title: At_BT_rep2

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

data_processing:
Library strategy: DNA-Seq
The raw reads were trimmed using Trimmomatic to remove adapter sequences. Reads with an averaged value of at least 15 in a 4 nt window were trimmed from both ends. After trimming, reads pairs with at least one mate shorter that 16 bp were discarded
The remaining sequences (in average 94% of raw reads) were aligned with segemehl v0.2.0 (Hoffmann et al., 2009), with 95% accuracy threshold, to the corresponding reference genome (A.thaliana TAIR10 and the B. vulgaris RefBeet-1.2.2) including also the sequence of the BCTIV genome (accession no. JX082259).
Split read junctions were called with testrealign.x (part of segemehl toolkit) with default parameters, and junctions with at least a coverage of 10 reads and comprising the virus genome were selected for downstream analysis using R (dplyr package)
Then, the reads spanning the 10 kb locus around each selected junctions were recovered together with their mates from the original fastq files, using samtools (Li et al., 2009) and BBMap (https://sourceforge.net/projects/bbmap/)
The filtered paired read lists were used as input in the A5_miseq pipeline (Coil et al., 2015) with default parameters, for reference-unbiased de novo assembly.
We then used blastn (BLAST v2.2.25+) with default parameters to filter only the assembled scaffolds matching both the reference and the BCTIV genome, to select minicircle candidates.
Genome_build: RefBeet-1.2.2
Genome_build: TAIR10
Genome_build: Beet curly top Iran virus-[Siv] (GenBank: JX082259)
Supplementary_files_format_and_content: Assembled scaffolds matching both the reference and the BCTIV genome were used to generate a list of sequences in fasta format. If none of the assembled scaffolds matched this alignment criteria, the file was not generated (this is the case of Arabidopsis samples and the B. vulgaris mock-inoculated plant).

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Plants were grown in soil in greenhouse at 20–28/16–20◦C (day/night), with a 16/8 h (light/dark) photoperiod and supplementary lighting

extract_protocol:
Total nucleic acids were extracted from plant samples (100 mg) using the TLES method (Noris et al., 1996)
Before library preparation, genomic DNA was fragmented to an average insert size of 350bp using 18 cycles of 30 seconds each on a Bioruptor® Diagenode sonication device, split into three groups of 6 cycles with 2.5 minutes on ice between each set. The genomic DNA sequencing libraries were prepared using the TruSeq DNA PCR-Free LT Library Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA), starting from 1.1µg of sonicated DNA. Libraries were validated using the High Sensitivity D1000 screentape on the 2200 Tapestation instrument (Agilent technologies, Santa Clara, CA) and the LightCycler® 480 Instrument II using the LightCycler® 480 SYBR Green I Master mix (Roche, Basel, Switzerland).

treatment_protocol: Plants were inoculated by agroinoculation, by delivery of agrobacteria carrying 1.4mer BCTIV-Siv clone (Soleimani et al., 2013) (accession no. JX082259) or pBIN19 as control (mock).

tag: ecotype

value: leaves

tag: developmental stage

value: 4 weeks post inoculation

tag: infected with

value: BCTIV


title: ATAC_LincGET_OE

status: Public on Dec 13 2018

type: SRA

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

country: China

institute: Institute of Zoology,CAS

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were performed quality controll and trimmed for adaptor sequence by FASTX-Toolki
Clean reads were then mapped to the mouse mm9 genome assembly by Bowtie2 (Langmead and Salzberg, 2012) using default settings. After this, reads with multiple genomic loci were discarded. Then, non-redundant reads were analyzed using MACS2 software (Zhang et al., 2008) to identify peaks (transcription factor binding sites) with a threshold of a p-value less than 1 × 10-5. Distributions of ATAC-seq read density around the transcription start sites (TSSs) regions (the upstream and downstream 1 kb regions, respectively) were plotted using Sitepro from the CEAS package (Shin et al., 2009) with a bin size of 20 bp. Finally, the ICM and TE specific genes were reanalyzed from the published single cell RNA-Seq data in the GEO database GSE70605 (Liu et al., 2016).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files produced by MACS2

molecule: genomic DNA

organism: Mus musculus

source_name: LincGET-overexpressing blastomeres at the 8-cell stage

growth_protocol: All experiments were performed in accordance with ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines and regulations. Two-cell stage embryos were collected from 6-week-old super-ovulated female ICR mice crossed with ICR males, 46 hours after the injection of human chorionic gonadotropin (hCG). 8-cell stage embryos was flushed from the reproductive tract at 68–70 h after hCG administration. The zona pellucida was removed using Tyrode’s solution. Zona-free embryos were incubated for 5 min in Ca2+ and Mg2+ free M2 before disaggregation by careful pipetting. Single cells were separeted into two tubes according to GFP positive or negtive.

extract_protocol:
Cells from ATAC-seq libraries created from approximately fifty 8-cell embryos were prepared as described previously (Wu et al., 2016). Briefly, samples were lysed in 5 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.15% NP-40) for 10 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD502). Then, the stop buffer was added directly into the reaction to end the tagmentation. PCR was then performed to amplify the library for 15 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s. This was by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 3 min, followed by 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2X AMPure (Backman, A63880) beads before proceeding to mitochondrial DNA depletion. A total of 400 sgRNAs targeting the mouse mitochondrial genome were provided as a gift by Wei Xie’s laboratory of School of Life Sciences, Tsinghua University. Next, in vitro transcription was performed to produce sgRNAs using the MEGAshortscript? Kit (Ambion, AM1354)). Each ATAC-seq library was incubated with 5 μg of sgRNA and 10 μg of Cas9 protein (PNA Bio, CP02-50) for 2 h at 37°C. After incubation, the reaction was treated by RNase A before being terminated by adding stop buffer (30% glycerol, 1.2% SDS, 250mM EDTA, pH 8.0).
The samples were then processed by an Illumina HiSeq 2500 sequencer with 50 bp paired-end sequencing reactions.

tag: strain

value: ICR

tag: tissue

value: 8-cell embryos

tag: operation

value: Overexpressing lincGET


title: αPM singlets_B [a_7]

city: Kyoto

first: Kenichiro

last: Furuyama

state: Kyoto

address: 53 Shogoinkawahara-cho, Sakyo-ku

department: Life Science Frontiers

country: Japan

institute: CiRA, Kyoto University

library_source: transcriptomic

data_processing:
The sequencing quality control was done with FASTQC v.0.11.2, followed by sequence alignment to the human reference genome (hg38) using the TopHat v2.0.13 (default parameters).
Biological quality control and summarization were done with the PicardTools v1.80.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each sample

molecule: total RNA

organism: Homo sapiens

source_name: αPM singlets

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Micro kit, and treated with RNase-free DNaseI (Qiagen)
Extracted RNA sample was assessed for the quality by Agilent bioanalyzer prior to library generation. Reverse transcription and cDNA amplification were performed using the SMARTer Ultra Low RNA kit (Clontech). cDNA library was prepared using Nextera XT DNA Sample Preparation kit (Illumina), and multiplexed.

value: pancreas

tag: cell type

value: alpha-cells

tag: cultured or grafted

value: 1 week

tag: transduction

value: PM


title: αPM grafted_C [a_8]

source_name: αPM grafted

value: grafted


title: αPM grafted_A [a_10]


title: αPM grafted_B [a_9]


title: s4662

city: Zürich

first: Konrad

last: Basler

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zürich

data_processing:
Mapping TopHat
Table of counts: Htseq
Normalization and DE testing: edgeR
Genome_build: Ensembl GRCm38.p4
Supplementary_files_format_and_content: differential fold changes between groups, in .xls

source_name: Vehicle treated SCC 4

extract_protocol:
TRIZOL followed by pure link mini kit (ambion)
GE3 center University of Geneva

treatment_protocol: 12 days after tumor induction, 6mg/kg/day per os

value: FVB

value: HPV induced squamous cell carcinoma (SCC)


title: ind26 2014

type: RNA

city: Haifa

first: Ayelet

last: Alpert

address: Techion

country: Israel

institute: Technion

description:
ind26
RNA expression value derived from Affymetrix Launcher software

hyb_protocol: Labeled complementary RNA (cRNA) was synthesized and amplified by in vitro transcription (IVT) of the second-stranded cDNA template using T7 RNA polymerase. Purified cRNA was fragmented by divalent cations and elevated temperature. 11ug of labelled and fragmented cRNA was hybridized onto the PrimeView GenChip, washed, scanned, and extracted by following the user guides: GeneChip Fluidics Station 450 User Guide AGCC (P/N 08-0295), the GeneChip Expression Wash, Stain, and Scan User Guide for Cartridge Arrays (PN 702731), and the GeneChip Command Console User Guide (P/N 702569).

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw data were processed in R for background correction and RMA normalization. Normalized expression data were log-transformed.

label: biotinylated UTP

source_name: whole blood

label_protocol: For each sample, 100 ng of total RNA were used for first-strand cDNA synthesis by using T7 oligo(dT) primer  at 42°C for 2 hr, then for at least 2 min at 4°C. Single-stranded cDNA was converted to double-stranded cDNA for 1 hr at 16°C, then for 10 min at 65°C, then for at least 2 min at 4°C.

growth_protocol: No growth protocol was applied on the cells.

extract_protocol: RNA was extracted from the PAXgene RNA blood tubes (PreAanalytiX GmbH,VWR part # 77776-026, USA) using the QIAcube automation RNA extraction procedure according to the manufacturer’s protocol (Qiagene Inc.,Valencia, CA, USA).

treatment_protocol: No additional treatment was applied on the samples.

