title: H3K4me3 PLAC-seq on embryonic 15.5 day mouse forebrain, biological replicate 2

data_processing:
The PLAC-seq data was processed using MAPS pipeline (https://github.com/ijuric/MAPS). In brief, the raw sequencing reads were mapped using BWA-MEM to mm10 reference genome in single-end mode for each of the two ends separately. The independently mapped ends were then paired-up and the read pairs were kept if they satisfy certain criteria. Then “samtools rmdup” is used to remove PCR duplicates.     We then partitioned the genome into 10Kb bins, and counted the number of paired-end reads in each 10Kb bin pair. Next, we defined the “AND”, “XOR” and “NOT” sets as 10Kb bin pairs where both two ends, only one end, and neither end contain replicated H3K4me3 ChIP-seq peaks from the corresponding tissue, respectively. We only kept the bin pairs in “AND” and “XOR” sets with >=1 counts for the downstream analysis of interaction calling. We assumed that the counts in the “AND” and “XOR” sets follow the positive Poisson distribution, and fitted a positive Poisson regression to adjust for systematic biases from effective fragment size, GC content, mappability, ChIP enrichment level (measured by the number of short-range [<1Kb] reads within each 10Kb bin), and 1D genomic distance. Next, we defined the normalized contact frequency as the ratio between the observed contact frequency and the expected contact frequency obtained from the positive Poisson regression. Finally, we identified long-range significant chromatin interactions at 10Kb resolution in autosomal chromosomes between 1D genomic distance range of 20Kb ~ 1Mb, such that these 10Kb bin pairs satisfied: (1) FDR<1% and (2) normalized contact frequency >=2. The significant interactions in the “AND” set are referred as “Promoter-to-Promoter” interactions and the ones in the “XOR” set are referred as “Promoter-to-Non-promoter” interactions.    The PLAC-seq data from the two biological replicates were combined by summing up the read counts in 10Kb bin pairs in the “AND” and “XOR” sets. To account for the variable sequencing depths, we further down-sampled above combined data. Specifically, for each of 19 autosomal chromosomes, we counted the total number of paired-end reads in the “AND” and “XOR” sets across 12 tissues. We identified the tissue with the minimal number of reads, and randomly down-sampled the paired-end reads in the “AND” and “XOR” sets in the remaining 11 tissues to match that minimal number. After such down-sampling procedure, we ensured that for each chromosome, the total number of paired-end reads in the “AND” and “XOR” sets are the same across 12 tissues. MAPS was applied to the combined, down-sampled data of each tissue as described above to identify long-range interactions.    For visualization, the deduped, valid read pairs were used to generate the raw contact matrix (without normalization) in the .hic format using Juicer.
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.     Peaks were called using MACS2 with regular peak calling at P threshold of 0.01. Such relaxed peak sets were generated for each biological/technical replicate, and also for the pooled replicates. Peaks from the pooled replicate set were defined as the replicated peak set if they overlapped (at least 1 bp) the peaks from both biological/technical replicates.
“combined_downsampled.hic” files were generated via Juicebox after combining the two biological replicates from the same tissue and further down-sampled to make all 12 tissues have the same number of usable reads.   “combined_downsampled_MAPS_call.bedpe” files were the long-range interactions called using combined, down-sampled datasets of each tissue.  “rep1/2_MAPS_call.bedpe” files were the long-range interactions called from each biological replicate.  A detailed description for each column in “MAPS_call.bedpe” files can be found at https://github.com/ijuric/MAPS.
Assembly: mm10
Library strategy: PLAC-Seq

extract_protocol:
In brief, 30-50mg tissues were dissociated, lysed and then digested 2 hours at 37oC using 100 U of MboI followed by biotin fill-in and proximity ligation at room temperature for 4 hours. Then the nuclei were further sonicated and immunoprecipitated against the antibodies. After immunoprecipitation, reverse crosslink was performed overnight at 65 oC after adding proteinase K to extract DNA.
DNA fragments containing ligation junctions were enriched with streptavidin beads followed by on-beads end repair, A-tail adding, adapter ligation and PCR amplification.

value: H3K4me3 (Millipore, 04-745)


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse craniofacial prominence, biological replicate 2

status: Public on Sep 02 2024

type: SRA

city: Cleveland

first: Ming

last: Hu

state: OH

address: 9500 Euclid Avenue

country: USA

institute: Cleveland Clinic

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: craniofacial prominence

tag: tissue

value: craniofacial prominence

tag: developmental stage

value: embryonic 12.5 day

tag: chip antibody


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse hindbrain, biological replicate 2

source_name: hindbrain

value: hindbrain


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse hindbrain, biological replicate 1


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse craniofacial prominence, biological replicate 1


title: TNNMH, rep 3

city: St. Louis

first: Jarret

last: Glasscock

state: MO

address: 4044 Clayton Ave

institute: Cofactor Genomics

description: TNNMH

library_source: transcriptomic

data_processing:
Fastq files were preprocessed with umitools version 1.1.1 to remove UMIs from the 5' end of each read.  Trim_galore/cutadapt version 0.4.1 was used to remove adapter sequences as well as reads with PHRED quality scores less than 20 and reads that were less than 20 basepairs.
The trimmed reads were aligned to the human genome GRCh38 with STAR version 2.5.2a using the two-pass method as previously described.  Duplicate alignments were removed with umitools version 1.1.1.
Read counts were generated using htseq-count version 0.9.1 and annotation from Gencode version 22.
Assembly: GRCh38
Supplementary files format and content: RNA-seq counts, tab separated file

molecule: total RNA

organism: Homo sapiens

source_name: R/M HNSCC

extract_protocol:
RNA was extracted using the RNAstorm™ FFPE RNA Extraction Kit (Biotium, Fremont, CA) according to the manufacturer’s instructions. RNA quantity was assessed with the High Sensitivity RNA Qubit assay (Thermo Fisher Scientific, Waltham, MA). RNA quality was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).
RNAseq libraries for OncoPrism-HNSCC ICI response prediction were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Inc., Greenland, NH), following the manufacturer’s instructions. Library RNA input was 40 ng total RNA for all samples unless otherwise specified. UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, Inc., Greenland, NH) replaced Second Strand Synthesis Mix 1 in the workflow. All samples were processed with two OncoPrism-HNSCC positive controls and a No Template Control. The positive (high or medium scoring) controls were RNA extracted from RM-HNSCC samples as described above. Final libraries were sequenced to a minimum depth of 10 million single-end 75 base pair reads on a NextSeq500 (Illumina, San Diego, CA), following the manufacturer’s protocols.

value: R/M HNSCC

tag: oncoprism score

tag: oncoprism group

value: High

tag: experiment type

value: Reproducibility

tag: experiment quantity


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse hindbrain, biological replicate 2

description: The library was sequenced twice on different machines with both single and paired-end reads.

data_processing:
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
Assembly: mm10

extract_protocol:
~30 mg fixed tissues were thawed on ice and the nuclei preparation was performed using truChIP® Chromatin Shearing Kit (Covaris) following the manufacturer’s instruction. The lysed nuclei were sheared using Covaris M220 with following setting: Setting: power, 75 W; duty factor, 8%; cycle per burst, 200; time, 12 min; temp, 7 °C. The sheared chromatins were cleared by centrifugation at 15,000×g for 12 min. The supernatant was collected and incubated with M-280 sheep anti-rabbit magnetic beads (Thermo Fisher, 11203D) for 3 hours at 4°C with slow rotation for preclearing. ~5% of precleared cell lysate was saved as input control after the incubation was done. The rest of precleared lysate was mixed M-280 sheep anti-rabbit magnetic beads that coupled with 0.9 μg of CTCF antibody (3418, Cell Signaling) and rotate at 4°C for 16 hours. On the next day, the beads were collected using magnetic stand and the supernatant was discarded. The beads are then washed with RIPA buffer three times, high-salt RIPA buffer (10 mM Tris, pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) twice, LiCl buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 0.1% sodium deoxycholate) once, TE buffer (10 mM Tris, pH 8.0, 0.1 mM EDTA) twice. Washed beads were treated with 10 μg Rnase A in extraction buffer (10 mM Tris, pH 8.0, 350 mM NaCl, 0.1 mM EDTA, 1% SDS) for 1 hours at 37°C, followed by reverse crosslinking in the presence of proteinase K (20 μg) overnight at 65°C. After reverse crosslinking the DNA was purified and quantified. The input control DNA was reverse crosslinked and purified in the same way as ChIPed DNA as described above.
Library preparation was performed using QIAseq Ultralow Input Library Kit (Qiagen) starting from 10–100 ng ChIPed DNA or input DNA. After PCR the amplified libraries were purified with SPRI Beads to extract fragments between 200-600bp for sequencing.


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse hindbrain, biological replicate 1


title: TNNMH, rep 2

description: TNNMH


title: PB6SN, rep 2


title: VLM8R, rep 3


title: VLM8R, rep 1


title: VLM8R, rep 2


title: Y292A, rep 1

value: Medium


title: Control ChIP-seq (input DNA) on embryonic 15.5 day mouse forebrain, biological replicate 1

source_name: forebrain

value: forebrain

value: embryonic 15.5 day


title: H3K4me3 PLAC-seq on embryonic 15.5 day mouse forebrain, biological replicate 1


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse forebrain, biological replicate 2


title: PB6SN, rep 3


title: Y292A, rep 2

value: Low


title: TNNMH, rep 1

description: TNNMH


title: PB6SN, rep 1


title: RDKM3, rep 3


title: CTCF ChIP-seq on embryonic 12.5 day mouse hindbrain, biological replicate 1

data_processing:
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
bigwig file represents the signal track for fold change over control from each replicate. Peak files are in narrowPeak format. Replicated peaks are the set of peak calls from the pooled replicates that are either observed in both biological/technical replicates, or are observed in two pseudoreplicates (https://www.encodeproject.org/chip-seq/histone/).
Assembly: mm10

value: CTCF (Cell Signaling, 3418, lot 3&4)


title: CTCF ChIP-seq on embryonic 12.5 day mouse hindbrain, biological replicate 2


