title: Untreated B (tumor CD8) Gene Expression

description:
Library name: untreated_b_tumor_cd8
Illumina HiSeq 2500 (rapid run)

data_processing:
Single-cell RNAseq analysis. 10X sequencing data was processed through the Cell Ranger pipeline (version 1.1, hg19 genome assembly) with default settings and filtered gene-barcode matrices were analyzed using the scanpy toolkit (Wolf FA et al. Genome Biol 2018). The gene expression values were log2 plus one transformed and normalized to 10,000 counts per cell. Cells with mitochondrial gene expression of >10% were filtered out. The resulting matrix was batch corrected by regressing out total UMI counts and percent mitochondrial genes using the scanpy function followed by scanpy implementation of ComBat (Johnson WE et al. Biostat Oxf Eng 2007). The adjusted matrix was scaled to a mean of zero and variance of 1. Highly variable genes were selected using the scanpy function followed by principal component analysis (PCA), Leiden clustering and UMAP plotting with default settings. CD4+ and CD8+ T cells were clustered together at a resolution of 0.9. DE analysis was carried out to identify marker genes that were upregulated in each individual cluster relative to all other single cells. Annotation of each unbiased population was performed by manual DE gene inspection.  Single-cell TCRseq analysis. For our overall patient TCR sequencing strategy, 10X barcodes of TCR were matched with 10X barcodes from cells with RNA sequences that passed filtering in the Cell Ranger pipeline. TRA and TRB CDR3s reads were aligned against known TRA and TRB CDR3 sequences and assembled into clonotype families using miXCR (Bolotin DA et al. Nat Methods 2015). For any given 10X barcode, the most abundant TRA or TRB clonotype was accepted for further analysis; if 2 TRA or TRB clonotypes were equally abundant for a given 10X barcode, the clonotype with the highest sequence alignment score was used for further analysis. Cells with paired TRA and TRB were used for further downstream analysis. For the specific results validating enrichment of tumor-matched TCRab clones in sorted KLRG1+ CD4+ T cells from PBMC (Patients 50 and 65, Supplemental Data 10), 10X Genomics Cell Ranger pipeline v8.0.1 was used.
Assembly: hg19
Supplementary files format and content: Gene expression: 10X Cellranger 1.1 outputs (barcodes.tsv, matrix.mtx, genes.tsv). TCR sequencing: processed TCRa and TCRb CDR3 and associated 10X GEX barcode (.csv). TCR sequencing from patients 50 and 65 (10X VDJ, Supplemental Data 10): filtered contig annotations (.csv)

value: Tumor

value: bladder cancer

value: T cells

value: untreated

value: pre-treatment


title: Brain, CD3+ SS2 KO A13 mouse 3 scRNAseq

status: Public on Apr 04 2025

type: SRA

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
SmartSeq2
SS2_20_017_5_A13

library_source: transcriptomic single cell

data_processing:
alignment was performed using kallisto v0.44.0
The transcript abundance files in hdf5 format (Hoefling and Annau 2020) from the pseudo alignment via kallisto v0.44.0 (Bray et al. 2016) were merged and converted into Transcripts per Kilobase Million (TPM) normalised gene expression matrices, with additional length scaling (”lengthScaledTPM”) and otherwise default parameters, via the package tximport v.1.18.0 (Soneson et al. 2015). For that purpose, the transcript to gene annotation file (tx2genes.csv) found in the sequencing results folders was used to associate the corresponding transcript ID to gene ID. The Ensembl IDs were transformed into gene symbols using biomaRt v.2.46.0 (Durinck et al. 2005; Durinck et al. 2009).
Assembly: mm10
Supplementary files format and content: all samples merged to one matrix: tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
To isolate immune cells, after perfusion, brains were digested for 45 min in RPMI containing 10 mM HEPES, 0.5 mg/ml Collagenase Type IV (Sigma Aldrich) and 0.05 mg/ml DNase I (Sigma Aldrich) at 37°C. Cells were then isolated using density gradient centrifugation. The isolated brain cells were directly sorted on an BD Aria III cell sorter for sequencing experiments. The left hemisphere was used to sort CD45+ cells to perform scRNAseq with SeqWell v3 (Aicher et al. 2019). The right hemisphere was used for index sorting of CD3+ cells into 384 well plates (Penter et al. 2018) for scRNAseq with SmartSeq2 (Picelli et al. 2014). Only cells isolated with a purity of > 98% were used for further analysis.
CNS T cells from the brains of B57BL/6 Zfyve26-/- 𝐶𝑋𝐶𝑅4;𝐶𝑟𝑒𝐸𝑅(𝑇2)−𝐼𝑅𝐸𝑆−𝐺𝐹𝑃;𝑅26𝐶𝐴𝐺−𝐿𝑆𝐿−𝑡𝑑𝑇 or Zfyve26+/- 𝐶𝑋𝐶𝑅4;𝐶𝑟𝑒𝐸𝑅(𝑇2)−𝐼𝑅𝐸𝑆−𝐺𝐹𝑃;𝑅26𝐶𝐴𝐺−𝐿𝑆𝐿−𝑡𝑑𝑇 animals were isolated as described above. Total RNA was isolated using the miRNeasy Mini Kit (QIAGEN) and transcriptome analysis was performed by SmartSeq2 (Picelli et al. 2014). Per sample, 500 pg RNA was denatured for 2 min at 95°C in 0.1% Triton X-100 containing 0.05 mM dNTP, 2 μM anchored oligodT (Smart dT30VN) primer and 1 U/μl RNase Inhibitor (Takara). Reverse transcription was carried out at 42°C for 90 min followed by 15 min inactivation at 70°C using 5 U/μl Superscript II reverse transcriptase (Thermo Fisher Scientific) in 1X Superscript II Buffer supplemented with 5 mM DTT, 1 M Betaine, 14 mM MgCl2, 1 μM Template Switching Oligo and 1 U/μl RNase Inhibitor. cDNA was then pre-amplified using KAPA HiFi HotStart ReadyMix (Kapa Biosystems) containing 1 nM ISPCR Primer. Amplification was carried out for 16 cycles consisting of 20 s denaturation at 98°C, 20 s annealing at 67°C and 6 min elongation at 72°C each after an initial denaturing at 98°C for 3 min. The pre-amplification reaction was then purified by using a 0.8:1 ratio of AMPure XP beads (Beckman Coulter). DNA was allowed to bind to beads for 3 min at RT followed by one wash in 80% Ethanol for 30 s. cDNA was then eluted from the beads in 15 μl of water before checking for cDNA quality on a Tapestation 2200 using a HighSensitivity D5000 assay (Agilent Genomics) according to manufacturer’s instructions. Tagmentation, PCR amplification and indexing of samples was performed using the Nextera XT DNA Library Preparation Kit (Illumina) according to manufacturer’s recommendations. After library preparation, DNA was purified with a 1:1 ratio of AMPure XP beads and sample. Quantification and quality check of libraries was done on a Tapestation 2200 using a HighSensitivity D5000 Assay. Library concentrations were adjusted to 2nM and pooled prior to sequencing SR 75 bp with two 8 bp index reads on an Illumina NextSeq 500 instrument using High Output v2 chemistry. RNA-seq data was demultiplexed using bcl2fastq2 v2.20 and pseudo aligned to Mus_musculus.GRCm38.cdna.all.fa.gz transcriptome using kallisto v0.44.0 (Bray et al. 2016). The sequences of all oligos used for SmartSeq2 can be found in Table S7. All oligos were biotinylated at the 5′ end to avoid the formation of concatemers.