tag: age

tag: ID

tag: gender

value: Female


title: At_BT_rep1

country: United Kingdom


title: αPM singlets_A [a_6]


title: ind109 2014

description:
ind109
RNA expression value derived from Affymetrix Launcher software


title: ind122 2014

description:
ind122
RNA expression value derived from Affymetrix Launcher software

value: Male


title: s4715

source_name: Vehicle treated SCC 3


title: αGFP singlets_A [a_5]

source_name: αGFP singlets

value: GFP


title: s4714

source_name: Vehicle treated SCC 2


title: α singlets_A [a_4]

source_name: α singlets


title: s4666

source_name: LGK974 treated SCC 4


title: αPM_A [a_2]

source_name: αPM


title: αPM_B [a_3]


title: ind39 2014

description:
ind39
RNA expression value derived from Affymetrix Launcher software


title: s4665

source_name: LGK974 treated SCC 3


title: s4711

source_name: LGK974 treated SCC 2


title: ind73 2014

description:
ind73
RNA expression value derived from Affymetrix Launcher software


title: s4710

source_name: LGK974 treated SCC 1


title: αPM grafted_1 [32_S32]


title: s4392

source_name: healthy skin 4

value: healthy skin


title: ind92 2014

description:
ind92
RNA expression value derived from Affymetrix Launcher software


title: ind82 2014

description:
ind82
RNA expression value derived from Affymetrix Launcher software


title: s4390

source_name: healthy skin 3


title: sVC83

source_name: Vehicle treated SCC 1


title: βGFP_6 [30_S30]

source_name: βGFP


title: s4716

source_name: healthy skin 2


title: βGFP_4 [28_S28]


title: ind80 2013

description:
ind80
RNA expression value derived from Affymetrix Launcher software


title: ind13 2013

description:
ind13
RNA expression value derived from Affymetrix Launcher software


title: βGFP_5 [29_S29]


title: ind66 2013

description:
ind66
RNA expression value derived from Affymetrix Launcher software


title: αPM grafted_2 [34_S33]

source_name: αPM grafted


title: s4717

source_name: healthy skin 1


title: αGFP_A [a_1]

source_name: αGFP


title: ind62 2013

description:
ind62
RNA expression value derived from Affymetrix Launcher software

source_name: whole blood


title: ind57 2013

description:
ind57
RNA expression value derived from Affymetrix Launcher software


title: βGFP_3 [27_S27]


title: RPE1_single_MidS_04

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

data_processing:
BrdUIP, Population early-S, 100-cells, Single-cell data: sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
BrdUIP, Population early-S, 100-cells, Single-cell data: trimmed reads were mapped into mm9, hg19, CBMS1-specific (CBA/MsM) diploid genome based on mm9 genome by using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 or hg19 were removed by using picard tool and the reads overlapped with mm9, hg19 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
BrdUIP data: we counted the reads of early and late S-phase BrdU-IP samples in sliding windows of 200 kb at 40-kb or 80-kb intervals (written in the processed data file as “w200sk40k” or “w200ks80k”, respectively) in non-overlapping 400-kb windows (“400k”) and performed rpm (reads per million) normalization. Then, the ratio of early-S to total read counts [(Early-S reads)/(Early-S reads + Late-S reads)] was calculated for each bin and their distribution converted to fit within a ± 1 scale, and this value was defined as the BrdU-IP RT score of each bin. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Population early-S data: we counted the reads of early-S and G1 in sliding windows of 200 kb at 40-kb intervals, performed rpm normalization in a manner identical to BrdU-IP data processing, and defined Log2[(Early-S reads)/(G1 reads)] as the population early-S RT score.
100-cells data: we counted the reads of 100 mid-S and G1 cells in sliding windows of 200 kb at 40-kb intervals and used the correctMappability command in the R package AneuFinder (http://bioconductor.org/packages/release/bioc/html/AneuFinder.html) for normalizing mid-S data based on G1 data. From the mappability corrected mid-S read counts, the genome-wide median was obtained and used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the 100-cell mid-S RT score.
Single-cell data (hTERT-RPE1): For the analysis of single mid-S cells, we counted the reads in sliding windows of 200 kb at 40-kb intervals, and used the AneuFinder’s correctMappability command sfor normalizing mid-S data based on the merged G1 control. From the mappability corrected mid-S read counts, the genome-wide median was obtained and was used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the single-cell mid-S RT score.
Single-cell data (CBMS1 un-resolved): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved data: after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy" ].
Binarized unresolved data: Sample_Name_80k_100S_MAP_2HMM2_eps0.01.binary.bedGraph, Binarized CBA data: Sample_name_cba_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph, Binarized MsM data: Sample_name_msm_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
RNA-seq: allele-specific RNA-seq analysis was performed using CBA/MsM diploid genome as described in Sakata et al. Development 2017. We defined genes with allelic expression imbalance as those with the percentage of either MsM- or CBA-specific reads above 60% (or >70%) among genes that show ≥10 total reads (i.e. CBA+MsM read numbers combined) and >0.1 FPKM (fragments per kilobase of exon per million fragments mapped, in a non-allelic manner) in three biological replicates (CBMS1_allele_specific_genetable.txt).
Genome_build: hg19 / mm9 / CBMS1 diploid genome
Supplementary_files_format_and_content: bedGraph, bigWig

growth_protocol: hTERT-RPE1 cells were grown in MEM-alpha supplemented with 10% FBS and penicillin/streptomycin. CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013).

extract_protocol:
For BrdU-IP samples, we followed our routine protocol as described (Ryba et al., Nat. Protoc. 2011). A Sony SH800 cell sorter was used in the ultra-purity mode, fractionating early and late S-phase populations. The BrdU-IP protocol has been described in detail (Ryba et al., Nat. Protoc. 2011), except that we used a Bioruptor UCD-250 (Sonic Bio) for gDNA sonication in high output mode, with ON/OFF pulse times of 30 sec/30 sec for 6 minutes. After BrdU-IP, immunoprecipitated DNA samples were subject to WGA with a SeqPlex kit (Sigma, SEQXE).   For early S-phase population samples, 200,000 cells from the first half of S-phase were sorted by Sony SH800 cell sorter, and gDNA was isolated using a Qiagen kit (Qiagen #69504, DNeasy Blood & Tissue Kit) and fragmented to 200–300 bp with a Covaris ultrasonciator (model: S220, tube: microTUBE snap-cap) according to the manufacturer’s instructions (peak incident power: 175, duty factor: 10%, cycles per burst: 200, treatment time: 120), followed by cleanup and size selection via Agencourt AMPure XP SPRI beads (Beckman Coulter).  For single or 100 cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).  For RNA-seq samples, cells were lysed in TRI Reagent (Molecular Research Center, Inc. cat. TR 118) to extract total RNA.
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80, 84, 127-bp length, single-read or paired-end read). For NGS on Ion Proton system, libraries were constructed using Ion Plus Core Module for AB Library Builder System (Thermo Fisher Scientific, #4477683) with Ion Xpress Barcode Adapters 1-16 Kit (Thermo Fisher Scientific, #4477683).  For RNA-seq, NGS library preparation was performed using 500ng of total RNA following the standard protocol of TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

value: Epithelial cells immortalized with hTERT

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: XX

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase

value: MidS


title: ind107 2013

description:
ind107
RNA expression value derived from Affymetrix Launcher software


title: βGFP_2 [26_S26]


title: Affected_F3

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

country: USA

institute: Medical College of Wisconsin

data_processing:
ThermoFisher Proton TMAP for reference alignment
ThermoFisher Proton AmpliSeq Plugin for counts
Used ThermoFisher RNA AmpliSeq target file as GTF
Genome_build: GRCh37
Supplementary_files_format_and_content: text file with raw counts

source_name: hiPSC-CM

extract_protocol:
RNA was isolated using a commercially available kit: PicoPure™ RNA Isolation Kit (Thermo Fisher, KIT0204) and RNase-Free DNase Set (Qiagen #79254).
Libraries were prepared using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (ThermoFisher, A26325) and sequenced on the Ion Torrent Proton System (Thermofisher Scientific) following manufacturer’s recommendations.

tag: donor id

value: F

tag: diagnosis

value: Affected

value: hiPSC-CM


title: ind32 2013

description:
ind32
RNA expression value derived from Affymetrix Launcher software


title: Affected_F2


title: RPE1_single_MidS_03

tag: strain


title: RPE1_single_MidS_02


title: ind21 2013

description:
ind21
RNA expression value derived from Affymetrix Launcher software


title: βGFP_1 [25_S25]

tag: tissue

value: pancreas

value: alpha-cells


title: ind64 2013

description:
ind64
RNA expression value derived from Affymetrix Launcher software


title: Affected_F1


title: ind36 2013

description:
ind36
RNA expression value derived from Affymetrix Launcher software


title: sorted β-cells_5 [24_S24]

source_name: sorted β-cells


title: RPE1_single_MidS_01


title: Affected_E3

value: E


title: sorted β-cells_4 [23_S23]


title: Affected_E2


title: sorted β-cells_3 [22_S22]


title: sorted β-cells_2 [21_S21]


title: Affected_E1


title: Affected_D3

value: D


title: ind24 2013

description:
ind24
RNA expression value derived from Affymetrix Launcher software


title: RPE1_single_G1_01

description: control


title: RPE1_100cells_MidS_rep3

value: 100 cells


title: sorted β-cells_1 [20_S20]


title: RPE1_100cells_MidS_rep2


title: ind9 2013

description:
ind9
RNA expression value derived from Affymetrix Launcher software


title: ind12 2013

description:
ind12
RNA expression value derived from Affymetrix Launcher software


title: NonAffected_C3

value: C

value: Non-Affected


title: RPE1_100cells_MidS_rep1


title: NonAffected_C2


title: αPM_3 [14_S14]

value: 1 week

value: PM


title: αPM_4 [15_S15]


title: RPE1_100cells_G1_rep1

description: control


title: Reh_rep2 (RACE)

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

description: cDNA from THE1B 5’ RACE

data_processing:
Trimming: cutadapt (1.4). RACE adapter and generic THE1B primer trimming was performed using zcat <fq.gz> | cutadapt -g TCATACACATACGATTTAGGTGACACTATAGAGCGGCCGCCTGCAGGAAA - | cutadapt -g CATGGCTGGGAGGCCTC -
Alignment: bowtie2 (2.1.0). Alignment was performed in paired-end mode using bowtie2 -x hg19 -1 <fq1> -2 <fq2> --very-sensitive-local
Read filtering on uniquely aligned reads: samtools (1.1). samtools view -hbq 2 <in.bam> -o <out.bam>
Peak detection and coverage track generation: MACS (1.4.1). macs14 -t <bam> -n <name> -g hs –keep-dup=all -w -S
Genome_build: hg19
Supplementary_files_format_and_content: Variable step 10bp bin wig format representing depth coverage

