title: Sample21: wild_type_gene_rep3

city: Zurich

first: Gianmarco

last: Meier

address: Gloriastrasse 28/30

department: Institute of medical microbiology

country: Switzerland

institute: University of Zurich

data_processing:
Adaptor sequences were trimmed with Cutadapt (V2.3)
Reads were mapped to the efrCD gene using BWA-mem (V0.7.17-r118) with default parameters. Alignment files were further processed by samtools (V1.9) and converted to BAM files.
Using a home-made Python program (DMS_ABC) sequences were quality-filtered and variants were counted.
Enrichment scores were calculated using Enrich2 (v1.2) software. Natural log ratios were used as scoring method and wt normalization as normalization method.
Assembly: efrCD from Enterococcus faecalis
Supplementary files format and content: CSV file containing score, standard error and raw counts for each variant

organism: Enterococcus faecalis

source_name: bacteria

growth_protocol: L.lactis NZ9000 ΔlmrCD ΔlmrA harbouring the EfrCD libraries were grown in M17, 0.5% glucose with 5 μg/ml chloramphenicol. Expression of EfrCD was induced for 30 min by the addition of a nisin-containing culture supernatant of L. lactis NZ9700 added at a dilution of 1:10’000 (v/v).

extract_protocol:
Plasmid DNA was extracted by alkaline lysis followed by precipitation in EtOH. The plasmids were purified again using the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel). To extract the efrCD genes, 7 μg plasmid was digested with 40 U of SfiI (NEB), separated on a 1% agarose gel and the band containing the efrCD genes were extracted with the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel).
500 ng DNA was sheared twice in a Covaris microTUBE on a Covaris E220 Focused-ultrasonicator to achieve a distribution with an average fragment length of 150 base pairs using peak power 175, duty factor 10, cycles/burst 200 for 280s at 7°C. In-between cycles the microTUBEs were spun down before a second round of shearing. 150 ng of sheared fragments was used as input for the TruSeq Nano DNA Library Prep Kit (Illumina). Illumina libraries were prepared following the manufacturer’s protocol with one modification to yield a narrow fragment distribution optimized for 150 bp inserts by using a ratio of 5.4 parts of sample purification beads to one part of water (135 μl SPB + 25 μl nuclease-free H2O) in the library size selection step.

treatment_protocol: OD600 was determined and normalized to 0.5. 24 ml of M17, 0.5% glucose, 5 μg/ml chloramphenicol containing nisin (1:10’000 (v/v)) with the respective drugs was inoculated with 1:100 of induced L. lactis cells containing the EfrCD libraries.

value: bacteria

tag: expression-strain

value: Lactococcus lactis NZ9000 delta-lmrCD delta-lmrA

tag: drug


title: RNA_6h_KCl_Harringtonin_rep2

status: Public on Aug 09 2022

type: SRA

city: Boston

first: Erin

middle: Elizabeth

last: Duffy

state: MA

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
In an effort to capture the most complete picture of translation, including the potential translation of brain-specific lncRNAs, RNA-seq and Ribo-seq reads were mapped to the lncRNA knowledge base (lncRNAKB) annotation.68 This annotation includes experimental evidence of lncRNA expression across 31 solid human normal tissues, including the brain, providing a comprehensive resource of transcripts and transcript isoforms in the human brain. Sequencing reads were aligned using Hisat2 (version 2.1.0) to the H. sapiens genome (GRCh30) and transcriptome (lncRNAKB). Alignments and analysis were performed on the Orchestra2 high performance computing cluster through Harvard Medical School. Aligned bam files were sorted using Picard Tools (version 2.8.0), stranded bedGraphs were generated using STAR, and reads were quantified over annotated exons using HTSeq-count (version 0.9.1).
Sequencing adapters were removed using Cutadapt (version 1.14), trimmed fastq files were aligned to hg38 ribosomal RNA sequences, and unaligned reads were mapped to the hg38 genome and lncRNAKB transcriptome68 using STAR (version 2.7.3a) with standard settings and the following modified parameters: --clip5pNbases 3, --seedSearchStartLmax 15, --outSJfilterOverhangMin 30 8 8 8, --outFilterScoreMin 0, -outFilterScoreMinOverLread 0.66, -outFilterMatchNmin 0, -outFilterMatchNminOverLread 0.66, --outSAMtype BAM Unsorted. Aligned bam files were sorted using Picard Tools (version 2.8.0) and stranded bedGraphs were generated using STAR. The RibORF pipeline was run on each sample individually using standard parameters. Due to template switching during library preparation, reads contained three untemplated bases at the 3’ end that were not included in the alignment but added to the length of each read. Therefore, reads 30-33 nt in length (corresponding to RNA fragments 27-30 nt) were analyzed for three-nucleotide periodicity within known protein-coding ORFs (RefSeq). For each sample we selected only the read lengths for which at least 50% of the reads matched the primary ORF of known protein-coding genes in a meta-gene analysis. Samples with fewer than two read lengths passing filtering were removed from further analysis. Read lengths were offset-corrected and RibORF was used to predict ORFs with a minimum length of 8 AA and translation probability >0.7. After running the RibORF pipeline on each brain sample individually, information from RibORF output files was used to generate GTF and BED files for all ORFs identified in each sample. ORFs with lengths of zero and ORFs annotated as non-coding despite being detected in protein coding genes were eliminated. Using Bedtools version 2.27.1 and the GRCh38 primary assembly human genome file, DNA sequences were associated with each exon of each remaining ORF. ORFs that did not end in stop codon sequences (“TGA”,”TAA”,”TAG”) were eliminated. Using the R library micropan version 2.1, DNA sequences for each complete ORF were translated into protein sequences. Of note, ORFs with start codons “GTG” or “TTG” are translated with a Methionine as the initial amino acid despite these sequences not typically encoding methionine in other positions in a protein-coding DNA sequence, per existing literature on non-canonical start codon usage in translation. Finally, all remaining ORF information was collapsed into one table, and duplicate ORFs, defined as ORFs in the same genomic position with identical protein sequences, were eliminated. When eliminating duplicates, ORFs identified of the most common ORF type identified by RibORF were conserved, according to the following order of priority, from highest to lowest: canonical, truncation, extension, overlap, uORF, internal, external, polycistronic, readthrough, and non-coding ORFs. ORFs annotated as type “seqerror” were eliminated. After combining ORF outputs from all samples, ORFs that were only detected in one sample were eliminated. After the removal of singleton ORFs, duplicate ORFs were once again eliminated according to the same priority scheme, leaving only one entry for each ORF that was detected in at least two samples in the dataset. The LncRNAKB annotation was used to assign a specific ORF type to each ORF. In order to be designated a sORF, an ORF had to be 100 amino acids or less in length, and not fully overlap in-frame with a canonical protein-coding ORF.
Assembly: hg38
Supplementary files format and content: counts

molecule: total RNA

organism: Homo sapiens

source_name: hESC-derived neurons

growth_protocol: The use of hESCs was approved by the Harvard Medical School Embryonic Stem Cell Research Oversight (ESCRO) Committee. We used the H9 NGN2 hESC line, harboring a doxycycline-inducible NGN2 construct in the AAVS1 locus, referred to here as H9 NGN267.  We collected human neurons from three independent differentiation cohorts, and each replicate exhibited characteristic gene expression patterns reported previously.

extract_protocol:
Ribosome profiling was performed using a protocol modified from McGlincy et al. Frozen brain tissue (~80 mg) was thawed on ice. Each sample was dounced 15x in 400 µL ice cold lysis buffer: 20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide (Sigma). The lysate was further sheared using a 26-gauge syringe. The lysate was clarified by centrifugation at 20,000 x g for 10 minutes at 4ºC. Supernatant (10 µL) was removed, added to 300 µL Trizol, and frozen at -80ºC for future RNA-seq library preparation. RNA concentration in the remaining supernatant was quantified using RNA Qubit. Lysate (30 µg) was subjected to RNase I digestion (0.5 U RNaseI per µg RNA) at room temperature for 15 minutes with gentle agitation. After RNase digestion, 10 µL SuperasIN (Thermo) was added to each sample, and the samples were transferred to ice. To isolate ribosome protected fragments, the RNase-digested lysate was transferred to Ultra-clear 11x34 mm centrifuge tubes (Beckman Coulter) and underlaid with 0.9 mL sucrose cushion. Samples were centrifuged in a TLS-55 rotor at 51,000 rpm for 2 hours at 4°C. The supernatant was discarded and the pellet was resuspended in 300 µL TRIzol. Ribosome-protected fragments were purified from TRIzol using the Zymo Direct-zol kit. RNA was precipitated by adding 38.5 µL RNase-free water, 1.5 µL Glycoblue, 10 µL 3 M sodium acetate pH 5.5, and 150 µL isopropanol to 100 µL eluted RNA. The mixture was incubated overnight at -20°C. Samples were centrifuged for 30 minutes at 20,000 x g at 4°C. The supernatant was discarded, and the RNA pellet was resuspended in 5 µL 10 mM Tris pH 8. Five µL 2X denaturing sample loading buffer (980 µL formamide, 20 µL 500 mM EDTA, 300 µg bromophenol blue) was added to each sample, then the sample was denatured at 80°C for 90 seconds. Ribosome-protected fragments, along with control oligos66, were run on a 15% polyacrylamide gel at 200 V with 12 µL NEB miRNA marker. The gel was stained with SYBR gold in 1X TBE. Gel fragments between 17 and 34 nucleotides were excised and placed in a microfuge tube with 400 µL gel extraction buffer. Samples were frozen on dry ice for 30 minutes, then thawed overnight with gentle agitation. After overnight gel extraction, 400 µL eluate was transferred to a new microfuge tube. The RNA was precipitated by adding 1.5 µL glycoblue and 500 µL isopropanol. After overnight incubation at -20°C, the sample was centrifuged at 20,000 x g for 30 minutes at 4°C. The supernatant was discarded, and precipitated RNA was resuspended in 4 µL 10mM Tris pH 8. Samples were then dephosphorylated using T4 PNK (4 µL RNA in 10 mM Tris pH 8, 0.5 µL T4 PNK enzyme, 0.5 µL T4 PNK buffer, and 0.5 µL Superasin) at 37°C for 1 hour. Samples were then subjected to SPRI clean up: 50 µL of sample in RNase-free water was added to 90 µL RNAclean beads and 270 µL isopropanol. After washing with 85% ethanol, beads were resuspended in 7 µL RNase-free water. The supernatant was collected, and we proceeded with next-generation sequencing library preparation using the Clontech smRNA library prep kit according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq S2 with single-end 1x50 nt reads. Samples were always processed in large batches of a maximum of 24 samples to avoid sample processing biases.
RNA-seq libraries were prepared from 10 ng total RNA using the SMARTer Stranded Total RNA-seq Pico Input Mammalian V2 kit (Takara Bio) according to the manufacturer’s instructions. Samples were multiplexed with Illumina TruSeq HT barcodes and sequenced on a NextSeq 2000 with single-end 1x75 nt reads. Samples were always processed in large batches of a maximum of 24 samples to avoid sample processing biases.

