title: K_Input_2

status: Public on Apr 03 2019

first: Suman Kumar

last: Vodnala

address: 10 Center Drive

department: Surgery Branch

institute: NCI

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2
Peaks were called usingHomer (findPeaks H3k9Ac_Veh_1 -i Input_V -region -size 1000 -minDist 2500), Common peaks between two conditions are merged into a sinle file using bedtools. significantly different peaks between Ctrl / K+ is caluclated using Deseq2 integrated in the homer package.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized bam files were processed to deeptools to generate bigwig files

source_name: Primary T cells cultured for 10 days in Potassium

growth_protocol: CD8+ T cells from pmel mice were stimulated in vitro with 1 μM human gp100 peptide (10 μg/ml) for 5 days and secondary re-stimulation was done for 48hrs with plate-bound anti-CD3 (1 μg/ml; BD Biosciences) and soluble anti-CD28 (1 μg/ml; BD Biosciences) and expanded in culture medium containing 60 IU/mL of IL-2.

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

value: CD8 T cell


title: K2_H3K27me3

type: SRA

city: Bethesda

state: MD

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: strain

tag: chip antibody

value: H3K27me3_ChIP Grade (ab195477)


title: V_Input_1

source_name: Primary T cells cultured for 10 days in Ctrl


title: SH-SY5Y-NOTCH3IC_off_24 hrs

status: Public on Apr 04 2019

type: RNA

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Cell lines were transfected with human NOTCH3-IC. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate mRNA expression profiles.

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: SH-SY5Y-NOTCH3IC cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: The NOTCH3-IC transgene in SH-SY5Y-NOTCH3IC cells was induced with 100 ng/ml doxycycline in the culture medium.

value: Neuroblastoma cell line SH-SY5Y with doxycycline inducible expression of human NOTCH3-IC


title: WT 0 Gy rep 1

city: New York

first: Sanjay

last: Mukherjee

state: NY

address: 630 W 168th street

institute: Columbia University

description: Gene expression in mock irradiated WT mice whole blood

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60○C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65┬░C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37○C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded.  Data were filtered to exclude features not positive and significant in 25% of the samples, or those without at least a 1.5-fold change in expression values across the samples.

source_name: Whole blood from Wild-type 24h post mock irradiation, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were housed under standard vivarium conditions, and all procedures were conducted under an approved IACUC protocol.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment, followed by globin reduction using GLOBINclear-Mouse/Rat.

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia at 24 hours post-irradiation. Each sample was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

tag: tissue

value: Whole Blood

tag: gender

value: Male


title: WT 0 Gy rep 2

source_name: Whole blood from Wild-type 24h post mock irradiation, replicate 2


title: SH-SY5Y-NOTCH3IC_off_336 hrs


title: K1_H3K27me3


title: SH-SY5Y-NOTCH3IC_off_0 hrs nb2151


title: Microdissected Rat Renal CCD, Lithium_12h, RNA-Seq, Transcriptome 01

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to Ensembl rat gene set (Rnor_6.0) using STAR v2.5.2b
Transcript abundances in TPM were caculated by RSEM/1.2.31
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file includes TPM  for each sample

molecule: polyA RNA

organism: Rattus norvegicus

growth_protocol: Pathogen-free male Sprague-Dawley rats weighing 120-160 g had free access to ad libitum drinking water and normal rodent chow before experiment. The rats were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 2 days before the experimental procedures.

extract_protocol:
After microdissecting cortical collecting duct and cortical collecting duct,  Total RNA were extracted using the Direct-zol™ RNA Kits (Zymo Research) and cDNA was synthesized by SMARTer V4 Ultra Low RNA kit (Clontech). The cDNA was then amplified for 15 PCR cycles, purified by AmPure XP magnetic beads (Beckman Coulter Genomics), and eluted with 15 μL Elution Buffer. The purified cDNA was further quantified by Qubit. Library size distribution was determined using the Agilent 2100 bioanalyzer using High-Sensitive DNA kit. The Nextera XT DNA Library Preparation Kits (Illumina) was used to generate the libraries with input of 1 ng.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats are exposed to food without (Control) or with 40mM lithium chloride (LiCl) /kg food for 0, 12, 24, 36, and 72 hrs

value: Sprague-Dawley

value: male

value: Kidney

tag: tissue sample

value: Microdissected Renal CCD

tag: agent

value: Lithium

tag: time


title: Kupffer cell MaR1 rep 1

city: Seoul

first: Yong-Hyun

last: Han

state: Seoul

address: Daehak-ro

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: replicate 1

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1. The probes of Log2 normalized signal intensity is filtered by Flag check.

source_name: Primary Mouse Kupffer cell

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: Kupffer cells were isolated from 8 weeks old, male C57BL/6 mice by perfusion of liver using collagenase type IV. For isolation of Kupffer cells, non-parenchymal sufficient supernatant was centrifuged in 50%/25% percoll  The layer containing Kupffer cells was plated with RPMI 1640 with 10% FBS.

extract_protocol: Cells were harvested in RLT buffer and RNA was extracted from cultured kupffer cells using the RNeasy micro KIT (Qiagen, Valencia, CA).

treatment_protocol: KCs were treated with 200 nM Maresin 1 (MaR1), or EtOH (Veh) for 24 h in 0.1% FBS containing RPMI medium.

tag: age

value: 8 weeks

value: Primary cultured Kupffer cells

tag: treatment

value: Maresin 1 (MaR1)-treated


title: Kupffer cell Veh rep 2

description: replicate 2

value: Vehicle


title: Kupffer cell Veh rep 1

description: replicate 1


title: AR Tumor replicate 2

city: Los Angeles

first: Sungyong

last: You

state: CA

address: 8700 Beverly Blvd

department: Surgery

institute: Cedars-Sinai Medical Center

description: AR transgenic

data_processing:
Quality of sequencing data was verified using MultiQC software. Sequence alignment and quantification were performed using the STAR-RSEM pipeline. Reads overlapping exons in the annotation of Genome Reference Consortium Mouse Build 38 (GRCm38) were identified, and would be excluded from further downstream analysis if they failed to achieve raw read counts of at least 2 across all the libraries. The trimmed mean of M-values normalization method (TMM) (version 1.6.1) was used for calculating normalized count data.  Three comparisons were performed between prostate tissues of different genotype mice using median difference test in this study.  For each gene, a P-value was computed by performing a two-tailed median difference test using the empirical distributions that were estimated by random permutations of the samples. Multiple testing correction was done by using Storey’s correction method
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM and expected_count were generated by RSEM

source_name: Mouse prostate (FFPE)

growth_protocol: All mice used in this study were from a C57BL/6 background. The Trp53 floxed mice, p53LoxP/LoxP mice, also named p53L/L, were obtained from Jackson Laboratory (stock:008462).  The AR transgenic mouse, R26hARLoxP/wt, also named R26hAR/+, was generated.  Osr1-Cre mice were kindly provided by Dr. Gail Martin.  Either p53L/+:R26hAR/+ or p53L/+:Osr1-Cre mice were first generated and then used to produce p53L/L:Osr1-Cre, p53L/+:Osr1-Cre, R26hAR/+:Osr1-Cre, p53L/+/R26hAR/+:Osr1-Cre and p53L/L/R26hAR/+:Osr1-Cre mice.  Mice were genotyped by PCR using specific primers for detecting either AR or trp53 targeted or deleted alleles. All animal experiments performed in this study were approved by the ethics committee of the Administrative Panel on Institutional Animal Care and Use Committee at Stanford University and Beckman Research Institute/City of Hope.

extract_protocol:
RNA samples were isolated from fresh mouse tissues using RNA-Bee (TEL-TEST, Inc., Friendswood, TX, USA) or from Fixed Paraffin Embedded (FFPE) slides using the Pinpoint Side RNA isolation Kit (Zymo Research, Cat R1007).
RNA sequencing libraries were prepared with Kapa RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Cat KR1351).
Sequencing runs were performed on Illumina Hiseq 2500 in the single read mode of 51 cycle of read 1 and 7 cycles of index with V4 Kits.

treatment_protocol: Tissues were formalin fixed and paraffin embedded.

value: Prostate

tag: mouse genotype


title: AR-P53 Tumor replicate 2

description: AR transgenic and TP53 knockout


title: Kupffer cell MaR1 rep 2

description: replicate 2


title: AR-P53 Tumor replicate 1

description: AR transgenic and TP53 knockout


title: PLC5-GSK343-16hr_2

city: New Taipei City

first: Pei-Ming

last: Yang

address: No. 301, Yuantong Rd., Zhonghe Dist.