source_name: Pro-B lymphoblastic leukemia cell line

growth_protocol: KM-H2, L1236 and L428 were cultured in IMDM, Namalwa and Reh cells in RPMI, both supplemented with 10% FCS, 2mM Glutamine, plus P/S. All cultures were incubated at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RACE was performed using the specific primer CATGGCTGGGGAGGCCTCA to amplify cDNA products containing a conserved region of the THE1B LTR and the transcription start site. RACE was carried out based on the ExactSTART™ Eukaryotic mRNA 5’-& 3’-RACE Kit (Epicentre) using the supplied protocol. However, due to the discontinuation of supply of the Tobacco Acid Pyrophosphatase enzyme, a number of modifications were made. To perform 5’ RACE RNA was treated with Alkaline Phosphatase for 15 minutes at 37°C (10 µl Apex Buffer, 5 µl Apex Heat-liable Alkaline Phosphatase (Epicentre), 1 µg RNA, made up to 100 µl with H2O). An Ampure RNA-clean bead purification was then carried out prior to treatment with RNA 5’ Pyrophosphohydrolase (RppH) for 1 hour at 37 °C (Purified RNA (40 µl), 10 x Thermopol Buffer (NEB)(5 µl), RppH Enzyme (NEB)(5 µl)). The RppH reaction was stopped by addition of 1 µl of 500 mM EDTA solution and then purified with a further Ampure RNA-clean bead purification and eluted in 16 µl H20. The 5’ RACE acceptor oligonucleotide was ligated at 37 °C for 30 minutes after addition of 4 µl H2O, 2 µl RNA ligase buffer, 1 µl 5’ acceptor oligonucleotide, 1 µl 2mM ATP solution and 1 µl T4 RNA ligase (NEB). First strand cDNA synthesis was carried out by addition of 14 µl H2O, 1 µl cDNA synthesis primer, 2 µl dNTP PreMix, 2 µl MMLV RT Buffer and 1 µl MMLV RT, the reaction was incubated at 37°C for 1 hour followed by 85°C for 10 minutes. The reaction then had 1 µl of RNase added and was incubated at 55°C for 5 minutes. The second strand cDNA synthesis reaction components were added at 55°C. The consensus biotinylated THE1B LTR primer CATGGCTGGGGAGGCCTCA (20 µM, 2 µl ) was used along with a primer complementary to the previously ligated 5’ RACE adaptor (5 µl ), 21 µl  H2O, 30 µl PCR mix and 1 µl (2.5 U) PfuUltra II polymerase and incubated for 21 cycles (95°C 30 seconds, 21 x 95°C 20 seconds, 60 °C 20 seconds, 72°C 3 minutes). Following second strand synthesis the fragments incorporating a biotinylated primer were selected using T1 Dynabeads (Thermo Fisher Scientific) as follows. T1 dynabeads (20 µl) were washed in B&W buffer (10 mM Tris-HCL, 1 mM EDTA, 2 M NaCl) using magnetic separation and re-suspended in 50 µl of 2 x buffer B&W buffer. An equal volume of RACE product was added and samples were mixed on a slow rotating wheel at room temperature for 1 hour. The beads were then captured using a magnetic separator washed with B&W buffer and TE andwere re-suspended in 33.75 µl 1 x TE. The selected DNA was amplified off the beads by a 3 cycle PCR (95°C 2 minutes, 3 x 95°C 20 seconds, 56 °C 20 seconds, 72°C 30 seconds and 72°C 3 minutes) using a non-biotinylated THE1B LTR primer (1.25 µl, 20µM), the 5’ RACE adaptor primer (4 µl), 5 µl dNTPs (10mM), 5 µl PFU Ultra Buffer and 1 µl PFU Ultra polymerase. Finally purification was carried out using the Qiagen MiniElute PCR Cleanup Kit and the final product was eluted in 11 µl elution buffer.
Libraries for genome wide RACE-Seq were produced using the MicroPlex Library Preparation Kit v2 (Diagenode). Purified RACE material (10 µl) was added to 2 µl of template preparation buffer and 1 µl of Template Preparation Enzyme and incubated at 22°C for 25 minutes followed by 55°C for 20 minutes. The prepared template was then mixed with 1 µl Library synthesis buffer according to the manufacturer’s instructions and 1 µl Library synthesis enzyme and incubated at 22°C for 40 minutes. The libraries were then mixed with amplification buffer (25 µl), amplification enzyme (1 µl), H2O (4 µl) and a Barcoded Indexing Reagent (5 µl) to allow for the samples to be multiplexed for sequencing. The mix was split into 2 reactions of 25 µl which were amplified at 12 and 14 cycles to allow for selection of enough material to sequence without introducing clonal amplification (Extension and Cleavage: 72°C 3 minutes, 85°C 2 minutes, Denaturation: 98°C 2 minutes, Addition of Indexed oligonucleotides: 4 x 98°C 20 seconds, 67°C 20 seconds, 72°C 40 seconds, Library Amplification: 12 or 14 x 98°C 20 seconds, 72°C 50 seconds). Finally size selection and purification of the libraries was carried out by running products on a 1.2% TAE agarose gel (with 0.05% ethidium bromide) and excising fragments between 190 and 300 bp. These were then extracted using the Qiagen mini-elute gel extraction kit and eluted twice in 12 µl H2O. The libraries were run on a Bioanalyzer 2100 with a High Sensitivity DNA Assay chip (Agilent) to determine the average fragment size and quantified by PCR using the Kappa Illumina Library Quantification Kit on an Applied Biosystems StepOne Plus RT PCR system. The indexed libraries were pooled and sequenced on Illumina MiSeq using the 150-Cycle paired end kit or a NextSeq 500 as a fraction of a 150 cycle flow cell.
RACE-Seq

treatment_protocol: PMA treatment was at 2 ng/ml media at a cell density of 1x106 / ml. Induction with doxycycline (2 μg/ml) was performed for 48 hours followed by sorted by fluorescence-activated cell sorting for GFP labeling.

tag: lymphoma type

value: Non-Hodgkin's lymphoma cell line

tag: treatment

tag: specific primer

value: CATGGCTGGGGAGGCCTCA

tag: 5' race primer+adapter


title: ind39 2013

description:
ind39
RNA expression value derived from Affymetrix Launcher software

tag: age

value: Female


title: αPM_2 [13_S13]

tag: cell type

tag: cultured or grafted

tag: transduction


title: ind88 2013

description:
ind88
RNA expression value derived from Affymetrix Launcher software

tag: ID

tag: gender


title: ind7 2013

description:
ind7
RNA expression value derived from Affymetrix Launcher software


title: Affected_D2


title: αPM_5 [16_S16]


title: NonAffected_C1


title: ind77 2013

description:
ind77
RNA expression value derived from Affymetrix Launcher software

value: Male


title: Reh_rep1 (RACE)

description: cDNA from THE1B 5’ RACE


title: Affected_D1


title: ind40 2013

description:
ind40
RNA expression value derived from Affymetrix Launcher software


title: αPM_1 [12_S12]


title: ind71 2013

description:
ind71
RNA expression value derived from Affymetrix Launcher software


title: ind74 2013

description:
ind74
RNA expression value derived from Affymetrix Launcher software


title: ind106 2013

description:
ind106
RNA expression value derived from Affymetrix Launcher software


title: ind135 2013

description:
ind135
RNA expression value derived from Affymetrix Launcher software


title: αGFP_6 [11_S11]

value: GFP


title: Reh_PMA_rep1 (RACE)

description: cDNA from THE1B 5’ RACE

value: PMA


title: ind92 2013

description:
ind92
RNA expression value derived from Affymetrix Launcher software


title: Namalwa_rep2 (RACE)

description: cDNA from THE1B 5’ RACE

source_name: Burkitt’s lymphoma cell line


title: αGFP_5 [10_S10]


title: NonAffected_B1

value: B


title: ind4 2013

description:
ind4
RNA expression value derived from Affymetrix Launcher software


title: ind134 2013

description:
ind134
RNA expression value derived from Affymetrix Launcher software


title: NonAffected_A3

value: A

value: hiPSC-CM


title: αGFP_4 [9_S9]

value: pancreas

value: alpha-cells


title: L428_rep1 (RACE)

description: cDNA from THE1B 5’ RACE

source_name: Hodgkin's lymphoma cell line

value: Hodgkin's lymphoma cell line


title: αGFP_3 [8_S8]


title: αGFP_2 [7_S7]


title: NonAffected_A2


title: L1236_rep1 (RACE)

description: cDNA from THE1B 5’ RACE


title: NonAffected_B3


title: KM-H2_rep1 (RACE)

description: cDNA from THE1B 5’ RACE


title: NonAffected_A1


title: αGFP_1 [6_S6]


title: sorted α-cells_5 [5_S5]

source_name: sorted α-cells


title: GM2_input_DNA_Rep2

city: Toronto

first: Chi-chung

last: Hui

state: Ontario

address: 686 Bay Street. Room 16-9712

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Adaptor sequences were trimmed using Trimmomatic 0.36 with adaptor sequence file TruSeq3-PE-2.fa
Reads were aligned to the mm9 reference genome using default parameters of BWA MEM
Aligned reads were filtered using bamtools to exclude unmappped reads, mapping quality < 5, and not proper pairs.
ENCODE blacklist regions in mm9 were filtered out using bedtools
Peaks were called using MACS2 with q = 0.05. --broad was enabled for histone ChIP, and disabled for Gli2 ChIP-Seq.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files are peaks called by MACS2.

source_name: input DNA

extract_protocol:
Tumours were dissected, cut into small pieces, and crosslinked in solution A (1% formaldehyde, 50mM Hepes-KOH, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA) for 20 minutes at room temperature. 1/20 volume of 2.5 M glycine was added to quench formaldehyde. Tissues were rinsed in ice-cold PBS and dounced in Wheaton tissue grinder. Cell suspensions were passed through a 100μm cell strainer to remove connective tissues, then centrifuged at 4 °C at 2500 × rcf for 3 min, followed by a wash in PBS. Olig2 antibody (EMD Millipore, ab15328) was incubated with pre-blocked magnetic beads in 250μL total volume for 8 hours at 4 °C, then washed and resuspended in 100μL 0.5% BSA (w/v) solution. Cell pellets were lysed by sequentially resuspending and centrifuging in LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100), and LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA). Pellet was resuspended in LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine) and sonicated into 200-400bp fragments. Sonicated lysates were diluted with LB3. After saving 50μL for input control, they were split into tubes containing 10% v/v Triton X-100 with Gli2 (homemade), H3K27ac (Millipore 05-1334 lot 2489078), or H3K36me3 (Abcam ab9050 lot GR204353-1) antibody, and incubated overnight. Beads were washed 6 times in RIPA buffer (50 mM Hepes-KOH, pH 7.5; 500 mM LiCl; 1mM EDTA; 1% NP-40 or Igepal CA-630; 0.7% Na-Deoxycholate), and once in TBS (20 mM Tris-HCl, pH 7.6; 150 mM NaCl). Protein-DNA complexes were eluted and crosslink reversed with 200 μL of elution buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS). The 50μL input lysate was also included in this step. Eluted DNA was diluted with 200 μL of TE, and treated with RNaseA for 30 min at 37°C, and subsequently with proteinase K for 2 hours at 55°C. Phenol:chloroform:isoamyl alcohol was used to extract DNA.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® kit.