treatment_protocol: On the day prior to cell harvest, neurons were silenced with TTX and APV, which antagonize sodium channels and NMDA receptors, respectively. H9 NGN2 cells were cultured in mTeSR Plus media (STEMCELL Technologies) on tissue culture plates coated with hESC-qualified matrigel (Corning). They were passaged using Dispase (1 mg/mL, Life Technologies) until ready for differentiation. A previously published protocol that combines developmental patterning and NGN2 induction was adapted to differentiate H9 NGN2 into neurons.57 At day 0, cells were treated with Accutase (StemPro Accutase, Life Technologies) and plated in single cells at 50,000 cells/cm2 in mTeSR Plus media supplemented with 10 µM Y-27632 (STEMCELL Technologies) on tissue culture plates coated with 336.67 µg/mL Growth Factor Reduced matrigel (Corning). On day 1, the medium was replaced with KSR media (Knockout DMEM medium, 15% knockout serum replacement (KOSR), 2 mM L-Glutamine, 1X MEM non-essential amino acids (MEM NEAA), 1X penicillin/streptomycin (pen/strep) and 1X 2-mercaptoethanol (all Gibco)) supplemented with 100 nM LDN193189, 2 µM XAV939 (STEMCELL Technologies), 10 µM SB431542 hydrate and 2 µg/mL doxycycline hyclate (Sigma). Day 2 media was 50% KSR media/50% NIM media supplemented with LDN/XAV/SB and 2 µg/mL doxycycline. NIM media consisted of DMEM/F-12 medium, 1X GlutaMAX, 1X MEM NEAA, 1X pen/strep, 0.16% D-glucose (Sigma) and 1X N2 supplement-B (STEMCELL Technologies). Day 3 media was NIM media supplemented with 2 µg/mL doxycycline. At day 4, cells were treated with Accutase and plated in single cells at 40,000 cells/cm2 in NB media (Neurobasal medium (without glutamine), 1X GlutaMAX, 1X MEM NEAA, 1X pen/strep and 1X N2 supplement-B) supplemented with 1X B27 without Vitamin A, 2-2.4 µg/mL mouse laminin (Gibco), 1 µM ascorbic acid, 2 µM dibutyryl cyclic-AMP (Sigma), 20 ng/mL brain-derived neurotrophic factor, 10 ng/mL glial-derived neurotrophic factor (rhBDNF and rhGDNF, Peprotech), 10 µM Y-27632 and 2 µg/mL doxycycline on the tissue culture plates coated with 336.67 µg/mL Growth Factor Reduced matrigel. The media at day 4 without Y-27632 and doxycycline is referred to as complete NB (cNB) media. On day 5 the media was replaced with cNB media. Thereafter, half of the media was replaced weekly with cNB2x, where concentrations of all the supplements to the NB media (except Y-27632) were doubled. In between each media change, media was directly supplemented with 2 µg/mL doxycycline on the third day of the week (days 8, 15 and 22). Cells were silenced on day 27 with TTX and APV, which antagonize sodium channels and NMDA receptors, respectively. Cells were collected at day 28 in 1X PBS supplemented with 1X cycloheximide after being stimulated with 55 mM KCl for 0 or 6 hours. For harringtonine treatment, 2 μg/mL harringtonine or an equal volume of DMSO was added to cell culture media and incubated at 37°C for 2 min before proceeding with Ribo-seq cell lysis and sample preparation as described above.

tag: tissue

value: Cultured Neurons

tag: agent


title: RNA_6h_KCl_Harringtonin_rep1


title: RNA_6h_KCl_DMSO_rep3


title: ChIP-Seq-spikein_RPB1_Untreated_rep1

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

country: China

institute: Peking University

description:
NEBNext Ultra II DNA Library Prep Kit (NEB, cat#E7645S)
ChIP-Seq-spikein_RPB1_Untreated.bw

library_source: genomic

data_processing:
ChIP-Rx raw data were processed using a custom pipeline that builds on published workflows with minor modifications. Briefly, raw reads after adapter trimming and quality control with cutadapt and RseQC were aligned to a concatenated genome comprised of mouse mm10 and fly dm6 assemblies using bowtie2 with options (-very-sensitive-local) as described in the ChIP-seq section.
Only properly paired and uniquely aligned reads were retained for subsequent processing. Reads mapped to the mouse genome were normalized to total reads originating from Drosophila spike-in cells, and the normalization factor was calculated as previously described (Jiang et al., 2020).
SAMtools (v 0.1.19) and sambamba (v0.7.0) were used to filter unmapped reads, multiple mapped reads, and potential PCR duplicates. The final BAM files were converted to bigwig and normalized to spike-in controls using bamCoverage from deeptools.
For visualization purposes, the bigWig format tracks from two biological replicates for each treatment were merged into an averaged signal using the mean operator from the WiggleTools (v1.2) package (Zerbino, Johnson, et al. 2014).
Assembly: mm10 and dm6
Supplementary files format and content: bigwig files

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells (V6.5)

growth_protocol: Pol II subunit degron cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 1 × nucleoside (Millipore, Cat#ES-008-D), 3 μM CHIR99021 (Selleck, Cat#S1263), 0.5 μM PD0325901 (Selleck, Cat#S1036), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) and maintained at 37℃ cell incubator with 5% CO2. ZBTB11-GFP inducible expressing HEK293T cells were constructed in our lab and used as spike-in cells, which were cultured in basic-DMEM (Thermo Fisher, Cat#C11995500BT) supplemented with 10% FBS (Gibco, Cat#10099141C).

extract_protocol:
Cross-linked cells were subjected to chromatin fraction isolation as reported (Ji et al., 2015), and the chromatin was pretreated with 40 U MNase (NEB, M0247), followed by sonication as previously described (Yongpeng et al., 2020). 1 μl GFP antibodies (Abcam, Ab290) and 30 μl Protein G beads (Thermo Fisher, 10004D) were used to enrich Pol II subunit-DNA complexes.
ChIP DNA were subjected to  library construction according to the instructions of the NEBNext Ultra II DNA Library Prep Kit (NEB, cat#E7645S). 200bp-400bp DNA libraries were gel-selected, purified, and delivered to Novogene company for sequencing.

treatment_protocol: For each RPB subunits ChIP-seq with reference exogenous genome, RPB degron cells were treated with 1μg/ml Dox for 12 h to induce TIR1 expression, and treated with or without 500 μM IAA for 1 h to degrade each RPB subunit. As the spike-in cells, the ZBTB11-GFP was induced by treating ZBTB11-GFP HEK293T cells with 1μg/ml Dox for 24 h. Then RPB degron cells were mixed with 10% ZBTB11-GFP HEK293T cells, and followed with cross-linking.

tag: treatment

value: RPB1-mAID-GFP degron mESCs treated with 1μg/ml Dox  for 12 h

tag: antibody


title: RNA_6h_KCl_Harringtonin_rep3


title: Sample18: EfrCD_nodrug_rep3_t1

tag: cell type

tag: timepoint


title: ChIP-Seq-spikein_RPB1_IAA_rep2

description:
NEBNext Ultra II DNA Library Prep Kit (NEB, cat#E7645S)
ChIP-Seq-spikein_RPB1_IAA.bw

value: RPB1-mAID-GFP degron mESCs treated with 1μg/ml Dox  for 12 h, then treated with 500 μM IAA for 1h


title: Sample16: EfrCD_nodrug_rep1_t1


title: Sample20: wild_type_gene_rep2


title: ChIP-Seq-spikein_RPB2_Untreated_rep1

description:
NEBNext Ultra II DNA Library Prep Kit (NEB, cat#E7645S)
ChIP-Seq-spikein_RPB2_Untreated.bw

value: RPB2-mAID-GFP degron mESCs treated with 1μg/ml Dox  for 12 h


title: Sample14: EfrCD_etbr_rep2_t1

value: EtBr


title: ChIP-Seq-spikein_RPB4_Untreated_rep1

description:
NEBNext Ultra II DNA Library Prep Kit (NEB, cat#E7645S)
ChIP-Seq-spikein_RPB4_Untreated.bw

value: RPB4-mAID-GFP degron mESCs treated with 1μg/ml Dox  for 12 h


title: Sample17: EfrCD_nodrug_rep2_t1


title: Sample19: wild_type_gene_rep1


title: Sample13: EfrCD_etbr_rep1_t1


title: Sample15: EfrCD_etbr_rep3_t1


title: Sample8: EfrCD_hoec_rep2_t1

value: Hoechst


title: Sample9: EfrCD_hoec_rep3_t1


title: Sample6: EfrCD_daun_rep3_t1

value: Daunorubicin


title: Sample10: EfrCD_etbr_nodrug_rep1_t0


title: Sample12: EfrCD_etbr_nodrug_rep3_t0


title: Sample11: EfrCD_etbr_nodrug_rep2_t0


title: Sample7: EfrCD_hoec_rep1_t1


title: Sample5: EfrCD_daun_rep2_t1


title: ChIP-Seq-spikein_RPB2_IAA_rep2

description:
NEBNext Ultra II DNA Library Prep Kit (NEB, cat#E7645S)
ChIP-Seq-spikein_RPB2_IAA.bw

value: RPB2-mAID-GFP degron mESCs treated with 1μg/ml Dox  for 12 h, then treated with 500 μM IAA for 1h


title: RNA_6h_KCl_DMSO_rep2


title: RNA_6h_KCl_DMSO_rep1


title: Sample4: EfrCD_daun_rep1_t1


title: Sample2: EfrCD_daun_hoechst_rep2_t0


title: Sample1: EfrCD_daun_hoechst_rep1_t0


title: Zebrafish perturbation atlas plates1-3

status: Public on Aug 08 2022

city: Seattle

first: Lauren

last: Saunders

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell
zperturb_full_cds.RDS
zperturb_full_raw_counts.RDS
zperturb_full_cell_metadata.csv
zperturb_full_gene_metadata.csv
zperturb_full_run1_hashTable.txt

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Brotman Baty sci-RNA-seq demultiplexing and processing pipelines (https://github.com/bbi-lab/bbi-dmux; https://github.com/bbi-lab/bbi-sci).
Count matrix was loaded into Monocle3 for further analysis
Assembly: GRCz11
Supplementary files format and content: Count Matrix (RDS file), Cell Metadata (comma separated values- .csv), Gene Metadata (comma separated values- .csv)
Supplementary files format and content: zperturb_pilot_cds.RDS monocle3 cell_data_set object
Supplementary files format and content: zperturb_pilot_raw_counts.RDS dgCMatrix with raw counts
Supplementary files format and content: zperturb_pilot_cell_metadata.csv cell metadata table (comma separated)
Supplementary files format and content: zperturb_pilot_gene_metadata.csv gene metadata table (comma separated)
Supplementary files format and content: zperturb_pilot_hashTable.txt hash oligo count table
Supplementary files format and content: reference_cds.RDS monocle3 cell_data_set object
Supplementary files format and content: reference_raw_counts.RDS dgCMatrix with raw counts
Supplementary files format and content: reference_cell_metadata.csv cell metadata table (comma separated)
Supplementary files format and content: reference_gene_metadata.csv gene metadata table (comma separated)
Supplementary files format and content: reference_expt1_hashTable.txt hash oligo count table
Supplementary files format and content: reference_expt2_hashTable.txt hash oligo count table
Supplementary files format and content: reference_expt3_hashTable.txt hash oligo count table
Supplementary files format and content: zperturb_full_cds.RDS monocle3 cell_data_set object
Supplementary files format and content: zperturb_full_raw_counts.RDS dgCMatrix with raw counts
Supplementary files format and content: zperturb_full_cell_metadata.csv cell metadata table (comma separated)
Supplementary files format and content: zperturb_full_gene_metadata.csv gene metadata table (comma separated)
Supplementary files format and content: zperturb_full_run1_hashTable.txt hash oligo count table
Supplementary files format and content: zperturb_full_run2_hashTable.txt hash oligo count table

molecule: polyA RNA

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Zebrafish embryos were raised in embryo media at 28.5C.