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

hyb_protocol: OneArray Plus Hybridization Protocol

scan_protocol: Agilent 0.1 XDR Protocol

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: PLC5, 10 uM, GSK343, 16hr, replicate 2

label_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, AM1753) to generate amino-allyl antisense RNA(aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridization. Purified coupled aRNA was quantified using NanoDrop ND-1000; pass criteria for CyDye incorporation efficiency at > 15 dye molecular/1000nt.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: HepG2 and PLC/PRF/5 (PLC5) cells were treated with drug in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line


title: AR Tumor replicate 1

description: AR transgenic


title: HepG2-GSK343-16hr_2

source_name: HepG2, 10 uM, GSK343, 16hr, replicate 2


title: HepG2-Control-16hr_1

source_name: HepG2, control, 16hr, replicate 1

value: Control


title: PLC5-GSK343-16hr_1

source_name: PLC5, 10 uM, GSK343, 16hr, replicate 1


title: Wild Type

description: Wild Type

value: Wild Type


title: RRBS: WT1

first: Ritu

last: Kumar

address: 1300 York Avenue

institute: Weill Cornell Medicine

description: RRBS

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
Genome_build: mm10

source_name: IPSC clone

growth_protocol: IPSCs were cultured in the presence of Serum/LIF

extract_protocol:
DNA was extracted using Qiagen Dneasy Blood and Tissue kit
RRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012).

treatment_protocol: No treatments were applied prior to genomic DNA extraction

value: IPSC clone from fibroblast

tag: genotype

value: WT

tag: reprogramming

value: Reprogrammed using OSKM

tag: passage


title: RRBS: WT3

description: RRBS


title: RRBS: WT2

description: RRBS


title: HepG2-GSK343-16hr_1

source_name: HepG2, 10 uM, GSK343, 16hr, replicate 1


title: HepG2-Control-16hr_2

source_name: HepG2, control, 16hr, replicate 2


title: PLC5-Control-16hr_1

source_name: PLC5, control, 16hr, replicate 1


title: A549-GSK343-6hr

treatment_protocol: HepG2 and A549 cells were treated with drug in DMEM supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 hours at 37 ºC in a humidified incubator with 5% CO2.


title: PLC5-Control-16hr_2

source_name: PLC5, control, 16hr, replicate 2


title: SH-SY5Y-NOTCH3IC_on_336 hrs nb2229

treatment_protocol: The NOTCH3-IC transgene in SH-SY5Y-NOTCH3IC cells was induced with 100 ng/ml doxycycline in the culture medium. Switching-off the NOTCH3-IC transgene was performed by wash-out of doxycycline from the culture medium.

value: Neuroblastoma cell line SH-SY5Y with doxycycline inducible expression of human NOTCH3-IC


title: WT_rep_1

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

hyb_protocol: Incubeted with rotation at 60 RPM for 16 hours at 45C

scan_protocol: Scanned with the Affymetrix® GeneChip Scanner 3000 7G using the Command Console software (Affymetrix®)

data_processing: Data summarized and normalized using the RMA-sketch routine as implemented in apt affimetrix software (apt-probeset-summarize)

label: Biotin

source_name: iNKT cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix manual target preparation for genechip ®  whole transcript expression array.

extract_protocol: Total RNA was extracted from frozen tissue samples using the RNeasy Mini Kit Plus protocol

value: WT control

tag: replicate


title: V_ALPHA_14_rep_1

value: V_alpha_14 cells


title: HepG2-Control-6hr

source_name: HepG2, control, 6hr


title: A549-Control-6 hr

source_name: A549, control, 6hr


title: V_ALPHA_14_rep_2


title: RRBS: AIDKO3

description: RRBS

value: AICDA KO


title: RRBS: AIDKO2

description: RRBS


title: HepG2-GSK343-6hr

source_name: HepG2, 10 uM, GSK343, 6hr


title: RNA-seq: WT3

description: RNA seq

data_processing:
Raw reads were aligned using STAR v2.3.0e_r291
Read counting was performed using htseq-count v0.6.0
Genome_build: mm10

source_name: iPSC

extract_protocol:
RNA was extracted using Qiagen RNeasy kit
Libraries prepared using IlluminaTruSeq RNA Sample Preparation Kits v2

treatment_protocol: No treatments were applied prior to RNA extraction


title: WT_rep_2


title: RNA-seq: AIDKO3

description: RNA seq


title: RNA-seq: AIDKO2

description: RNA seq


title: RNA-seq: WT1

description: RNA seq


title: RNA-seq: WT2

description: RNA seq


title: RNA-seq: AIDKO1

description: RNA seq


title: RAG1A:control-2:2

city: Beijing

first: Mengzhu

last: Liu

address: Yiheyuan Road No.5

country: China

institute: Peking University

data_processing:
Library strategy: PEM-seq
For initial reads preprocessing, both Illumina adapter sequences and ending low quality sequences (QC < 30) were trimmed by cutadapt (http://cutadapt.readthedocs.io/en/stable/); remaining reads shorter than 25bp were discarded. Then reads were de-multiplexed using fastq-multx (https://github.com/brwnj/fastq-multx) to distinguish index.
For reads alignment and clustering, we adapted corresponding pipeline used in LAM-HTGTS9 to perform reads mapping and translocation break point detection. Note that we used the hg38 genome as reference.
For reads deduplicates, A molecular barcode clustering algorithm32 was adapted to remove PCR duplicates at an editing distance of 2.
Break-site and neighbor ±5bp region was analyzed for indels; reads containing large deletions resulting from resection and rejoining in the break-site ±250kb region were also categorized as indels (I). Reads without any detected mutations around break point were identified as germline (G). Genome-wide translocation (T) was identified as before.
A pipeline named superQ was developed to process data of PEM-seq.
Genome_build: hg38
Supplementary_files_format_and_content: tab files generated by superQ.

growth_protocol: DMEM + 10%FBS

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
All the biotinylated primers are placed within 100-bp from the cut site. In general, PEM-seq can be divided into 3 steps: primer-extension, bridge adapter (with RMB on it) ligation and PCR amplification for Illumina sequencing. For primer extension, Bst polymerase 3.0 (NEB) was used to perform primer extension: 65°C 10min, 80°C 5min. Beads-cleaned products were incubated at 95°C for 5 min and quickly put on the ice for 5min for DNA denaturation. Biotinylated PCR products were enriched by Dynabeads™ MyOne™ Streptavidin C1 (Thermo Fisher). In the bridge adapter ligation step, ligation reaction was performed in 15% PEG8000 (Sigma) at room temperature overnight. Finally, ligation products underwent nested PCR (Taq, Transgene, China) with I5 and I7 sequence primers for 16 cycles and another PCR (Fastpfu, Transgene, China) tagged with Illumina P5 and P7 sequence. All the PEM-seq libraries were sequenced by Hiseq with 150bp ×2.

treatment_protocol: Cas9 nucleases were transfected by CaPO4 for 48 hrs before genomic DNA extraction

tag: bait locus


title: RAG1A:control-0:4


title: RAG1A:control-3:1


title: RAG1A:control-1:3


title: RAG1A:control-4:0


title: RAG1A-figure6a-control


title: RAG1A-K562-control


title: MYC-locus2-figure6c-control


title: RAG1A-U2OS-control


title: EMX1-figure4-control


title: RAG1A-HCT116-control


title: SaCas9-myc1-RAG1A-arcIIA4-control


title: RAG1C-Figure3-control


title: RAG1A-xCas9-control


title: MYC1-FigureS3-control


title: wt treated with 0.27 mg/L nystatin rep1

city: Parma

first: Luca

last: Pagano

address: Parco Area delle Scienze 11/A

department: Chemistry Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description: Gene expression data from wt BY4742 grew on YPD medium for 24h and treated with nystatin for another 24h

hyb_protocol: Hybridization, washing and staining were performed according the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip® Expression 3’ Amplification Reagent Hybridization Controls (Cat# 900454; Lot# 4211830) and the Hybridization Module of GeneChip® Hybridization, Wash and Stain Kit (Cat# 900720; Lot# 4139834) and mixed with aRNA samples. GeneChip® Yeast Genome 2.0 Array (Cat# 900554; Lot# 4244368) were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 16 hours in the GeneChip® Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip® Fluidics Station 450. Biolityx AG (Witterswil, CH).

scan_protocol: Scanning was done with GeneChip® Scanner 3000 (Affymetrix). Biolityx AG (Witterswil, CH).

data_processing: QC analysis for generated array data in this study was performed with the Expression Console of the Affymetrix GeneChip® Command Console (AGCC) using RMA (Robust Multi-Array Average)

organism: Saccharomyces cerevisiae

source_name: wt treated with 0.27 mg/L nystatin (1/10 MIC)

label_protocol: 200 ng of total RNA were used for amplification which was performed with the GeneChip 3’ IVT Express Kit (Cat # 901228, Lot# 0908014, Affymetrix). For fragmentation 7.5 μg aRNA were used. Biolityx AG (Witterswil, CH).

growth_protocol: yeast cells were grown in liquid YPD medium at 30°C, 120 rpm

extract_protocol: Qiagen RNeasy Mini kit

treatment_protocol: after 24h of growth yeast cell cultures were transferred in liquid YPD medium suppremented of 0 mg/L, nystatin 0.27 mg/L or nystatin 0.27 mg/L + CdS QDs 100 mg/L for other 24h at 30°C.