tag: developmental stage

value: medulloblastoma

tag: genotype

value: SmoM2 overexpression

tag: chip antibody


title: sorted α-cells_4 [4_S4]


title: NonAffected_B2

tag: donor id

value: Non-Affected


title: Reh_rep2

data_processing:
Alignment: tophat2 (2.0.11), using tophat -G hg19_refFlat.gtf --library-type fr-firststrand hg19 <R1.fq> <R2.fq>
FPKM quantification: cuffnorm (2.2.1) using cuffnorm --library-type fr-firststrand -o <outdir> -L <labels> hg19_refFlat.gtf <bam1_rep1><bam1_rep2> […] <bamx_rep1><bamx_rep2>
Coverage track generation: bedtools genomecov (2.19), using bedtools genomecov -ibam <bam> -g hg19.chrom.sizes -bg -split -trackline -trackopts ‘name=<name> description=<description>’
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph format representing read depth coverage, tsv format representing normalised FPKM values

extract_protocol:
RNA was isolated using a Nucleospin RNA extraction column with on-column DNase treatment (Machery Nagel, France).
RNA Sequencing libraries were produced in duplicate using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina).

treatment_protocol: PMA treatment was at 2 ng/ml media at a cell density of 1x106 / ml.


title: sorted α-cells_3 [3_S3]


title: Reh_rep1


title: Namalwa_rep1 (RACE)

description: cDNA from THE1B 5’ RACE


title: ind79 2013

description:
ind79
RNA expression value derived from Affymetrix Launcher software


title: Namalwa_rep2


title: ind86 2013

description:
ind86
RNA expression value derived from Affymetrix Launcher software


title: ind82 2013

description:
ind82
RNA expression value derived from Affymetrix Launcher software


title: Namalwa_rep1


title: RPE1_BrdUIP_LateS

description: RPE1_rpm_w200ks40k_BrdUIP_Percent_q0.05.bedGraph

value: Epithelial cells immortalized with hTERT

tag: sample state

value: BrdUIP

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase

value: LateS


title: RPE1_BrdUIP_EarlyS

tag: strain

value: EarlyS


title: ind122 2013

description:
ind122
RNA expression value derived from Affymetrix Launcher software

tag: age


title: sorted α-cells_1 [1_S1]

tag: tissue

tag: cell type


title: ind73 2013

description:
ind73
RNA expression value derived from Affymetrix Launcher software


title: ind5 2013

description:
ind5
RNA expression value derived from Affymetrix Launcher software

value: Female


title: L428_rep1

tag: lymphoma type

tag: treatment


title: KKAy_Liver_42w_rep2 [expression]

city: Taichung

first: Fuu-Jen

last: Tsai

address: No.2, Yude Rd., North Dist.

department: Department of Medical Research

country: Taiwan

institute: China Medical University Hospital

description:
42Y-2
Gene expression data from liver of KK.Cg-Ay/J mouse at 42 weeks old.

hyb_protocol: The arrays were hybridised for 17 hours at 45°C and 60 rpm and then subsequently washed (Affymetrix Fluidics Station 450) and lastly stained with streptavidin-phycoerythrin (GeneChip® Hybridization, Wash, and Stain Kit, 900720).

scan_protocol: The samples were scanned on an Affymetrix GeneChip® Scanner 3000 following the protocols of the commercial manufacturer.

data_processing:
The raw output data was processed by using Expression Console software (Affymetrix) with default RMA parameters.
The analysis of differential expression was performed by Transcriptomic analysis Console (TAC). It was set up with the default settings include eBayes algorithm. In the details of filtering option, the general analysis of gene expression was set up with Fold change ≥ 1.2, Fold change ≤ -1.2 and P-value < 0.05. Due to specialized the genes, the analysis of essential genes had the different parameters as Fold change ≥ 1.5 and Fold change ≤ -1.5.

label: biotin

source_name: Liver tissue of KK.Cg-Ay/J mice at 42 weeks old

label_protocol: 300 ng of each sample was amplified and labeled using the GeneChip WT Sense Target Labeling and Control Reagents (900652) for Expression Analysis.

growth_protocol: The pathogenesis-grouped mice were isolated by following the experimental design with the stages and classified groups and the cages of these mice were put in a sterile room with securely controlling in temperature (22-25°C), relative humidity (50-70%), and applying to natural photoperiod with nearly 12-h light/12-h dark.

extract_protocol: The mouse liver tissues were weighted proportionally 40 mg were scraped and collected by centrifugation, and total RNA was subsequently isolated by RNeasy Mini Kit (QIAGEN, P/N 74104). RNA quantity and purity were assessed at 260 nm and 280nm using a Nanodrop (ND-1000; Labtech. International).

treatment_protocol: These mice were fed barely with LabDiet 5k52 (St. Louis, MO, USA), which contains 19.3% protein, 13.2% total fat and 4.3% fiber.

tag: strain/background

tag: genotype/variation

value: mutant-Ay (Ay/a)

tag: phenotype

tag: gender

value: Male

value: Liver

value: 42 weeks

tag: Stage

value: Late developing


title: KKAy_Liver_42w_rep1 [expression]

description:
42Y-1
Gene expression data from liver of KK.Cg-Ay/J mouse at 42 weeks old.


title: ind124 2013

description:
ind124
RNA expression value derived from Affymetrix Launcher software

tag: ID


title: sorted α-cells_2 [2_S2]

tag: cultured or grafted

tag: transduction


title: KKAy_Liver_16w_rep1 [expression]

description:
16Y-1
Gene expression data from liver of KK.Cg-Ay/J mouse at 16 weeks old.

source_name: Liver tissue of KK.Cg-Ay/J mice at 16 weeks old

value: 16 weeks

value: Early developing


title: KKAy_Liver_16w_rep2 [expression]

description:
16Y-2
Gene expression data from liver of KK.Cg-Ay/J mouse at 16 weeks old.


title: ind61 2013

description:
ind61
RNA expression value derived from Affymetrix Launcher software


title: ind55 2013

description:
ind55
RNA expression value derived from Affymetrix Launcher software


title: L1236_rep1


title: pant_1_jurkat_vdj_t_rep2

city: Stanford

first: Calvin

last: Kuo

state: CA

address: 265 Campus Dr.

department: Department of Medicine, Division of Hematology

institute: Stanford University

description:
Single cell 5' VDJ-seq
Pan_T_Healthy_Donor_1%_Jurkat_VDJ_T_Enrichment_Rep2
The percentages represent the amount of GM12878 and Jurkat cells that were spiked into the healthy donor. For example, 0.1% GM12878 means 0.1% GM12878 was mixed with CD19 B cells from a healthy donor.

data_processing:
The Cell Ranger (CR) Software Suite (version 2.1.0) was used for 5’ gene counting and V(D)J sequence assembly and paired clonotype calling.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv, tsv, mtx files

source_name: Pan T cells from a healthy donor

growth_protocol: Tumor tissues were minced finely, washed twice in ADMEM/F12 (Invitrogen) containing 1X Normocin (InvivoGen), resuspended in Type I collagen gel (Trevigen), and layered in a double dish air-liquid culture system as previously described8. Organoids were cultured in human organoid medium (ADMEM/F12 supplemented with 50% Wnt3a, RSPO1, Noggin-conditioned media (L-WRN, ATCC), HEPES (1mM, Invitrogen), Glutamax (1X, Invitrogen), Nicotinamide (10 mM, Sigma), N-Acetylcysteine (1 mM, Sigma), B-27 without vitamin A (1X, Invitrogen), A83-01 (0.5 μM, Tocris), Pen-Strep Glutamine (1X, Invitrogen), Gastrin (10 nM, Sigma), SB-202190 (10 μM, Sigma), and EGF (50 ng/mL, Invitrogen). Organoids were passaged every 14-30 days by dissociation with 200 units ml−1 collagenase IV (Worthington) at 37 °C for 30 min, followed by three 5-min washes with 100% FBS and replating at a 1:4 split into new air-liquid interface collagen gels. Additionally, in some cases, media was supplemented with recombinant human IL-2 (Peprotech) at 600 or 6000 IU/ml.

extract_protocol:
Tumor tissues were obtained through the Stanford Tissue Bank from patients undergoing surgical resection at Stanford University Medical Center (SUMC). All experiments utilizing human material were approved by SUMC’s Institutional Review Board and performed under protocol #28908. Written informed consent for research was obtained from donors prior to tissue acquisition. Samples were confirmed to be tumor by pathological assessment at SUMC.
Cellular suspensions were loaded on a ChromiumTM Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs. Single-cell RNA-Seq libraries were prepared using the ChromiumTM Single Cell 5’ Library & Gel Bead Kit (P/N 1000006, 10x Genomics). GEM-RT was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad; P/N 1851197):  53 °C for 45 min, 85 °C for 5 min; held at 4 °C and stored at -20 °C. The GEMs were shipped to 10x Genomics on dry ice, then broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific; P/N 37002D) . Barcoded, full length cDNA was amplified using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98 °C for 45 s; cycled 13 ×: 98 °C for 20 s, 67 °C for 30 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit (0.6 × SPRI; Beckman Coulter; P/N B23318) . Barcoded, full-length V(D)J segments were enriched from amplified cDNA with primers specific to TCR constant regions. The target enrichment 1 was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98 °C for 45 s; cycled 10 ×: 98 °C for 20 s, 67 °C for 30 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. The target enrichment 1 was cleaned up with the SPRIselect Reagent Kit (0.8 × SPRI). The target enrichment 2 was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98 °C for 45 s; cycled 10 ×: 98 °C for 20 s, 67 °C for 30 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. The target enrichment 2 was cleaned up twice with the SPRIselect Reagent Kit (0.5 × and 0.8 × SPRI). The enrichment primers can be found in Supplementary Table 4. 5’ gene expression and enriched libraries were constructed using the reagents in the ChromiumTM Single Cell 3’/5’ Library Construction kit (P/N 1000020). For 5’ gene expression library construction, these steps were followed: (1) fragmentation, end repair and A-tailing; (2) post fragmentation, end repair and A-tailing cleanup with SPRIselect; (3) adaptor ligation; (4) post ligation cleanup with SPRIselect; (5) sample index PCR and cleanup. For the enriched library construction, these steps were followed: (1) fragmentation, end repair and A-tailing; (2) adaptor ligation; (3) post ligation cleanup with SPRIselect; (4) sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824). Sequencing libraries were loaded at concentrations on sequencers with the read configuration as specified in Table S5.

