. The columns refer to: chromosome, start, end, chromosome, start, end, interaction score.

tag: cell line

value: B-Lymphocyte


title: Setdb1 ChIP in female Setdb1+/gt Xist∆A/+ MEFs replicate 1

value: Setdb1+/gt Xist-deltaA/+

value: Setdb1 (Santa Cruz Biotechnology, sc-66884, lot L1812)


title: Human CHi-C Biological Replicate 3


title: TCR59A.BC2

description:
TCR-alpha RNA
G11-Blood-TCRA

source_name: patient 11 (glioblastoma), TCR-alpha repertoire of peripheral blood

value: peripheral blood


title: TCR59B.BC4

description:
TCR-beta RNA
G11-Brain-TCRB

source_name: patient 11 (glioblastoma), TCR-beta repertoire of brain tumor tissue

value: TCR-beta


title: Setdb1 ChIP in Male Setdb1+/+ X/Y MEFs replicate 3

value: Setdb1+/+ X/Y


title: G11-Brain-RNAseq_JJ10

description:
poly(A)+ RNA
G11-Brain-RNAseq

data_processing:
TCRseq libraries, error correction:  Raw paired-end data (FASTQ output option on MiSeq) was processed for sequencing error correction using a custom software pipeline.  Each mate-pair was first validated using the Burrows-Wheeler Aligner local alignment algorithm, then fully aligned (Smith-Waterman) for site-by-site comparison. Overlapping regions were individually scanned for nucleotide consistency at every position. Mismatches were resolved as follows:  1) If the mismatch occurred at a mapped position, the reference allele was selected. 2) If the location was unmapped or varied from the reference, the nucleotide identity was selected from the mate-paired stands by base quality, if the difference in quality differed by an order of magnitude. 3) If the quality score of the site on both paired reads was similar (<10x difference), the nucleotide identity from R1 was used by default. The output reads were constructed by merging the mate-pair overlapping, corrected regions, and appending the 3’ and 5’ overhangs.
TCRseq libraries, demultiplexing:  Internal 6mer barcode sequences (available through the support documents at [http://media.wix.com/ugd/c9f231_5f7f780864ec41f8a5cc57ffcb2a3277.pdf] were identified within the merged, error-corrected reads using string-search algorithm with linear average search time, whereby a 14-nt sliding window scanned the read from the end proximal to the barcode location (J cassette), the first eight nucleotides corresponding to the end of the conserved constant region of either alpha –chain or beta –chain, and the remaining six nucleotides constituting the manufacturer barcode. Every possible combination of 14-nucleotides was searched for simultaneously using a preprocessed hash table, with a single nucleotide mismatch allowed in each of the constant region and the barcode region, resulting in the assignment of each read to a barcode, or flagging it as “unmatched.”  All reads and their assigned barcode ID proceeded to CDR3 motif filtering.
TCRseq libraries, in silico translation and filtering:  Error corrected output files were in silico translated as previously described, using a custom pipeline writen in Perl, then filtered for sequences encoding an in-frame C/FXFG motif with no intervening stop codons, and thus a productive CDR3.  This output was tabulated by V-J cassette combination, aaCDR3, and combined VJ+aaCDR3 clonotype identifier, totCDR3 (Supplementary Table S2), in which a single count represents an error corrected R1-R2 mate pair of reads.
TCRseq libraries, V and J cassette mapping:  The presence of V or J cassettes was initially identified based on the coordinates to which the read was mapped in a GRCh37.p8 human reference, in which the Beta-chain on Chr. 7 had been masked (location 7q34 91557-667340) and replaced by a patch from Genbank (GRCh37.p9), which offered more up-to-date sequence data on this locus. Our cassette reference contained the entire set of amino acid sequences and CDR3 associated motifs, including pseudogenes, provided by the ImMunoGeneTics (IMGT) information system, for a comprehensive analysis. Sequences were translated into all three reference frames, and the correct CDR3 sequence identified based on the conserved cysteine in the V cassette and the conserved four residue motif in the J cassette.  In order to define the interval on which the TRAV and TRBV cassette family members might be resolved, we used the TCRseq data from all subjects to find the most uptream nucleotide position for each V in the reference sequence included in ≥95% of its mapped reads (for V).  Within this interval and exclusive of the final 5nt, the hamming distances between members of the same family were calculated.  All cases in which two or more validated cassettes were found to have a hamming distance of 0 within the shorter of the two nt intervals were annotated as indistinguishable (e.g. TRBV6-2/3).  Non-validated (pseudogene and ORF) V and J cassettes to which < 100 reads per library were mapped (across all libraries in this study) were considered spurious and discarded, while non-validated but productive, sequence-resolvable cassettes to which > 100 reads per library were mapped were included in the final data set despite their lack of previous validation (TRBV12-2, TRBV26, and TRBV7-1).
RNAseq libraries were mapped to the GRCh37 genome and Illumina iGenomes transcriptome using Tophat 2 and uniquely mapped read counts were computed using HTSeq. The resulting read counts were then normalized using the 'estimateSizeFactors' function in DESeq2.
Genome_build: GRCh37.p8, with TCRb locus (7q34 91557-667340) masked and replaced by a patch from Genbank (GRCh37.p9); V and J cassette sequences for reference mapping imported from IMGT
Supplementary_files_format_and_content: [TCRseq]  text files in tsv format that contain the VJ cassette combination, number of reads, VJ cassette gene names, amino acid CDR3 sequence, nucleotide CDR3 sequence, and insertion length for each observed clone.
Supplementary_files_format_and_content: [RNAseq] Excel spreadhseet containing the number of uniquely mapped reads associated with each gene calculated using HTSeq.