tag: growth protocol

value: wt grew on YPD medium for 24h

value: treated with nystatin for another 24h


title: wt treated with 0.27 mg/L nystatin + 100 mg/L CdS QDs rep1

description: Gene expression data from wt BY4742 grew on YPD medium for 24h and treated with nystatin+CdS QDs for another 24h

source_name: wt treated with 0.27 mg/L nystatin (1/10 MIC) + 100 mg/L CdS QDs (1/5 MIC)

tag: strain


title: wt treated with 0.27 mg/L nystatin + 100 mg/L CdS QDs rep2

value: treated with nystatin+CdS QDs for another 24h


title: wt control rep1

description: Gene expression data from wt BY4742 grew on YPD medium for 48h (untreated control)

source_name: wt untreated

value: transferred on fresh YPD for another 24h of growth (untreated control)


title: SaCas9-MYC1-RAG1A-arcIIA4-1:1-rep3


title: SaCas9-MYC1-RAG1A-arcIIA4-1:1-rep2


title: wt control rep2


title: SaCas9-MYC1-RAG1A-arcIIA4-1:0-rep3


title: SaCas9-MYC1-RAG1A-arcIIA4-1:1-rep1


title: SaCas9-MYC1-RAG1A-arcIIA4-1:0-rep1


title: wt treated with 0.27 mg/L nystatin rep2


title: MYC2-acrIIA4-1:1-figure6C-rep3


title: RAG1B-Figure3-control


title: MYC2-acrIIA4-1:1-figure6C-rep2


title: MYC2-acrIIA4-1:0-figure6C-rep2


title: MYC2-acrIIA4-1:0-figure6C-rep3


title: SaCas9-MYC1-RAG1A-arcIIA4-1:0-rep2


title: MYC1-acrIIA4-1:0-figure6C-rep1


title: MYC1-acrIIA4-1:1-figure6C-rep1


title: MYC1-acrIIA4-1:0-figure6C-rep2


title: RAG1A-Figure4-control


title: MYC1-acrIIA4-1:1-figure6C-rep2


title: MYC1-acrIIA4-1:0-figure6C-rep3


title: MYC2-acrIIA4-1:0-figure6C-rep1


title: EMX1-acrIIA4-1:1-figure6C-rep3


title: EMX1-acrIIA4-1:0-figure6C-rep3


title: EMX1-acrIIA4-1:0-figure6C-rep2


title: EMX1-acrIIA4-1:1-figure6C-rep2


title: EMX1-acrIIA4-1:1-figure6C-rep1


title: EMX1-acrIIA4-1:0-figure6C-rep1


title: RAG1B-acrIIA4-1:1-figure6C-rep1


title: RAG1B-acrIIA4-1:1-figure6C-rep3


title: RAG1B-acrIIA4-1:0-figure6C-rep3


title: RAG1A-acrIIA4-1:1-figure6C-rep1


title: RAG1A-acrIIA4-1:1-figure6C-rep2


title: RAG1A-acrIIA4-1:1-figure6C-rep3


title: MYC2-acrIIA4-1:1-figure6C-rep1


title: RAG1B-acrIIA4-1:0-figure6C-rep1


title: RAG1A-acrIIA4-1:0-figure6C-rep2


title: RAG1A-acrIIA4-1:3-fig6A-rep2


title: RAG1A-acrIIA4-1:0-figure6C-rep1


title: RAG1A-acrIIA4-1:3-fig6A-rep3


title: RAG1A-acrIIA4-1:1-fig6A-rep3


title: RAG1A-acrIIA4-1:0-figure6C-rep3


title: RAG1A-acrIIA4-1:1-fig6A-rep2


title: MYC1-acrIIA4-1:1-figure6C-rep3


title: RAG1A-acrIIA4-3:1-fig6A-rep2


title: RAG1B-acrIIA4-1:0-figure6C-rep2


title: RAG1A-acrIIA4-1:0-fig6A-rep2


title: RAG1A-acrIIA4-1:0-fig6A-rep3


title: RAG1A-acrIIA4-3:1-fig6A-rep1


title: RAG1A-acrIIA4-3:1-fig6A-rep3


title: RAG1A-acrIIA4-1:0-fig6A-rep1


title: MYC-locus1-FeSpCas9-rep2


title: MYC-locus1-FeSpCas9-rep1


title: MYC-locus1-HF2-rep2


title: MYC-locus1-HF2-rep3


title: MYC-locus1-FeSpCas9-rep3


title: MYC-locus1-HF1-rep3


title: MYC-locus1-HF1-rep2


title: MYC-locus1-eSp-rep2


title: MYC-locus1-HF1-rep1


title: RAG1B-acrIIA4-1:1-figure6C-rep2


title: RAG1A-acrIIA4-1:1-fig6A-rep1


title: RAG1A-acrIIA4-1:3-fig6A-rep1


title: MYC-locus1-D1135E-rep2


title: MYC-locus1-D1135E-rep3


title: MYC-locus1-rep3


title: EMX1-FeSpCas9-rep2


title: EMX1-FeSpCas9-rep3


title: MYC-locus1-rep2


title: EMX1-FeSpCas9-rep1


title: EMX1-eSp-rep2


title: EMX1-eSp-rep3


title: EMX1-D1135E-rep3


title: EMX1-D1135E-rep2


title: EMX1-eSp-rep1


title: EMX1-D1135E-rep1


title: MYC-locus1-HF2-rep1


title: MYC-locus1-eSp-rep1


title: MYC-locus1-eSp-rep3


title: EMX1-rep1


title: EMX1-rep3


title: RAG1A-FeSpCas9-rep3


title: EMX1-rep2


title: MYC-locus1-D1135E-rep1


title: RAG1A-eSp-rep3


title: RAG1A-eSp-rep2


title: RAG1A-eSp-rep1


title: RAG1A-D1135E-rep1


title: RAG1A-D1135E-rep2


title: RAG1A-FeSpCas9-rep1


title: RAG1A rep2


title: RAG1A rep3


title: MYC-locus1-rep1


title: RAG1A-D1135E-rep3


title: RAG1A-U2OS-rep1


title: RAG1A rep1


title: RAG1A-U2OS-rep2


title: RAG1A-K562-rep3


title: RAG1A-U2OS-rep3


title: RAG1A-HCT116-rep2


title: RAG1A-K562-rep2


title: RAG1A-HCT116-rep3


title: RAG1A-K562-rep1


title: RAG1A-FeSpCas9-rep2


title: RAG1A-HCT116-rep1


title: RAG1C-rep3


title: RAG1C-rep2


title: RAG1B-rep2


title: RAG1B-rep1


title: RAG1B-rep3


title: RAG1A-rep2

data_processing:
For initial reads preprocessing, both Illumina adapter sequences and ending low quality sequences (QC < 30) were trimmed by cutadapt (http://cutadapt.readthedocs.io/en/stable/); remaining reads shorter than 25bp were discarded. Then reads were de-multiplexed using fastq-multx (https://github.com/brwnj/fastq-multx) to distinguish index.
For reads alignment and clustering, we adapted corresponding pipeline used in LAM-HTGTS9 to perform reads mapping and translocation break point detection. Note that we used the hg38 genome as reference.
For reads deduplicates, A molecular barcode clustering algorithm32 was adapted to remove PCR duplicates at an editing distance of 2.
Break-site and neighbor ±5bp region was analyzed for indels; reads containing large deletions resulting from resection and rejoining in the break-site ±250kb region were also categorized as indels (I). Reads without any detected mutations around break point were identified as germline (G). Genome-wide translocation (T) was identified as before.
A pipeline named superQ was developed to process data of PEM-seq.
Genome_build: hg38
Supplementary_files_format_and_content: tab files generated by superQ.

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
All the biotinylated primers are placed within 100-bp from the cut site. In general, PEM-seq can be divided into 3 steps: primer-extension, bridge adapter (with RMB on it) ligation and PCR amplification for Illumina sequencing. For primer extension, Bst polymerase 3.0 (NEB) was used to perform primer extension: 65°C 10min, 80°C 5min. Beads-cleaned products were incubated at 95°C for 5 min and quickly put on the ice for 5min for DNA denaturation. Biotinylated PCR products were enriched by Dynabeads™ MyOne™ Streptavidin C1 (Thermo Fisher). In the bridge adapter ligation step, ligation reaction was performed in 15% PEG8000 (Sigma) at room temperature overnight. Finally, ligation products underwent nested PCR (Taq, Transgene, China) with I5 and I7 sequence primers for 16 cycles and another PCR (Fastpfu, Transgene, China) tagged with Illumina P5 and P7 sequence. All the PEM-seq libraries were sequenced by Hiseq with 150bp ×2.
PEM-seq


title: RAG1A-rep1


title: RAG1A-rep3


title: RAG1C-rep1


title: AB4835

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out. read2 used to read cell and molecule barcodes only
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample and Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: (BSA/CpG) NP+ DC

growth_protocol: 8 to 12 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were euthanized and popliteal and inguinal LNs were dissected. Cells were collected, filtered through a 70µm cell strainer, washed and maintained strictly at 4°C. Dendritic cells were enriched by negative selection. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation; Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header

treatment_protocol: sub-cutaneous hock immunization

tag: mouse age

value: 8 weeks

value: Popliteal and inguinal lymph nodes

tag: cell type

value: Dendritic cell enriched fraction

tag: selection marker

value: CD45+ TCRb- CD19- NK1.1- Ly6G- PDCA-1- MHC II+

tag: antigen/adjuvant

value: BSA/CpG

tag: time point

value: 20h post-immunization

value: sub-cutaneous injection of antigen and adjuvant carrying nanoparticles

tag: animal pooling

value: 2 mice

tag: replicate id

value: BSA rep1


title: AB4834

source_name: (OVA/CpG) NP+ DC

tag: tissue

value: OVA/CpG

tag: treatment

value: OVA rep2


title: WT_cd11b_1

city: Ulsan

first: Sungho

last: Park

address: 50 UNIST-gil, Eonyang-eup

department: Life Science

institute: Ulsan National Institute of Science and Technology

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed.
the SureCell RNA Single-Cell App in BaseSpace Sequence Hub
Single cell RNA-seq analysis was performed using Seurat (Butler et al., 2018).
Genome_build: mm9

source_name: Skin macrophages

growth_protocol: Dorsal skin was removed, and 8-mm biopsy punches were obtained from the wounded region. Skin was finely minced before digestion in Liberase TM (13 U/ml) and then dispase II (2.42 U/ml). After Fc blocking, cells were washed and  stained with CD45, F4/80 and CD11b antibodies (1:100).