value: Pan T cells from a healthy donor

tag: condition

value: Cryopreserved


title: KM-H2_rep1

value: Hodgkin's lymphoma cell line


title: pant_0.1_jurkat_vdj_t_rep2

description:
Single cell 5' VDJ-seq
Pan_T_Healthy_Donor_0.1%_Jurkat_VDJ_T_Enrichment_Rep2
The percentages represent the amount of GM12878 and Jurkat cells that were spiked into the healthy donor. For example, 0.1% GM12878 means 0.1% GM12878 was mixed with CD19 B cells from a healthy donor.


title: ind125 2013

description:
ind125
RNA expression value derived from Affymetrix Launcher software


title: ind38 2013

description:
ind38
RNA expression value derived from Affymetrix Launcher software


title: pant_1_jurkat_vdj_t_rep1

description:
Single cell 5' VDJ-seq
Pan_T_Healthy_Donor_1%_Jurkat_VDJ_T_Enrichment_Rep1
The percentages represent the amount of GM12878 and Jurkat cells that were spiked into the healthy donor. For example, 0.1% GM12878 means 0.1% GM12878 was mixed with CD19 B cells from a healthy donor.


title: SUDHL4_Input_si

city: New York

first: Katerina

last: Hatzi

state: NY

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

data_processing:
For ChIP-seq, raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg38) using BWA 0.6.2. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifacts and were excluded from the analysis. Read density tracks were visualized using the UCSC browser. Peak calling was performed using MACS. Each ChIP-seq dataset was normalized to its corresponding input. Peaks were annotated based on the RefSeq database (hg38). Peaks localized +/2kb of the TSS were defined as promoter peaks, peaks localized +/2kb of the TES were defined as 30 end peaks, and peaks > 2kb away from genes were defined intergenic.
H3K4me1 signals from SUDHL4 cells were normalized based on the scaling factor calculated from the ratio of human and Drosophila mapped reads as previously described (Egan et al. 2016, PLoS One).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: BIGWIG files: Continuous value CHIPseq signal.
Supplementary_files_format_and_content: BED files: Genomic locations of called peaks.

source_name: SUDHL4 cells (lymphoma)

growth_protocol: RPMI 10% FBS, antibiotics.

extract_protocol:
Briefly, SUDHL4 were fixed, lysed, and sonicated to generate fragments less than 400 bp. Sonicated lysates were incubated with antibodies against LSD1 (abcam 17721), BCL6 (Santa Cruz N3, sc-858), or H3K4me1 (abcam, ab8895), and after increasing stringency washes, immunocomplexes were recovered and DNA was isolated. H3K4me1 ChIPs also contained Drosophila spike-in chromatin control (750ng per ChIP, Active Motif, 53083) added during precipitation along with Drosophila antibody (2ug, Active Motif, 61686) per manufacturer’s recommendation for proper signal normalization.
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacturer’s instructions with minor modifications. Briefly, 10ng of purified ChIP DNA (quantified using Qubit 2.0 fluorometer, Invitrogen) was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 30 ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adaptor ligation, DNA was separated by electrophoresis and size selected by isolating a gel band of 250 ± 25bp. Size selected fragments were PCR amplified for 15 cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30 s at 98oC, 15cycles of 10 at 98oC, 30 s at 65oC, 30 s at 72oC and 5min extension at 75oC). Q-PCR was repeated to confirm retention of relative enrichment.

treatment_protocol: For ChIP-seq experiments with cells treated with siRNAs, SUDHL4 cells were transfected using Nucleofector 96-well Shuttle system (Lonza) with 1uM siRNA against BCL6 (HSS100968) or non-targeted siRNA (46-2001) (Stealth RNAi, Invitrogen) for 24h.

tag: cell line

value: lymphoma cell line

tag: sirna

tag: chip antibody


title: pant_0.1_jurkat_vdj_t_rep1

description:
Single cell 5' VDJ-seq
Pan_T_Healthy_Donor_0.1%_Jurkat_VDJ_T_Enrichment_Rep1
The percentages represent the amount of GM12878 and Jurkat cells that were spiked into the healthy donor. For example, 0.1% GM12878 means 0.1% GM12878 was mixed with CD19 B cells from a healthy donor.


title: cd19b_1_gm12878_vdj_t_rep2

description:
Single cell 5' VDJ-seq
CD19_B_Healthy_Donor_1%_GM12878_VDJ_B_Enrichment_Rep2
The percentages represent the amount of GM12878 and Jurkat cells that were spiked into the healthy donor. For example, 0.1% GM12878 means 0.1% GM12878 was mixed with CD19 B cells from a healthy donor.

source_name: CD19+ B cells from a healthy donor

value: CD19+ B cells from a healthy donor


title: ind25 2013

description:
ind25
RNA expression value derived from Affymetrix Launcher software

tag: age


title: cd19b_1_gm12878_vdj_t_rep1

description:
Single cell 5' VDJ-seq
CD19_B_Healthy_Donor_1%_GM12878_VDJ_B_Enrichment_Rep1
The percentages represent the amount of GM12878 and Jurkat cells that were spiked into the healthy donor. For example, 0.1% GM12878 means 0.1% GM12878 was mixed with CD19 B cells from a healthy donor.


title: SUDHL4_H3K4me1_si


title: SUDHL4_Input_NT

value: control


title: cd19b_0.1_gm12878_vdj_t_rep2

description:
Single cell 5' VDJ-seq
CD19_B_Healthy_Donor_0.1%_GM12878_VDJ_B_Enrichment_Rep2
The percentages represent the amount of GM12878 and Jurkat cells that were spiked into the healthy donor. For example, 0.1% GM12878 means 0.1% GM12878 was mixed with CD19 B cells from a healthy donor.


title: SUDHL4_H3K4me1_NT


title: KKa_Liver_42w_rep2 [expression]

description:
42K-2
Gene expression data from liver of KK-a/a mouse at 42 weeks old.

source_name: Liver tissue of KK-a/a mice at 42 weeks old

value: KK-a/a

value: wild-type (a/a)

tag: tissue


title: ind34 2013

description:
ind34
RNA expression value derived from Affymetrix Launcher software


title: KKa_Liver_42w_rep1 [expression]

description:
42K-1
Gene expression data from liver of KK-a/a mouse at 42 weeks old.


title: KKAy_Liver_6w_rep2 [expression]

description:
6Y-2
Gene expression data from liver of KK.Cg-Ay/J mouse at 6 weeks old.

source_name: Liver tissue of KK.Cg-Ay/J mice at 6 weeks old

value: 6 weeks

value: Pre-developing


title: ind110 2013

description:
ind110
RNA expression value derived from Affymetrix Launcher software


title: ind67 2013

description:
ind67
RNA expression value derived from Affymetrix Launcher software

value: Female


title: ind129 2013

description:
ind129
RNA expression value derived from Affymetrix Launcher software

value: Male


title: SUDHL4_LSD1

tag: cell type


title: LIN28B_X0_let7_transfection_Total_RNA_Human

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
processed data file:
Polysomes_Let7_RPKM.csv
sample name in processed data file:
a9_input

data_processing:
Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner
RPKM values were calculated for all polysome and rnaseq samples. For eCLIP samples, read densities were calculated to identify eCLIP peaks. eCLIP peaks were identified using clipper
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: RPKM files for all polysome samples. eCLIP input normalized peaks in BED format

growth_protocol: standard cell culture in 10% FBS in DMEM

extract_protocol:
Total and polysome derived RNA were extracted using Trizol reagent; small RNA isolation was performed using miRvana kit
Various: Illumina polyA Total RNA kit, Illumina Small RNA kit

treatment_protocol: LIN28B transgenes were induced using 10ng/ml Doxycycline; mature let-7a miRNAs (10nM) were introduced using Lipofectamine RNAiMAX


title: KKa_Liver_16w_rep2 [expression]

description:
1-5
Gene expression data from liver of KK-a/a mouse at 16 weeks old.

source_name: Liver tissue of KK-a/a mice at 16 weeks old

value: Liver


title: KKAy_Liver_6w_rep1 [expression]

description:
6Y-1
Gene expression data from liver of KK.Cg-Ay/J mouse at 6 weeks old.

value: mutant-Ay (Ay/a)


title: KKa_Liver_6w_rep2 [expression]

description:
6K-2
Gene expression data from liver of KK-a/a mouse at 6 weeks old.

source_name: Liver tissue of KK-a/a mice at 6 weeks old


title: SUDHL4_BCL6


title: LIN28B_X0_let7_transfection_Polysome_Human

description:
processed data file:
Polysomes_Let7_RPKM.csv
sample name in processed data file:
a9_polysome

data_processing:
Library strategy: ribosome profiling
Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner
RPKM values were calculated for all polysome and rnaseq samples. For eCLIP samples, read densities were calculated to identify eCLIP peaks. eCLIP peaks were identified using clipper
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: RPKM files for all polysome samples. eCLIP input normalized peaks in BED format


title: LIN28B_X3_wt_total_smallRNA

description:
small RNA
processed data file:
human_small_rnaseq_counts.txt
sample name in processed data file:
b8p100_smallrnaseq_hek293_x3_wt_total_S22_L002_R1_


title: ind59 2013

description:
ind59
RNA expression value derived from Affymetrix Launcher software

source_name: whole blood


title: KKa_Liver_6w_rep1 [expression]

description:
6K-1
Gene expression data from liver of KK-a/a mouse at 6 weeks old.


title: LIN28B_X3_wt_ip_smallRNA

description:
small RNA
processed data file:
human_small_rnaseq_counts.txt
sample name in processed data file:
b8p100_smallrnaseq_hek293_x3_wt_ip_S26_L002_R1_001

tag: antibody

value: anti-AGO2 Clone 9E8.2, Millipore, Cat# 04-642


title: LIN28B_X3_let7_total_smallRNA

description:
small RNA
processed data file:
human_small_rnaseq_counts.txt
sample name in processed data file:
b8p100_smallrnaseq_hek293_x3_l7_total_S24_L002_R1_


title: KKa_Liver_16w_rep1 [expression]

description:
1-3
Gene expression data from liver of KK-a/a mouse at 16 weeks old.

value: 16 weeks


title: LIN28B_KO_wt_total_smallRNA

description:
small RNA
processed data file:
human_small_rnaseq_counts.txt
sample name in processed data file:
b8p100_smallrnaseq_hek293_ko_wt_total_S21_L002_R1_


title: ind102 2013

description:
ind102
RNA expression value derived from Affymetrix Launcher software


title: ind120 2013

description:
ind120
RNA expression value derived from Affymetrix Launcher software


title: ind37 HIMC_2024 2013

description:
ind37 HIMC_2024
RNA expression value derived from Affymetrix Launcher software


title: Ptch1KO_mb_rep2

hyb_protocol: Sample preparation and hybridization to Affymetrix Mouse Gene ST 1.0 arrays, washing, and scanning were performed according to the Affymetrix standard protocol

scan_protocol: Scanning was performed according to the Affymetrix standard protocol

data_processing: CEL files were imported and normalized using the Bioconductor R packages oligo, and annotated using the mogene10sttranscriptcluster.db package.