title: R69R3, rep 2


title: OODZN, rep 1

description: OODZN


title: RDKM3, rep 2


title: 0USCU, rep 3


title: Y292A, rep 3


title: 0USCU, rep 1


title: R69R3, rep 1


title: OODZN, rep 2

description: OODZN


title: RDKM3, rep 1


title: JI4XZ, rep 3


title: GU1HL, rep 2


title: R69R3, rep 3


title: JI4XZ, rep 1


title: GM9DV, rep 2


title: FBZXI, rep 3

description: FBZXI


title: GU1HL, rep 3


title: 0USCU, rep 2


title: BO62V, rep 3


title: BO62V, rep 2


title: GU1HL, rep 1


title: GM9DV, rep 3


title: FBZXI, rep 1

description: FBZXI


title: GM9DV, rep 1


title: OODZN, rep 3

description: OODZN


title: FBZXI, rep 2

description: FBZXI


title: B3VRM, rep 1


title: JI4XZ, rep 2


title: B3VRM, rep 2


title: BO62V, rep 1


title: 12CU1, 17.0 % DV200, incubation time 4 min, rep C


title: 12CU1, 17.0 % DV200, incubation time 4 min, rep A


title: 12CU1, 13.0 % DV200, incubation time 5 min, rep B


title: 12CU1, 17.0 % DV200, incubation time 4 min, rep B


title: 12CU1, 13.0 % DV200, incubation time 5 min, rep C


title: 12CU1, 23.0 % DV200, incubation time 3 min, rep B


title: 12CU1, 23.0 % DV200, incubation time 3 min, rep A


title: B3VRM, rep 3


title: 12CU1, 23.0 % DV200, incubation time 3 min, rep C


title: 12CU1, 33.0 % DV200, incubation time 2 min, rep A


title: 12CU1, 33.0 % DV200, incubation time 2 min, rep B


title: 12CU1, 60.0 % DV200, incubation time 0 min, rep B


title: 12CU1, 60.0 % DV200, incubation time 0 min, rep C


title: 12CU1, 46.0 % DV200, incubation time 1 min, rep A


title: RNA-11, 29.0 % DV200, incubation time 4 min, rep 39


title: RNA-11, 35.0 % DV200, incubation time 3 min, rep 38


title: RNA-11, 22.0 % DV200, incubation time 5 min, rep 41


title: RNA-11, 43.0 % DV200, incubation time 2 min, rep 36


title: RNA-11, 29.0 % DV200, incubation time 4 min, rep 40


title: RNA-11, 22.0 % DV200, incubation time 5 min, rep 42


title: 12CU1, 13.0 % DV200, incubation time 5 min, rep A


title: 12CU1, 60.0 % DV200, incubation time 0 min, rep A


title: RNA-11, 35.0 % DV200, incubation time 3 min, rep 37


title: RNA-11, 57.0 % DV200, incubation time 1 min, rep 33


title: RNA-11, 76.0 % DV200, incubation time 0 min, rep 32


title: RNA-11, 57.0 % DV200, incubation time 1 min, rep 34


title: RNA-11, 43.0 % DV200, incubation time 2 min, rep 35


title: 12CU1, 33.0 % DV200, incubation time 2 min, rep C


title: RNA-11, 76.0 % DV200, incubation time 0 min, rep 31


title: RNA-08, 24.0 % DV200, incubation time 5 min, rep 26


title: RNA-08, 35.0 % DV200, incubation time 3 min, rep 22


title: RNA-08, 35.0 % DV200, incubation time 3 min, rep 23


title: 12CU1, 46.0 % DV200, incubation time 1 min, rep C


title: RNA-08, 46.0 % DV200, incubation time 2 min, rep 21


title: RNA-08, 27.0 % DV200, incubation time 4 min, rep 24


title: RNA-08, 24.0 % DV200, incubation time 5 min, rep 27


title: 12CU1, 46.0 % DV200, incubation time 1 min, rep B


title: RNA-08, 54.0 % DV200, incubation time 1 min, rep 18


title: RNA-08, 54.0 % DV200, incubation time 1 min, rep 19


title: RNA-08, 46.0 % DV200, incubation time 2 min, rep 20


title: RNA-08, 76.0 % DV200, incubation time 0 min, rep 17


title: RNA-08, 76.0 % DV200, incubation time 0 min, rep 16


title: RNA-02, 12.0 % DV200, incubation time 5 min, rep 12


title: RNA-02, 12.0 % DV200, incubation time 5 min, rep 11


title: RNA-02, 26.0 % DV200, incubation time 3 min, rep 7


title: RNA-02, 18.0 % DV200, incubation time 4 min, rep 10


title: RNA-02, 26.0 % DV200, incubation time 3 min, rep 8


title: RNA-02, 18.0 % DV200, incubation time 4 min, rep 9


title: RNA-08, 27.0 % DV200, incubation time 4 min, rep 25


title: RNA-02, 35.0 % DV200, incubation time 2 min, rep 5


title: RNA-02, 35.0 % DV200, incubation time 2 min, rep 6


title: KU09D, 0 % gDNA, rep R1

value: gDNA %


title: KU09D, 0 % gDNA, rep R3


title: KU09D, 5 % gDNA, rep R2


title: RNA-02, 62.0 % DV200, incubation time 0 min, rep 2


title: KU09D, 0 % gDNA, rep R2


title: KU09D, 5 % gDNA, rep R3


title: RNA-02, 48.0 % DV200, incubation time 1 min, rep 4


title: RNA-02, 62.0 % DV200, incubation time 0 min, rep 1


title: KU09D, 20 % gDNA, rep R2


title: KU09D, 30 % gDNA, rep R2


title: KU09D, 20 % gDNA, rep R3


title: KU09D, 30 % gDNA, rep R3


title: KU09D, 5 % gDNA, rep R1


title: KU09D, 30 % gDNA, rep R1


title: KU09D, 20 % gDNA, rep R1


title: KU09D, 10 % gDNA, rep R1


title: OCYVO, 0 % gDNA, rep R2

description: OCYVO


title: OCYVO, 0 % gDNA, rep R3

description: OCYVO


title: KU09D, 10 % gDNA, rep R2


title: RNA-02, 48.0 % DV200, incubation time 1 min, rep 3


title: OCYVO, 30 % gDNA, rep R2

description: OCYVO


title: OCYVO, 5 % gDNA, rep R2

description: OCYVO


title: OCYVO, 30 % gDNA, rep R3

description: OCYVO


title: OCYVO, 30 % gDNA, rep R1

description: OCYVO


title: OCYVO, 5 % gDNA, rep R3

description: OCYVO


title: OCYVO, 20 % gDNA, rep R1

description: OCYVO


title: OCYVO, 20 % gDNA, rep R2

description: OCYVO


title: OCYVO, 20 % gDNA, rep R3

description: OCYVO


title: OCYVO, 10 % gDNA, rep R1

description: OCYVO


title: LNRMW, 0 % gDNA, rep R3

description: LNRMW


title: OCYVO, 10 % gDNA, rep R3

description: OCYVO


title: LNRMW, 5 % gDNA, rep R3

description: LNRMW


title: LNRMW, 0 % gDNA, rep R1

description: LNRMW


title: LNRMW, 5 % gDNA, rep R1

description: LNRMW


title: LNRMW, 5 % gDNA, rep R2

description: LNRMW


title: LNRMW, 30 % gDNA, rep R1

description: LNRMW


title: OCYVO, 10 % gDNA, rep R2

description: OCYVO


title: LNRMW, 30 % gDNA, rep R3

description: LNRMW


title: KU09D, 10 % gDNA, rep R3


title: LNRMW, 0 % gDNA, rep R2

description: LNRMW


title: OCYVO, 0 % gDNA, rep R1

description: OCYVO


title: LNRMW, 20 % gDNA, rep R2

description: LNRMW


title: LNRMW, 30 % gDNA, rep R2

description: LNRMW


title: LNRMW, 20 % gDNA, rep R1

description: LNRMW


title: LNRMW, 20 % gDNA, rep R3

description: LNRMW


title: LNRMW, 10 % gDNA, rep R1

description: LNRMW


title: GU1HL, 0 % gDNA, rep R1


title: LNRMW, 10 % gDNA, rep R3

description: LNRMW


title: LNRMW, 10 % gDNA, rep R2

description: LNRMW


title: GU1HL, 5 % gDNA, rep R2


title: GU1HL, 0 % gDNA, rep R2


title: GU1HL, 5 % gDNA, rep R3


title: GU1HL, 5 % gDNA, rep R1


title: GU1HL, 0 % gDNA, rep R3


title: OCYVO, 5 % gDNA, rep R1

description: OCYVO


title: GU1HL, 30 % gDNA, rep R1


title: GU1HL, 30 % gDNA, rep R2


title: GU1HL, 20 % gDNA, rep R2


title: GU1HL, 30 % gDNA, rep R3


title: R69R3, 80 ng RNA input, rep C

value: RNA input (ng)


title: GU1HL, 10 % gDNA, rep R2


title: GU1HL, 10 % gDNA, rep R3


title: R69R3, 60 ng RNA input, rep B


title: GU1HL, 20 % gDNA, rep R3


title: R69R3, 40 ng RNA input, rep A


title: R69R3, 40 ng RNA input, rep B


title: GU1HL, 10 % gDNA, rep R1


title: R69R3, 80 ng RNA input, rep A


title: R69R3, 40 ng RNA input, rep C


title: GU1HL, 20 % gDNA, rep R1


title: R69R3, 60 ng RNA input, rep C


title: R69R3, 80 ng RNA input, rep B


title: R69R3, 30 ng RNA input, rep B


title: R69R3, 30 ng RNA input, rep C


title: R69R3, 20 ng RNA input, rep A


title: R69R3, 30 ng RNA input, rep A


title: R69R3, 20 ng RNA input, rep C


title: R69R3, 10 ng RNA input, rep B


title: R69R3, 10 ng RNA input, rep C


title: GU1HL, 80 ng RNA input, rep C


title: Pam3sck4_3h_3

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to mm10 using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2CPM (count per million) values for each sample

source_name: bone-marrow-derived macrophage

growth_protocol: BMDMs were isolated from 7 week-old mice, and red blood cells were lysed with ACK lysis buffer. The cells were cultured in DMEM containing 10% FBS and 50 ng/ ml GM-CSF. The medium was changed with complete medium every 2 days.

extract_protocol:
RNA-seq : Total RNA was isolated from cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
RNA-seq : TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
RNA-seq : The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: BMDMs of 2x106 cells/well in 2ml DMEM containing 10% FBS were treated with 0.5mm AmTARS or 10ng/ml Pam3csk4 for 1h and 3h.

tag: cell type

value: bone-marrow-derived macrophage

tag: molecular subtype

value: total RNA

tag: origin


title: R69R3, 60 ng RNA input, rep A


title: Pam3sck4_3h_2


title: GU1HL, 80 ng RNA input, rep A


title: Pam3sck4_1h_1


title: GU1HL, 60 ng RNA input, rep C


title: GU1HL, 80 ng RNA input, rep B


title: GU1HL, 60 ng RNA input, rep B


title: Control_3


title: Pam3sck4_1h_3


title: AmTARS_1h_2


title: AmTARS_3h_1


title: GU1HL, 60 ng RNA input, rep A


title: Control_2


title: GU1HL, 40 ng RNA input, rep C


title: GU1HL, 30 ng RNA input, rep B


title: AmTARS_1h_3


title: R69R3, 20 ng RNA input, rep B


title: GU1HL, 40 ng RNA input, rep A


title: R69R3, 10 ng RNA input, rep A


title: GU1HL, 30 ng RNA input, rep C


title: GU1HL, 20 ng RNA input, rep C


title: Genomic DNA from H3 K27M DMG 24

type: genomic

city: Regensburg

first: Annika

middle: K

last: Wefers

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

country: Germany

institute: Regensburg University Hospital

description: DMG 24

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC BeadChip using the standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing:
Statistical analysis was performed using the minfi package version 1.46.0 with the statistical programming language R version 4.3.0
Processed data contains: Average beta-values after combining arrays and normalization using the Noob method

label: Cy5 and Cy3

source_name: H3 K27M DMG 24

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the RSC FFPE Plus DNA Kit (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean and Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

tag: localisation

value: Thalamus

tag: Sex

value: f

tag: age

tag: os [months]