extract_protocol: Live flow-sorted cells (DAPI negative) were prepared for single-cell sequencing, using the SureCell WTA 3′Library Prep Kit for the ddSeq  System (Bio-Rad).

treatment_protocol: Full-thickness wounds were created by excision of 4-mm punches on either side of midline (Chia et al., 2016).

value: Skin

value: macrophages


title: AB4836

value: BSA rep2


title: AB4833

value: OVA rep1


title: WT_cd11b_3


title: WT_cd11b_2


title: OT_T_cells_BSA_CpG_NP_2

description:
20h post-immunizatio
processed data file:
20171221_CC_exons_raw_OTcells_DESeq.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
alignment: hisat 0.1.6  with deafult parameters
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
UMI location: in fastq header, sample barcode N7 + UMI N8
UMI were filtered if 2 reads got same UMI in 3kb area
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count exons -condenseGenes -strand +  -raw
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
Mice were euthanized and popliteal and inguinal LNs were dissected. Cells were collected, filtered through a 70µm cell strainer, washed and maintained strictly at 4°C. Dendritic cells were enriched by negative selection. Cells were stained with FACS antibodies. 10^4-10^5 cells from each dendritic cell or T cell subpopulation were sorted in 40 ul of Lysis/Binding Buffer (Life technologies), lysed for 5 min and frozen at -80°C. Cell lysates were thawed and mRNA was captured with 12 ul of Dynabeads oligo(dT) (Life technologies), and washed according to manufacture guidelines. Purified messenger RNA was eluted at 70°C with 10 ul of 10 mM Tris-Cl pH 7.5 and stored at -80°C
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.
3' RNA-seq for digital gene expression quantitation

tag: strain background

tag: genotype/variation

value: OT-II

tag: age

value: 8-12 weeks

value: popliteal and inguinal lymph node

value: nanoparticles immunization

value: CD4+ OT-II T cells


title: WT_cd11b_F480_2


title: CC_NP_DC_BSA_CpG_NP_3

description:
20h post-immunizatio
processed data file:
20171221_CC_exons_raw_DC_DESeq.txt

value: wild-type

value: lymph node dendritic cells


title: CC_NP_DC_BSA_CpG_NP_4


title: OT_T_cells_OVA_CpG_NP_2


title: OT_T_cells_BSA_CpG_NP_3


title: CC_NP_DC_BSA_CpG_NP_2


title: CC_NP_DC_BSA_CpG_NP_1


title: OT_T_cells_BSA_CpG_NP_1


title: CC_NP_DC_OVA_CpG_NP_4


title: CC_NP_DC_OVA_CpG_NP_5


title: CC_NP_DC_OVA_CpG_NP_2


title: CC_NP_DC_OVA_CpG_NP_3


title: CC_NP_DC_OVA_CpG_NP_1


title: WT_cd11b_F480_1


title: WT_cd11b_F480_3


title: CC_NP_DC_NI_control_4

description:
non-immunized control
processed data file:
20171221_CC_exons_raw_DC_DESeq.txt


title: CC_NP_DC_NI_control_3


title: OT_T_cells_OVA_CpG_NP_3


title: OT_T_cells_OVA_CpG_NP_1


title: CC_DC_wt_OVA_OT_12H_2

description:
12h hours post-immunization
processed data file:
20170430B_exons_raw_CC_DESEQ2f_12h.txt


title: CC_DC_wt_OVA_12H_1

description:
12 hours post-immunization
processed data file:
20170430B_exons_raw_CC_DESEQ2f_12h.txt


title: CC_DC_wt_OVA_12H_2


title: CC_NP_DC_NI_control_1


title: CC_NP_DC_NI_control_2


title: CC_DC_wt_BSA_OT_12H_3


title: CC_NP_DC_BSA_CpG_NP_5


title: CC_DC_ko_OVA_OT_12H_2


title: CC_DC_wt_BSA_OT_12H_1


title: CC_imm_LN_DC_OVA_CpG_NP_24h_2

description:
24h hours post-immunization
processed data file:
20161218_UMI_exons_raw_CC_20180717_DESeq.txt


title: CC_DC_wt_OVA_OT_12H_1


title: CC_DC_ko_OVA_OT_12H_1


title: CC_imm_LN_DC_OVA_CpG_NP_12h_2

description:
12 hours post-immunization
processed data file:
20161218_UMI_exons_raw_CC_20180717_DESeq.txt


title: CC_imm_LN_DC_CpG_NP_24h_1


title: CC_imm_LN_DC_CpG_NP_12h_2


title: CC_imm_LN_DC_OVA_CpG_NP_12h_1


title: CC_imm_LN_DC_OVA_CpG_NP_24h_1


title: CC_imm_LN_DC_CpG_NP_12h_1


title: CC_NP_DC_NI_control_5


title: CC_imm_LN_DC_CpG_NP_24h_2


title: CC_imm_LN_DC_control_non_imm_2

description:
non-immunized control
processed data file:
20161218_UMI_exons_raw_CC_20180717_DESeq.txt


description:
used for supp fig 1B
BB_Rescue_P19_macrophages_IL10R_littermate_abx_491.M
processed data file: p19_abx_rescue_macrophages.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8 (single end protocol read2 used to split to samples (7N) and UMI (8N))
alignment: hisat 0.1.6  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
10^4-10^5 cells from each macrophage subpopulation were sorted in 100-200 ul of Lysis/Binding Buffer (Life technologies), lysed for 5 min and frozen at -80°C. Cell lysates were thawed and mRNA was captured with 12 ul of Dynabeads oligo(dT) (Life technologies), and washed according to manufacture guidelines. Purified messenger RNA was eluted at 70°C with 10 ul of 10 mM Tris-Cl pH 7.5 and stored at -80°C
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.
3' RNA-seq for digital gene expression quantitation

value: 6-7 weeks

value: antibiotics in drinking water

value: colonic lamina propria


description:
used for supp fig 1B
BB_Rescue_P19_macrophages_IL10R_littermate_abx_496.M
processed data file: p19_abx_rescue_macrophages.txt


title: Rescue_P19_macrophages_CX_1

description:
used for Fig3A-C
BB_Rescue_P19_macrophages_CX_1.M
processed data file: p19_abx_rescue_macrophages.txt


title: Rescue_P19_macrophages_CX_3

description:
used for Fig3A-C
BB_Rescue_P19_macrophages_CX_3.M
processed data file: p19_abx_rescue_macrophages.txt


description:
used for supp fig 1B
BB_Rescue_P19_macrophages_IL10R_littermate_abx_490.M
processed data file: p19_abx_rescue_macrophages.txt


description:
used for supp fig 1B
BB_Rescue_P19_macrophages_5C5_IL10R_abx_161.M
processed data file: p19_abx_rescue_macrophages.txt


description:
used for supp fig 1B
BB_Rescue_P19_macrophages_5C5_IL10R_abx_495.M
processed data file: p19_abx_rescue_macrophages.txt


description:
used for supp fig 1B
BB_Rescue_P19_macrophages_5C5_IL10R_abx_160.M
processed data file: p19_abx_rescue_macrophages.txt


description:
used for Fig3A-C
BB_Rescue_P19_macrophages_5C5_IL10R_P19_105.M
processed data file: p19_abx_rescue_macrophages.txt


description:
used for Fig3A-C
BB_Rescue_P19_macrophages_5C5_IL10R_P19_100.M
processed data file: p19_abx_rescue_macrophages.txt


description:
used for Fig3A-C
BB_Rescue_P19_macrophages_5C5_IL10R_P19_107.M
processed data file: p19_abx_rescue_macrophages.txt


description:
used for Fig3A-C
BB_Rescue_P19_macrophages_5C5_IL10R_P19_106.M
processed data file: p19_abx_rescue_macrophages.txt


title: Rescue_P19_macrophages_5C5_IL10R_68

description:
used for Fig3A-C
BB_Rescue_P19_macrophages_5C5_IL10R_68.M
processed data file: p19_abx_rescue_macrophages.txt


title: Rescue_P19_macrophages_5C5_IL10R_67

description:
used for Fig3A-C
BB_Rescue_P19_macrophages_5C5_IL10R_67.M
processed data file: p19_abx_rescue_macrophages.txt


title: Rescue_P19_macrophages_5C5_IL10R_27

description:
used for Fig3A-C
BB_Rescue_P19_macrophages_5C5_IL10R_27.M
processed data file: p19_abx_rescue_macrophages.txt


title: Rescue_P19_macrophages_5C5_IL10R_61

description:
used for Fig3A-C
BB_Rescue_P19_macrophages_5C5_IL10R_61.M
processed data file: p19_abx_rescue_macrophages.txt


title: Rescue_P19_macrophages_5C5_IL10R_32

description:
used for Fig3A-C
BB_Rescue_P19_macrophages_5C5_IL10R_32.M
processed data file: p19_abx_rescue_macrophages.txt