extract_protocol:
Embryos were transferred, one by one, into separate wells of a 96-well V-bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope, which took between 20-40 minutes depending on embryo stage (e.g. 20 minutes for 18hpf and 40 minutes for 72hpf). Stop solution [1x dPBS, 5% FBS ] was then added to each well to quench the proteases.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

value: Whole embryo

tag: developmental stage

tag: strain

value: AB

tag: genotype

value: ctrl-cr, tbx16, tbx16-tbx16l, tbx16-msgn1, cdx4, cdx4-cdx1a, tbxta, tbx16, tbx16l, msgn1, wnt3a-wnt8a, noto, smo, tbx1, hand2, egr2b, epha4a, hoxb1a, mafba, zc4h2, phox2a, foxi1, hgfa, met, foxd3, tfap2a, tfap2a-foxd3


title: zebrafish single nucleus developmental reference, expt 1

description:
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell
reference_cds.RDS
reference_raw_counts.RDS
reference_cell_metadata.csv
reference_gene_metadata.csv
reference_expt1_hashTable.txt

value: wild type


title: pilot tbx16-msgn1 snRNAseq, rep1

description:
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell
zperturb_pilot_cds.RDS
zperturb_pilot_raw_counts.RDS
zperturb_pilot_cell_metadata.csv
zperturb_pilot_gene_metadata.csv
zperturb_pilot_hashTable.txt

value: 24 hpf (prim-5)

value: AB, AB/Wik

value: ctrl-cr, tbx16-cr, tbx16 null, tbx16 null; msgn1 MO, tbx16-cr; msgn1-cr


title: Sample3: EfrCD_daun_hoechst_rep3_t0

value: bacteria

value: Lactococcus lactis NZ9000 delta-lmrCD delta-lmrA


title: zebrafish single nucleus developmental reference, expt 3

description:
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell
reference_cds.RDS
reference_raw_counts.RDS
reference_cell_metadata.csv
reference_gene_metadata.csv
reference_expt3_hashTable.txt


title: pilot tbx16-msgn1 snRNAseq, rep2


title: Zebrafish perturbation atlas plates4-6

description:
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell
zperturb_full_cds.RDS
zperturb_full_raw_counts.RDS
zperturb_full_cell_metadata.csv
zperturb_full_gene_metadata.csv
zperturb_full_run2_hashTable.txt


title: zebrafish single nucleus developmental reference, expt 2

description:
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell
reference_cds.RDS
reference_raw_counts.RDS
reference_cell_metadata.csv
reference_gene_metadata.csv
reference_expt2_hashTable.txt


title: PD1lo TIL Ndufs4KO B16 H3K27me3 2

status: Public on Aug 04 2022

city: Pittsburgh

first: B. Rhodes

last: Ford

state: PA

address: 4401 Penn Ave.

department: Department of Pediatrics

institute: University of Pittsburgh

description: CUT&Tag DNA

data_processing:
trimmed high quality reads were aligned to genome using bowtie2
bedgraph files were generated from alignment files using bedtools
BigWig files were generated using bedGraphToBigWig
peaks were determined using MACS2 for peak calling, followed by idr
Differential peak analysis determined using DESeq2 on concatenated and merged peak files with cutoffs of 2 fold and p value<0.05
Assembly: mm10_ensembl
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

source_name: Ndufs4-deficient B16 melanoma tumor

growth_protocol: Mice were injected intradermally with 2.5 × 10^5 cells of either WT or Ndufs4-deficient B16 melanoma. Mice were sacrificed and dLN and TIL harvested on day 14, when tumors were typically 8-10 mm in diameter.

extract_protocol:
CD8 T cells were isolated from tumors by surgical excision followed by flow sorting. CUT&Tag was performed as previously described (Kaya-Okur et al., 2020).
Libraries were amplified within CUT&Tag protocol as described (Kaya-Okur et al., 2020). Cluster generation and 75-bp paired-end, dual-indexed sequencing were performed on the Illumina NextSeq 500 system.

value: CD8+ T cell

tag: disease state

value: B16 melanoma

value: Day 14 post-tumor

tag: sorting scheme


title: pilot tbx16-msgn1 snRNAseq, rep3


title: PD1hiTim3+ TIL Ndufs4KO B16 H3K27me3 1

description: CUT&Tag DNA


title: PD1hiTim3+ TIL Ndufs4KO B16 H3K4me3 1

description: CUT&Tag DNA


title: PD1lo TIL Ndufs4KO B16 H3K27me3 1

description: CUT&Tag DNA


title: PD1lo TIL Ndufs4KO B16 H3K4me3 2

description: CUT&Tag DNA


title: PD1lo TIL WT B16 H3K4me3 1

description: CUT&Tag DNA

source_name: WT B16 melanoma tumor


title: PD1hiTim3+ TIL Ndufs4KO B16 H3K4me3 2

description: CUT&Tag DNA


title: PD1lo TIL WT B16 H3K27me3 1

description: CUT&Tag DNA


title: PD1hiTim3+ TIL WT B16 H3K27me3 1

description: CUT&Tag DNA

value: Day 8 post-infection


title: PD1hiTim3+ TIL WT B16 H3K4me3 2

description: CUT&Tag DNA


title: Pmel PD1hiTim3+ RNAseq 2

description:
Pmel_PD1Tim3_rep2
TPM_TIL_Pmel.csv

data_processing:
trimmed high quality reads were aligned to genome using HISAT2
Transcripts per Million (TPMs) calculated using Subread
Differentially expressed genes (DEG) determined using DEseq2 with cutoffs of 2 fold and padj<0.05
Assembly: mm10 ensembl
Supplementary files format and content: TPM_TIL_Pmel.csv: Transcripts per Million (TPM) file, normalized counts.

source_name: B16-OVA melanoma tumor

growth_protocol: Mice were injected intradermally with 2.5 × 10^5 cells of. Thy1.1+ pmel-1 T cells were transferred at day 2 and 7 post-tumor injection. Mice were sacrificed and dLN and TIL harvested on day 14, when tumors were typically 8-10 mm in diameter.

extract_protocol:
CD8 T cells were isolated from tumors by surgical excision followed by flow sorting. cDNA was prepared from ~1,000 cells using the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Libraries were prepared using the Nextera XT DNA Library Preparation kit. Libraries were denatured and diluted using the NextSeq 500 protocol Revision D.Cluster generation and 75-bp paired-end, dual-indexed sequencing were performed on the Illumina NextSeq 500.

value: B16-OVA melanoma

value: Day 12 post-cell transfer


title: PD1lo TIL Ndufs4KO B16 H3K4me3 1

description: CUT&Tag DNA


title: PD1hiTim3+ TIL Ndufs4KO B16 H3K27me3 2

description: CUT&Tag DNA


title: Pmel PD1hiTim3+ RNAseq 3

description:
Pmel_PD1Tim3_rep3
TPM_TIL_Pmel.csv


title: PD1hiTim3+ TIL WT B16 H3K4me3 1

description: CUT&Tag DNA


title: PD1lo TIL WT B16 H3K27me3 2

description: CUT&Tag DNA


title: Pmel PD1lo RNAseq 3

description:
Pmel_PD1lo_rep3
TPM_TIL_Pmel.csv

value: Day 7 post-cell transfer


title: Pmel PD1hiTim3+ RNAseq 1

description:
Pmel_PD1Tim3_rep1
TPM_TIL_Pmel.csv


title: Pmel PD1lo RNAseq 2

description:
Pmel_PD1lo_rep2
TPM_TIL_Pmel.csv


title: PD1hiTim3+ TIL WT B16 H3K27me3 2

description: CUT&Tag DNA


title: Pmel PD1lo RNAseq 1

description:
Pmel_PD1lo_rep1
TPM_TIL_Pmel.csv


title: trunk neural crest + tetracycline repeat 2 [tNC2pos]

status: Public on Aug 03 2022

city: Sheffield

first: Anestis

last: Tsakiridis

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Sequencing adapters were removed, and the low-quality reads were filtered using the fastp (0.20.1) software. Alignment of the short reads on GRCh38 was performed using Bowtie2 (2.4.1) with the “-very-sensitive” parameter. PCR duplicates were marked using samblaster (0.1.24), and the reads mapped to the ENCODE black-listed regions were discarded prior to peak calling.
To detect the open chromatin regions, we performed peak calling using the MACS2 (2.2.7.1) software with the “--nomodel”, “--keep-dup auto” and “--extsize 147” options. Finally, HOMER findMotifs (4.11) was used for motif enrichment analysis over the detected open chromatin regions.
Assembly: GRCh38
Supplementary files format and content: peak lists in UCSC Genome Browser BED format

source_name: trunk neural crest

extract_protocol:
After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 μl 2xTD buffer, 2 μl TDE1 (Illumina), 10.25 μl nuclease-free water, and 0.25 μl 1% digitonin (Promega)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 12 μl, 1 μl of eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles.
The remaining 11 μl of each library were amplified for the number of cycles corresponding to the Cq value (i.e., the cycle number at which fluorescence has increased above background levels) from the qPCR. Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers.

treatment_protocol: shRNA knockdown hESCs were first differentiated towards NMPs (Day 3) and subsequently either trunk neural crest (tNC; upon culture in BMP/WNT agonists for 5 days) or pre-neural spinal cord progenitors (PNE; upon culture in WNT/high FGF for 4 days) in the presence (Pos) or absence (Neg) of Tetracycline.