source_name: patient 11 (glioblastoma), RNA-Seq of brain tumor tissue


title: TCR93B.BC6

description:
TCR-beta RNA
G10-Blood-TCRB

source_name: patient 10 (glioblastoma), TCR-beta repertoire of peripheral blood

value: patient 10 (glioblastoma)


title: TCR59A.BC3

description:
TCR-alpha RNA
G11-Brain-TCRA

source_name: patient 11 (glioblastoma), TCR-alpha repertoire of brain tumor tissue

value: TCR-alpha


title: G13-Brain-RNAseq_JJ1

description:
poly(A)+ RNA
G13-Brain-RNAseq

source_name: patient 13 (glioblastoma), RNA-Seq of brain tumor tissue

value: brain


title: Human CHi-C Biological Replicate 1


title: G08-Brain-RNAseq_PC048

description:
poly(A)+ RNA
G08-Brain-RNAseq

source_name: patient 8 (glioblastoma), RNA-Seq of brain tumor tissue

value: patient 8 (glioblastoma)


title: TCR93A.BC7

description:
TCR-alpha RNA
G10-Brain-TCRA

source_name: patient 10 (glioblastoma), TCR-alpha repertoire of brain tumor tissue


title: G10-Brain-RNAseq_PC051

description:
poly(A)+ RNA
G10-Brain-RNAseq

source_name: patient 10 (glioblastoma), RNA-Seq of brain tumor tissue


title: G09-Brain-RNAseq_JJ8

description:
poly(A)+ RNA
G09-Brain-RNAseq

source_name: patient 9 (glioblastoma), RNA-Seq of brain tumor tissue

value: patient 9 (glioblastoma)


title: TCR93B.BC8

description:
TCR-beta RNA
G10-Brain-TCRB

source_name: patient 10 (glioblastoma), TCR-beta repertoire of brain tumor tissue


title: TCR69A.BC5

description:
TCR-alpha RNA
G09-Blood-TCRA

source_name: patient 9 (glioblastoma), TCR-alpha repertoire of peripheral blood


title: G12-Brain-RNAseq_PC049

description:
poly(A)+ RNA
G12-Brain-RNAseq

source_name: patient 12 (glioblastoma), RNA-Seq of brain tumor tissue

value: patient 12 (glioblastoma)


title: TCR69B.BC4

description:
TCR-beta RNA
G09-Brain-TCRB

source_name: patient 9 (glioblastoma), TCR-beta repertoire of brain tumor tissue


title: L06-Brain-RNAseq_JJ2

description:
poly(A)+ RNA
L06-Brain-RNAseq

source_name: patient 6 (low-grade glioma), RNA-Seq of brain tumor tissue

value: patient 6 (low-grade glioma)


title: G07-Brain-RNAseq_JJ021

description:
poly(A)+ RNA
G07-Brain-RNAseq

source_name: patient 7 (glioblastoma), RNA-Seq of brain tumor tissue

value: patient 7 (glioblastoma)


title: TCR69A.BC3

description:
TCR-alpha RNA
G09-Brain-TCRA

source_name: patient 9 (glioblastoma), TCR-alpha repertoire of brain tumor tissue


title: L04-Brain-RNAseq_JJ4

description:
poly(A)+ RNA
L04-Brain-RNAseq

source_name: patient 4 (low-grade glioma), RNA-Seq of brain tumor tissue

value: patient 4 (low-grade glioma)


title: L05-Brain-RNAseq_JJ9

description:
poly(A)+ RNA
L05-Brain-RNAseq

source_name: patient 5 (low-grade glioma), RNA-Seq of brain tumor tissue

value: patient 5 (low-grade glioma)


title: TCR93A.BC5

description:
TCR-alpha RNA
G10-Blood-TCRA

source_name: patient 10 (glioblastoma), TCR-alpha repertoire of peripheral blood


title: N03-Brain-RNAseq_BJ025

description:
poly(A)+ RNA
N03-Brain-RNAseq

source_name: patient 3 (non-glioma), RNA-Seq of brain tissue

value: patient 3 (non-glioma)


title: TCR94A.BC5

description:
TCR-alpha RNA
G08-Blood-TCRA

source_name: patient 8 (glioblastoma), TCR-alpha repertoire of peripheral blood


title: G14-Brain-RNAseq_JJ016

description:
poly(A)+ RNA
G14-Brain-RNAseq

source_name: patient 14 (glioblastoma), RNA-Seq of brain tumor tissue

value: patient 14 (glioblastoma)


title: N02-Brain-RNAseq_JJ015

description:
poly(A)+ RNA
N02-Brain-RNAseq

source_name: patient 2 (non-glioma), RNA-Seq of brain tissue

value: patient 2 (non-glioma)