title: CC_imm_LN_DC_control_non_imm_1

description:
non-immunized control
processed data file:
20161218_UMI_exons_raw_CC_20180717_DESeq.txt


description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_6_ko_ly6g.M
processed data file: macrophages_in_neuts_depletion.txt

value: 4 weeks post chimerism

value: BM chimeras injected with anti-ly6g antibody


description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_5_ko_ly6g.M
processed data file: macrophages_in_neuts_depletion.txt


title: Neuts_depletion_sorted_colonic_mfs_3_wt

description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_3_wt.M
processed data file: macrophages_in_neuts_depletion.txt


title: Neuts_depletion_sorted_colonic_mfs_4_wt

description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_4_wt.M
processed data file: macrophages_in_neuts_depletion.txt


title: Neuts_depletion_sorted_colonic_mfs_1_wt

description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_1_wt.M
processed data file: macrophages_in_neuts_depletion.txt


description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_14_ko_igg.M
processed data file: macrophages_in_neuts_depletion.txt


description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_18_ko_igg.M
processed data file: macrophages_in_neuts_depletion.txt


title: Neuts_depletion_sorted_colonic_mfs_2_wt

description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_2_wt.M
processed data file: macrophages_in_neuts_depletion.txt


description:
used for supp fig 1B
BB_Rescue_P19_macrophages_5C5_IL10R_abx_497.M
processed data file: p19_abx_rescue_macrophages.txt


title: IL10R_colonic_MFs3

description:
used for fig1A-B
BB_IL10R_colonic_MFs3.M
processed data file: IL10R_macrophages.txt


title: IL10R_colonic_MFs2

description:
used for fig1A-B
BB_IL10R_colonic_MFs2.M
processed data file: IL10R_macrophages.txt


title: CXhet_colonic_MFs1

description:
used for fig1A-B
BB_CXhet_colonic_MFs1.M
processed data file: IL10R_macrophages.txt


title: CXhet_colonic_MFs3

description:
used for fig1A-B
BB_CXhet_colonic_MFs3.M
processed data file: IL10R_macrophages.txt


title: CXhet_colonic_MFs2

description:
used for fig1A-B
BB_CXhet_colonic_MFs2.M
processed data file: IL10R_macrophages.txt


description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_16_ko_igg.M
processed data file: macrophages_in_neuts_depletion.txt


title: AB5318

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: [metadata.txt]  file associating each single cell with its amplification batch and index sorting readouts

source_name: Brain parenchyma, excluding choroid plexus

growth_protocol: 16 to 19 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were intracardially perfused with PBS. Brains were dissected, dissociated using the gentleMACS™ dissociator (Miltenyi Biotec), and loaded on a Percoll gradient (GE Healthcare) to isolate leukocytes. Cells were collected, filtered through a 70µm cell strainer, washed with FACS buffer and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

treatment_protocol:
(1)Mice were anesthetized and TAT-CRE recombinase was injected intraventricularly. PBS was injected to control animals.
(2)Mice were exposed to two sessions of electrical foot shocks on consecutive days. On day 1, mice received 14 shocks of 1 mA, 1 s in duration over 85 min at variable intervals. . On day 2, the same mice received 5 shocks of 0.7 mA, 1 s in duration over 5 min at fixed intervals.

tag: organ

value: Brain

value: T cells

tag: icv injected material

value: PBS

tag: time point after stress

value: Intracerebroventricular injection of PBS

value: Foot-shock stress

value: Sham 218

value: 16 weeks


title: AB5317

value: Sham 216

value: 19 weeks


title: AB5316

value: TAT-CRE recombinase

value: Intracerebroventricular injection of TAT-CRE recombinase

value: CRE 215


title: AB5314

value: CRE 207

value: 18 weeks


title: AB5315

value: CRE 208


title: MycOE_Input

first: Ramon

last: Parsons

address: 1425 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
ChIP-seq: Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 1.1.1) with parameters –l 50 –n 2 –S –best –k 1 –m 1. BAM files were generated using SAMtools. bigwig files were generated from BAM files using MACS2 (version 2.1.0) with parameters nomodel -extsize 150 -keep-dup 2 -SPMR
ChIP-seq (double crosslinking): Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 1.1.1) with parameters –l 50 –n 2 –S –best –k 1 –m 1. BAM files were generated using SAMtools. bigwig files were generated from BAM files using MACS2 (version 2.1.0) with parameters nomodel -extsize 150 -keep-dup 2 -SPMR
RNA-seq: Custom-built software was used to map the reads to the human genome (GRCh38/hg38) and estimate the coverage of each gene. Briefly, the reads were split into three 32 bp parts after trimming 2 bp at each end and mapped to the genome using a suffix-array based approach. The median of coverage across the transcript was used as an estimate of gene expression. The expression values were quantile normalized and log-ratios were calculated.
Genome_build: GRCh37/hg19, GRCh38/hg38, or NCBI37/mm9
Supplementary_files_format_and_content: fastq - raw illumina reads. bigwig - aligned reads pileup.

source_name: cell culture

extract_protocol:
ChIP-seq: Lysates were clarified from sonicated nuclei and prtein-DNA complexes were isolated with antibody
RNA-seq: RNA was extracted from cell pellets using Qiagen RNeasy Kit.
ChIP-seq: 2-10 ng of DNA were subject to end-repair, A-tailing, and ligation with Illumina Truseq adapters using NEB enzymes (NEB), followed by size-selection of 300-400 bp and amplification for 10-15 cycles using the KAPA HiFi Library Amplification Kit (Kapa Biosystems).
RNA-seq: Illumina TruSeq RNALibrary Prep Kit v2 (RS 122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries

value: mouse breast tumor cells

tag: chip antibody

tag: growth protocol

value: grown in DMEM supplemented with 10% FBS, penicillin and streptomycin, and 2mM L-glutamine

value: Pten WT


description:
used for fig7E-F
BB_Neuts_depletion_sorted_colonic_mfs_7_ko_ly6g.M
processed data file: macrophages_in_neuts_depletion.txt

tag: strain

value: 4 weeks post chimerism

value: BM chimeras injected with anti-ly6g antibody

value: colonic lamina propria


title: MycOE_Pten_Null_RNAPII

tag: cell type

value: RNAPII (Santa Cruz, Sc-899)

value: Pten Null


title: MEF_Pten_KO_RNAPII

value: primary mouse embryonic fibroblasts (passage 6-8)


title: MycOE_Pik3ca_mut_RNAPII


title: MEF_Pten_WT_RNAPII


title: K562_input

city: Liège

first: Nor Eddine

last: Sounni

address: avenue de l'Hôpital 11

department: Medical oncology

country: Belgium

institute: Liège University (ULG - ULiège)

data_processing:
Basecalling pipeline : NextSeq Control Software 2.1.0.31; RTA 2.4.11 ; bcl2fastq2.17 v2.17.1.14
ChIPseq reads were aligned to the hg19 reference genome using BWA
Removal of duplicates, filtering of ENCODE blacklisted regions and removal of multimapping reads with bedtools
Peak calling done with SICER v 1,1 using the following settings : window size 3000 bp; gap size 21000 bp and FDR 0.3.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: human blood (chronic myelogenous leukemia)

extract_protocol:
Chromatin was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001) to an average of 150-200 bp fragments as assessed by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.).
Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA (starting amount 1ng) using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Library amplification is assessed using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). Libraries were then double size-selected and purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analyzed by High Sensitivity DNA Analysis Kit on a 2100 Bioanalyzer system (Agilent).

value: K562 cell line - Somatic cells


title: K562_4

extract_protocol:
Chromatin was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001) to an average of 150-200 bp fragments as assessed by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). ChIP was performed manually with the iDeal ChIP-seq kit for Histones (Diagenode Cat# C01010059)
Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA (starting amount 1ng) using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Library amplification is assessed using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). Libraries were then double size-selected and purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analyzed by High Sensitivity DNA Analysis Kit on a 2100 Bioanalyzer system (Agilent).

value: H4K20me3 antibody (Diagenode Premium, C15410207)


title: K562_3


title: K562_5


title: MEF_input

value: grown in DMEM supplemented with 10% FBS, penicillin and streptomycin


title: IL10R_colonic_MFs1

description:
used for fig1A-B
BB_IL10R_colonic_MFs1.M
processed data file: IL10R_macrophages.txt

value: 6-7 weeks

tag: selection marker


title: D63_Input

source_name: Motile human sperm

extract_protocol:
Nucleosomal fraction of the chromatin was digested with 30 U micrococcal nuclease (MNase) for 5 min, cleaned and used as input.
Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA (starting amount 1ng) using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Library amplification is assessed using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). Libraries were then double size-selected and purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analyzed by High Sensitivity DNA Analysis Kit on a 2100 Bioanalyzer system (Agilent).

value: Sperm cells


title: K562_2


title: D31_Input


title: D31

extract_protocol:
Nucleosomal fraction of the chromatin was digested with 30 U micrococcal nuclease (MNase) for 5 min before incubation overnight with 2µg of antibody and cleaning of the immunoprecipitated chromatin.
Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA (starting amount 1ng) using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Library amplification is assessed using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). Libraries were then double size-selected and purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analyzed by High Sensitivity DNA Analysis Kit on a 2100 Bioanalyzer system (Agilent).