extract_protocol: P13 mouse cerebellum or medulloblastoma tumor was dissected and frozen at -80°C prior to RNA isolation using PureLink RNA Mini Kit (Invitrogen).

value: medulloblastoma tumor

tag: genotype

tag: developmental stage


title: Ptch1KO_mb_rep3

label_protocol: Sample preparation and hybridization to Affymetrix Mouse Gene ST 1.0 arrays, washing, and scanning were performed according to the Affymetrix standard protocol


title: PSNSF2

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
raw file: PSNSF12_252828211744_4.txt
Gene expression in hypothalamic paraventricular node of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 2

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two rats were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

organism: Rattus norvegicus

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Time-pregnant Sprague-Dawley rats were purchased from approved source (Taconic Farms, Germantown, NY). The rats were housed individually during the remainder of their pregnancy in the animal facility with free access to standard rat chow and water on the regular 12 hour light-dark cycle with the lights on at 07:00 am.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE).

treatment_protocol: On G15, some pregnant rats received vehicle (normal saline). Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four males and four females. Pups were treated with saline to act as a control, on days 13, 14 and 15.

tag: Sex

value: female

tag: strain

value: Sprague-Dawley

value: hypothalamic paraventricular node


title: PSNSF4

description:
raw file: PSNSF34_252828211744_3.txt
Gene expression in hypothalamic paraventricular node of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 4


title: LIN28B_KO_wt_ip_smallRNA

description:
small RNA
processed data file:
human_small_rnaseq_counts.txt
sample name in processed data file:
b8p100_smallrnaseq_hek293_ko_wt_ip_S25_L002_R1_001


title: ind93 2013

description:
ind93
RNA expression value derived from Affymetrix Launcher software

tag: gender


title: SufuKO_cb_rep3

value: cerebellum

value: SufuKO


title: LIN28B_X3_let7_ip_smallRNA

description:
small RNA
processed data file:
human_small_rnaseq_counts.txt
sample name in processed data file:
b8p100_smallrnaseq_hek293_x3_l7_ip_S28_L002_R1_001


title: LIN28B_KO_let7_total_smallRNA

description:
small RNA
processed data file:
human_small_rnaseq_counts.txt
sample name in processed data file:
b8p100_smallrnaseq_hek293_ko_l7_total_S23_L002_R1_


title: PSNSF3

description:
raw file: PSNSF34_252828211744_3.txt
Gene expression in hypothalamic paraventricular node of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 3


title: SufuKO_cb_rep2


title: ind26 2013

description:
ind26
RNA expression value derived from Affymetrix Launcher software


title: wildtype_cb_rep3

value: wildtype


title: ind37 HIMC_2017 2013

description:
ind37 HIMC_2017
RNA expression value derived from Affymetrix Launcher software


title: PSNSF1

description:
raw file: PSNSF12_252828211744_4.txt
Gene expression in hypothalamic paraventricular node of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 1


title: ind58 2013

description:
ind58
RNA expression value derived from Affymetrix Launcher software


title: PSNSM4

description:
raw file: PSNSM34_252828211742_3.txt
Gene expression in hypothalamic paraventricular node of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 4

value: male


title: LIN28B_KO_let7_ip_smallRNA

description:
small RNA
processed data file:
human_small_rnaseq_counts.txt
sample name in processed data file:
b8p100_smallrnaseq_hek293_ko_l7_ip_S27_L002_R1_001


title: cd19b_0.1_gm12878_vdj_t_rep1

description:
Single cell 5' VDJ-seq
CD19_B_Healthy_Donor_0.1%_GM12878_VDJ_B_Enrichment_Rep1
The percentages represent the amount of GM12878 and Jurkat cells that were spiked into the healthy donor. For example, 0.1% GM12878 means 0.1% GM12878 was mixed with CD19 B cells from a healthy donor.

value: CD19+ B cells from a healthy donor

value: Cryopreserved


title: wildtype_cb_rep2


title: SufuKO_cb_rep1


title: PSNSM2

description:
raw file: PSNSM2-PBYAF4_252828211750_3.txt
Gene expression in hypothalamic paraventricular node of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 2


title: Lin28B_X4_Total_RNA_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
x4_input


title: PSNSM3

description:
raw file: PSNSM34_252828211742_3.txt
Gene expression in hypothalamic paraventricular node of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 3


title: ind98 2013

description:
ind98
RNA expression value derived from Affymetrix Launcher software


title: wildtype_cb_rep1


title: ind83 2013

description:
ind83
RNA expression value derived from Affymetrix Launcher software


title: ATAC_LSD1 KO1

description: omni-ATAC-seq

data_processing:
ATAC-seq paired-end sequencing reads were trimmed to remove adapter sequences using NGmerge with option “-a”, and trimmed reads were aligned to mm10 reference genome using bowtie2 with options “-X2000 –local”. Alignments were filtered using samtools v1.8 to retain only uniquely mapping read pairs and to discard mitochondrial mapping reads. Read duplicates were detected and removed using the MarkDuplicates program in Picard Tools 2.18.11.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BIGWIG files: Continuous value ATACseq signal.
Supplementary_files_format_and_content: BED files: Genomic locations of differential opening or closing peaks.

source_name: mouse GC B cells

extract_protocol:
Fifty thousand purified GC B cells were resuspended in 1ml of ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) and centrifuged at 500 r.c.f. and 4°C for 5 min. Supernatant was aspirated by pipetting and cells were resuspended in 50ul of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin and incubated on ice for 3 min. Following lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 was added, and nuclei were centrifuged at 500 r.c.f. and 4°C for 10 minutes. Supernatant was then aspirated by pipetting and nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer, 2.5 μl tagment DNA enzyme, 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) and incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m.
Reactions were cleaned up with Zymo DNA Clean and Concentrator columns.
DNA libraries were prepared as described (Corces et al. Nat. Methods, 2017) and sequenced on a Hi-Seq 2000 (Illumina).

treatment_protocol: Sorted viable mouse GC B splenocytes (GL7+Fas+B220+).

value: GC B splenocytes (GL7+Fas+B220+)

tag: genotype/variation

value: LSD1 KO (C<gamma>1-Cre;Lsd1fl/fl)


title: ind27 2013

description:
ind27
RNA expression value derived from Affymetrix Launcher software

tag: ID

value: Female


title: Lin28B_X3_Total_RNA_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
x3_input


title: Lin28B_X2_Total_RNA_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
x2_input


title: ATAC_LSD1 WT2

description: omni-ATAC-seq

value: LSD1 WT (Lsd1fl/fl)


title: AM_untreated_d5

city: Saarbruecken

first: Jessica

last: Hoppstaedter

address: Campus C2 3

department: Pharmacy

institute: Saarland University

description:
miRNA
Donor 5 Co
Alveolar macrophages - untreated

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Array-chips were scanned in a high resolution microarray scanner from Agilent Technologies using Scan Control 8.5.1 software, 3 microns resolution in double path mode.

data_processing: Signal intensity values were extracted from the raw data file using Feature Extraction software (Agilent Technologies). The gTotalProbeSignals were summed up to calculate the total expression value for each miRNA per sample. Quantile normalization was applied to normalize expression values across the arrays using the preprocessCore package of the programming language R. After that we log2-transformed the expression values.

source_name: Alveolar macrophages, untreated, donor 5

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit.

growth_protocol: Alveolar macrophages were isolated by lavage of human lung tissue obtained from patients undergoing lung resection. Cells were enriched by plastic adherence (> 95% purity as shown by CD68 staining).

extract_protocol: Total RNA including small RNAs was isolated using miRNeasy Micro Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Cells were either left untreated or treated as follows: 1 µg/mL LPS for 2 h; 1 µg/mL Pam3CSK4 for 2 h; 10 µg/mL Poly(I:C) for 2 h; 0.1 µg LPS for 24 h (chronic low-dose exposure to induce LPS tolerance); 0.1 µg LPS for 24 h followed by rechallenge with 1 µg/mL LPS for 2 h; 1 µg Poly(I:C) for 24 h (chronic low-dose exposure).

value: alveolar macrophages

tag: lung tissue donor

tag: treatment

value: untreated


title: AM_PIC_24h_d5

description:
miRNA
Donor 5 PIC 24 h
Alveolar macrophages - Poly(I:C) 1 µg/ml, 24 h

source_name: Alveolar macrophages, Poly(I:C), 24 h, donor 5

value: PIC 24h


title: ATAC_LSD1 WT1

description: omni-ATAC-seq


title: Lin28B_X1_Total_RNA_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
x1_input


title: AM_LPS_24+2h_d3

description:
miRNA
Donor 3 LPS 24+2 h
Alveolar macrophages - LPS 0.1 µg/ml, 24 h followed by rechallenge with LPS 1 µg/ml, 2 h

source_name: Alveolar macrophages, LPS, 24+2 h, donor 3

value: LPS 24+2h


title: Lin28B_X0_Total_RNA_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
a9_input


title: AM_LPS_24h_d3

description:
miRNA
Donor 3 LPS 24 h
Alveolar macrophages - LPS 0.1 µg/ml, 24 h

source_name: Alveolar macrophages, LPS, 24 h, donor 3

value: LPS 24h


title: ind1 2013

description:
ind1
RNA expression value derived from Affymetrix Launcher software

value: Male


title: Lin28B_X4_Polysome_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
x4_polysome


title: AM_PIC_2h_d3

description:
miRNA
Donor 3 PIC 2 h
Alveolar macrophages - Poly(I:C) 10 µg/ml, 2 h

source_name: Alveolar macrophages, Poly(I:C), 2 h, donor 3

value: PIC 2h


title: ind84 2013

description:
ind84
RNA expression value derived from Affymetrix Launcher software


title: AM_Pam_2h_d3

description:
miRNA
Donor 3 Pam 2 h
Alveolar macrophages - Pam3CSK4 1 µg/ml, 2 h

source_name: Alveolar macrophages, Pam3CSK4, 2 h, donor 3

value: Pam3CSK4 2h


title: PSNSM1

description:
raw file: PSNSM1-PBYAF3_252828211742_4.txt
Gene expression in hypothalamic paraventricular node of prenatally expossed to saline_no infantile spasms_postnatally treated with saline P15_Replicate 1

value: Sprague-Dawley

value: hypothalamic paraventricular node


title: ind56 2013

description:
ind56
RNA expression value derived from Affymetrix Launcher software