value: trunk neural crest

value: tetracycline


title: trunk neural crest + tetracycline repeat 3 [tNC3pos]


title: trunk neural crest - tetracycline repeat 3 [tNC3neg]


title: SP-C C121G Day 7

city: Philadelphia

first: Apoorva

last: Babu

address: SCTR, 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
Fastq files were aligned to the mm39 reference genome using STARSolo
Downstream processing was performed using Seurat v4
Assembly: mm39
Supplementary files format and content: Seurat processed h5ad files

source_name: lung

extract_protocol:
To enrich for EPCAM+ cells, a single cell suspension was prepared by physical and enzymatic dissociation (Collagenase, DNase, Dispase) followed by MACS sorting by LS columns with CD45+ cell removal using CD45 micobeads followed by EPCAM+ cell enrichment using EPCAM microbeads.
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Day 3 and 7 mice received 400mg/kg IP tamoxifen

tag: age

value: EPCAM+

value: Sp-C C121G


title: trunk neural crest + tetracycline repeat 1 [tNC1pos]


title: PD1lo TIL WT B16 H3K4me3 2

description: CUT&Tag DNA


title: trunk neural crest - tetracycline repeat 1 [tNC1neg]


title: pre-neural spinal cord progenitors - tetracycline repeat 3 [PNE3neg]

source_name: pre-neural spinal cord progenitors

value: pre-neural spinal cord progenitors


title: pre-neural spinal cord progenitors + tetracycline repeat 3 [PNE3pos]


title: pre-neural spinal cord progenitors - tetracycline repeat 1 [PNE1neg]


title: pre-neural spinal cord progenitors - tetracycline repeat 2 [PNE2neg]


title: pre-neural spinal cord progenitors + tetracycline repeat 2 [PNE2pos]


title: AOCS_174_31_8

status: Public on Aug 02 2022

city: Melbourne

first: Dale

middle: W

last: Garsed

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Initial QC on the raw FASTQ files were done using FastQC (v0.11.8)
Reads were trimmed for low quality, adapters, N content and poly-A tails using fastq-mcf (v1.05)
Contamination was checked using FastQ Screen (v0.11.4)
Reads were mapped to the human reference GRCh37.92 using the STAR two pass method (v2.6.0b)
Mapped reads were sorted using Picard Tools (v2.17.3)
Additional QC after mapping was performed using Picard Tools CollectRnaSeqMetrics (v2.17.3) and RSeQC (v 2.6.4)
Counts were generated on the ensemble release GRCh37.92 GTF annotation using HTSeq (v0.10.0). Counts were done on the exons only using the “intersection-nonempty” mode
Assembly: hg19
Supplementary files format and content: Raw counts, gene by sample matrix. The GeneID column is in the format "EnsemblID|Chromosome|Start|End|Strand|Whole_Gene_Length|Exon_Only_Length|Gene_Symbol|Gene_Biotype", eg.. "ENSG00000000003|X|99883667|99894988|-|11322|2968|TSPAN6|protein_coding"

source_name: FT - normal control

extract_protocol:
RNA was isolated using the mirVana miRNA Isolation kit (Ambion/Life Technologies)
Between 500 ng and 2 μg of total RNA (RNA integrity number >7, except for autopsy samples) was used for library preparation using the TruSeq RNA Sample Preparation v2 kit (Illumina) as per the manufacturer’s instructions using the Low-Throughput protocol.

tag: case id

tag: gender

value: Female

value: FT - normal control

value: Fallopian Tube

tag: run batch

tag: library prep_batch

tag: library strand_orientation

value: unstranded


title: AOCS_176_31_3

tag: tissue


title: AOCS_177_31_6


title: AOCS_178_31_9


title: AOCS_175_31_0


title: AOCS_172_31_2


title: AOCS_170_4_9

source_name: Ascites

value: Ascites

value: High Grade Serous Ovarian Cancer


title: AOCS_170_2_1

source_name: PrimaryTumour

value: PrimaryTumour


title: pre-neural spinal cord progenitors + tetracycline repeat 1 [PNE1pos]


title: trunk neural crest - tetracycline repeat 2 [tNC2neg]


title: AOCS_171_4_1


title: SP-C C121G Day 3


title: AOCS_171_2_4


title: SP-C C121Gneo

value: SP-C C121Gneo


title: AOCS_169_2_4


title: AOCS_168_2_1


title: AOCS_167_29_7_WT

description: Whole tissue section

source_name: AutopsyTumour

value: AutopsyTumour


title: AOCS_167_29_7_MD

description: Tumour enriched by macrodissection


title: AOCS_167_4_6


title: AOCS_167_27_X_WT

description: Whole tissue section


title: AOCS_165_2_3


title: AOCS_164_2_0


title: AOCS_167_27_X_MD

description: Tumour enriched by macrodissection


title: AOCS_163_2_8


title: AOCS_162_2_5


title: AOCS_161_2_2


title: AOCS_159_2_2


title: AOCS_173_31_5


title: AOCS_160_2_X


title: AOCS_157_2_7


title: AOCS_155_4_9


title: AOCS_153_2_6


title: AOCS_152_2_3


title: AOCS_158_2_X


title: AOCS_150_4_5


title: AOCS_148_2_8


title: AOCS_142_4_9


title: AOCS_143_2_4


title: AOCS_144_2_7


title: AOCS_141_4_6


title: AOCS_145_2_X


title: AOCS_147_2_5


title: AOCS_166_2_6


title: AOCS_146_2_2


title: AOCS_139_7_7MD

description: Tumour enriched by macrodissection


title: AOCS_139_26_6WT

description: Whole tissue section


title: AOCS_139_2_9


title: AOCS_139_24_9WT

description: Whole tissue section


title: AOCS_138_4_3


title: AOCS_137_4_0


title: AOCS_139_7_7WT

description: Whole tissue section


title: AOCS_139_24_9MD

description: Tumour enriched by macrodissection


title: AOCS_137_10_2


title: AOCS_139_26_6MD

description: Tumour enriched by macrodissection


title: AOCS_135_4_5


title: AOCS_150_10_7


title: AOCS_134_4_2


title: AOCS_149_2_0


title: AOCS_130_2_4


title: AOCS_132_2_X


title: AOCS_133_2_2


title: AOCS_126_2_9


title: AOCS_124_2_3


title: AOCS_120_4_X


title: AOCS_123_2_0


title: AOCS_128_2_4


title: AOCS_119_4_2


title: AOCS_125_2_6


title: AOCS_117_4_7


title: AOCS_115_2_4


title: AOCS_141_10_8


title: AOCS_114_2_1


title: AOCS_116_2_7


title: AOCS_111_2_3


title: AOCS_113_2_9


title: AOCS_109_2_3


title: AOCS_112_2_6


title: AOCS_135_10_7


title: AOCS_105_2_2


title: AOCS_104_2_X


title: AOCS_106_2_5


title: AOCS_108_2_0


title: AOCS_095_4_5


title: AOCS_107_2_8


title: AOCS_097_2_3


title: AOCS_096_2_0


title: AOCS_095_2_8


title: AOCS_094_4_2

source_name: RelapseTumour

value: RelapseTumour


title: AOCS_094_2_5


title: AOCS_131_2_7


title: AOCS_093_8_4


title: AOCS_092_4_7


title: AOCS_122_2_8


title: AOCS_093_4_X


title: AOCS_091_4_4


title: AOCS_093_2_2


title: AOCS_092_2_X


title: AOCS_090_4_1


title: AOCS_086_4_6


title: AOCS_085_2_6


title: AOCS_088_4_1


title: AOCS_084_2_3


title: AOCS_088_2_4


title: AOCS_086_2_9


title: AOCS_081_2_5


title: AOCS_078_2_2


title: AOCS_080_2_2


title: AOCS_076_2_7


title: AOCS_075_2_4


title: AOCS_077_2_X


title: AOCS_065_2_2


title: AOCS_079_2_5


title: AOCS_064_4_7


title: AOCS_065_4_X


title: AOCS_061_2_1


title: AOCS_060_2_9


title: AOCS_059_2_1


title: AOCS_058_2_9


title: AOCS_091_2_7


title: AOCS_055_2_0


title: AOCS_034_4_1


title: AOCS_064_2_X


title: AOCS_090_2_4


title: AOCS_057_2_6


title: AOCS_034_2_4


title: AOCS_083_2_0


title: AOCS_056_2_3


title: AOCS_005_2_1


title: AOCS_002_2_3

description: The only Low Grade Serous Ovarian Cancer sample that was sequenced in the project

value: Low Grade Serous Ovarian Cancer


title: AOCS_001_2_0


title: Ishikawa_Input

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Reads were aligned to hg19 using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2
SAMtools was used to sort and convert SAM files to BAM files
Peaks with a P-value cutoff of 1 x 10-10 and an mfold parameter between 15 and 100 were called by Model Based Analysis of ChIP-seq-2 (MACS2)
Assembly: hg38
Supplementary files format and content: BigWig files
Supplementary files format and content: narrowPeak files from MACS2

source_name: Ishikawa

growth_protocol: HCI-EC-23 and Ishikawa was cultured in RPMI 1640 (Gibco, 11875119) supplemented with 10% fetal bovine serum (Gibco, 26140079) and 1% penicillin-streptomycin (Gibco, 15140163). Hormone deprived media consisted of phenol red-free RPMI1640 (Gibco, 11835055) supplemented with 10% charcoal-stripped fetal bovine serum (Sigma Aldrich, F6765) and 1% penicillin-streptomycin (Gibco, 15140163). HCI-EC-23 or Ishikawa cell lines were cultured in hormone-deprived media for at least five days prior to experiments using hormones. Cells were incubated at 37°C with 5% CO2.

extract_protocol:
Cells were fixed using 1% formaldehyde (Sigma Aldrich, 252549) for 10 minutes at room temperature to cross-link DNA and proteins. Cross-linking was stopped by addition of glycine (Fisher Scientific, BP381) to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via scraping in Farnham lysis buffer supplemented with protease and phosphatase inhibitors (Thermo Scientific, A32959).
Chromatin immunoprecipitation was performed as previously described (Reddy et al. Genome Research 2009) with an Anti-Estrogen receptor alpha (ESR1) antibody (Millipore Sigma, 06-935) or H3K27ac antibody (Active Motif, 39133).

treatment_protocol: Media was changed and cells were treated with either 0.1% DMSO (vehicle) for 8 hr (H3K27ac ChIPs) or 10 nM E2  for 1 hour (ER ChIPs) in hormone-deprived media.

tag: cell line

value: Ishikawa

value: endometrioid adenocarcinoma

tag: chip antibody

value: pooled input


title: Ishikawa_1hrE2_rep2

value: ESR1 (Millipore Sigma, 06-935)

tag: treatment

value: 10 nM E2


title: Ishikawa_1hrE2_rep1

tag: cell type


title: AOCS_004_2_9


title: HCI-EC-23_1hrE2_rep2


title: AOCS_063_2_7


title: ATAC HSPC, 0th day, rep1

status: Public on Aug 01 2022

city: Ann Arbor

first: Joshua

last: Welch

state: MI

address: 500 S State St

department: DCMB

institute: University of Michigan

description:
3423-MV-1_barcodes.tsv.gz
3423-MV-1_features.tsv.gz
3423-MV-1_matrix.mtx.gz
3423-MV-1_feature_linkage.bedpe

data_processing:
Raw sequencing data were mapped and preprocessed to gene expressions and peaks using CellRanger ARC 2.0.0.
Secondary analyses by CellRanger ARC produced feature linkages between peaks and genes.
Unspliced and spliced mRNA expressions were quantified using Velocyto (v0.17.17) (La Manno et al. 2018) with the GTF (GRCh38) provided in CellRanger.
Assembly: GRCh38
Supplementary files format and content: Combined RNA and ATAC count data from CellRanger in zipped Matrix Market format
Supplementary files format and content: CellRanger linkage file in text format
Supplementary files format and content: ATAC peak annotation file in text format
Supplementary files format and content: Unspliced and spliced counts from Velocyto in loom format

source_name: Blood

growth_protocol: Cells were either immediately prepared for single-cell processing or maintained at 37ºC with 5% CO2 in Stemspan II medium supplemented with 100 ng/ml stem cell factor, 100 ng/ml thrombopoietin, 100 ng/ml Flt3 ligand (all from Stemcell Technologies), and 100 ng/ml insulin-like growth factor binding protein 2 (R&D Systems) for seven days.

extract_protocol:
Cells were washed in PBS supplemented with 0.04% BSA and sorted using fluorescence actived cell sorting. Nuclei were isolated following the 10X Genomics Nuclei Isolation Signle Cell multiome ATAC + Gene expression Sequencing demonstrrated Low Cell Input protocol.
Single Cell Multiome ATAC and Gene Expression libraries were prepared according to the 10X Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide for standard Illumina paired-end sequencing.

value: Blood

value: Primary Cells

value: Mobilized CD34+ Hematopoietic Stem and Progenitor Cells


title: ATAC HSPC, 7th day, rep1

description:
3423-MV-2_barcodes.tsv.gz
3423-MV-2_features.tsv.gz
3423-MV-2_matrix.mtx.gz
3423-MV-2_feature_linkage.bedpe


title: HCI-EC-23_1hrE2_rep1


title: T47D_537_LSD1_rep1

city: Miami

first: Liliana

last: Garcia-Martinez

state: Florida

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami

data_processing:
ChIP-seq: Single-end ChIP-seq fastq files were processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4, and peaks with fold change > 3.5 compared to input and a FDR < 0.05 were used for subsequent analysis. Only default parameters were used.
Homer annotatePeaks v4.8.3 was used for peak  annotation and for assigning peaks to genes.
Bedtools v2.26.0 intersect was used to determine peak overlaps.
Assembly: hg19
Supplementary files format and content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were were culture in estrogen deprived conditions for 3 days. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL). Cells were treated with DMSO for 72h.