title: D63


title: D93_Input


title: SNW1_RNAi

city: Baltimore

first: Andrew

last: Holland

address: 725 N Wolfe St PCTB 704

institute: Johns Hopkins University School of Medicine

data_processing:
Basecalls were derived using the standard Illumina NextSeq500 software
Sequenced reads were mapped to hg38 using RSEM with parameters -p 8 --star --calc-ci --paired-end
Read counts mapping back to exons or introns were calculated using bedtools multicov
Percent of intron retention was calculated using IRFinder for transcripts with a minimum of 4 reads across
Genome_build: hg38
Supplementary_files_format_and_content: tab-deliminated files of the IRFinder results, including the ratio of transcripts containing each intron compared to the total number of transcripts across that splice junction (IRratio) for the experimental condition (A) and control condition (B)

source_name: colorectal adenocarcinoma cell line

growth_protocol: DMEM 10% FBEssence 5% Penn-Strep-Glut

extract_protocol:
Cells were lysed and RNA was isolated using Qiagen RNeasy kit for mRNA purification with Dnase treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: colorectal adenocarcinoma cell line

value: DLD-1 LacZeo

tag: passages

value: 100nM SNW1 siRNA 72hr


title: WBP11_Auxin

value: DLD-1 LacZeo osTIR1

value: 500uM auxin 48hr


title: Control

description: WBP11rnai-vs-CTRLrnai.txt, SNW1rnai-vs-CTRLrnai.txt


title: Control_Auxin


title: WBP11_RNAi

value: 100nM WBP11 siRNA 72hr


title: K562_1


title: PWT-W1

city: Mexico

first: Rosaura

state: Cd. de Mexico

address: Av. Instituto Politécnico Nacional # 2508

department: Biomedicine

country: Mexico

institute: CINVESTAV

data_processing:
A total of 35,205,405 and 34,046,499 paired-end RNA-seq reads for the PANC1 wild type and PZT2 knockdown respectively were adapter and quality trimmed using Trim Galore! version 0.4.1.
Transcript-level abundance was estimated using kallisto  version 0.43.0. Quantification algorithm were run on paired-end RNA-seq files from the biological samples, using an index created from a FASTA file containing the RefSeq annotated transcripts, with bootstraps parameter set at 100 (-b 100). Kallisto output abundance files were analysed to calculate differential expression, using sleuth version 0.29.0.  Wald tests were performed to establish expression patterns by comparing PZT2 versus PANC-1 wild type samples.
Genome_build: hg19
Supplementary_files_format_and_content: tabular text files include pval, qval and b values

source_name: pancreatic cancer cell line (WT)

growth_protocol: The PZT-2 and PANC-1 cell line were grown in DMEM medium (ATCC® 30-2002TM) supplemented with 10% FBS. The cell lines were incubated in a humid atmosphere, with 5% CO2 and at a temperature of 37ºC. The absence of Mycoplasma in our cell lines was confirmed by PCR.

extract_protocol:
Total RNA extraction was carried out using the TRIZOL method
The integrity of the total RNA samples for the preparation of the RNA-seq libraries was determined by Automated Capillary Electrophoresis using the Bioanalyzer 2100 system (Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA 6000 Nano chip, the values of RIN obtained for the samples were >8. The mRNA was enriched by magnetic beads. The construction of the RNA-seq libraries was performed using the Illumina TruSeq Stranded mRNA sample prep kit (Illumina, Inc., SanDiego, CA). Subsequently, the RNA was fragmented in a range of  200-600 bp. Both ends of the double-stranded cDNA were repaired to subsequently bind the specific Illumin adapters, using T4 DNA polymerase and T4 DNA ligase, respectively. Finally, each library was amplified by PCR with specific oligonucleotides for the P5 and P7 adapters of Illumina and thus increase the number of molecules for the massive sequencing. Each library was analyzed by Automated Capillary Electrophoresis (Bioanalyzer 2100, Agilent Technologies, Inc., Santa Clara, CA) using the DNA High Sensitivity chip. Finally, the libraries were quantified using the Qubit® fluorometer with the Qubit ds DNA HS Assay kit (Invitrogen). The libraries were clonally amplified in the Flowcell and sequenced with the NextSeq 500 platform of the Illumina brand (Illumina, Inc., SanDiego, CA) and with the NextSeq 500/550 Mid Output kit v2 (150 cycles) with a run configuration Paired-End 2X76 indexed and following the protocol described by the manufacturer.

value: Wild type

tag: passage


title: P2T2-2-2

source_name: pancreatic cancer cell line (KD of three H2A.Z isoforms)

value: KD of three H2A.Z isoforms


title: P2T2-2-1


title: D93


title: DM017: Patient29_Plate4

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

data_processing:
Reads were aligned to the human genome reference GRCh38 using STAR (version 2.5). During alignment, reads with more than 1 mapping were recorded as unmapped using the arguments ‘--outFilterMultimapNmax 1’ and ‘--outSAMunmapped Within’. Alignment counts were generated using Subread’s featureCounts (version 1.6) with default parameters. Reads were assigned to cell and unique molecular indicator (UMI) barcodes using UMI-tools.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-separated value files containing UMI counts for each gene and cell in each 96-well plate, meta-data files are comma-separated value files containing the CD4/CD8, donor/recipient, CD69 expression, and CD103 expression status of each cell from FACS

source_name: T cells from bronchoalveolar lavage

extract_protocol:
Single CD3+T cells from patient BAL were sorted directly into wells of 96-well plates; each well contained 7.5uL lysis buffer: 0.2% Triton X-100 (Sigma), 1 U/uL SUPERaseIN (ThermoFisher), 2mM dNTPs (ThermoFisher), 2uM RT primer (Integrated DNA Technologies). Primer annealing was performed at 72°C for 3 minutes. Reverse transcription was performed by adding 7.5uL RT mix to each well (2M Betaine (Affymetrix), 2X Protoscript Buffer (New England Biolabs), 12mM MgCl2 (ThermoFisher), 10mM DTT (ThermoFisher), 5.3U Protoscript II Reverse Transcriptase (New England Biolabs), 0.53U SUPERaseIN (ThermoFisher), 2uM Template Switching Oligo (Integrated DNA Technologies, table S6). Reverse transcription was performed at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes, 42°C for 2 minutes, 70°C for 10 minutes, followed by a 4°C hold. Excess primers were removed by adding 2ul Exonuclease I (ThermoFisher) mix to each well (1.875U ExoI in water) and incubating at 37°C for 30 minutes, 85°C for 15 minutes, 75°C for 30 seconds, 4°C hold. All wells were pooled into a single 15-ml falcon tubes and cDNA was purified and concentrated using Dynabeads™ MyOne™ Silane beads (ThermoFisher) according to the manufacturer’s instructions. The cDNA was split into duplicate reactions containing 25ul cDNA, 25ul 2x HIFI HotStart Ready Mix (Kapa Biosystems), and 0.2M SMART PCR Primer (table S6), PCR amplified as above, and duplicate reactions were combined and purified using 0.7 volumes AMPure XP beads (Beckman Coulter). The amplified cDNA was visualized on an Agilent TapeStation and quantified using a Qubit II fluorometer (ThermoFisher). Sequencing libraries were constructed using Nextera XT (Illumina) with modifications. A custom i5 primer was used (NexteraPCR, table S6) with 0.6ng input cDNA and 10 cycles of amplification was performed. Unique i7 indexes were used for each plate. After amplification, the library was purified with two rounds of AMPure XP beads, visualized on the TapeStation and quantified using the Qubit II fluorometer. Libraries were sequenced on an Illumina NextSeq 500 using the 75 cycle High Output kit (read lengths 26(R1) x 8(i) x 58(R2)). Custom sequencing primers were used for Read 1 (SMART_R1seq and ILMN_R1seq, see table S6). With each plate we targeted ~70M reads. Library pools were loaded at 1.8pM with 30% PhiX (Illumina).
Pooled, 3'-end single-cell RNA-seq

value: FAC-sorted T cells from bronchoalveolar lavage

tag: origin

value: pooled sample (see supplementary data)

tag: cd69 expression status

tag: cd103 expression status


title: DM015: Patient29_Plate2

tag: tissue


title: DM018: Patient29_Plate5


title: DM016: Patient29_Plate3


title: DM013: Patient19_Plate4


title: HeLa_CRISPR-PTEN_SPT5

value: HeLa

value: SPT5 (Bethyl Laboratories, A300-868A)

tag: genotype/variation

value: CRISPR-PTEN KO


title: HeLa_CRISPR-PTEN_RNAPII_Ser5P

value: RNAPII Ser5P (abcam, ab5408)


title: HeLa_CRISPR-PTEN_RNAPII

value: RNAPII (Santa Cruz, Sc-899)

value: grown in DMEM supplemented with 10% FBS, penicillin and streptomycin


title: DM012: Patient19_Plate3


title: DM010: Patient19_Plate2


title: HeLa_PTEN_WT_SPT5

value: PTEN WT


title: HeLa_CRISPR-PTEN_PTEN_AB1and2

value: PTEN 6H2.1 (Millipore, 04-035) and PTEN 138G6 (Cell Signaling, 9559)


title: HeLa_PTEN_WT_RNAPII_Ser2P

value: RNAPII Ser2P (abcam, ab5095)