title: Lin28B_X3_Polysome_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
x3_polysome


title: ind89 2013

description:
ind89
RNA expression value derived from Affymetrix Launcher software


title: ind11 2013

description:
ind11
RNA expression value derived from Affymetrix Launcher software


title: ind53 2013

description:
ind53
RNA expression value derived from Affymetrix Launcher software


title: AM_LPS_2h_d3

description:
miRNA
Donor 3 LPS 2 h
Alveolar macrophages - LPS 1 µg/ml, 2 h

source_name: Alveolar macrophages, LPS, 2 h, donor 3

value: LPS 2h


title: Lin28B_X2_Polysome_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
x2_polysome


title: CTRD: bone marrow sample of healthy individual from ALLCELLS

first: Genta

last: Ishikawa

address: One Gustave L. Levy Place Box 1232

department: Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

description:
control
Gene expression data from control subject

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human RNA micro array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Its concentrations were measured with NanoDrop (Thermo Scientific, Wilmington, DE, USA) and samples were run on the Illumina microarray Human HT-12_v4 Bead Chip gene expression array

source_name: Human bone marrow sample from a healthy subject

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted and purified with RNeasy Mini Kit (#79104 QIAGEN GmbH, Germany)

value: bone marrow

tag: condition

value: Healthy human control


title: ind63 2013

description:
ind63
RNA expression value derived from Affymetrix Launcher software


title: ind116 2013

description:
ind116
RNA expression value derived from Affymetrix Launcher software


title: CTRB: bone marrow sample of healthy individual from ALLCELLS


title: CTRC: bone marrow sample of healthy individual from ALLCELLS


title: Lin28B_X1_Polysome_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
x1_polysome

tag: cell line


title: AM_PIC_24h_d6

description:
miRNA
Donor 6 PIC 24 h
Alveolar macrophages - Poly(I:C) 1 µg/ml, 24 h

source_name: Alveolar macrophages, Poly(I:C), 24 h, donor 6


title: AM_untreated_d3

description:
miRNA
Donor 3 Co
Alveolar macrophages - untreated

source_name: Alveolar macrophages, untreated, donor 3


title: Lin28B_X0_Polysome_Human

description:
processed data file:
human_polysome_samples_rpkms.txt
sample name in processed data file:
a9_polysome


title: ID9: essential thrombocythemia

description:
essential thrombocythemia
Gene expression data from subject with essential thrombocythemia

source_name: Human bone marrow sample from a patient with essential thrombocythemia

value: Patient with essential thrombocythemia


title: ind97 2013

description:
ind97
RNA expression value derived from Affymetrix Launcher software


title: ID8: essential thrombocythemia


title: AM_LPS_24+2h_d2

description:
miRNA
Donor 2 LPS 24+2 h
Alveolar macrophages - LPS 0.1 µg/ml, 24 h followed by rechallenge with LPS 1 µg/ml, 2 h

source_name: Alveolar macrophages, LPS, 24+2 h, donor 2


title: cleavage fragment sequencing

city: Hong Kong

first: S. Chul

last: Kwon

address: L1-05, Laboratory Block, 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: degenerate DNA library made by PCR

data_processing:
The base calling was done by RTA (Real Time Analysis. v1.18)
For the "dictionary" which contains the barcode and variant pair information, fastq-join was first used to join the paired-end reads (maximum difference: 5%; -p 5). Then, after filtering reads through fastq_quality_filter (minimum quality score: 30, minimum percent of bases having the quality: 90; -q 30 -p 90), cutadapt was used tandemly two times (default parameters); first, for the trimming of the 3′ flanking sequence; second, for the split of the barcode and variants. After the initial filter, sequencing error-containing reads were discarded, and the unique barcode-variant pairs were reported as "processed dictionary file". Note that this file contains sequences that were not initially designed variants; i.e., errors during oligo synthesis, PCR, or sequencing.
For the "input" library, first, cutadapt was used to trim the adapter (minimum trimmed read length: 25, maximum trimmed read length: 35; -m 25 -M 35), and then fastq_quality_filter was applied (minimum quality score: 30, minimum percent of bases having the quality: 100; -q 30 -p 100). The "processed input file" contains count numbers per each barcode.
For the "cleavage" library, after trimming the 3p adapter using cutadapt (minimum trimmed read length: 30; -m 30), Fastq_quality_filter was used (minimum quality score: 30, minimum percent of bases having the quality: 95; -q 30 -p 95). Then, because of the random tetramer from the 3p adapter, 4 nucleotides from the 3′-end of reads were trimmed by fastx_trimmer (-t 4), and the barcode-variants pairs were splitted by using cutadapt. Subsequently, sequencing error-containing reads were discarded. The "processed cleavage fragment file" contains barcodes and 5′ cleavage fragments.
For the "variant_counts", only initially designed pri-miRNA variants were considered and remained.
Genome_build: n/a
Supplementary_files_format_and_content: Provided are tab-delimited text files which contains "barcode-variant pairs" for dictionary, "barcode-count pairs" for input, and "barcode-fragment pairs" for cleavage files. "variant_counts.txt" contains all merged information derived from initially designed pri-miRNA sequences.
Supplementary_files_format_and_content: dictionary.txt: barcode-variant pairs
Supplementary_files_format_and_content: input_barcode_counts.txt: barcode-input count pairs
Supplementary_files_format_and_content: barcode_cleavage_frag.txt: barcode-cleavage fragment pairs
Supplementary_files_format_and_content: designed_variants.txt: initially designed pri-miRNA variants
Supplementary_files_format_and_content: variant_counts.txt: merged information of variant-input count-cleavage fragment

organism: synthetic construct

source_name: synthetic

extract_protocol:
pri-miRNA variants containing 29–31-nucleotide barcodes and random sequences at two junctional positions were prepared by oligonucleotide annealing, extension, and PAGE gel purification. After quantification of the initial pools using NEBNext library quantitation kit (NEB), 16,000,000 molecules per pri-miRNA group were reamplified by PCR to decrease barcode complexity. An aliquot from the amplified DNA was sequenced as "dictionary". Next, T7 in vitro transcription was used to produce pri-miRNAs from the above DNA pools, and a subset of the RNA was sequentially treated with alkaline phosphatase and T4 polynucleotide kinase to be traced using gamma ATP. An aliquot from the transcribed RNA was stored as "input". In vitro DROSHA processing was carried out to the "input" pri-miRNAs, and 5′ cleavage fragments were purified and ligated with a 3′ adapter which contains 4-nucleotide random sequences. Next, reverse transcription using SuperScript III (Thermo Fisher) was carried out on "cleavage fragment" as well as "input" RNAs. After amplification using PCR, a 6% native PAGE gel was used to purify DNA libraries.
Illumina adapter sequences were incorporated to the libraries using PCR.

tag: barcode

value: CCGTCC


title: AM_LPS_24h_d2

description:
miRNA
Donor 2 LPS 24 h
Alveolar macrophages - LPS 0.1 µg/ml, 24 h

source_name: Alveolar macrophages, LPS, 24 h, donor 2


title: dictionary sequencing

description: degenerate DNA library made by PCR

value: ACAGTG


title: AM_PIC_2h_d2

description:
miRNA
Donor 2 PIC 2 h
Alveolar macrophages - Poly(I:C) 10 µg/ml, 2 h

source_name: Alveolar macrophages, Poly(I:C), 2 h, donor 2


title: Patient 79

type: genomic

city: Salt Lake City

first: Roberto

middle: Henrique

last: Nussenzveig

state: Utah

address: 2000 Circle of Hope

department: Oncology

institute: University of Utah/Huntsman Cancer Institute

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 79

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing:
The scanned data files were processed by GenomeStudio Genotyping using the cluster file HumanOmniExpress_24v1.0 (GPL21168), HumanOmniExpress_24v1.1 (GPL22678), and InfiniumOmniExpress_24v1.2  (Platform_InfiniumOmniExpress-24v1-2_A1.txt) all provided by Illumina.
Genotype: AA,AB,BB,or NC (no call)

label: C-Bio and A-DNP

source_name: Prostate Cancer

label_protocol: Standard Illumina labelling protocol

extract_protocol: Extraction of genomic DNA from separated leukocytes was performed using ice-cold alkaline phenol-chloroform extraction and precipitation with isopropanol followed by ethanol.

tag: disease state

value: Prostate Cancer

tag: abir. start date

tag: abir. failure date

tag: failure (yes=1, no=0)

tag: pfs (months)

tag: logpsa (at abir start)

value: BB

value: AB

value: whole blood


title: Patient 78

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 78

value: AA

tag: tissue


title: AM_Pam_2h_d2

description:
miRNA
Donor 2 Pam 2 h
Alveolar macrophages - Pam3CSK4 1 µg/ml, 2 h

source_name: Alveolar macrophages, Pam3CSK4, 2 h, donor 2

tag: cell type

value: alveolar macrophages


title: JFE018x: gras54

city: Québec

first: Julie

last: Fradette

state: Québec

department: Chirurgie

institute: Université Laval

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Lipoaspirated Fat

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cells were differenciated or not into adipocytes according to the protocol described in the associated publication. Reconstructed tissues were analysed at day 35 of culture.

extract_protocol: RNA was extracted with RNeasy Lipid tissue Mini Kit (Qiagen), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Lipoaspirated Fat

tag: age

value: 54 years


title: JFE017: gras41

value: 41 years


title: JFE016: gras35

value: 35 years


title: input sequencing

description: degenerate DNA library made by PCR

value: AGTCAA


title: AM_LPS_2h_d2

description:
miRNA
Donor 2 LPS 2 h
Alveolar macrophages - LPS 1 µg/ml, 2 h

source_name: Alveolar macrophages, LPS, 2 h, donor 2

value: LPS 2h


title: ind45 2013

description:
ind45
RNA expression value derived from Affymetrix Launcher software

data_processing: Raw data were processed in R for background correction and RMA normalization. Normalized expression data were log-transformed.

source_name: whole blood

extract_protocol: RNA was extracted from the PAXgene RNA blood tubes (PreAanalytiX GmbH,VWR part # 77776-026, USA) using the QIAcube automation RNA extraction procedure according to the manufacturer’s protocol (Qiagene Inc.,Valencia, CA, USA).