tag: material

value: FROZEN

tag: classification result v11b4

tag: classification score


title: Genomic DNA from H3 K27M DMG 25

description: DMG 25

source_name: H3 K27M DMG 25

value: FFPE


title: Genomic DNA from H3 K27M DMG 26

description: DMG 26

source_name: H3 K27M DMG 26

value: m

tag: OS status


title: GU1HL, 30 ng RNA input, rep A

tag: tissue

value: R/M HNSCC


title: GU1HL, 20 ng RNA input, rep B

value: High


title: Genomic DNA from H3 K27M DMG 23

description: DMG 23

source_name: H3 K27M DMG 23


title: Genomic DNA from H3 K27M DMG 27

description: DMG 27

source_name: H3 K27M DMG 27


title: GU1HL, 20 ng RNA input, rep A


title: GU1HL, 10 ng RNA input, rep C


title: Genomic DNA from H3 K27M DMG 21

description: DMG 21

source_name: H3 K27M DMG 21

value: Pons


title: Genomic DNA from H3 K27M DMG 22

description: DMG 22

source_name: H3 K27M DMG 22


title: AmTARS_3h_3


title: GU1HL, 10 ng RNA input, rep A


title: Genomic DNA from H3 K27M DMG 28

description: DMG 28

source_name: H3 K27M DMG 28


title: GU1HL, 40 ng RNA input, rep B


title: VA8LQ, 80 ng RNA input, rep C


title: Genomic DNA from H3 K27M DMG 20

description: DMG 20

source_name: H3 K27M DMG 20


title: VA8LQ, 80 ng RNA input, rep B


title: Genomic DNA from H3 K27M DMG 18

description: DMG 18

source_name: H3 K27M DMG 18


title: Genomic DNA from H3 K27M DMG 17

description: DMG 17

source_name: H3 K27M DMG 17


title: VA8LQ, 60 ng RNA input, rep C


title: Genomic DNA from H3 K27M DMG 16

description: DMG 16

source_name: H3 K27M DMG 16


title: VA8LQ, 80 ng RNA input, rep A


title: Genomic DNA from H3 K27M DMG 15

description: DMG 15

source_name: H3 K27M DMG 15


title: VA8LQ, 60 ng RNA input, rep B


title: VA8LQ, 60 ng RNA input, rep A


title: Genomic DNA from H3 K27M DMG 14

description: DMG 14

source_name: H3 K27M DMG 14

value: Sella


title: Genomic DNA from H3 K27M DMG 13

description: DMG 13

source_name: H3 K27M DMG 13

value: Spinal cord


title: VA8LQ, 40 ng RNA input, rep B

source_name: R/M HNSCC


title: Genomic DNA from H3 K27M DMG 11

description: DMG 11

source_name: H3 K27M DMG 11


title: VA8LQ, 40 ng RNA input, rep A


title: GU1HL, 10 ng RNA input, rep B


title: VA8LQ, 30 ng RNA input, rep B


title: Genomic DNA from H3 K27M DMG 10

description: DMG 10

source_name: H3 K27M DMG 10


title: Genomic DNA from H3 K27M DMG 9

description: DMG 09

source_name: H3 K27M DMG 09


title: Genomic DNA from H3 K27M DMG 8

description: DMG 08

source_name: H3 K27M DMG 08


title: VA8LQ, 30 ng RNA input, rep A


title: VA8LQ, 20 ng RNA input, rep C


title: Genomic DNA from H3 K27M DMG 19

description: DMG 19

source_name: H3 K27M DMG 19


title: VA8LQ, 20 ng RNA input, rep B


title: VA8LQ, 20 ng RNA input, rep A


title: Genomic DNA from H3 K27M DMG 7

description: DMG 07

source_name: H3 K27M DMG 07


title: Genomic DNA from H3 K27M DMG 6

description: DMG 06

source_name: H3 K27M DMG 06


title: VA8LQ, 10 ng RNA input, rep C


title: VA8LQ, 10 ng RNA input, rep B


title: Genomic DNA from H3 K27M DMG 4

description: DMG 04

source_name: H3 K27M DMG 04


title: Genomic DNA from H3 K27M DMG 3

description: DMG 03

source_name: H3 K27M DMG 03


title: Genomic DNA from H3 K27M DMG 2

description: DMG 02

source_name: H3 K27M DMG 02


title: 8J361, 80 ng RNA input, rep C

value: Medium


title: VA8LQ, 10 ng RNA input, rep A

value: Low


title: Genomic DNA from H3 K27M DMG 1

description: DMG 01

source_name: H3 K27M DMG 01


title: VA8LQ, 30 ng RNA input, rep C


title: 8J361, 80 ng RNA input, rep B


title: Genomic DNA from H3 K27M DMG 12

description: DMG 12

source_name: H3 K27M DMG 12


title: 8J361, 80 ng RNA input, rep A


title: 8J361, 60 ng RNA input, rep A


title: 8J361, 40 ng RNA input, rep C


title: 8J361, 60 ng RNA input, rep B


title: Genomic DNA from H3 K27M DMG 5

description: DMG 05

source_name: H3 K27M DMG 05


title: 8J361, 40 ng RNA input, rep A


title: 8J361, 40 ng RNA input, rep B


title: 8J361, 30 ng RNA input, rep B


title: 8J361, 30 ng RNA input, rep A


title: 8J361, 20 ng RNA input, rep C


title: 8J361, 30 ng RNA input, rep C


title: SCtrl, Library 2

city: Miami

first: James

middle: S

last: Choi

state: FL

address: 1095 NW 14th Terrace

institute: University of Miami Miller School of Medicine

description:
mCEL-Seq2
svz_mat.mtx
barcodes.tsv
genes.tsv

library_source: transcriptomic single cell

data_processing:
Six libraries with 192 cells each were sequenced per lane on an Illumina HiSeq 3000 sequencing system (pair-end multiplexing run) at a depth of !130,000–200,000 reads per cell.
De-multiplexing of the raw data was performed by running bcl2fastq (version 2.17.1.14.).
Assembly: GRCm39
Supplementary files format and content: svz_mat.mtx contains a sparse matrix in the Matrix Market format for the count matrix for all cells that passed downstream quality control and were used for analysis in the published study.
Supplementary files format and content: genes.tsv contains, in exact order, the gene names for the rows of the count matrix in svz_mat.mtx.
Supplementary files format and content: barcodes.tsv contains, in exact order, the unique cell barcode names for the columns of the count matrix in svz_mat.mtx.

molecule: polyA RNA

source_name: Subventricular zone

growth_protocol: Nestin-CreERT2 mice15 were crossed with R26-yfp mice, resulting in Nestin-CreERT2:R26-yfp mice.

extract_protocol:
Mice were anesthetized with ketamine and xylazine, and transcardially perfused with PBS. Brains were immediately harvested and placed in the dissection solution (0.8% glucose and 15 mM HEPES in HBSS) on ice. The lateral SVZ from the hemisphere ipsilateral to the cortical PT site was microdissected according to published protocols53. The SVZ tissue was digested with papain (Worthington, 1200 units per 5 mice) in PIPES solution [120 mM NaCl, 5 mM KCl, 50 mM PIPES (Sigma-Aldrich), 0.6% glucose, 1× Pen/Strep in water, pH adjusted to 7.6] for 10 min at 37°C, and mechanically dissociated into single cells with fire-polished glass Pasteur pipettes after adding ovomucoid (Worthington, 0.7 mg per 5 mice) and DNase I (Invitrogen,  1,000 units per 5 mice) as described54. Myelin debris was removed by centrifuging in 22% Percoll (Sigma-Aldrich) for 10 min at 4ºC without brakes.
Single-cell RNA sequencing was performed using the mCEL-Seq2 protocol, an automated and miniaturized version of CEL-Seq2 on a mosquito nanoliter-scale liquid-handling robot. Eight libraries with 192 cells each were synthesized.

treatment_protocol: 20 minutes after injection of the photosensitive dye Rose Bengal (Sigma–Aldrich; 10 μl/g body weight, intraperitoneal), a cold light illuminator was positioned stereotaxically to deliver light (150 W) to the cortex (AP, 0 mm; ML, −2.4 mm, according to Paxinos and Watson). The region of interest (4-mm diameter) was illuminated for 4 min, and after the light exposure ended, the wound was sutured.

value: Subventricular zone

value: FACS-sorted

tag: genotype

tag: treatment

value: Control


title: S7d, Library 2

value: 7 days post-PT


title: SCtrl, Library 1


title: S7d, Library 1


title: 8J361, 20 ng RNA input, rep B

tag: oncoprism score

tag: oncoprism group

value: RNA input (ng)


title: S1d, Library 2

value: 1 day post-PT


title: 8J361, 20 ng RNA input, rep A

tag: experiment type

tag: experiment quantity


title: 8J361, 10 ng RNA input, rep B


title: S1d, Library 1

tag: cell type


title: PE patients umbilical cord blood exosomes -rep1

type: RNA

city: Linhai city

first: Xiang

last: Ying

address: No.150 Ximen Road

country: China

institute: Taizhou hospital

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: umbilical cord blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The Exosomes were isolated by ultracentrifugation. The umbilical cord blood and trophoblast conditional medium was centrifugated at 300 x g for 30 min followed by 2000 x g for 0.5 hour, then removed the pellet and centrifugated at 10,000 x g for 0.5 hour. Next, supernatant was centrifugated twice at 100,000 x g for1 hour, 4°C with a SW-41 rotor (Beckman Coulter Ltd),RNA was prepared using the Versagene Blood RNA Purification kit.

value: umbilical cord

tag: disease

value: preeclampsia


title: PE patients umbilical cord blood exosomes-rep2


title: Normal patients umbilical cord blood exosomes -rep1

value: normal


title: Normal patients umbilical cord blood exosomes -rep2


title: 8J361, 60 ng RNA input, rep C


title: Normal patients umbilical cord blood exosomes -rep3


title: PE patients umbilical cord blood exosomes -rep3


title: 8J361, 10 ng RNA input, rep C


title: VA8LQ, 40 ng RNA input, rep D


title: 8J361, 10 ng RNA input, rep A


title: VS8KQ, operator 2, lot B, day 2, rep C

value: Intermediate Precision


title: VS8KQ, operator 2, lot B, day 2, rep A

value: R/M HNSCC


title: THWJ7, operator 2, lot B, day 2, rep B


title: THWJ7, operator 2, lot B, day 2, rep A


title: THWJ7, operator 2, lot B, day 2, rep C


title: S2MX9, operator 2, lot B, day 2, rep C

value: High


title: S2MX9, operator 2, lot B, day 2, rep A


title: S2MX9, operator 2, lot B, day 2, rep B


title: 0USCU, operator 2, lot B, day 2, rep C


title: 0USCU, operator 2, lot B, day 2, rep A


title: VS8KQ, operator 2, lot B, day 2, rep B


title: 0USCU, operator 2, lot B, day 2, rep B


title: VCNJ7, operator 2, lot B, day 2, rep C


title: VCNJ7, operator 2, lot B, day 2, rep A


title: OODZN, operator 2, lot B, day 2, rep C

description: OODZN


title: OODZN, operator 2, lot B, day 2, rep B

description: OODZN


title: OODZN, operator 2, lot B, day 2, rep A

description: OODZN


title: 195NM, operator 2, lot B, day 2, rep C


title: ACHN_YY1, CUT&Tag

city: Wuhan

first: Jie

last: Xiong

address: 185, Donghu road

institute: Wuhan University

data_processing:
Basecalls were performed using fastq Novaseq output.
CUT&Tag reads were trimmed with fastp.
CUT&Tag reads were aligned to the hg38 and mm10 genome using Bowtie2 (v2.4.2).
Peaks were called uing MACS v2.2.7.1 (q-value takes default setting).
BigWig files were obtained by deepTools (v3.5.1).
Assembly: Heatmap and metaplot files were made by plotHeatmap and plotProfile of deepTools (v3.5.1).
Supplementary files format and content: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: ACHN_YY1, CUT&Tag

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
The Cleavage Under Targets and Tagmentation (CUT&Tag) assay was conducted according to the manual instruction of Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro(Vazyme, TD904). ChIP-grade anti-KDM5C antibody (Bethyl, A301-034A) and anti-YY1 (CST, D5D9Z) was used for immunoprecipitation specific bounding to chromatin. Rabbit IgG (ABclonal, AC042) was used as a negative control.
The library was built by TruePrep Index Kit V2 for Illumina(Vazyme, TD202).