title: HeLa_PTEN_WT_RNAPII_Ser5P


title: HeLa_PTEN_WT_AB1

value: PTEN 6H2.1 (Millipore, 04-035)


title: HeLa_PTEN_WT_AB2

value: PTEN 138G6 (Cell Signaling, 9559)


title: HeLa mRNA-seq PTEN KO rep3


title: DM019: Patient29_Plate6


title: HeLa_CRISPR-PTEN_RNAPII_Ser2P


title: DM014: Patient29_Plate1


title: HeLa mRNA-seq PTEN WT rep1


title: PWT-W2


title: HeLa mRNA-seq PTEN WT rep3


title: HeLa mRNA-seq PTEN KO rep1


title: HeLa mRNA-seq PTEN WT rep2


title: DM009: Patient19_Plate1


title: YX_1009900102_B4_S28

city: Stanford

first: Yuan

last: Xue

address: 318 Campus Drive

institute: Stanford University

description:
3.5 weeks old Schistosome cell 360
schisto3.5_tpm_unfiltered.csv.gz

data_processing:
Read alignment, STAR, 2.5.0a,  –outSAMstrandField intronMotif --runThreadN {threads} --outFileNamePrefix {wdir} --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS NM MD --outReadsUnmapped Fastx --clip3pAdapterSeq CTGTCTCTTATACACATCT --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1; gene count, htseq-count, 0.10.0, -s no -t exon -r pos -f bam -i Parent -m intersection-strict
Genome_build: schistosoma_mansoni.PRJEA36577.WBPS9.genomic.ercc.fa
Supplementary_files_format_and_content: Comma-separated values of normalized gene count (tpm) matrix where rows are genes and columns are sample names.

organism: Schistosoma mansoni

source_name: Schistosoma mansoni stem cells

extract_protocol:
Triton X-100 was used to lyse individual cells, Smart-seq2 protocol was followed to reverse transcribe and amplify mRNA.
Nextera XT DNA

value: stem cells

tag: mouse strain with s. mansoni

value: Swiss  Webster NR-21963

tag: worm age

value: 3.5 weeks


title: YX_1009900102_G7_S151

description:
3.5 weeks old Schistosome cell 365
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D1_S73

description:
3.5 weeks old Schistosome cell 359
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F11_S131

description:
3.5 weeks old Schistosome cell 363
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P17_S77

description:
3.5 weeks old Schistosome cell 366
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E12_S108

description:
3.5 weeks old Schistosome cell 364
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O19_S55

description:
3.5 weeks old Schistosome cell 362
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C7_S55

description:
3.5 weeks old Schistosome cell 356
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H16_S184

description:
3.5 weeks old Schistosome cell 357
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P16_S76

description:
3.5 weeks old Schistosome cell 358
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O11_S47

description:
3.5 weeks old Schistosome cell 355
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N7_S19

description:
3.5 weeks old Schistosome cell 367
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P21_S81

description:
3.5 weeks old Schistosome cell 361
schisto3.5_tpm_unfiltered.csv.gz


title: HeLa_PTEN_WT_RNAPII


title: YX_1009900102_N11_S23

description:
3.5 weeks old Schistosome cell 354
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G5_S149

description:
3.5 weeks old Schistosome cell 350
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H20_S188

description:
3.5 weeks old Schistosome cell 352
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K22_S262

description:
3.5 weeks old Schistosome cell 351
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I5_S197

description:
3.5 weeks old Schistosome cell 349
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G6_S150

description:
3.5 weeks old Schistosome cell 348
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D17_S89

description:
3.5 weeks old Schistosome cell 347
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H5_S173

description:
3.5 weeks old Schistosome cell 344
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F9_S129

description:
3.5 weeks old Schistosome cell 343
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G23_S167

description:
3.5 weeks old Schistosome cell 342
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G13_S157

description:
3.5 weeks old Schistosome cell 345
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I6_S198

description:
3.5 weeks old Schistosome cell 346
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O8_S44

description:
3.5 weeks old Schistosome cell 341
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B12_S36

description:
3.5 weeks old Schistosome cell 336
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P2_S62

description:
3.5 weeks old Schistosome cell 340
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D4_S76

description:
3.5 weeks old Schistosome cell 337
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P1_S61

description:
3.5 weeks old Schistosome cell 334
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A23_S23

description:
3.5 weeks old Schistosome cell 329
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C17_S65

description:
3.5 weeks old Schistosome cell 330
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E22_S118

description:
3.5 weeks old Schistosome cell 353
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C2_S50

description:
3.5 weeks old Schistosome cell 333
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F21_S141

description:
3.5 weeks old Schistosome cell 338
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L10_S274

description:
3.5 weeks old Schistosome cell 331
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M20_S8

description:
3.5 weeks old Schistosome cell 335
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L17_S281

description:
3.5 weeks old Schistosome cell 339
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H15_S183

description:
3.5 weeks old Schistosome cell 332
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C21_S69

description:
3.5 weeks old Schistosome cell 328
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I8_S200

description:
3.5 weeks old Schistosome cell 325
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C10_S58

description:
3.5 weeks old Schistosome cell 323
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H7_S175

description:
3.5 weeks old Schistosome cell 326
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F13_S133

description:
3.5 weeks old Schistosome cell 327
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B1_S25

description:
3.5 weeks old Schistosome cell 322
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I19_S211

description:
3.5 weeks old Schistosome cell 324
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I11_S203

description:
3.5 weeks old Schistosome cell 321
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N19_S31

description:
3.5 weeks old Schistosome cell 320
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J17_S233

description:
3.5 weeks old Schistosome cell 319
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C15_S63

description:
3.5 weeks old Schistosome cell 318
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H18_S186

description:
3.5 weeks old Schistosome cell 317
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D10_S82

description:
3.5 weeks old Schistosome cell 315
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N5_S17

description:
3.5 weeks old Schistosome cell 314
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A21_S21

description:
3.5 weeks old Schistosome cell 313
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E23_S119

description:
3.5 weeks old Schistosome cell 312
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L15_S279

description:
3.5 weeks old Schistosome cell 316
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K13_S253

description:
3.5 weeks old Schistosome cell 310
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A9_S9

description:
3.5 weeks old Schistosome cell 306
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O21_S57

description:
3.5 weeks old Schistosome cell 311
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L9_S273

description:
3.5 weeks old Schistosome cell 309
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J23_S239

description:
3.5 weeks old Schistosome cell 307
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F4_S124

description:
3.5 weeks old Schistosome cell 303
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G9_S153

description:
3.5 weeks old Schistosome cell 302
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N22_S34

description:
3.5 weeks old Schistosome cell 304
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M6_S294

description:
3.5 weeks old Schistosome cell 299
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J8_S224

description:
3.5 weeks old Schistosome cell 298
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B13_S37

description:
3.5 weeks old Schistosome cell 297
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G17_S161

description:
3.5 weeks old Schistosome cell 301
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G16_S160

description:
3.5 weeks old Schistosome cell 300
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O5_S41

description:
3.5 weeks old Schistosome cell 293
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H8_S176

description:
3.5 weeks old Schistosome cell 296
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D9_S81

description:
3.5 weeks old Schistosome cell 292
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H17_S185

description:
3.5 weeks old Schistosome cell 295
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O22_S58

description:
3.5 weeks old Schistosome cell 294
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O1_S37

description:
3.5 weeks old Schistosome cell 305
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I14_S206

description:
3.5 weeks old Schistosome cell 291
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G18_S162

description:
3.5 weeks old Schistosome cell 290
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I15_S207

description:
3.5 weeks old Schistosome cell 289
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G12_S156

description:
3.5 weeks old Schistosome cell 287
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D12_S84

description:
3.5 weeks old Schistosome cell 288
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O18_S54

description:
3.5 weeks old Schistosome cell 286
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E10_S106

description:
3.5 weeks old Schistosome cell 279
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M4_S292

description:
3.5 weeks old Schistosome cell 282
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G2_S146

description:
3.5 weeks old Schistosome cell 278
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B20_S44

description:
3.5 weeks old Schistosome cell 280
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P20_S80

description:
3.5 weeks old Schistosome cell 284
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L18_S282

description:
3.5 weeks old Schistosome cell 276
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O10_S46

description:
3.5 weeks old Schistosome cell 275
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N12_S24

description:
3.5 weeks old Schistosome cell 281
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G1_S145

description:
3.5 weeks old Schistosome cell 273
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E19_S115

description:
3.5 weeks old Schistosome cell 308
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L23_S287

description:
3.5 weeks old Schistosome cell 270
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C11_S59

description:
3.5 weeks old Schistosome cell 271
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E1_S97

description:
3.5 weeks old Schistosome cell 269
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F6_S126

description:
3.5 weeks old Schistosome cell 267
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D7_S79

description:
3.5 weeks old Schistosome cell 277
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B6_S30

description:
3.5 weeks old Schistosome cell 274
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B17_S41

description:
3.5 weeks old Schistosome cell 268
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N9_S21

description:
3.5 weeks old Schistosome cell 265
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G8_S152

description:
3.5 weeks old Schistosome cell 264
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K12_S252

description:
3.5 weeks old Schistosome cell 263
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H11_S179

description:
3.5 weeks old Schistosome cell 266
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K16_S256

description:
3.5 weeks old Schistosome cell 262
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I10_S202

description:
3.5 weeks old Schistosome cell 285
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A1_S1