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and fixed with 11% solution containing formaldehyde (Thermo Fisher #28908), 50mM HEPES-KOH(pH 7.5), 100mM Nacl, 0.5M EDTA, 0.5M EGTA for 10 min. 1/20 of the plates volume equivalent of freshly prepared Glycine 2.5M(stock) was added to quench the reaction for 5min . The supernatant was aspirated, and the cells were washed twice with 5 ml PBS and harvested on ice using cell scrapers . Cells were pelleted at 2950 x g for 10 min at 4°C, washed 1x with 10 ml cold PBS, and pelleted once more. Cell pellets were flash freeze in liquid nitrogen and store at -80°C until processing day. Cell pellet collected from 6 plates of cells was resuspended in 5 ml of Lysis Buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), allowed to rotate for 10 min at 4°C, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 5 ml of Lysis Buffer 2 (10 mM Tris-HCL pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), allowed to rotate for 10 min at room temperature, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 3 ml of Lysis Buffer 3 (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 then transfer to 15ml sonication tubes (Diagenode cat# C01020031). Cells were sonicated on a Bioruptor Pico at 4°C for 20min of 30’’ ON-OFF cycles with 1.2 g of sonication beads. After sonication, samples were transferred to 2 separate 1.5 ml microtube and centrifuged at 20,000 x g for 15 minutes at 4°C. The supernatant was transferred to new 15 ml tubes. To check sonication efficiency, 50µl of sonicated samples was transferred to a new microtube with 50µl PBS and incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm to decrosslink. DNA was purified with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H20. 1 ug of decrosslinked chromatin from each sample were run in a 1% agarose gel at 100V for 45min and imaged on a Bio-rad ChemiDoc XRS+. DNA concentration in the sonicated decrosslinked samples were measured via qubit, and this concentration was then used to estimate the concentration of chromatin in the un-decrosslinked samples.  10ug of Antibody (see Key Resources table for list of antibodies) along with 2ug of Spike-in antibodies (Active Motif 61686) were bound to 50 ul of Dynabeads Protein G (Thermo Fisher 10004D), previously washed with 1 ml of 0.5% BSA in 1x PBS three times, and rotated end-to-end overnight at 4°C (Eppendorf cat# 0030108051). After binding of the antibodies , beads were washed with 1 ml of 0.5% BSA in 1x PBS three times. 30ug of chromatin and 50 ng of Spike-in chromatin (Active Motif 53083) were added to 1.5ml LoBind tube (Eppendorf cat# 0030108051) containing pre-bound antibodies beads and brought up to 500µl final volume with Lysis Buffer and rotated end-to-end overnight at 4°C.  5 µl was removed as input material (1%) and placed in a separate microtube at 4°C completing the volume to 50uL with Lysis Buffer 3.  Beads were washed 6 times with 1 ml Wash Buffer (50 mM Hepes-KOH, pH 7.6; 500 mM LiCl, 1 mM EDTA, 1% NP-40; 0.5% Na-Deoxycholate) and once with 1 ml TE containing 50 mM NaCl. Beads were dried after the last wash by removing as much TE as possible. 210 ul of Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) was added to each sample and  150 ul elution buffer were added to each input sample that was previously set aside. To elute immunocomplexes from beads, samples were incubated at 65°C for 15 minutes on an Eppendorf Thermomixer shaking at 1000rpm. Tubes were centrifuged for 3min at 960xg at RT and 200µl of supernatant was transferred to a new tube and reverse crosslinked overnight at 65°C. Next day, 200 ul of TE was added to each decrosslinked sample and input, and the samples were treated sequentially with 0.2 mg/ml RNAse A (Sigma R5503) at 37°C and 0.2 ug/ml Proteinase K (NEB P8107S) at 55°C for two hours each. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H2O and quantified by Qubit.
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

tag: cell source

value: ATCC #HTB-133

tag: modifications

value: Y537S Point mutation in ESR1

value: Anti-KDM1 / LSD1 antibody - ChIP Grade (ab17721)


title: T47D_WT_FLAG

city: Charlestown

first: Ioannis

last: Sanidas

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Sequencing reads were trimmed using trim-galore, aligned to the human genome (build hg19) using bwa-mem, then duplicate-marked using sambamba, and filtered to remove reads that were duplicates, had mapping quality <30, had >2 mismatches, or had >1/3 of their sequence soft-clipped.
Filtered BAMs were sorted and indexed, and deeptools-bamCoverage was used to generate CPM-normalized bigwig files for peak visualization, and bedtools-coverage was used to count reads in 200bp genomic windows tiling the genome.
Assembly: human genome (build hg19)
Supplementary files format and content: CPM-normalized bigwig files were generated using deeptools-bamCoverage

source_name: T47D breast cancer cells

growth_protocol: The telomerase-expressing non-transformed human retina epithelial cells RPE1 and skin fibroblasts BJ cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 5% Fetal Bovine Serum (FBS) and antibiotics (100 units/ml Penicillin and 100 μg/ml Streptomycin; P/S). The MCF10A human breast epithelial cell line were cultured in DMEM/Nutricient mixture F12 medium supplemented with 5% horse serum (Gibco, Cat. No. 16050122), 20 ng/ml human EGF (ThermoFisher, Cat. No. PHG0311), 0.5 µg/ml hydrocortisone (Sigma, Cat. No. H-0888), 100 ng/ml cholera toxin (Sigma, Cat. No. C-8052), 10 µg/ml insulin (Sigma, Cat. No. I-1882) and antibiotics (P/S). The human breast cancer cell line T47D was cultured in RPMI 1640 medium supplemented with 10% FBS and antibiotics (P/S).

extract_protocol:
ChIP assays were carried out on RPE1, BJ, MCF10A and T47D cell cultures using approximately 5 million cells per sample and per epitope. Cells were washed once with PBS and fixed with 1.5 mM ethylene glycol bis(succinimidyl succinate) (Thermo Scientific, Cat. No. 21565) for 30 min at 25oC and 1% formaldehyde (Sigma, Cat. No. F8775) for 10 min at 37oC. 20mM Tris-HCl pH7.5 and 150 mM Glycine were used to quench cross-linking. Cell pellets were washed twice with ice-cold PBS and lysates were prepared using 300 µl lysis buffer (50mM Tris-HCl pH 7.4, 1% SDS, 0.25% DOC) supplement with protease and phosphatase inhibitors cocktail (PPI) (Thermo Scientific, Cat. No. 78442) for 10 min on ice. Cell lysates were diluted with 900 µl ChIP dilution buffer (50mM Tris-HCl pH 7.4, 0.1% SDS, 150mM NaCl, 1.84% Triton-X) supplement with PPI and chromatin was fragmented to a size of 200 – 700 bases with Branson 250 sonifier. Solubilized chromatin was further diluted with 1800 µl ChIP dilution buffer and immunoprecipitated with the indicated antibodies overnight at 4°C. Anti-DYKDDDDK Tag (Cell Signaling, Cat. No. 14793) was used for FLAG-RB ChIP. Antibody-chromatin complexes were pulled down with protein G-Dynabeads (Life Technologies, Cat. No. 10004D) for 2 hours at 4°C and washed 3 times with RIPA 150 Wash Buffer (0.1% SDS, 0.1% DOC 1% Triton X-100, 1mM EDTA, 10mM Tris-HCl pH 8, 150mM NaCl), 3 times with RIPA 500 Wash Buffer (0.1% SDS, 0.1% DOC 1% Triton X-100, 1mM EDTA, 10mM Tris-HCl pH 8, 500mM NaCl), 3 times with LiCl wash buffer (10mM Tris-HCl, pH 8, 250mM LiCl, 0.5% Triton X-100, 0.5% DOC) and once with ice-cold 10mM Tris-HCl, pH 8. Chromatin complexes were eluted from the beads using elution buffer (10mM Tris-HCl pH 8, 0.1% SDS, 150mM NaCl, 5 mM DTT) for 1 hour at 65°C and treated with RNase A (Roche, Cat. No. 11119915001) for 30 min at 37oC. Proteinase K (Thermo Scientific, Cat. No. 25530049) treatment and reverse cross-linking was performed for 3 hours at 65°C. After crosslink reversal, immunoprecipitated DNA was extracted with AMP Pure XP beads (Beckman Coulter, Cat. No. A63881). ChIP DNA was quantified with Qubit dsDNA HS Assay kit (Thermo Scientific, Cat. No. Q32851).
1-2 ng ChIP DNA samples were used to prepare sequencing libraries, using the Ovation Ultralow System V2 kit (TECAN, Cat. No. 0344NB-A01).

treatment_protocol: RB1 knock down or replacement of the endogenous by exogenous RB protein in cells transduced with pINDUCER11 and/or pINDUCER20 constructs were induced by addition of 0.5 μg/ml DOX (Sigma, Cat. No. D9891) for the indicating time. Expression of the dominant negative A-FOS or the dominant negative DP1_aa127-410 in cells transduced with pLenti-CMVtight puro constructs were induced by addition of 0.5 μg/ml DOX for 48 hours. Contact inhibition experiments performed by maintaining RPE1 cells in confluent culture for 6 days.

value: pINDUCER11-shRB1, pINDUCER20-FLAG-RBWT

value: anti-DYKDDDDK Tag (Cell Signaling Technology, 14793)

value: 48 hours doxycycline


title: MCF10A_WT_input

source_name: MCF10A breast epithelial cells

value: input


title: T47D_537_input_rep2

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were were culture in estrogen deprived conditions for 21 months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL).Cells were treated for 72h with 500nM of compound Corin (MedChem Express


title: T47D_537_LSD1_rep3


title: T47D_dCDK_FLAG


title: MCF10A_dCDK_FLAG


title: T47D_537_LSD1_rep2

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were were culture in estrogen deprived conditions for 3 days. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL).Cells were treated with DMSO for 72h.