tag: cell line

value: ACHN

value: ccRCC

tag: chip antibody

value: KDM5C(Bethyl, A301-034A)


title: patient 32, 3 months post mepolizumab treatment

city: Nottingham

first: Ian

last: Sayers

state: Nottinghamshire

address: Biodiscovery Institute, Science Road, University Park

country: United Kingdom

institute: University of Nottingham

data_processing:
Trimmomatic
Star
Limma
Assembly: GRCh38
Supplementary files format and content: counts matrix

source_name: nasal swab

extract_protocol:
Norgen RNA/DNA purification kit (SKU 48700)
Ilumina v1.5

value: nasal swab

tag: Sex

value: female

tag: responder

value: yes

value: mepolizumab


title: VCNJ7, operator 2, lot B, day 2, rep B

source_name: R/M HNSCC

value: Medium


title: ACHN_KDM5C, CUT&Tag

source_name: ACHN_KDM5C, CUT&Tag


title: ACHN_IgG,CUT&Tag


title: patient 32 baseline


title: 195NM, operator 2, lot B, day 2, rep A


title: VS8KQ, operator 1, lot B, day 2, rep B


title: VS8KQ, operator 1, lot B, day 2, rep C


title: patient 31 baseline

value: no


title: patient 29, 3 months post mepolizumab treatment


title: patient 31, 3 months post mepolizumab treatment


title: VS8KQ, operator 1, lot B, day 2, rep A


title: patient 29 baseline


title: patient 28, 3 months post mepolizumab treatment

value: male


title: patient 27, 3 months post mepolizumab treatment


title: THWJ7, operator 1, lot B, day 2, rep B

value: Low


title: THWJ7, operator 1, lot B, day 2, rep A


title: THWJ7, operator 1, lot B, day 2, rep C


title: genomic DNA from dry core biopsy malignant tissue sample 8

city: Kolkata

first: Amlan

last: Ghosh

state: West Bengal

address: 86/1, College Street

department: Life Sciences

country: India

institute: Presidency University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850k Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: RnBeads

label: Cy3 and Cy5

source_name: needle biopsy

label_protocol: Standard MethylationEPIC array protocol

extract_protocol: genomic DNA was extracted using the phenol-chloroform method according to standard protocol

tag: gender

value: Male

tag: disease state

value: malignant


title: S2MX9, operator 1, lot B, day 2, rep C


title: patient 27 baseline


title: genomic DNA from prostatic fluid sample 4

source_name: prostatic fluid

value: normal


title: genomic DNA from dry core biopsy benign tissue sample 8

value: benign


title: patient 28 baseline


title: S2MX9, operator 1, lot B, day 2, rep A

value: R/M HNSCC

value: Intermediate Precision


title: patient 25, 3 months post mepolizumab treatment


title: patient 26 baseline


title: 195NM, operator 2, lot B, day 2, rep B

value: High


title: genomic DNA from dry core biopsy benign tissue sample 7


title: 0USCU, operator 1, lot B, day 2, rep B


title: patient 25 baseline


title: patient 24, 3 months post mepolizumab treatment


title: VCNJ7, operator 1, lot B, day 2, rep C


title: genomic DNA from dry core biopsy malignant tissue sample 3


title: genomic DNA from dry core biopsy malignant tissue sample 4


title: patient 24 baseline


title: genomic DNA from dry core biopsy benign tissue sample 6


title: VCNJ7, operator 1, lot B, day 2, rep B


title: genomic DNA from dry core biopsy benign tissue sample 2


title: genomic DNA from prostatic fluid sample 3


title: patient 21, 3 months post mepolizumab treatment


title: VCNJ7, operator 1, lot B, day 2, rep A


title: patient 21 baseline


title: genomic DNA from dry core biopsy malignant tissue sample 2


title: patient 20, 3 months post mepolizumab treatment


title: genomic DNA from dry core biopsy benign tissue sample 3


title: 0USCU, operator 1, lot B, day 2, rep C


title: patient 26, 3 months post mepolizumab treatment


title: OODZN, operator 1, lot B, day 2, rep C

description: OODZN


title: genomic DNA from prostatic fluid sample 2


title: OODZN, operator 1, lot B, day 2, rep B

description: OODZN


title: patient 20 baseline


title: OODZN, operator 1, lot B, day 2, rep A

description: OODZN


title: patient 19, 3 months post mepolizumab treatment


title: genomic DNA from dry core biopsy benign tissue sample 5


title: 195NM, operator 1, lot B, day 2, rep C


title: genomic DNA from dry core biopsy malignant tissue sample 5


title: patient 19 baseline


title: genomic DNA from dry core biopsy benign tissue sample 1


title: patient 18, 3 months post mepolizumab treatment


title: 195NM, operator 1, lot B, day 2, rep A


title: genomic DNA from dry core biopsy malignant tissue sample 1


title: patient 18 baseline


title: genomic DNA from dry core biopsy malignant tissue sample 6


title: S2MX9, operator 1, lot B, day 2, rep B


title: VS8KQ, operator 1, lot A, day 2, rep C


title: patient 17, 3 months post mepolizumab treatment


title: patient 17 baseline


title: VS8KQ, operator 1, lot A, day 2, rep A


title: VS8KQ, operator 1, lot A, day 2, rep B


title: patient 15, 3 months post mepolizumab treatment


title: genomic DNA from dry core biopsy benign tissue sample 4


title: THWJ7, operator 1, lot A, day 2, rep B


title: THWJ7, operator 1, lot A, day 2, rep C


title: THWJ7, operator 1, lot A, day 2, rep A


title: patient 14 baseline


title: patient 13, 3 months post mepolizumab treatment


title: S2MX9, operator 1, lot A, day 2, rep B


title: genomic DNA from dry core biopsy malignant tissue sample 7


title: patient 13 baseline


title: patient 14, 3 months post mepolizumab treatment


title: patient 12 baseline


title: 0USCU, operator 1, lot A, day 2, rep C


title: S2MX9, operator 1, lot A, day 2, rep A


title: patient 11 baseline


title: genomic DNA from prostatic fluid sample 1


title: patient 11, 3 months post mepolizumab treatment


title: patient 9, 3 months post mepolizumab treatment


title: VCNJ7, operator 1, lot A, day 2, rep C


title: patient 15 baseline


title: patient 9 baseline


title: VCNJ7, operator 1, lot A, day 2, rep B


title: S2MX9, operator 1, lot A, day 2, rep C


title: VCNJ7, operator 1, lot A, day 2, rep A


title: patient 12, 3 months post mepolizumab treatment


title: OODZN, operator 1, lot A, day 2, rep C

description: OODZN


title: 0USCU, operator 1, lot A, day 2, rep B


title: patient 7 baseline


title: patient 7, 3 months post mepolizumab treatment


title: patient 8 baseline


title: OODZN, operator 1, lot A, day 2, rep B

description: OODZN


title: 0USCU, operator 1, lot A, day 2, rep A


title: OODZN, operator 1, lot A, day 2, rep A

description: OODZN


title: 195NM, operator 1, lot A, day 2, rep A


title: patient 6 baseline


title: patient 6, 3 months post mepolizumab treatment


title: VS8KQ, operator 2, lot A, day 2, rep B


title: patient 5, 3 months post mepolizumab treatment


title: VS8KQ, operator 2, lot A, day 2, rep C


title: THWJ7, operator 2, lot A, day 2, rep C


title: VS8KQ, operator 2, lot A, day 2, rep A


title: patient 5 baseline


title: patient 4, 3 months post mepolizumab treatment


title: THWJ7, operator 2, lot A, day 2, rep B


title: patient 4 baseline


title: patient 8, 3 months post mepolizumab treatment


title: patient 3, 3 months post mepolizumab treatment


title: THWJ7, operator 2, lot A, day 2, rep A


title: patient 2, 3 months post mepolizumab treatment


title: 195NM, operator 1, lot A, day 2, rep B


title: S2MX9, operator 2, lot A, day 2, rep C


title: S2MX9, operator 2, lot A, day 2, rep B


title: patient 2 baseline


title: S2MX9, operator 2, lot A, day 2, rep A


title: patient 1, 3 months post mepolizumab treatment


title: 0USCU, operator 2, lot A, day 2, rep C


title: patient 1 baseline


title: 0USCU, operator 1, lot B, day 2, rep A


title: 0USCU, operator 2, lot A, day 2, rep A


title: b342cor_min60_na

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

data_processing:
scRNA libraries were pooled and sequenced using the NovaSeq 6000 instrument (Illumina) generating 100-bp paired end reads. Sequencing was performed by the Genomics Division of the Iowa Institute of Human Genetics. FASTQ files were generated from base calls with the bcl2fastq software (Illumina), and reads were mapped to the pre-built GRCh38 reference (refdata-gex-GRCh38-2020-A) with Cell Ranger v7.0.0 (10X Genomics) using the ‘count’ function with the following parameters: --expect-cells=8000 --localcores=56. Only cells passing the default Cell Ranger call were analyzed further. All timepoints and controls for the four dissociations performed were integrated using canonical correlation analysis (CCA) in Seurat v4.0.3 (40). Only cells with between 2,000 and 6,000 unique genes (features) were included in the analysis. Only cells with < 10% of reads mapping to mtDNA-encoded genes were included. Counts data were normalized using the NormalizeData function (Seurat) with the following parameters: normalization.method = "LogNormalize", scale.factor = 10000. 2,000 variable features were identified with the FindVariableFeatures function using the vst selection method. Integration anchors were identified using the FindIntegrationAnchors function using 25 dimensions. An assay “Integrated” was generated for the 2000 variable features using the IntegrateData function using 25 dimensions.
30 principal components were identified out of the integrated dataset described above using the RunPCA function (Seurat) (40). Uniform manifold approximation and projection (UMAP) was performed using the RunUMAP function using 25 principal components. Cells were then clustered using Seurat’s FindNeighbors and FindClusters functions with the following parameters: k.param = 20, reduction=”pca”, dims=1:25 (for FindNeighbors); resolution=0.5 (FindClusters) using the original Louvain algorithm as implemented by Seurat. As shown in Supplemental Figure 1, the expression patterns of genes previously shown to be markers of retinal organoid cell types (cite Sridhar et al) were then examined in these clusters and were used to manually annotate each cluster with a cell type. In all calculations of photoreceptor purity, cells contained in clusters which highly express CRX were counted as fate-committed photoreceptors and all other clusters were treated as non-photoreceptor cells. Dot plot of cluster expression was generated using scCustomize (Marsh SE (2021). scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing. https://doi.org/10.5281/zenodo.5706430. RRID:SCR_024675).
Assembly: GRCh38
Supplementary files format and content: For scRNAseq data, raw and log normalzied counts are provided for each library (*_counts.csv and *_normalized.csv, respectively). Counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@counts. Normalized counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@data.

source_name: retinal organoid

growth_protocol: Retinal differentiation was performed as described previously with minor modifications (20, 39). Briefly, iPSCs were cultured on laminin 521 coated plates in E8 medium. Embryoid bodies (EBs) were lifted with ReLeSR (STEMCELL Technologies, Cambridge, MA) and transitioned from E8 to neural induction medium (NIM) over a four-day period. On day 6, NIM was supplemented with 1.5 nM BMP4 (R&D Systems, Minneapolis, MN). On day 7, EBs were adhered to CELLstart coated plates (Thermo Fisher Scientific). BMP4 was gradually transitioned out of the NIM over seven days. On day 16, the media was changed to retinal differentiation medium (RDM). On day 25-30 the entire EB outgrowth was mechanically lifted and transferred to ultra-low attachment flasks in 3D-RDM (RDM plus 10% KnockOut Serum Replacement (KSR)); Thermo Fisher Scientific), 100 µM taurine (Sigma-Aldrich), 1:1000 chemically defined lipid concentrate (Thermo Fisher Scientific), and 1 µM all-trans retinoic acid (until day 100; Sigma-Aldrich). The cells were fed three times per week with 3D-RDM until harvest at Day 160.

extract_protocol:
For each sample tested, approximately 20 organoids were selected for staged partial dissociation along with 10 organoids which were fully dissociated in one step. Both populations were placed in 1.5mL Eppendorf tubes and suspended in 0.5mL of 30U/mL papain (Worthington) and 120U/mL DNase (Worthington) in Earle’s balanced salt solution (EBSS) (Worthington). These tubes were then placed in a rotating incubator at 37°C. Every 20 minutes, the organoids being partially dissociated were allowed to settle, after which the supernatant containing liberated cells were collected. These organoids were washed once with papain and then placed in fresh papain solution for continued dissociation. The cells in the supernatant were passed through a 100 µm filter and counted using a Moxi Go II coulter counter (Orflo). After 60 minutes of total dissociation, any remaining solid aggregates in both the experimental and control tubes were fully dissociated via trituration (i.e., mechanical aspiration and expulsion via a 1mL pipette), counted, pelleted and prepared for scRNA-seq. All samples were pelleted and resuspended in 8µg/mL recombinant albumin (New England Biolabs) in dPBS[-/-] for encapsulation with the Chromium X instrument (10X Genomics). Approximately 8,000 cells were targeted for encapsulation per sample.
Single cells were partitioned and barcoded with the Chromium Controller instrument (10X Genomics) and Single Cell 3' Reagent (v3.1 chemistry) kit (10X Genomics) according to the manufacturer’s specifications with no modification (Rev E). Final libraries were quantified using the Qubit dsDNA HS Assay Kit (Life Technologies) and diluted to 3ng/µL in buffer EB (Qiagen). Library quality was confirmed using the Bioanalyzer High Sensitivity DNA Assay (Agilent) prior to sequencing.