description:
3.5 weeks old Schistosome cell 260
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F18_S138

description:
3.5 weeks old Schistosome cell 283
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C5_S53

description:
3.5 weeks old Schistosome cell 259
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K4_S244

description:
3.5 weeks old Schistosome cell 258
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E3_S99

description:
3.5 weeks old Schistosome cell 261
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I17_S209

description:
3.5 weeks old Schistosome cell 272
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M19_S7

description:
3.5 weeks old Schistosome cell 254
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B19_S43

description:
3.5 weeks old Schistosome cell 255
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D15_S87

description:
3.5 weeks old Schistosome cell 252
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F5_S125

description:
3.5 weeks old Schistosome cell 250
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L22_S286

description:
3.5 weeks old Schistosome cell 249
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M11_S299

description:
3.5 weeks old Schistosome cell 247
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I2_S194

description:
3.5 weeks old Schistosome cell 246
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J7_S223

description:
3.5 weeks old Schistosome cell 248
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I21_S213

description:
3.5 weeks old Schistosome cell 245
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I13_S205

description:
3.5 weeks old Schistosome cell 244
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K9_S249

description:
3.5 weeks old Schistosome cell 242
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C9_S57

description:
3.5 weeks old Schistosome cell 241
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O15_S51

description:
3.5 weeks old Schistosome cell 239
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E16_S112

description:
3.5 weeks old Schistosome cell 237
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N6_S18

description:
3.5 weeks old Schistosome cell 236
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E7_S103

description:
3.5 weeks old Schistosome cell 234
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G19_S163

description:
3.5 weeks old Schistosome cell 235
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F20_S140

description:
3.5 weeks old Schistosome cell 257
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A18_S18

description:
3.5 weeks old Schistosome cell 256
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F16_S136

description:
3.5 weeks old Schistosome cell 232
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O9_S45

description:
3.5 weeks old Schistosome cell 251
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P22_S82

description:
3.5 weeks old Schistosome cell 253
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B2_S26

description:
3.5 weeks old Schistosome cell 231
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C3_S51

description:
3.5 weeks old Schistosome cell 228
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M16_S4

description:
3.5 weeks old Schistosome cell 230
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M1_S289

description:
3.5 weeks old Schistosome cell 243
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N15_S27

description:
3.5 weeks old Schistosome cell 226
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B10_S34

description:
3.5 weeks old Schistosome cell 233
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M2_S290

description:
3.5 weeks old Schistosome cell 229
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C13_S61

description:
3.5 weeks old Schistosome cell 225
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O6_S42

description:
3.5 weeks old Schistosome cell 221
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J1_S217

description:
3.5 weeks old Schistosome cell 227
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H22_S190

description:
3.5 weeks old Schistosome cell 240
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A22_S22

description:
3.5 weeks old Schistosome cell 224
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H9_S177

description:
3.5 weeks old Schistosome cell 223
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K21_S261

description:
3.5 weeks old Schistosome cell 222
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A8_S8

description:
3.5 weeks old Schistosome cell 220
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L6_S270

description:
3.5 weeks old Schistosome cell 238
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E2_S98

description:
3.5 weeks old Schistosome cell 215
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N8_S20

description:
3.5 weeks old Schistosome cell 216
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E21_S117

description:
3.5 weeks old Schistosome cell 219
schisto3.5_tpm_unfiltered.csv.gz


title: HeLa Input DNA


title: HeLa mRNA-seq PTEN KO rep2


title: YX_1009900102_J19_S235

description:
3.5 weeks old Schistosome cell 217
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G10_S154

description:
3.5 weeks old Schistosome cell 214
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N20_S32

description:
3.5 weeks old Schistosome cell 213
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N16_S28

description:
3.5 weeks old Schistosome cell 212
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G21_S165

description:
3.5 weeks old Schistosome cell 211
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H3_S171

description:
3.5 weeks old Schistosome cell 210
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O14_S50

description:
3.5 weeks old Schistosome cell 208
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D18_S90

description:
3.5 weeks old Schistosome cell 207
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G3_S147

description:
3.5 weeks old Schistosome cell 209
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B18_S42

description:
3.5 weeks old Schistosome cell 206
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J10_S226

description:
3.5 weeks old Schistosome cell 204
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M18_S6

description:
3.5 weeks old Schistosome cell 203
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L2_S266

description:
3.5 weeks old Schistosome cell 205
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O13_S49

description:
3.5 weeks old Schistosome cell 202
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I1_S193

description:
3.5 weeks old Schistosome cell 199
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P5_S65

description:
3.5 weeks old Schistosome cell 200
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I7_S199

description:
3.5 weeks old Schistosome cell 197
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I18_S210

description:
3.5 weeks old Schistosome cell 195
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F10_S130

description:
3.5 weeks old Schistosome cell 194
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O2_S38

description:
3.5 weeks old Schistosome cell 218
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J9_S225

description:
3.5 weeks old Schistosome cell 196
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_G22_S166

description:
3.5 weeks old Schistosome cell 193
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P11_S71

description:
3.5 weeks old Schistosome cell 192
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C20_S68

description:
3.5 weeks old Schistosome cell 189
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M9_S297

description:
3.5 weeks old Schistosome cell 187
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O16_S52

description:
3.5 weeks old Schistosome cell 191
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F12_S132

description:
3.5 weeks old Schistosome cell 188
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J15_S231

description:
3.5 weeks old Schistosome cell 185
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P8_S68

description:
3.5 weeks old Schistosome cell 186
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H13_S181

description:
3.5 weeks old Schistosome cell 183
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E8_S104

description:
3.5 weeks old Schistosome cell 182
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O12_S48

description:
3.5 weeks old Schistosome cell 180
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M14_S2

description:
3.5 weeks old Schistosome cell 181
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O7_S43

description:
3.5 weeks old Schistosome cell 178
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P10_S70

description:
3.5 weeks old Schistosome cell 198
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H2_S170

description:
3.5 weeks old Schistosome cell 177
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D23_S95

description:
3.5 weeks old Schistosome cell 176
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H6_S174

description:
3.5 weeks old Schistosome cell 174
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E11_S107

description:
3.5 weeks old Schistosome cell 175
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J3_S219

description:
3.5 weeks old Schistosome cell 201
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L5_S269

description:
3.5 weeks old Schistosome cell 172
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I4_S196

description:
3.5 weeks old Schistosome cell 171
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A12_S12

description:
3.5 weeks old Schistosome cell 179
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E15_S111

description:
3.5 weeks old Schistosome cell 170
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I23_S215

description:
3.5 weeks old Schistosome cell 169
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A4_S4

description:
3.5 weeks old Schistosome cell 173
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N1_S13

description:
3.5 weeks old Schistosome cell 166
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N4_S16

description:
3.5 weeks old Schistosome cell 168
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H4_S172

description:
3.5 weeks old Schistosome cell 190
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L4_S268

description:
3.5 weeks old Schistosome cell 164
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B9_S33

description:
3.5 weeks old Schistosome cell 162
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B5_S29

description:
3.5 weeks old Schistosome cell 161
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A6_S6

description:
3.5 weeks old Schistosome cell 159
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L19_S283

description:
3.5 weeks old Schistosome cell 158
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E14_S110

description:
3.5 weeks old Schistosome cell 167
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I3_S195

description:
3.5 weeks old Schistosome cell 163
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D16_S88

description:
3.5 weeks old Schistosome cell 160
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_F19_S139

description:
3.5 weeks old Schistosome cell 156
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N23_S35

description:
3.5 weeks old Schistosome cell 157
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A15_S15

description:
3.5 weeks old Schistosome cell 155
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H21_S189

description:
3.5 weeks old Schistosome cell 184
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D11_S83

description:
3.5 weeks old Schistosome cell 153
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B21_S45

description:
3.5 weeks old Schistosome cell 154
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_E9_S105

description:
3.5 weeks old Schistosome cell 152
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P19_S79

description:
3.5 weeks old Schistosome cell 149
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B16_S40

description:
3.5 weeks old Schistosome cell 151
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P3_S63

description:
3.5 weeks old Schistosome cell 150
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N10_S22

description:
3.5 weeks old Schistosome cell 148
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K14_S254

description:
3.5 weeks old Schistosome cell 165
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K6_S246

description:
3.5 weeks old Schistosome cell 147
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L12_S276

description:
3.5 weeks old Schistosome cell 146
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I9_S201

description:
3.5 weeks old Schistosome cell 144
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B22_S46

description:
3.5 weeks old Schistosome cell 145
schisto3.5_tpm_unfiltered.csv.gz


title: V2_H3K27me3

first: Suman Kumar

last: Vodnala

address: 10 Center Drive

institute: NCI

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2
Peaks were called usingHomer (findPeaks H3k9Ac_Veh_1 -i Input_V -region -size 1000 -minDist 2500), Common peaks between two conditions are merged into a sinle file using bedtools. significantly different peaks between Ctrl / K+ is caluclated using Deseq2 integrated in the homer package.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized bam files were processed to deeptools to generate bigwig files

source_name: Primary T cells cultured for 10 days in Ctrl

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

value: CD8 T cell

value: H3K27me3_ChIP Grade (ab195477)


title: YX_1009900102_J16_S232

description:
3.5 weeks old Schistosome cell 143
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L8_S272

description:
3.5 weeks old Schistosome cell 142
schisto3.5_tpm_unfiltered.csv.gz