title: RBKO1_2_RB

source_name: retina epithelial cells RPE1

value: sgRB1 (Nicolay et al. 2015)

value: anti-RB (Cell Signaling Technology, 9309)


title: T47D_dCDK_input


title: MCF10A_dCDK_input


title: T47D_537_ER_rep2

data_processing:
ATAC-seq: Paired-end ATAC-seq fastq files were processed using the ATAC-seq Pipeline from the Kundaje Lab (https://github.com/kundajelab/atac_dnase_pipelines). Reads were trimmed using cutadapt v1.9.1 using the following parameters: -m 5. Reads were aligned to the hg19 genome using Bowtie2 v2.2.6, and the SAMtools v1.7 was used to convert the output files into the BAM format using default parameters. Duplicate reads were removed using Picard tool v1.126 using default parameters. Shuf was used to subsample reads to 50 million. Peaks were called using MACS2 v2.1.0 using default parameters
Assembly: hg19
Supplementary files format and content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061 ).

value: Anti-Estrogen Receptor alpha antibody (ab3575)


title: T47D_WT_input


title: RBWT_RB

value: sgControl (Nicolay et al. 2015)


title: T47D_537_ER_rep1


title: HCI-EC-23_Input

value: endometrioid adenocarcinoma

value: pooled input


title: iPSC_chimera

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

description: single cell

data_processing:
CellRanger v6 used for demultiplexing + read mapping + barcode assignment + UMI counting
Seurat v4.2.1 used for quality control + normalization + dimensionality reduction + clustering
Mouse Cell Atlas, PanglaoDB and published literaure used for cell type annotation
Assembly: GRCm38.p6
Supplementary files format and content: Count matrices from Cell Ranger (raw for iPSC chimera, filtered for KO-Pesa and KO-Testis)

source_name: Cauda epididymes

extract_protocol:
Chromium Single Cell 3’ Reagents kits v3.1 user guide RevD
Single Cell 3’ v3.1 chemistry

value: Cauda epididymes

value: Spermatids, spermatozoa

tag: line

value: Pax7-nGFP iPS x goGermline


title: Tsc22d3_KO

description: single cell

value: Epididymal cells

value: goGermline


title: HK6acc_DAA_inhibition_24hrs_AtNUDX23_rep2

status: Public on Jul 31 2022

city: Copenhagen N

first: Jeppe

last: Vinther

address: Ole Maaloes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

description:
CapZyme-seq protocol
FeatureCount_HK6acc_DAA_output.txt

data_processing:
Illumina bcl2fastq was used to create fastq files
Sequenced reads were trimmed for adaptor sequence (cutadapt -a AGATCGGAAGAGCACACGTCT -q 20 -m 15) and mapped to RNA sequences (viral RNA, rRNA, snoRNA, tRNA and mRNA (TPM>2) using  (bowtie2 --norc --very-sensitive)
Counts for the 5' end of different RNA were obtained using the featureCounts function from the Subread package using a SAF file specifing the first 100 nts of each RNA.
Example code for the processing of the sequencing data is available at https://github.com/jeppevinther/CapZyme
Supplementary files format and content: Tab-delimited text files include FeatureCounts output, raw counts
Supplementary files format and content: Matrix table with raw 5'  counts for every RNA (first 100nt) and every sample in experiment
Library strategy: CapZyme-seq

organism:
Homo sapiens
Hepacivirus hominis

source_name: Huh7.5 hepatoma cells

extract_protocol:
RNA extraction was performed by Trizol treatment followed on-column DNase I digestion and RNA purification using RNA Clean & Concentrator kit-5
RNA was enzymatically treated with de-capping enzymes that specifically convert different 5’ cap structures to 5’ monophosphates. 5’-phosphate dependent adapter ligation was performed followed by reverse transcription. Libraries were generated using PCR with custom Illumina compatible primers.

value: Huh7.5 hepatoma cells

tag: enzymatic treatment

tag: virus

value: HCV genotype 6a:HK6acc

tag: molecule subtype

value: TEX treated total RNA


title: HK6acc_DAA_inhibition_24hrs_AtNUDX23_rep3


title: HK6acc_DAA_inhibition_8hrs_neg_rep3

value: negative


title: HK6acc_DAA_inhibition_24hrs_neg_rep3


title: HK6acc_DAA_inhibition_8hrs_Rpp_rep3

value: Rpp


title: HK6acc_DAA_inhibition_8hrs_neg_rep2


title: HK6acc_DAA_inhibition_24hrs_Rpp_rep3


title: HK6acc_DAA_inhibition_8hrs_AtNUDX23_rep2


title: HK6acc_DAA_inhibition_24hrs_Rpp_rep1


title: HK6acc_DAA_inhibition_8hrs_Rpp_rep2


title: HK6acc_DAA_inhibition_24hrs_Rpp_rep2


title: HK6acc_DAA_inhibition_24hrs_AtNUDX23_rep1


title: HK6acc_DAA_inhibition_24hrs_neg_rep1


title: HK6acc_DAA_inhibition_24hrs_neg_rep2


title: HK6acc_DAA_inhibition_0hrs_AtNUDX23_rep3


title: HK6acc_DAA_inhibition_0hrs_neg_rep3


title: HK6acc_DAA_inhibition_8hrs_AtNUDX23_rep1


title: HK6acc_DAA_inhibition_8hrs_Rpp_rep1


title: HK6acc_DAA_inhibition_8hrs_neg_rep1


title: HK6acc_DAA_inhibition_0hrs_AtNUDX23_rep2


title: HK6acc_DAA_inhibition_8hrs_AtNUDX23_rep3


title: HK6acc_DAA_inhibition_0hrs_Rpp_rep3


title: T47D_537_INPUT

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-133

value: Y537S Point mutation in ESR1

value: N\A


title: HK6acc_DAA_inhibition_0hrs_AtNUDX23_rep1


title: V26-1

status: Public on Jul 30 2022

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
scRNA-Seq:Read 2 was used to obtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences;Read 1 was picked in each cell according to the cell ID in read2 and the UMI information was aligned to it,and then these raw reads were trimmed to remove TSO or polyA sequence;Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data;TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each single cell RNA samples
Supplementary_files_format_and_content: The *Info.txt files at the foot of each sample page include the cell barcode sequence and its associated ID.

source_name: patient 26 adjacent normal tissue region 1

extract_protocol:
Briefly, single cells were picked into the RNA lysis buffer by a mouth pipette. Then disrupt the cells by vigorously vortexing for 40 seconds, and the released RNAs were incubated at 72℃ for 3min to open the secondary structure. The remaining cell suspension was centrifuged at 500g for 10min and the supernatant was discarded. Then the cell pellets were used for genomic DNA extraction with DNeasy Blood & Tissue Kit.
Single-cell cDNA amplification was based on a modified STRT-seq protocol. Briefly, the released mRNAs were reverse transcribed into cDNA by poly (T) primers anchored with 8bp cell-specific barcodes and 8bp unique molecular identifiers (UMIs), followed by second strand cDNA synthesis and pre-amplification. The amplified cDNA from different cells can be pooled together, fragmented to around 300bp, and the 3’ ends were enriched by the affinity interaction with Dynabeads® MyOne™ Streptavidin C1 beads for library construction using Kapa Hyper Prep Kit. The constructed libraries were sequenced on Illumina HiSeq 4000 system as paired-end 150bp reads.

treatment_protocol: Fresh lung tumor tissues and adjacent normal tissues were dissected in RPMI-1640 medium + 10% FBS on ice, and washed with ice-cold DPBS. Then transfer the tissues to a tube , cut it into small pieces with a scissor and resuspend it in 1ml of digestion buffer consisting of Collagenase Type I(2mg/ml; Gibco), Dispase II(1mg/ml; Millipore) and DNase I (0.2mg/ml; Roche) in RPMI-1640 medium. After incubation at 37°C for 30-40 min with frequent agitation, 500ul of RPMI-1640 medium was added to stop digestion. The tissues were pipetted up and down for 40-50 times and the cell suspension was filtered through a 100-um mesh filters. Then the cells were centrifuged at 500g for 10 min at 4°C, the pelleted cells were re-suspended in red blood cell lysis buffer and incubated at RT for 3min. The cell pellets were washed again and re-suspended with RPMI-1640 medium +10 % FBS.

tag: subject id

value: patient 26

tag: patient diagnosis

value: non-small cell lung cancer (NSCLC)

value: adjacent normal tissue


title: HK6acc_DAA_inhibition_0hrs_Rpp_rep1


title: V27-1

description: The file GSE119911_mixed_sample_phenotypes.xlsx includes the tumor vs  non-tumor status of each cell ID and barcode.

source_name: patient 27 tumor tissue and adjacent normal tissue region 1

value: patient 27

value: tumor tissue and adjacent normal tissue


title: V22-4

source_name: patient 22 tumor tissue

value: patient 22

value: tumor tissue


title: HK6acc_DAA_inhibition_0hrs_neg_rep1


title: Tsc22d3_KO-Testis

description: single cell

source_name: Testis

value: Testis

value: Testicular cells

value: goGermline


title: V22-2

source_name: patient 22 adjacent normal tissue region 1


title: V22-5

source_name: patient 22 adjacent normal tissue region 2


title: V22-3


title: MCF10A_WT_FLAG

tag: genotype

value: pINDUCER11-shRB1, pINDUCER20-FLAG-RBWT

value: anti-DYKDDDDK Tag (Cell Signaling Technology, 14793)

value: 48 hours doxycycline


title: V20-5

source_name: patient 20 adjacent normal tissue region 2

value: patient 20


title: V20-2


title: V22-1


title: V20-6

source_name: patient 20 tumor tissue


title: HK6acc_DAA_inhibition_0hrs_Rpp_rep2

value: Huh7.5 hepatoma cells

value: Rpp

value: HCV genotype 6a:HK6acc

value: TEX treated total RNA


title: HK6acc_DAA_inhibition_0hrs_neg_rep2

value: negative


title: V20-4

source_name: patient 20 adjacent normal tissue region 1

value: non-small cell lung cancer (NSCLC)

value: adjacent normal tissue


title: V20-1


title: V19-5

source_name: patient 19 adjacent normal tissue region 3

value: patient 19


title: V19-4

source_name: patient 19 adjacent normal tissue region 1


title: T47D_537_FOXA1_rep2

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-133

value: Y537S Point mutation in ESR1

value: Anti-FOXA1 antibody - ChIP Grade (ab23738)


title: V25-1

source_name: patient 25 adjacent normal tissue region 1 and region 2

value: patient 25


title: T47D_537_FOXA1_rep1


title: V19-3

source_name: patient 19 tumor tissue

value: tumor tissue


title: T47D_537_RNApol_rep2

value: Rpb1 NTD (D8L4Y) Rabbit mAb #14958 Cell Signaling Technology


title: V17-2

source_name: patient 17 adjacent normal tissue region 2

value: patient 17


title: V17-4

source_name: patient 17 tumor tissue


title: V19-2

source_name: patient 19 adjacent normal tissue region 2


title: V17-3


title: V26-2

source_name: patient 26 tumor tissue and adjacent normal tissue region 2

value: patient 26

value: tumor tissue and adjacent normal tissue


title: V17-1

source_name: patient 17 adjacent normal tissue region 1


title: V25-2

source_name: patient 25 tumor tissue


title: V16-1

source_name: patient 16 normal tissue region 1

value: patient 16

value: normal tissue


title: V16-2


title: V15-7

source_name: patient 15 tumor tissue region 2

value: patient 15


title: V20-3

value: patient 20


title: V15-8

source_name: patient 15 tumor tissue region 3

value: non-small cell lung cancer (NSCLC)