tag: gender

value: Female


title: Patient 77

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 77


title: ind78 2013

description:
ind78
RNA expression value derived from Affymetrix Launcher software

value: Male


title: ID7: essential thrombocythemia, 2nd measurement

description:
essential thrombocythemia
Gene expression data from subject (obtained from the same subject and at the same time for ET 3 (1)) with essential thrombocythemia

value: bone marrow

value: Patient with essential thrombocythemia


title: ind52 2013

description:
ind52
RNA expression value derived from Affymetrix Launcher software


title: AM_untreated_d2

description:
miRNA
Donor 2 Co
Alveolar macrophages - untreated

source_name: Alveolar macrophages, untreated, donor 2

value: untreated


title: DLB-1 cells infected for 72 h

city: MURCIA

first: ALBERTO

last: CUESTA

state: MURCIA

address: CAMPUS UNIVERSITARIO ESPINARDO, FACULTAD BIOLOGIA

department: CELL BIOLOGY AND HISTOLOGY

country: Spain

institute: UNIVERSITY OF MURCIA

description:
DLB-1_NNV 72 h
AB7717
processed data file: COUNTS_CUESTA_03_samples12_13_17.txt

data_processing:
Images analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA 1.8.
RNA-seq data were aligned to the Dicentrarchus labrax assembly with GEM v1.7.
RNA-seq paired-end reads were mapped against the DicLab assembly with STAR.
Differentially expressed genes (DEGs) were determined with RSEM.
Genome_build: Dicentrarchus labrax assembly with GEM v1.7
Supplementary_files_format_and_content: COUNTS_CUESTA_03_samples12_13_17.txt: Tab-delimited text file includes raw counts.

organism: Dicentrarchus labrax

source_name: DLB-1 cells infected for 72 h

extract_protocol:
Total RNA from cells was isolated by PureLink® RNA Mini Kit.
Libraries from the total RNA were prepared using the TruSeq® Stranded mRNA LT Sample Prep Kit from 0.5 µg of RNA.
Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp.

value: Brain cell line

value: NNV infection

tag: time


title: JFE015: gras30

value: 30 years


title: DLB-1 cells infected for 12 h

description:
DLB-1_NNV 12 h
AB7713
processed data file: COUNTS_CUESTA_03_samples12_13_17.txt

source_name: DLB-1 cells infected for 12 h


title: AM_untreated_d6

description:
miRNA
Donor 6 Co
Alveolar macrophages - untreated

source_name: Alveolar macrophages, untreated, donor 6


title: ID7: essential thrombocythemia, 1st measurement

description:
essential thrombocythemia
Gene expression data from subject with essential thrombocythemia


title: ID5 & 6: primary myelofibrosis, bone marrows of ID 5 & 6 were mixed for RNA microarray analysis due to their low amount

description:
primary myelofibrosis
Gene expression data from subject with primary myelofibrosis

source_name: Human bone marrow sample from a patient with primary myelofibrosis

value: Patient with primary myelofibrosis


title: ID7: essential thrombocythemia, the same patient as ID7 analyzed 1 year prior

description:
essential thrombocythemia
Gene expression data from subject (obtained from the same subject for ET 3 (1) and ET 3 (2) but obtained 1 year prior) with essential thrombocythemia


title: Patient 76

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 76

value: Prostate Cancer

tag: last f/u

value: BB

value: AA

value: whole blood


title: Control cells

description:
DLB-1 control
AB7712
processed data file: COUNTS_CUESTA_03_samples12_13_17.txt

source_name: DLB-1 control cells

value: Mock infection


title: ind15 2013

description:
ind15
RNA expression value derived from Affymetrix Launcher software

tag: ID


title: ID4: primary myelofibrosis, 1st measurement


title: JFE014: BM37 NI

source_name: Engineered human connective tissue

value: Bone marrow-derived human stromal/stem cells differentiated into connective tissue


title: Ptch1KO_mb_rep1

value: medulloblastoma tumor

tag: genotype

tag: developmental stage


title: Patient 75

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 75

value: AB


title: ind33 2013

description:
ind33
RNA expression value derived from Affymetrix Launcher software


title: ID4: primary myelofibrosis, 2nd measurement

description:
primary myelofibrosis
Gene expression data from subject (obtained from the same subject and at the same time for PMF 1 (1))) with primary myelofibrosis

tag: condition


title: JFE012: BM19 NI


title: JFE011: BM37 Ind

source_name: Engineered human adipose tissue

value: Bone marrow-derived human stromal/stem cells differentiated into adipocyte tissue


title: ccRCC_2_or_gex_rep2

description: Single cell 5' RNA-seq

data_processing:
The Cell Ranger (CR) Software Suite (version 2.1.0) was used for 5’ gene counting and V(D)J sequence assembly and paired clonotype calling.
Genome_build: GRCh38

source_name: CD45+ cells from an organoid sample

growth_protocol: Tumor tissues were minced finely, washed twice in ADMEM/F12 (Invitrogen) containing 1X Normocin (InvivoGen), resuspended in Type I collagen gel (Trevigen), and layered in a double dish air-liquid culture system as previously described8. Organoids were cultured in human organoid medium (ADMEM/F12 supplemented with 50% Wnt3a, RSPO1, Noggin-conditioned media (L-WRN, ATCC), HEPES (1mM, Invitrogen), Glutamax (1X, Invitrogen), Nicotinamide (10 mM, Sigma), N-Acetylcysteine (1 mM, Sigma), B-27 without vitamin A (1X, Invitrogen), A83-01 (0.5 ?M, Tocris), Pen-Strep Glutamine (1X, Invitrogen), Gastrin (10 nM, Sigma), SB-202190 (10 ?M, Sigma), and EGF (50 ng/mL, Invitrogen). Organoids were passaged every 14-30 days by dissociation with 200 units ml?1 collagenase IV (Worthington) at 37 °C for 30 min, followed by three 5-min washes with 100% FBS and replating at a 1:4 split into new air-liquid interface collagen gels. Additionally, in some cases, media was supplemented with recombinant human IL-2 (Peprotech) at 600 or 6000 IU/ml.

extract_protocol:
Tumor tissues were obtained through the Stanford Tissue Bank from patients undergoing surgical resection at Stanford University Medical Center (SUMC). All experiments utilizing human material were approved by SUMC’s Institutional Review Board and performed under protocol #28908. Written informed consent for research was obtained from donors prior to tissue acquisition. Samples were confirmed to be tumor by pathological assessment at SUMC.
Cellular suspensions were loaded on a ChromiumTM Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs. Single-cell RNA-Seq libraries were prepared using the ChromiumTM Single Cell 5’ Library & Gel Bead Kit (P/N 1000006, 10x Genomics). GEM-RT was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad; P/N 1851197):  53?°C for 45 min, 85?°C for 5?min; held at 4?°C and stored at -20?°C. The GEMs were shipped to 10x Genomics on dry ice, then broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific; P/N 37002D) . Barcoded, full length cDNA was amplified using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98?°C for 45 s; cycled 13 ×: 98?°C for 20?s, 67?°C for 30?s, and 72?°C for 1?min; 72?°C for 1?min; held at 4?°C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit (0.6 × SPRI; Beckman Coulter; P/N B23318) .  Barcoded, full-length V(D)J segments were enriched from amplified cDNA with primers specific to TCR constant regions. The target enrichment 1 was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98?°C for 45 s; cycled 10 ×: 98?°C for 20?s, 67?°C for 30?s, and 72?°C for 1?min; 72?°C for 1?min; held at 4?°C. The target enrichment 1 was cleaned up with the SPRIselect Reagent Kit (0.8 × SPRI).  The target enrichment 2 was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98?°C for 45 s; cycled 10 ×: 98?°C for 20?s, 67?°C for 30?s, and 72?°C for 1?min; 72?°C for 1?min; held at 4?°C. The target enrichment 2 was cleaned up twice with the SPRIselect Reagent Kit (0.5 × and 0.8 × SPRI). The enrichment primers can be found in Supplementary Table 4. 5’ gene expression and enriched libraries were constructed using the reagents in the ChromiumTM Single Cell 3’/5’ Library Construction kit (P/N 1000020). For 5’ gene expression library construction, these steps were followed: (1) fragmentation, end repair and A-tailing; (2) post fragmentation, end repair and A-tailing cleanup with SPRIselect; (3) adaptor ligation; (4) post ligation cleanup with SPRIselect; (5) sample index PCR and cleanup. For the enriched library construction, these steps were followed: (1) fragmentation, end repair and A-tailing; (2) adaptor ligation; (3) post ligation cleanup with SPRIselect; (4) sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824). Sequencing libraries were loaded at concentrations on sequencers with the read configuration as specified in Table S5.

value: CD45+ cells from an organoid sample

tag: treatment

value: Organoid


title: ccRCC_2_or_vdj_t_rep1

description: Single cell 5' VDJ-seq


title: ccRCC_2_or_gex_rep1

description: Single cell 5' RNA-seq


title: ccRCC_2_or_vdj_t_rep2

description: Single cell 5' VDJ-seq


title: Patient 74

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 74

tag: disease state


title: Patient 72

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 72

tag: abir. start date


title: JFE010: BM33 Ind


title: JFE013: BM33 NI


title: ccRCC_2_ft_vdj_t_rep2

description: Single cell 5' VDJ-seq

source_name: CD45+ cells from a fresh kidney tumor sample

value: Fresh tumor


title: JFE009: BM19 Ind


title: ccRCC_2_ft_vdj_t_rep1

description: Single cell 5' VDJ-seq

value: CD45+ cells from a fresh kidney tumor sample


title: AM_LPS_24+2h_d1

description:
miRNA
Donor 1 LPS 24+2 h
Alveolar macrophages - LPS 0.1 µg/ml, 24 h followed by rechallenge with LPS 1 µg/ml, 2 h

source_name: Alveolar macrophages, LPS, 24+2 h, donor 1

value: alveolar macrophages

tag: lung tissue donor

value: LPS 24+2h


title: Patient 71

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 71

tag: abir. failure date

tag: failure (yes=1, no=0)


title: AM_LPS_24h_d1

description:
miRNA
Donor 1 LPS 24 h
Alveolar macrophages - LPS 0.1 µg/ml, 24 h

source_name: Alveolar macrophages, LPS, 24 h, donor 1

value: LPS 24h


title: AM_Pam_2h_d1

description:
miRNA
Donor 1 Pam 2 h
Alveolar macrophages - Pam3CSK4 1 µg/ml, 2 h

source_name: Alveolar macrophages, Pam3CSK4, 2 h, donor 1

value: Pam3CSK4 2h


title: Patient 70

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 70

source_name: Prostate Cancer

value: Prostate Cancer

tag: pfs (months)

tag: logpsa (at abir start)


title: Patient 69

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 69

value: BB

tag: tissue


title: JFE008: LA44 NI

value: Adipose-derived human stromal/stem cells differentiated into connective tissue


title: ccRCC_2_ft_gex_rep2

description: Single cell 5' RNA-seq

tag: cell type


title: JFE007: LA40 NI