value: retinal organoid

tag: line

value: line 1

tag: dissociation timepoint

tag: organization quality


title: b342cor_min40_na

tag: tissue


title: VCNJ7, operator 2, lot A, day 2, rep A


title: b342cor_full_na

value: full


title: VCNJ7, operator 2, lot A, day 2, rep B


title: b342cor_control_na

value: control


title: VCNJ7, operator 2, lot A, day 2, rep C


title: patient 3 baseline

value: nasal swab

value: female

value: yes

tag: treatment


title: OODZN, operator 2, lot A, day 2, rep B

description: OODZN

tag: oncoprism score


title: b342cor_min20_na


title: OODZN, operator 2, lot A, day 2, rep C

description: OODZN

tag: oncoprism group


title: OODZN, operator 2, lot A, day 2, rep A

description: OODZN

tag: experiment type


title: b1737_min40_well_organized

value: line 3

value: well organized


title: 195NM, operator 2, lot A, day 2, rep C

tag: experiment quantity


title: b1737_min40_poorly_organized

value: poorly organized


title: b1737_min60_well_organized


title: 195NM, operator 2, lot A, day 2, rep B


title: b1737_min60_poorly_organized


title: 0USCU, operator 2, lot A, day 2, rep B

value: Low


title: b1737_min20_well_organized


title: b1737_min20_poorly_organized


title: 195NM, operator 2, lot A, day 2, rep A


title: VS8KQ, operator 2, lot B, day 1, rep B


title: b1737_full_well_organized


title: VS8KQ, operator 2, lot B, day 1, rep A


title: b1737_control_well_organized


title: THWJ7, operator 2, lot B, day 1, rep C


title: b1737_full_poorly_organized


title: b1737_control_poorly_organized


title: THWJ7, operator 2, lot B, day 1, rep A


title: b1427_min20_na

value: line 2


title: S2MX9, operator 2, lot B, day 1, rep C


title: b1427_full_na


title: S2MX9, operator 2, lot B, day 1, rep B


title: b1427_control_na


title: S2MX9, operator 2, lot B, day 1, rep A


title: BrUseq_STK19-KO rescue 12J16h

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description:
averages_min5to100kb_TOP3000Above25kbGenesn1473.txt
averages_min5to100kb_TOP3000Above50kbGenesn787.txt
averages_min5to100kb_TOP3000Above100kbGenesn308.txt

library_source: other

data_processing:
For each BrU-seq sample, a sequencing quality profile was generated using FastQC (Version 0.11.9). Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the Human Genome 38 using STAR (Version 2.7.7a) with genome file GCA_000001405.15_GRCh38 and splice junction file Homo_sapiens.GRCh38.94.correctedContigs.gtf. Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2) (Heinz et al., 2010, Mol Cell). Example genome tracks were generated in IGV (Version 2.4.3). A list of 49,948 gene-coordinates was obtained from the UCSC genome database (https://genome.ucsc.edu/cgi-bin/hgTables) selecting the known Canonical table containing the canonical transcription start sites per gene. To prevent contamination of binding profiles, genes were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). From this, a set of 3,000 actively transcribed genes was selected based on the BrU-seq signal in the first 3 kb of genes in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings. These 3,000 actively transcribed genes were used in downstream analyses, unless stated otherwise. Read-densities around transcription start sites (TSSs) were quantified using the AnnotatePeaks.pl tool of HOMER using default settings and 200bp resolution. Individual datasets were subsequently processed into heatmaps or density profiles using R (Version 4.0.5) and Rstudio (Version 1.1.423). To quantitatively compare different read-density profiles, each profile was normalized to nascent transcript levels, as quantified by 5-EU labeling (RRS protocol), relative to the control in their specific cell type. For example, RPE1 iCas9 cells 3 h after UV irradiation showed 32% nascent transcription relative to mock-treated RPE1 iCas9 cells, so we multiplied the read-density in each 200-bp bin by 0.32.
Assembly: hg38
Supplementary files format and content: averages_min5to100kb_TOP3000Above25kbGenesn1473.txt: tab-delimited text file containing the average read-density at the indicated distance from the TSS of the actively transcribed genes that are >25kb in length (1473 genes of the 3000 selected actively transcribed genes). Counts are normalized to 10M total reads
Supplementary files format and content: averages_min5to100kb_TOP3000Above50kbGenesn787.txt: tab-delimited text file containing the average read-density at the indicated distance from the TSS of the actively transcribed genes that are >50kb in length (787 genes of the 3000 selected actively transcribed genes). Counts are normalized to 10M total reads
Supplementary files format and content: averages_min5to100kb_TOP3000Above100kbGenesn308.txt: tab-delimited text file containing the average read-density at the indicated distance from the TSS of the actively transcribed genes that are >100kb in length (308 genes of the 3000 selected actively transcribed genes). Counts are normalized to 10M total reads
Supplementary files format and content: TagCountAroundTSS_200kbWindow_BrUseq_WT_mock_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of 9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: TagCountAroundTSS_200kbWindow_BrUseq_STK19KO_mock_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of 9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: TagCountAroundTSS_200kbWindow_BrUseq_STK19resc_mock_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of 9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: TagCountAroundTSS_200kbWindow_BrUseq_WT_12J3h_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of 9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: TagCountAroundTSS_200kbWindow_BrUseq_STK19KO_12J3h_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of 9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: TagCountAroundTSS_200kbWindow_BrUseq_STK19resc_12J3h_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of 9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: TagCountAroundTSS_200kbWindow_BrUseq_WT_12J16h_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of 9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: TagCountAroundTSS_200kbWindow_BrUseq_STK19KO_12J16h_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of 9944 non-overlapping genes with a minimal size of 3 kb.
Supplementary files format and content: TagCountAroundTSS_200kbWindow_BrUseq_STK19resc_12J16h_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of 9944 non-overlapping genes with a minimal size of 3 kb.
Library strategy: nascent RNA-seq

molecule: other

source_name: RPE1 iCas9 p53/puro-dKO STK19-KO+STK19-TY

growth_protocol: DMEM GlutaMAX +8-10% Fetal Calf Serum + antibiotics

extract_protocol:
Immediately after BrU pulse-labeling the cells were washed with PBS and lysed in TRIzol reagent (Invitrogen) and BrU-containing RNA was isolated as previously described (Van der Weegen et al.,2021, Nat Cell Biol; Andrade-Lima et al., 2015, Nucleic Acids Res; Van den Heuvel et al., 2021, Nat Commun)
cDNA libraries were made from the BrU-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan DNA Sequencing Core.

treatment_protocol: Cells were either mock-treated or irradiated with UV-C light (12 J/m2). Cells were then incubated in conditioned media for different periods of time (0, 3 and 16 h) before incubation with 2 mM bromouridine (BrU, Sigma) at 37 °C for a 30 min

tag: cell type

value: Retina pigment epithelium

value: Cells were irradiated with 12J/m2 UV-C, followed by 30min BrU pulse-labeling 15.5h later

tag: pulldown antibody

value: Mouse anti-BrdU; BD Pharmingen, 555627

tag: type of_material

value: Nascent RNA


title: BrUseq_WT 12J16h

source_name: RPE1 iCas9 p53/puro-dKO WT

tag: cell line

value: RPE1 iCas9 p53/puro-dKO WT


title: 0USCU, operator 2, lot B, day 1, rep C

value: R/M HNSCC

value: Intermediate Precision


title: VS8KQ, operator 2, lot B, day 1, rep C

value: High


title: 0USCU, operator 2, lot B, day 1, rep A


title: BrUseq_STK19-KO rescue 12J3h

value: RPE1 iCas9 p53/puro-dKO STK19-KO+STK19-TY

value: Cells were irradiated with 12J/m2 UV-C, followed by 30min BrU pulse-labeling 2.5h later


title: BrUseq_STK19-KO 12J16h

source_name: RPE1 iCas9 p53/puro-dKO STK19-KO

value: RPE1 iCas9 p53/puro-dKO STK19-KO


title: b1427_min40_na

value: retinal organoid


title: VCNJ7, operator 2, lot B, day 1, rep C

value: Medium


title: VCNJ7, operator 2, lot B, day 1, rep B


title: BrUseq_STK19-KO 12J3h


title: VCNJ7, operator 2, lot B, day 1, rep A


title: THWJ7, operator 2, lot B, day 1, rep B


title: BrUseq_WT 12J3h


title: BrUseq_STK19-KO rescue mock

value: Cells were 30min BrU pulse-labeled


title: OODZN, operator 2, lot B, day 1, rep C

description: OODZN


title: OODZN, operator 2, lot B, day 1, rep A

description: OODZN


title: BrUseq_WT mock


title: GC6

city: Hefei

first: Zhenya

last: Tan

address: 81th Meishan Road

institute: Anhui Medical University

data_processing:
10X Genomics Chromium Single-Cell 3’ kit (V3) was used to load 10x Chromium for capturing a maximum of 13000 single cell form single cell suspensions, and following cDNA amplification and library construction were performed according to the manufacturer’s instructions. Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. Cell Ranger (vision 5.0.0) pipeline was used for sample demultiplexing, barcode processing and gene counting. For dimensional reduction, clustering and downstream analysis, Cell Ranger output was loaded to Seurat (version 3.1.1) after genome aligning. The STAR aligner was used for generating elementary data, including reads to transcriptome, normalized matrix of gene counts versus cells across samples.
In detail, we employed the FindVariableGenes function (with mean.function = FastExpMean and dispersion.function = FastLogVMR) to identify the most variable genes in Seurat. Subsequently, we applied the normalized expression values of these variable genes to conduct PCA (Principal component analysis) analysis. Clusters were then generated based on gene expression using the FindClusters package. We visualized cell clusters from 3D to 2D space using tSNE dimensional reduction in Seurat. To identify cell cluster markers, we employed the FindAllMarkers package to recognize gene counts that specifically express in a given cluster compared to other cells. We employed SingleR with the reference transcriptome 'Human Primary Cell Atlas' for cell type recognition. All cell types were subsequently revalidated using well-acknowledged cell markers.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5

source_name: stomach

extract_protocol:
Viable cells were used for sequencing following the 10× Genomics protocol. Libraries were prepared using the Single Cell 5′ Library Kit V2 (10× Genomics). Transcriptome profiles of individual cells were determined by Tissue dissociation buffer (2mg/ml papain, 0.35% collagenase I and 120Units/ml DNase I) was used for tissue dissociation. Tumor tissue-tissue dissociation buffer mix was shaken for 20 min at 100rpm in 37 centigrade water baths. The same volume of PBS containing 10% FBS (V/V) was added for digestion termination. Then cell suspension was passed through 30-70 um stacked cell strainer to gotten single cell suspension. Cell suspension was centrifuged at 300g for 5 min at 4 °C and discarded supernatant. To remove erythrocytes in cell pellet, 1 ml 1× red blood cell lysis buffer (MACS 130-094-183,) was added. The cell pellet was resuspended and incubated at room temperature for 5 min. Then the suspension was centrifuged at 300g for 5 min at room temperature.
10× Genomics-based droplet sequencing and libraries were sequenced with paired-end reads on an Illumina NovaSeq 6000