title: T47D_537_RNApol_rep1


title: V15-4

source_name: patient 15 lymphatic metastasis tissue

value: lymphatic metastasis tissue


title: V15-5


title: V15-2

source_name: patient 15 tumor tissue region 1


title: V15-3


title: V15-6

source_name: patient 15 adjacent normal tissue

value: adjacent normal tissue


title: V13-6

source_name: patient 13 adjacent normal tissue

value: patient 13


title: V15-1


title: V13-5


title: V13-4

source_name: patient 13 second tumor tissue region 3


title: V13-3

source_name: patient 13 second tumor tissue region 2


title: V19-1

source_name: patient 19 adjacent normal tissue region 1

value: patient 19


title: V12-5

source_name: patient 12 tumor tissue region 1 and adjacent normal tissue

value: patient 12


title: V16-3

source_name: patient 16 normal tissue region1 and region 2


title: V12-4

source_name: patient 12 tumor tissue region 2


title: V12-1

source_name: patient 12 lymphoid tissue

value: lymphoid tissue


title: V11-4

source_name: patient 11 tumor tissue region 1

value: patient 11


title: V12-2

source_name: patient 12 tumor tissue region 1

value: tumor tissue


title: V11-3

source_name: patient 11 tumor tissue region 3


title: V11-2

source_name: patient 11 tumor tissue region 2


title: V11-1


title: V10-6

source_name: patient 10 adjacent normal tissue

value: patient 10


title: V11-6

source_name: patient 11 adjacent normal tissue


title: V13-2

source_name: patient 13 second tumor tissue region 1


title: V10-4

source_name: patient 10 tumor tissue region 3


title: V10-5


title: V10-2

source_name: patient 10 tumor tissue region 1


title: V10-1


title: V10-3

source_name: patient 10 tumor tissue region 2


title: V09-8

source_name: patient 9 lymphoid tissue

value: patient 9


title: V09-7


title: V09-6


title: V09-9


title: V09-4

source_name: patient 9 tumor tissue region 4


title: V13-1

source_name: patient 13 first tumor tissue


title: V09-3

source_name: patient 9 tumor tissue region 3


title: V09-2

source_name: patient 9 tumor tissue region 2


title: V09-1

source_name: patient 9 tumor tissue region 1


title: V09-5


title: V11-5


title: V09-11

source_name: patient 9 adjacent normal tissue


title: V09-10


title: V06-8

source_name: patient 6 tumor tissue region 3

value: patient 6


title: V11-7

source_name: patient 11 tumor tissue region 1


title: V06-5

source_name: patient 6 tumor tissue region 1 and region 3


title: V06-7

source_name: patient 6 adjacent normal tissue


title: V06-4

source_name: patient 6 tumor tissue region 2


title: V06-6

source_name: patient 6 tumor tissue region 3 and adjacent normal tissue

value: tumor tissue and adjacent normal tissue


title: V05-5

source_name: patient 5 tumor tissue region 1 and region 2

value: patient 5


title: V06-2

source_name: patient 6 tumor tissue region 1


title: V06-3


title: V05-2

source_name: patient 5 tumor tissue region 2


title: V05-3

source_name: patient 5 tumor tissue region 3


title: V05-6

source_name: patient 5 tumor tissue region 3 and adjacent normal tissue


title: V05-4

source_name: patient 5 adjacent normal tissue


title: V04-6

source_name: patient 4 tumor tissue region 3 and adjacent normal tissue

value: patient 4


title: V04-3

source_name: patient 4 tumor tissue region 3


title: V04-2

source_name: patient 4 tumor tissue region 2


title: V04-4

source_name: patient 4 adjacent normal tissue


title: V04-5

source_name: patient 4 tumor tissue region 1 and region 2


title: V04-1

source_name: patient 4 tumor tissue region 1


title: V03-6

source_name: patient 3 adjacent normal tissue

value: patient 3


title: V03-3

source_name: patient 3 tumor tissue region 1 and region 2


title: V03-4


title: V03-2

source_name: patient 3 tumor tissue region 2


title: V03-5


title: V06-1


title: V02-6

source_name: patient 2 tumor tissue region 2 and adjacent normal tissue

value: patient 2


title: 293T-VEGFA-sgRNADel-PD_rep1

first: Howard

last: MENG

state: Beijing

address: No.5 Yiheyuan Road Haidian District

data_processing:
Detect-seq raw FASTQ files are remove Illumina sequencing adapters with cutadapt software (version 1.18). Working command and key parameters are: cutadapt --times 1 -e 0.1 -O 3 --quality-cutoff 25 -m 50. After adapter removal, FASTQ files are mapped to the reference genome (hg38) with Bismark(version 0.22.3) aligner without special settings. Then the unmapped and low MAPQ (MAPQ < 20) FASTQ reads are re-mapped by BWA MEM (version 0.7.17) with default behavior. The Bismark-generated BAM and BWA-generated BAM are merged, then sorted by reference coordinate with samtools sort command (version 1.9). Sored BAM files are removed duplications by Picard MarkDuplicates (version 2.0.1) with default settings. Considering of CBE usually generate indel byproducts, BAM files are needed to be re-aligned with GATK RealignerTargetCreator and IndelRealigner (version 3.8.1) with default settings, and SNP know sites are download from NCBI dbSNP.
After Detect-seq mapping steps, several computation and analysis steps should perform to achieve final Detect-seq off-targets. While making it an easy-achieve analysis pipeline, we offer Detect-seq tools on GitHub (https://github.com/menghaowei/Detect-seq), which contains several useful Python scripts. And those tools can help to perform Detect-seq analysis like off-targets finding, sgRNA alignment, and result visualization.
Assembly: hg38
Supplementary files format and content: The bed files are the final off-target results generated by the Detect-seq protocol

source_name: Human embryonic kidney

growth_protocol: The HEK293T and MCF7 is separately cultivated in DMEM and MEM with 10% FBS and 1% PS at 37°C cultivator with 5% CO2. The subculture of cells was performed every 2–3 days and only passage 3-10 were used for experiments. All the cells were routinely tested for Mycoplasma contamination with TransDetect PCR Mycoplasma Detection Kit (TRANSGEN BIOTECH, FM311-01).

extract_protocol:
Genomic DNA was freshly extracted using CWBIO universal genomic DNA kit (CWbiotech, CW2298M) and stored in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) at -80 °C.
Extracted genomic DNA was fragmented into ~300 bp through Covaris Focused-ultrasonicator™ Instrument (ME220), followed by a purification using DNA Clean & Concentrator-5 (Vistech, DC2005). ~5 ug DNA fragments and 10 pg spike-in model sequences were subjected to end repair with NEBNext End Repair Module (NEB, E6050), and 1 μl E. coli ligase (NEB, M0205) was added to repair nicks in DNA. Then hydroxylamine protection of endogenous 5fC was performed in 100 mM MES buffer (pH 5.0), 10 mM O-ethylhydroxylamine (EtONH2, Aldrich, 274992) at 37 °C for 6 h. The product underwent 5fC protection was diluted 2.5 times and purified with DNA Clean & Concentrator-5. Next, dA-tailing procedure was carried out using NEBNext dA-Tailing Module (NEB, E6053) followed by a DNA purification with 1.8 × AMPure XP beads. DNA damage that may interfere the subsequent labeling step was repaired in a mixture of 2 μl endonuclease IV (Endo IV, NEB, M0304), 1 μl Bst full-length polymerase (NEB, M0328), 2 μl Taq ligase (NEB, M0208), 1 μl NAD+ (NEB, B9007), 1 μl dNTP (2.5 mM each) in NEBuffer 3 for 1 h at 37 °C and 1 h at 45 °C. DNA was purified and subjected to in vitro BER labeling reaction containing a mixture of 1 μl UDG (NEB, M0280), 1.5 μl Endo IV, 0.8 μl Bst full-length polymerase, 1.7 μl Taq ligase, 1 μl NAD+, 200 nM biotin-dUTP, 800 nM d5fCTP, 200 nM dATP and 200 nM dGTP in NEBuffer 3 for 40 min at 37 °C. The DNA was incubated with 75 mM of malononitrile in 10 mM Tris-HCl (pH 7.0) at 37°C for 20 h in an enclosed thermomixer (Eppendorf, 850 rpm), away from light. The reaction product was then purified with 1.8 × AMPure XP beads. Labeled fragments were enriched by streptavidin C1 beads (Invitrogen) following the manufacturer's instruction. Y adaptor (see Supplementary Note 1) was ligated (NEBNext Quick Ligation Module, E6056) to double-stranded DNA on streptavidin C1 beads so that free adaptor can be removed by three-times washing of 1×B&W buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20). After washing once with 1× SSC buffer (pH 7.0), beads with biotinylated DNA strands were resuspended in freshly prepared 0.15 M NaOH and incubated at room temperature for 10 min, followed by a sequential washing of 1× SSC buffer (7.0) and 1× TE buffer (pH 7.5) for once. The DNA was eluted from C1 beads using deionized water after heating at 95 °C for 3 min. Eluted DNA was finally subjected to library amplification with indexed primers (NEB). To obtain sufficient DNA template, 2 rounds of amplification were first performed by using MightyAmp DNA polymerase (Takara), which was proved to read through regions containing biotin-dU and d5fC-malononitrile sites more easily. The PCR product was recovered via DNA Clean & Concentrator-5 and then PCR amplified for ~12 cycles using NEBNext® Q5® Hot Start HiFi PCR Master Mix (NEB, M0543). The constructed libraries were checked using the Agilent 2100 bioanalyzer. Sequencing was performed by Illumina Hiseq X Ten.

treatment_protocol: 6.4 × 106 of HEK293T cells or 2.5 × 106 of MCF-7 cells were seeded into 6-well culture plates (Corning) for 16 h growth. Adherent cells were transfected with 4 μg BE and 2720 ng sgRNA plasmids per well using lipofectamine LTX following the manufacturer’s protocol. Cells were then collected after 72 h of transfection.

value: Human embryonic kidney

tag: trait info

value: VEGFA-sgRNADel-PD


title: 293T-VEGFA-sgRNADel-PD_rep2


title: V02-5

source_name: patient 2 tumor tissue region 2

value: non-small cell lung cancer (NSCLC)


title: 293T-VEGFA-UGIDel-PD_rep1

value: VEGFA-UGIDel-PD


title: 293T-VEGFA-UGIDel-PD_rep2


title: 293T-VEGFA-Empty-PD_rep1

value: VEGFA-Empty-PD


title: 293T-VEGFA-APODel-PD_rep2

value: VEGFA-APODel-PD


title: V02-1

source_name: patient 2 tumor tissue and adjacent normal tissue


title: V03-1

source_name: patient 3 tumor tissue region 1


title: V05-1

source_name: patient 5 tumor tissue region 1


title: V02-2.3

source_name: patient 2 tumor tissue region 1


title: V01-5

source_name: patient 1 tumor tissue and adjacent normal tissue

value: patient 1


title: 293T-VEGFA-APODel-PD_rep1


title: 293T-VEGFA-All-Input_rep2

value: VEGFA-All-Input


title: V01-2

source_name: patient 1 tumor tissue

value: tumor tissue


title: 293T-VEGFA-All-PD_rep2

value: VEGFA-All-PD


title: EV hepatocytes, rep2

status: Public on Jul 29 2022

first: Takeshi

last: Katsuda

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

data_processing:
Reads were aligned to the mouse genome (mm10) using Bowtie2 with options ‘--very-sensitive -X 1000 --dovetail -1’
duplicates were removed using Picard (http://broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: The bigwig files (.bw) are generated by aligning the sequence tags to mm10 by bowtie2 with default parameters and converting the bam files to bigwig using bamCoverage.
Supplementary files format and content: Peak calling was performed using MACS2 with the options ‘--nomodel --extsize 200 --shift -100’.

source_name: Liver

extract_protocol:
Nuclei were isolated from sorted cells using a solution of 10 mM Tris-HCl pH 7.4/10 mM NaCl/3 mM MgCl2/0.1% IGEPAL CA-630.
Immediately following isolation, the transposition reaction was conducted using Tn5 transposase and TD buffer (Illumina) for 30 minutes at 37 °C.
Transposed DNA fragments were purified using a Qiagen MinElute Kit, barcoded, and PCR amplified for xx cycles using NEBNext High Fidelity 2x PCR master mix (New England Biolabs), and then the libraries were purified with AMPure XP beads.

treatment_protocol: AAV8-TBG-Cre (EV) or AAV8-TBG-HA-Sox4-P2A-Cre (Sox4OE) were retro-orbitally injected. 4 days post injection, hepatocytes were harvsted.

value: Liver

value: Hepatocyte

value: WT

value: AAV8-TBG-Cre injected; harvested 4 days post injection


title: EV hepatocytes, rep3


title: EV hepatocytes, rep1


title: V02-4


title: CAR T cells in blood of Pt129 on day 7: TCR

status: Public on Jul 28 2022

city: Stanford

first: Zinaida

last: Good

state: California

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute, Department of Biomedical Data Science

institute: Stanford University School of Medicine

description:
pt129-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt129-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt129-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt129-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt129-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds

data_processing:
Cell Ranger count or vdj pipelines for scRNA-seq and CITE-seq, or scTCR-seq (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: An h5 file containing Cell Ranger count pipeline output for filtered cell-feature data: columns contain UMI counts across cells; rows contain features (genes for scRNA-seq or proteins for CITE-seq).
Supplementary files format and content: An HTML file containing Cell Ranger alignment summary statistics.
Supplementary files format and content: A CSV file containing Cell Ranger vdj pipeline output for all or filtered alpha-beta TCR clonotype data: columns contain cells; rows contain TCR clonotype parameters quantified.
Supplementary files format and content: seurat-day7-car-t.rds: Seurat object for all patients.
Library strategy: scTCR-seq

source_name: Live circulating CAR+ T cells

extract_protocol:
Droplet-based single-cell sequencing on 10X Genomics Chromium platform.
10X Genomics Single Cell 5' kit.

tag: patient id

tag: diagnosis

value: Large B-cell lymphoma (LBCL)

tag: time after axi-cel

value: day 7

value: CAR+ T cells

tag: library type

value: scTCR-seq


title: CAR T cells in blood of Pt129 on day 7

description:
pt129-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt129-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt129-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds

data_processing:
Cell Ranger count or vdj pipelines for scRNA-seq and CITE-seq, or scTCR-seq (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: An h5 file containing Cell Ranger count pipeline output for filtered cell-feature data: columns contain UMI counts across cells; rows contain features (genes for scRNA-seq or proteins for CITE-seq).
Supplementary files format and content: An HTML file containing Cell Ranger alignment summary statistics.
Supplementary files format and content: A CSV file containing Cell Ranger vdj pipeline output for all or filtered alpha-beta TCR clonotype data: columns contain cells; rows contain TCR clonotype parameters quantified.
Supplementary files format and content: seurat-day7-car-t.rds: Seurat object for all patients.

value: scRNA-seq and CITE-seq


title: CAR T cells in blood of Pt125 on day 7

description:
pt125-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt125-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt125-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt125 on day 7: TCR

description:
pt125-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt125-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt125-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt125-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt125-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt116 on day 7

description:
pt116-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt116-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt116-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt116 on day 7: TCR

description:
pt116-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt116-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt116-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt116-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt116-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt110 on day 7

description:
pt110-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt110-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt110-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt110 on day 7: TCR

description:
pt110-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt110-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt110-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt110-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt110-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: 293T-VEGFA-All-PD_rep1

tag: tissue

value: Human embryonic kidney

tag: cell line


title: V01-4

value: non-small cell lung cancer (NSCLC)


title: CAR T cells in blood of Pt263 on day 7: TCR

description:
pt263-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt263-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt263-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt263-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt263-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds

tag: cell type


title: CAR T cells in blood of Pt282 on day 7: TCR

description:
pt282-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt282-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt282-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt282-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt282-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt253 on day 7

description:
pt253-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt253-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt253-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt276 on day 7

description:
pt276-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt276-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt276-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt282 on day 7

description:
pt282-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt282-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt282-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: V01-3


title: CAR T cells in blood of Pt276 on day 7: TCR

description:
pt276-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt276-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt276-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt276-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt276-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt245 on day 7: TCR

description:
pt245-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt245-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt245-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt245-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt245-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt263 on day 7

description:
pt263-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt263-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt263-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: V01-1

description: The file GSE119911_mixed_sample_phenotypes.xlsx includes the tumor vs  non-tumor status of each cell ID and barcode.

value: tumor tissue and adjacent normal tissue


title: CAR T cells in blood of Pt245 on day 7

description:
pt245-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt245-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt245-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: TREG HA CAR - rep5

city: Memphis

first: Tian

last: Mi

state: TN

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
Sequencing reads were aligned to the hg38 genome using the BSMAP v.2.90 software
CpG methylation levels were determined by methratio.py script from BSMAP
Assembly: hg38
Supplementary files format and content: txt files with columns of chr, loc, cov, meth

source_name: HA-CAR T cells

growth_protocol: Naïve Tregs were flow-sorted as live CD4+CD127loCD25hi CD45RA+CD62Lhi cells and naïve CD4+ Tconvs cells were sorted as live CD4+ CD45RA+CD62Lhi. Cells were resuspended at 1x10^6 cells/ml in XH media (X-Vivo 15 (Lonza) with 5% human serum, 1% penicillin/streptavidin, 1% glutamine and phenol red) containing 300U IL2/ml (Proleukin) and were stimulated with a 3 bead : 1 cell ratio of Dynabead. On day 2 and 3, cells were transduced with a retrovirus containing a non-tonic signaling CAR (non-TS-CAR; CD19) or a TS one (HA CAR). At day 7, cells were collected and live CAR+ were flow sorted  and resuspended at 0.5x10^6 cells/ml in XH media containing 300U IL2/ml for an addition 3 days for conventional T cells and 4 days for Tregs. Then the beads were magnetically removed and cells were rested overnight. DNA was then extracted for DNA methylation.

extract_protocol:
DNA was extracted from the sorted cells by using a DNA-extraction kit (Qiagen) and then bisulfite treated using an EZ DNA methylation kit (Zymo Research).
Bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicentre) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina HiSeq 4000 and NovaSeq 6000 systems

value: CD4+ TREG cells

tag: treatment

value: HA CAR


title: 293T-VEGFA-All-Input_rep1

value: VEGFA-All-Input


title: TREG HA CAR - rep4

treatment_protocol: retrovirus containing a non-tonic signaling CAR (non-TS-CAR; CD19) or a TS one (HA CAR).


title: TREG HA CAR - rep2


title: TREG HA CAR - rep3


title: ChIP-seq with anti Gfi1 antibody

city: Montréal

first: Tarik

last: Moroy

state: Québec

address: 110 Avenue des Pins

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

data_processing:
Quality control: FastQC v0.11.5 and MultiQC v1.6
Trimming: Trimmomatic v0.36
Alignment (ChIP-Seq, ATAC-Seq): BWA v0.7.17
Peak calling (ChIP-Seq, ATAC-Seq): Macs2 v2.1.0
Pseudoalignment: Kallisto v0.44.0
Assembly: mm10
Supplementary files format and content: Peak calling results in narrowPeak and broadPeak format.

source_name: bone marrow

extract_protocol:
RNA was extracted using MagMax-96 Total RNA Isolation kit (Ambion) and quality-checked with RNA 6000 Pico kit (Agilent). RNA-seq libraries were prepared from the RNA extracts using the Illumina TruSeq Stranded mRNA Kit according to the manufacturer’s instructions, and sequenced using the TruSeq PE Clusterkit v3-cBot-HS on an Illumina HiSEq 2000 system. Sequencing reads were aligned to the mm10 genome using Tophat v2.0.10. Reads were processed with Samtools and then mapped to Ensembl transcripts using HTSeq. Differential expression was tested using the DESeq R package (Anders & Huber, 2010)(R Core Team 2015, http://www.r-project.org/). A genome coverage file was generated and scaled to RPM using Bedtools.
ChIPs were performed on 1-20x106 sorted cells. The cells were cross-linked with 1.5mM EGS for 20 minutes and 1% formaldehyde for 8 minutes before quenching with 125mM glycine. Cells were lysed in lysis buffer and sonicated using a Covaris E220 to generate 200-600bp fragments (Lee, Johnstone, & Young, 2006). Samples were immuno-precipitated with 2-5 µg of either anti- GFI1 (AF3540, R&D systems), anti-H3K4me1 (ab8895, Abcam), anti-H3K4me2 (ab11946; Abcam), anti-H3K4me3 (ab8580; Abcam) or anti-H3K9me2 (ab1220; Abcam). Libraries were generated according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads. External datasets were obtained in the form of .bed files of peaks and .wig visualization tracks, aligned to the mm9 build, with the exception of LSD1, which only included the .bed peak file.

tag: strain

value: GMP

tag: age

value: adult 6-12 weeks

value: wild type

tag: antibody

value: anti Gfi1


title: TREG HA CAR - rep1


title: TREG CD19 CAR - rep4

source_name: CD19-CAR T cells

value: CD19 CAR


title: TREG CD19 CAR - rep3


title: TREG CD19 CAR - rep5


title: TREG CD19 CAR - rep2


title: CAR T cells in blood of Pt253 on day 7: TCR

description:
pt253-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt253-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt253-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt253-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt253-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: TREG CD19 CAR - rep1


title: TCONV CD19 CAR - rep1

value: CD4+ TCONV cells


title: TCONV HA CAR - rep2


title: TCONV CD19 CAR - rep3


title: TCONV HA CAR - rep4


title: TCONV HA CAR - rep3


title: TCONV CD19 CAR - rep2