value: gastric adenocarcinoma


title: OODZN, operator 2, lot B, day 1, rep B

description: OODZN


title: BrUseq_STK19-KO mock


title: 195NM, operator 2, lot B, day 1, rep C


title: GC5


title: GC3


title: GC4


title: 195NM, operator 2, lot B, day 1, rep B


title: 195NM, operator 2, lot B, day 1, rep A


title: GC2


title: GC1


title: VS8KQ, operator 2, lot A, day 1, rep C


title: VS8KQ, operator 2, lot A, day 1, rep B


title: VS8KQ, operator 2, lot A, day 1, rep A


title: MEC1/CART, CARC

city: Boston

first: Alexandria

last: Maurer

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

description:
all timepoints for each experiment (CARA, CARB, CARC, CARD) were pooled together for sequencing  and then demultiplexed in post-processing, described in methods of paper)
CARC_

data_processing:
10x genomics pipeline
CellRanger 3.1.0
Assembly: GRCh38
Supplementary files format and content: zipped csv file for counts opf genes as well as cluster assignments

extract_protocol:
CD19 CAR-T cells were generated by transducing healthy donor T cells with 3rd generation lentiviral vectors encoding a bicistronic construct containing either FMC63 CD19 scFv-CD28-CD3z and green fluorescent protein (GFP) or FMC63 CD19 scFv-41BB-CD3z. Peripheral blood mononuclear cells were re-suspended at 2*10^6/ml and seeded at 1ml per 24 well plate and activated with CD3/CD28 Beads. The next day, fresh media was added with IL-2 to a final concentration of 100IU/ml. Six hours later cells were harvested, counted and re-suspended at 0.6*10^6/ml and 0.5ml was seeded into a 24 well plate pre-coated with retronectin. 1.5ml of lentiviral supernatant was added to each well with fresh IL-2 to a final concentration of 100IU/ml and spun for 40 minutes at 1000G. Two days later cells were harvested, re-suspended at 0.5*10^6/ml with 50IU/ml of IL-2 and left to expand and split every 48 hours. Transduction efficiency was assessed by determining the percentage of GFP+ T cells.
Co-cultures were harvested together and stained with hashing antibodies (Biolegend), normalized and prepared for single-cell RNA sequencing on the Chromium 10X platform.

value: CAR-T

tag: time point

value: mixed, multiplexed

value: co-culture


title: MEC1/CART, CARD

description:
all timepoints for each experiment (CARA, CARB, CARC, CARD) were pooled together for sequencing  and then demultiplexed in post-processing, described in methods of paper)
CARD


title: MEC1/CART, CARB

description:
all timepoints for each experiment (CARA, CARB, CARC, CARD) were pooled together for sequencing  and then demultiplexed in post-processing, described in methods of paper)
CARB


title: THWJ7, operator 2, lot A, day 1, rep B

value: Low


title: MEC1/CART, CARA

description:
all timepoints for each experiment (CARA, CARB, CARC, CARD) were pooled together for sequencing  and then demultiplexed in post-processing, described in methods of paper)
CARA


title: THWJ7, operator 2, lot A, day 1, rep A


title: S2MX9, operator 2, lot A, day 1, rep C


title: SP025-H,scTCR-seq

city: Shanghai

first: Zilu

last: Wen

address: No. 2901, Caolang Road, Jinshan District, Shanghai

institute: SHANGHAI PUBLIC HEALTH CLINICAL CENTER

description:
190684G_SP025_High_TCR
10x Genomics

data_processing:
Sequencing reads were segregated from the same cells based on their barcodes, aligned to the Human GRCh38 reference genome, and then filtered to create matrices of expression counts representing features (genes) and barcodes (cells). Cells with <300, >6000 genes or with >20% mitochondrial reads were discarded.
Marker genes for each cell types against the rest of all other cell types were calculated by Seurat’s FindAllMarkers function using a Wilcoxon Rank Sum test with the threshold of log2(fold-change) > 0.25 and being expressed at least 25% of the cells in the cell type.
scTCR-seq was performed using 10x Genomics 5′ Single Cell Immune Profiling technology and then sequenced using the Illumina NovaSeq 6000 (Novogene).
scTCR-seq was integrated with single-cell transcriptomes based on unique cell barcode sequences using the combineExpression function from scRepertoire (ver. 1.6.0).
Cells possessing identical CDR3 sequences for both the α-chain and the β-chain with different cell barcode sequences were considered as clonally expanded.
Assembly: GRCh38-3.0
Supplementary files format and content: counts

source_name: lung

extract_protocol:
Resected lung tissues were processed in the BSL2+ laboratory and digested with Collagenase IV (100 U/ml) and Benzonase (50 U/ml) in RPMI 1640 medium without serum for 45 min at room temperature with rocking. Debris was removed using Dead Cell Removal Kit (Miltenyi Biotec). Cells were collected by centrifugation, resuspended in 1x DPBS on ice, and passed through a 40mm strainer. Cell viability measured by trypan blue staining was above 75%.
Single cell samples were processed using Chromium Single Cell 5’ GEM, Library & Gel Bead Kit v3 and, after cDNA amplification, removed from BSL2+ laboratory for subsequent library construction and sequencing.scTCR-seq was performed using 10x Genomics 5′ Single Cell Immune Profiling technology and then sequenced using the Illumina NovaSeq 6000 (Novogene).

value: lung

value: lung tissue with 18F-FDG avidity

value: immune cells

value: Fresh resected human lung tissue


title: S2MX9, operator 2, lot A, day 1, rep A

value: R/M HNSCC

value: Intermediate Precision


title: S2MX9, operator 2, lot A, day 1, rep B

value: High


title: 0USCU, operator 2, lot A, day 1, rep C


title: 0USCU, operator 2, lot A, day 1, rep B


title: SP019-H,scTCR-seq

description:
190684A_sp019_High_TCR
10x Genomics


title: SP023-H,scTCR-seq

description:
190684E_SP023_High_TCR
10x Genomics


title: SP021-H,scTCR-seq

description:
190684C_SP021_High_TCR
10x Genomics


title: VCNJ7, operator 2, lot A, day 1, rep C


title: TT_bulkATAC_iberdomide_rep4

city: Cambridge

first: Tristan

last: Tay

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

data_processing:
Bulk ATAC-seq data was processed as previously described (Buenrostro et al., 2015). Briefly, reads were trimmed and aligned using Bowtie 2 (v2.3.3.1) and the same peakset from the single-cell ATAC sequencing experiments was utilized.
Assembly: hg38

source_name: Human PBMCs

growth_protocol: CD3+ T cells were isolated from healthy donor leukopaks (Stemcell Technologies) using bead separation (Stemcell Technologies) and cryopreserved. Thawed T cells were resuspended in RPMI medium supplemented with heat-inactivated FBS, Pen/Strep, HEPES, non-essential amino acids, sodium pyruvate, Glutamax and 2-mercapto-ethanol (all Gibco). 10 million cells were plated in a T25 tissue culture flask at a density of 1 million/mL.

extract_protocol:
The ATAC-seq protocol was performed as previously described (Buenrostro et al., 2013; Ludwig et al., 2019). Briefly, cell samples were thawed and 50,000 cells were washed twice in PBS. Pelleted cells were then directly transposed using an all-in-one transposition buffer (Tris pH 7.5, MgCl2, DMF 5%, PBS 0.3X, NP-40 0.1%, Illumina Tn5 1X, ddH20 to 50 uL). The transposition reaction was completed with thermomixing at 37°C for 30 minutes at 300 rpm on a thermoshaker.
Transposed DNA was purified with MinElute column clean-up (Qiagen), then minimally amplified for sequencing as previously described (Buenrostro et al., 2015). Prepared libraries were purified with MinElute column clean-up (Qiagen) and digested with ExoI (NEB). Libraries were quantified with a Qubit dsDNA HS Assay kit (Invitrogen).

treatment_protocol: 250 µL of ImmunoCult Human CD3/CD28 T Cell Activator Mix (StemCell Technology) was added to the cells and incubated at 37°C for 6 hours.

tag: drug

value: Iberdomide

tag: replicate

value: Replicate 4


title: TT_bulkATAC_iberdomide_rep5

value: Replicate 5


title: VCNJ7, operator 2, lot A, day 1, rep A

value: Medium


title: TT_bulkATAC_iberdomide_rep2

value: Replicate 2


title: VCNJ7, operator 2, lot A, day 1, rep B


title: THWJ7, operator 2, lot A, day 1, rep C


title: OODZN, operator 2, lot A, day 1, rep C

description: OODZN


title: TT_bulkATAC_iberdomide_rep3

value: Replicate 3


title: OODZN, operator 2, lot A, day 1, rep B

description: OODZN


title: TT_bulkATAC_iberdomide_rep1

value: Replicate 1


title: OODZN, operator 2, lot A, day 1, rep A

description: OODZN


title: 195NM, operator 2, lot A, day 1, rep C


title: TT_bulkATAC_untreated_rep4

value: Control


title: 195NM, operator 2, lot A, day 1, rep B


title: TT_bulkATAC_untreated_rep5


title: TT_bulkATAC_untreated_rep3


title: 195NM, operator 2, lot A, day 1, rep A


title: 195NM, operator 1, lot B, day 2, rep B


title: TT_bulkATAC_untreated_rep6

value: Replicate 6


title: VS8KQ, operator 1, lot B, day 1, rep C


title: TT_bulkATAC_untreated_rep2


title: TT_bulkATAC_untreated_rep1


title: 0USCU, operator 2, lot A, day 1, rep A

value: Low


title: RNA_DonorPool_2

data_processing:
The data is processed using share-seq alignment v2 pipeline (https://github.com/masai1116/SHARE-seq-alignmentV2)
Assembly: hg38

extract_protocol:
After stimulation, cells were harvested and washed twice with ice cold 1x PBS + 0.1% BSA and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter.
scRNA-seq libraries were generated using the SHARE-seq protocol (https://www.protocols.io/workspaces/shareseq).

treatment_protocol: 250 µL of ImmunoCult Human CD3/CD28 T Cell Activator Mix (StemCell Technology) was added to the cells and incubated at 37°C. After 3 days of culture, cells were transferred to fresh culture medium and stimulated again. After 3 rounds of stimulation, cells were washed and stimulated for a final cytokine assessment 24hr post the last round (chronic stim).

tag: donorpool

value: DonorPool 2


title: 0USCU, operator 2, lot B, day 1, rep B

data_processing:
Fastq files were preprocessed with umitools version 1.1.1 to remove UMIs from the 5' end of each read.  Trim_galore/cutadapt version 0.4.1 was used to remove adapter sequences as well as reads with PHRED quality scores less than 20 and reads that were less than 20 basepairs.
The trimmed reads were aligned to the human genome GRCh38 with STAR version 2.5.2a using the two-pass method as previously described.  Duplicate alignments were removed with umitools version 1.1.1.
Read counts were generated using htseq-count version 0.9.1 and annotation from Gencode version 22.
Assembly: GRCh38
Supplementary files format and content: RNA-seq counts, tab separated file


title: RNA_DonorPool_1

value: DonorPool 1


title: VS8KQ, operator 1, lot B, day 1, rep B


title: SP024-H,scTCR-seq

description:
190684F_SP024_High_TCR_1
10x Genomics

value: lung

value: lung tissue with 18F-FDG avidity

value: immune cells


title: THWJ7, operator 1, lot B, day 1, rep C

value: R/M HNSCC

value: Intermediate Precision


title: ATAC_DonorPool_1

data_processing:
The data is processed using share-seq alignment v2 pipeline (https://github.com/masai1116/SHARE-seq-alignmentV2)
Assembly: hg38
Supplementary files format and content: Peak file (BED) contains chromsome, start and end coordinates for determined chromatin accessibility peak window ranges. cellMeta file contains single cell barcode information for the final set of filtered scATAC stimulation cells used in the analysis. Fragments.tsv.gz files contain all Tn5-corrected coordinates for aligned fragments, which can be used to overlap with peaks to get counts of Tn5 insertions falling within peaks for each cell barcode.

extract_protocol:
After stimulation, cells were harvested and washed twice with ice cold 1x PBS + 0.1% BSA and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter.
scATAC-seq libraries were generated using the SHARE-seq protocol (https://www.protocols.io/workspaces/shareseq).


title: S2MX9, operator 1, lot B, day 1, rep A

extract_protocol:
RNA was extracted using the RNAstorm™ FFPE RNA Extraction Kit (Biotium, Fremont, CA) according to the manufacturer’s instructions. RNA quantity was assessed with the High Sensitivity RNA Qubit assay (Thermo Fisher Scientific, Waltham, MA). RNA quality was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).
RNAseq libraries for OncoPrism-HNSCC ICI response prediction were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Inc., Greenland, NH), following the manufacturer’s instructions. Library RNA input was 40 ng total RNA for all samples unless otherwise specified. UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, Inc., Greenland, NH) replaced Second Strand Synthesis Mix 1 in the workflow. All samples were processed with two OncoPrism-HNSCC positive controls and a No Template Control. The positive (high or medium scoring) controls were RNA extracted from RM-HNSCC samples as described above. Final libraries were sequenced to a minimum depth of 10 million single-end 75 base pair reads on a NextSeq500 (Illumina, San Diego, CA), following the manufacturer’s protocols.

value: High


title: S2MX9, operator 1, lot B, day 1, rep B


title: THWJ7, operator 1, lot B, day 1, rep A


title: 0USCU, operator 1, lot B, day 1, rep C


title: 0USCU, operator 1, lot B, day 1, rep B


title: Treg_02 [L49929_Track-90483]

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description:
RawExpressionCountTable.csv
TCR_data.csv

data_processing:
library strategy: Plate base Single cell RNA seq (SMARTseq2)
Fragments were aligned to the human reference genome hg38 with support of Ensembl 98 splice sites using the aligner gsnap (v2019-06-10).
Counts per gene and cell were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1)
T-cell receptor sequences were assembled per cell using TraCeR (v0.5)
Assembly: hg38
Supplementary files format and content: Counts per gene per cell, CSV
Supplementary files format and content: T-cell receptor sequences, CSV

source_name: Blood

growth_protocol: 2.5-5x10^7 PBMCs were plated in 2 ml RPMI-1640 medium (GIBCO), supplemented with 5% (v/v) human AB-serum (Sigma Aldrich, Schnelldorf, Germany) in 6-well cell culture plates.

extract_protocol:
CD154+ memory cells were isolated by MACS and further purified by FACS sorting on a FACS Aria Fusion (BD Bioscience, San Jose, CA, USA) based on dual expression of CD154 and CD69 and expression of CD45RO. Cells were directly sorted into skirted 96-well PCR plates which were equipped with 2 µl lysis buffer (nuclease-free water with 0.2% Triton-X 100 solution (Roche Diagnostics GmbH, Mannheim, Germany) with 4 U/µL RNase Inhibitor (New England Biolabs)) in advance. After FACS sorting plates were shortly centrifuged (30 sec, 200xg) and immediately frozen at -80°C until shipment.
Library preparation and sequencing was performed at the DRESDEN-concept Genome Center (DcGC, TU Dresden, Germany). The workflow was based on the previously described SMARTseq2 protocol 81. After thawing the samples, 2 ul of a primer mix was added (5 mM dNTP (Invitrogen), 0.5 uM dT-primer*, 4 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription was performed at 42°C for 90 min after filling up to 10 ul with RT buffer mix for a final concentration of 1X superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 uM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using 2X Kapa HiFi HotStart Readymix (Roche) at a final 1X concentration and 0.1 uM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 22 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6X volume of hydrophobic Sera-Mag Beads (Cytvia: GE24152105050250,) and DNA was eluted in 12 ul nuclease free water. The cDNA quality and concentration of a few representative samples was determined with the Fragment Analyzer (Agilent). For library preparation, 2 µl amplified cDNA was tagmented in 1X Tagmentation Buffer using 0.8 µl bead-linked transposome (Illumina DNA Prep, (M) Tagmentation, Illumina) at 55°C for 15 min in a total volume of 4 µL. The reaction was stopped by adding 1 µl of 0.1 % SDS (37°C, 15 min). Magnetic beads were bound to a magnet, the supernatant was removed, beads were resuspended in 4 µl indexing PCR Mix containing 1x KAPA Hifi HotStart Ready Mix (Roche). After adding 700 nM unique dual indexing primers (i5 and i7) using Echo Acoustic Liquid Handler (Echo 525, Beckman Coulter), the reaction mixture was subjected to a PCR (72°C 3 min, 98°C 30 sec, 12 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min). After PCR, libraries are quantified with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium) and equimolarly pooled using Echo Acoustic Liquid Handler (Echo 525, Beckman Coulter GmbH). The pooled libraries were then purified with 0.9x volume Sera-Mag SpeedBeads, followed by a double size selection with 0.6x and 0.9x volume of beads. Re-double size selection with 0.6x and 0.9x volume of beads was performed if needed.

treatment_protocol: PBMC were stimulated for 7 h in presence of 1 µg/ml CD40 pure antibody (Miltenyi Biotec, Bergisch Gladbach, Germany) with AQP4, Influenza A H1N1 (HA) and C.albicans MP65 peptide pools or PMA/Ionomycin

value: Blood

value: CD4 T cell

value: Regulatory T cell

value: PMA and Ionomycin


title: Treg_02 [L49941_Track-90503]


title: Treg_02 [L49905_Track-90389]


title: 0USCU, operator 1, lot B, day 1, rep A


title: Treg_02 [L49893_Track-90446]


title: Treg_02 [L49917_Track-90456]


title: VS8KQ, operator 1, lot B, day 1, rep A


title: VCNJ7, operator 1, lot B, day 1, rep B

value: Medium


title: Treg_02 [L49869_Track-90374]


title: Treg_02 [L49857_Track-90482]


title: Treg_01 [L49845_Track-90487]


title: Treg_02 [L49881_Track-90468]


title: Treg_01 [L49833_Track-90546]


title: Treg_01 [L49821_Track-90496]


title: THWJ7, operator 1, lot B, day 1, rep B


title: VCNJ7, operator 1, lot B, day 1, rep A


title: ATAC_DonorPool_2


title: VCNJ7, operator 1, lot B, day 1, rep C


title: OODZN, operator 1, lot B, day 1, rep B

description: OODZN


title: Treg_01 [L49809_Track-90476]


title: 195NM, operator 1, lot B, day 1, rep C


title: Treg_01 [L49797_Track-90519]


title: 195NM, operator 1, lot B, day 1, rep A


title: 195NM, operator 1, lot B, day 1, rep B


title: Treg_01 [L49785_Track-90474]


title: VS8KQ, operator 1, lot A, day 1, rep C


title: OODZN, operator 1, lot B, day 1, rep C

description: OODZN


title: T-HD_03 [L76184_Track-119508]

value: T cell

value: AQP4 peptide pool


title: OODZN, operator 1, lot B, day 1, rep A

description: OODZN


title: T-HD_03 [L76185_Track-119381]


title: Treg_01 [L49761_Track-90494]


title: THWJ7, operator 1, lot A, day 1, rep C


title: VS8KQ, operator 1, lot A, day 1, rep B


title: THWJ7, operator 1, lot A, day 1, rep B


title: THWJ7, operator 1, lot A, day 1, rep A


title: T-HD_03 [L76182_Track-119473]


title: 0USCU, operator 1, lot A, day 1, rep C


title: T-HD_03 [L76181_Track-119576]


title: T-HD_03 [L76179_Track-119464]


title: T-HD_03 [L76183_Track-119388]


title: S2MX9, operator 1, lot A, day 1, rep B


title: T-HD_03 [L76178_Track-119438]


title: 0USCU, operator 1, lot A, day 1, rep A


title: 0USCU, operator 1, lot A, day 1, rep B


title: VCNJ7, operator 1, lot A, day 1, rep C


title: T-HD_03 [L76176_Track-119555]


title: VCNJ7, operator 1, lot A, day 1, rep B


title: T-HD_03 [L76177_Track-119433]


title: Treg_01 [L49773_Track-90517]


title: VCNJ7, operator 1, lot A, day 1, rep A


title: T-HD_03 [L76174_Track-119547]


title: T-HD_03 [L76173_Track-119493]


title: OODZN, operator 1, lot A, day 1, rep C

description: OODZN


title: VS8KQ, operator 1, lot A, day 1, rep A


title: T-HD_03 [L76180_Track-119421]


title: OODZN, operator 1, lot A, day 1, rep B

description: OODZN


title: T-HD_03 [L76172_Track-119371]


title: OODZN, operator 1, lot A, day 1, rep A

description: OODZN


title: 195NM, operator 1, lot A, day 1, rep B


title: T-HD_03 [L76170_Track-119453]


title: T-HD_03 [L76167_Track-119501]


title: VS8KQ, operator 1, lot B, day 2, rep C, alternate sequencer

value: Intermediate Precision - Alternate Sequencer


title: 195NM, operator 1, lot A, day 1, rep C


title: T-HD_03 [L76168_Track-119454]


title: VS8KQ, operator 1, lot B, day 2, rep A, alternate sequencer


title: 195NM, operator 1, lot A, day 1, rep A


title: T-HD_03 [L76169_Track-119648]


title: T-HD_03 [L76166_Track-119686]


title: VS8KQ, operator 1, lot B, day 2, rep B, alternate sequencer


title: THWJ7, operator 1, lot B, day 2, rep C, alternate sequencer

value: Low


title: T-HD_03 [L76164_Track-119743]


title: THWJ7, operator 1, lot B, day 2, rep A, alternate sequencer


title: T-HD_03 [L76175_Track-119463]


title: THWJ7, operator 1, lot B, day 2, rep B, alternate sequencer


title: T-HD_03 [L76162_Track-119748]


title: T-HD_03 [L76163_Track-119740]


title: T-HD_03 [L76165_Track-119472]


title: S2MX9, operator 1, lot B, day 2, rep C, alternate sequencer


title: T-HD_03 [L76161_Track-119361]


title: S2MX9, operator 1, lot B, day 2, rep B, alternate sequencer


title: S2MX9, operator 1, lot B, day 2, rep A, alternate sequencer


title: T-HD_03 [L76159_Track-119517]


title: T-HD_03 [L76171_Track-119682]


title: T-HD_03 [L76158_Track-119592]


title: 0USCU, operator 1, lot B, day 2, rep B, alternate sequencer


title: T-HD_03 [L76157_Track-119670]


title: VCNJ7, operator 1, lot B, day 2, rep C, alternate sequencer


title: T-HD_03 [L76156_Track-119415]


title: VCNJ7, operator 1, lot B, day 2, rep A, alternate sequencer


title: T-HD_03 [L76154_Track-119507]


title: T-HD_03 [L76153_Track-119766]


title: OODZN, operator 1, lot B, day 2, rep B, alternate sequencer

description: OODZN


title: T-HD_03 [L76151_Track-119628]


title: OODZN, operator 1, lot B, day 2, rep C, alternate sequencer

description: OODZN


title: T-HD_03 [L76150_Track-119477]


title: 195NM, operator 1, lot B, day 2, rep C, alternate sequencer


title: T-HD_03 [L76152_Track-119753]


title: 195NM, operator 1, lot B, day 2, rep A, alternate sequencer


title: 195NM, operator 1, lot B, day 2, rep B, alternate sequencer


title: T-HD_03 [L76147_Track-119500]


title: VS8KQ, operator 2, lot A, day 1, rep C, alternate sequencer


title: T-HD_03 [L76160_Track-119739]


title: T-HD_03 [L76145_Track-119652]


title: VS8KQ, operator 2, lot A, day 1, rep B, alternate sequencer


title: 0USCU, operator 1, lot B, day 2, rep C, alternate sequencer


title: VS8KQ, operator 2, lot A, day 1, rep A, alternate sequencer


title: THWJ7, operator 2, lot A, day 1, rep C, alternate sequencer


title: VCNJ7, operator 1, lot B, day 2, rep B, alternate sequencer


title: T-HD_03 [L76143_Track-119356]


title: T-HD_03 [L76142_Track-119581]


title: THWJ7, operator 2, lot A, day 1, rep B, alternate sequencer


title: THWJ7, operator 2, lot A, day 1, rep A, alternate sequencer


title: T-HD_03 [L76148_Track-119734]


title: 0USCU, operator 1, lot B, day 2, rep A, alternate sequencer


title: S2MX9, operator 2, lot A, day 1, rep B, alternate sequencer


title: T-HD_03 [L76139_Track-119462]


title: T-HD_03 [L76138_Track-119519]


title: T-HD_03 [L76140_Track-119566]


title: 0USCU, operator 2, lot A, day 1, rep B, alternate sequencer


title: T-HD_03 [L76146_Track-119636]


title: T-HD_03 [L76149_Track-119475]


title: T-HD_03 [L76136_Track-119727]


title: S2MX9, operator 2, lot A, day 1, rep C, alternate sequencer


title: 0USCU, operator 2, lot A, day 1, rep A, alternate sequencer


title: S2MX9, operator 2, lot A, day 1, rep A, alternate sequencer


title: VCNJ7, operator 2, lot A, day 1, rep C, alternate sequencer


title: T-HD_03 [L76135_Track-119755]


title: 0USCU, operator 2, lot A, day 1, rep C, alternate sequencer


title: OODZN, operator 1, lot B, day 2, rep A, alternate sequencer

description: OODZN


title: VCNJ7, operator 2, lot A, day 1, rep B, alternate sequencer


title: T-HD_03 [L76133_Track-119442]


title: T-HD_03 [L76144_Track-119760]


title: VCNJ7, operator 2, lot A, day 1, rep A, alternate sequencer


title: T-HD_03 [L76132_Track-119757]


title: T-HD_03 [L76141_Track-119615]


title: OODZN, operator 2, lot A, day 1, rep C, alternate sequencer

description: OODZN


title: OODZN, operator 2, lot A, day 1, rep B, alternate sequencer

description: OODZN


title: T-HD_03 [L76131_Track-119410]


title: T-HD_03 [L76134_Track-119437]


title: OODZN, operator 2, lot A, day 1, rep A, alternate sequencer

description: OODZN


title: 195NM, operator 2, lot A, day 1, rep C, alternate sequencer


title: 195NM, operator 2, lot A, day 1, rep B, alternate sequencer


title: T-HD_03 [L76128_Track-119749]


title: T-HD_03 [L76127_Track-119363]


title: T-HD_03 [L76129_Track-119487]


title: T-HD_03 [L76137_Track-119635]


title: T-HD_03 [L76155_Track-119385]


title: TCRseq_CSBKO_12J8h_rep1

data_processing:
After sequencing, a quality profile was generated for each sample, using FastQC (Version 0.11.9). Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the Human Genome 38 using bwa-mem tools (BWA (Version 0.7.17) and reference genome GCA_000001405.15_GRCh3847. Only uniquely mapping and high-quality reads (> q30) were included in the analyses. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2) (Heinz et al., 2010, Mol Cell). Example genome tracks were generated in IGV (Version 2.4.3). Stranded metagene profiles were generated for the 3,000 actively transcribed genes defined in our BrU-seq data, using the makeMetaGeneProfile.pl tool of HOMER with default settings.
Assembly: hg38
Supplementary files format and content: TCRseq_MetaGeneProfile_Stranded_TOP3000.txt: tab-delimited text file containing the average stranded read-density/10M total reads at the indicated distance from the TSS/TTS of the selected 3000 actively transcribed genes.
Library strategy: TCR-Seq

extract_protocol:
Cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed once with PBS followed by incubation with 1% PFA for 20 min at RT. Fixation was stopped by addition of glycine in PBS to a final concentration of 0.1 M for 3 min at RT. This was followed by washing with cold PBS and collection of the cells in 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), and 20 mM Hepes (pH 7.6) in miliQ. Chromatin was pelleted by centrifugation for 5 min at 400 × g and incubated in 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) in miliQ for 10 min at 4 °C. Chromatin was again pelleted by centrifugation and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6) in miliQ) to a final concentration of 15 × 106 cells/mL. Chromatin was sonicated to approximately one nucleosome using the Bioruptor Pico (Diagenode), 8 cycles of 30 s ON/30 s OFF in a 4°C water bath. ChIP was performed on 280-300ul sonicated material (~25 µg of chromatin per sample) with 3 µg of rat anti-RNAPII-S2 antibody (Millipore, clone 3E10) by overnight incubation at 4 °C, followed by a 1.5 h protein-chromatin pull-down with 20 µl protein G Dynabeads (Thermo Fisher, 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 h at 65 °C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit.
Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex adapters or xGen UDI-UMI adapters. Samples were sequenced using an Illumina NextSeq500 or HiSeq X, using paired-end sequencing with 42 or 151 bp from each end.

treatment_protocol: Cells were either mock-treated or irradiated with UV-C light (12 J/m2). Cells were then incubated in conditioned media for either 1 hour or 8 hours as indicated per sample.

value: RPE1 iCas9 p53/puro-dKO STK19-KO

value: Retina pigment epithelium

value: Cells were irradiated with 12J/m2 UV-C and incubated in conditioned medium for 8 hour at 37C

value: Rat anti-RNAPII-S2 antibody (Millipore, clone 3E10)


title: T-HD_03 [L76126_Track-119509]


title: TCRseq_STK19KO7_12J8h_rep1

value: RPE1 iCas9 p53/puro-dKO STK19-KO+STK19-TY


title: TCRseq_STK19KO7_12J1h_rep1

value: Cells were irradiated with 12J/m2 UV-C and incubated in conditioned medium for 1 hour at 37C


title: T-HD_03 [L76124_Track-119521]


title: TCRseq_WT_12J8h_rep1

value: RPE1 iCas9 p53/puro-dKO WT


title: T-HD_03 [L76121_Track-119512]


title: TCRseq_WT_12J1h_rep1


title: T-HD_03 [L76123_Track-119461]


title: T-HD_03 [L76125_Track-119751]


title: T-HD_03 [L76120_Track-119744]


title: T-HD_03 [L76119_Track-119449]


title: T-HD_03 [L76130_Track-119387]


title: T-HD_03 [L76122_Track-119708]


title: TCRseq_CSBKO_12J1h_rep1


title: 195NM, operator 2, lot A, day 1, rep A, alternate sequencer

value: R/M HNSCC

value: High


title: pHLFs TGF-B1 treated replicate 3

city: London

first: Greg

last: Contento

state: Greater London

address: Rayne Institute, 5 University Street

department: UCL Respiratory

institute: University College London

description: DEGs.txt

data_processing:
Data analysis was performed with the Illumina Basespace platform.
Reads pre-processing and alignment to the genome (Homo sapiens UCSC hg38) were performed using HISAT2 and DEGs defined by DESeq2
Counts files for each individual sample were generated with Featurecounts.
Assembly: hg38
Supplementary files format and content: Processed data files are in tab-delimited txt or FASTQ format.

source_name: Lung

growth_protocol: Primary human lung fibroblasts were grown in Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% Fetal bovine serum (FBS), 1% Penicillin/Streptomycin, 5 mM glucose and 0.7 mM L-glutamine. They were maintained at 37 degC and at 10% CO2. Cells were passaged when 80% confluent.

extract_protocol:
RNA was extracted using Rneasy Kit
Poly(A)-taled RNA enrichment and library preparation were performed using the KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KAPABiosystems), following the manufacturer's instructions.

treatment_protocol: 90% confluent cells were serum starved for 24h before treatment. Cells were treated with 1ng/mL TGFβ1  and incubated for 24h.

value: Lung

value: primary

value: fibroblast

tag: individual

value: Male former smoker


title: TCRseq_CSBKO_mock_rep1

value: Untreated


title: T-HD_03 [L76117_Track-119532]

value: Blood

value: CD4 T cell

value: T cell

value: AQP4 peptide pool


title: T-HD_03 [L76116_Track-119662]


title: TCRseq_STK19KO7_mock_rep1

value: Retina pigment epithelium


title: T-HD_03 [L76118_Track-119380]


title: T-HD_03 [L76110_Track-119373]


title: T-HD_03 [L76114_Track-119690]


title: pHLFs TGF-B1 treated replicate 2

description: DEGs.txt


title: pHLFs untreated replicate 1

description: DEGs.txt

value: control


title: T-HD_03 [L76112_Track-119573]


title: KMS34_ChIPSeq, rep2

city: Yakushiji

first: NAOKI

last: OSADA

address: Tochigi

department: Center for Molecular Medicine

country: Japan

institute: Jichi Medical University

data_processing:
Basecalls performed using bcl2Fastq version 2.20
ChIP-seq reads were aligned to the hg38 genome assembly using bwa version 0.7.12
Spike-in protocols and normalization were used. For comparative analysis, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group. The normalization is implemented through random deletion of test sample tags (down-sampling). The normalization factor shows the adjustment relative to standard normalized tag numbers (where the usable tags for each sample within a normalization group would be adjusted to the same number).
The two main peak callers used at Active Motif are MACS(v2.1.0) and SICER(v1.1) .MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II).
Assembly: hg38
Supplementary files format and content: BW

source_name: Multiple Myeloma

growth_protocol: We cultured KMS34 cells in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and isolated with anti-histone H3K36me2 antibody.
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.

treatment_protocol: No treatment

tag: disease state

value: Multiple Myeloma

value: Hematopoietic cells

tag: chip antibody

value: anti-H3K36me2 (Abcam#ab9049)


title: RDEB fibroblasts, Givinostat, patient 434

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trim Galore! (parameter - quality: 20)
Trimmed sequence reads were aligned to Ensembl transcripts (Homo_sapiens.GRCh38.cdna.all.fa.gz) and read counts were extracted using kallisto with default parameters
Read count normalization was performed using DeSeq2 R package
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw Kallisto counts for each Sample
Supplementary files format and content: tab-delimited text files include rlog nomalized values for each Sample

source_name: fibroblasts

growth_protocol: Primary dermal fibroblasts isolated from the skin of RDEB patients were grown in Dulbecco modified Eagle’s medium (DMEM) with 25 mM glucose containing 10% FBS, 50 mg per ml penicillin and streptomycin, and 4 mM L-glutamine.

extract_protocol:
Total RNA was extracted from fibroblasts using Direct-zol RNA MicroPrep (Zymo Research). 300 ng of total RNA were used for the construction of sequencing libraries.
RNA libraries were prepared using TruSeq Stranded mRNA (TruSeq RNA-Seq v2) Library Preparation Kit following manufacturer's protocols.

treatment_protocol: Subconfluent RDEB fibroblasts were starved overnight in 0.1% BSA and then treated for 30 hours with 250 nM Givinostat or 2 mM VPA, or DMSO as vehicle.

value: fibroblasts

tag: patient

value: Givinostat


title: pHLFs untreated replicate 2

description: DEGs.txt

tag: tissue

tag: treatment


title: pHLFs TGF-B1 treated replicate 1

description: DEGs.txt


title: T-HD_03 [L76105_Track-119675]


title: RDEB fibroblasts, untreated, patient 434


title: pHLFs untreated replicate 3

description: DEGs.txt


title: T-HD_03 [L76115_Track-119398]


title: TCRseq_WT_mock_rep1

value: RPE1 iCas9 p53/puro-dKO WT

value: Rat anti-RNAPII-S2 antibody (Millipore, clone 3E10)


title: T-HD_03 [L76107_Track-119510]


title: T-HD_03 [L76108_Track-119728]


title: T-HD_03 [L76109_Track-119730]


title: RDEB fibroblasts, VPA, patient 434

value: Valproic acid


title: KMS34_ChIPSeq, rep1


title: T-HD_03 [L76111_Track-119677]


title: T-HD_03 [L76106_Track-119386]


title: RDEB fibroblasts, VPA, patient 3248


title: RDEB fibroblasts, Givinostat, patient 3248


title: T-HD_03 [L76113_Track-119664]


title: RDEB fibroblasts, VPA, patient 2175


title: RDEB fibroblasts, Givinostat, patient 2175