tag: tissue

value: Brain

tag: strain

tag: Sex

value: male

tag: genotype

value: KO

tag: age

value: 15 months


title: Untreated B (tumor CD4) Gene Expression

city: San Francisco

first: David

last: Oh

state: CA

address: 513 Parnassus Ave, HSE301, Box 0519

country: USA

institute: University of California, San Francisco

description:
Library name: untreated_b_tumor_cd4
Illumina HiSeq 2500 (rapid run)

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Blood processing. Whole blood was collected in heparinized tubes and processed within 24h. Whole blood was diluted 1:1 with PBS (Ca2+ and Mg2+ free) and centrifuged with Ficoll. PMBC was removed from the white cell interface and washed 2x with PBS before freezing in 10% DMSO and 12.5% of human serum albumin in RPMI-1640.  Tumor processing. Cystectomy surgical specimens were obtained fresh from the operating field, and dissected in pathology where grossly apparent tumor or adjacent bladder not grossly affected by tumor (“normal” adjacent tissue) were isolated, minced, and transported at room temperature in L15 media with 15 mM HEPES and 600 g/L glucose. These were further minced and digested using freshly prepared 200 mg/ml Liberase and 100 mg/ml DNAse in RPMI-1640 at 37°C for 1 h with the gentleMACS dissociator (Milteny Biotec). Cells were washed with 10% heat inactivated FBS in RPMI-1640 and passed through a 100 mm cell strainer. Single cell suspensions were counted for viability and stained for cell sorting.
Single-cell RNA sequencing. CD3+CD4+ and CD3+CD8+ T cells were sorted from digested tumor and non-malignant tissues, or Ficoll-purified and previously cryopreserved PBMC from the same patients, into 500 ml of PBS with 0.04% BSA. Double-positive (ie CD4+ and CD8+ by protein expression) cells were excluded from the sort strategy and therefore do not contribute to the observed population of cytotoxic CD4+ (single-positive) T cells. Cells were centrigued and resuspended into a concentration of 1000 cells/ml and all cells sorted were used when not exceeding the maximum number recommended by manufacturer. Droplet-based single-cell RNA sequencing was performed using the 10X Genomics Chromium Single Cell 3′ platform, version 1, according to manufacturer’s instructions. Following library preparation, sequencing was performed on an Illumina HiSeq 2500 (Rapid Run mode).  Single-cell TCR sequencing. For our overall patient TCR sequencing strategy, targeted PCR with NEBNext Ultra II Q5 Master Mix (New England Biolabs) used a pool of forward Va and Vb primers containing the TruSeq Read 1 primer sequence with a reverse P7 primer to amplify CDR3 sequences as well as the 10X Genomics barcodes. A second PCR with forward primers containing the Illumina P5, i5 and TruSeq Read 1 sequences was used with reverse P7 primer to generate TCR libraries for sequencing. Sequencing used an Illumina NovaSeq S1 with separate lanes for TCRa and TCRb sequencing. Read 1 contained 280 bp of the TCRa and TCRb CDR3 sequence, and the i7 read contained the 14 bp 10X Genomics barcode. For the specific results validating enrichment of tumor-matched TCRab clones in sorted KLRG1+ CD4+ T cells from PBMC (Patients 50 and 65, Supplemental Data 10), 10X Genomics Human Single Cell V(D)J reagents were used.

tag: disease state

tag: cell type

tag: treatment

tag: timepoint


title: Brain, CD3+ SS2 KO F13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F13


title: CRC2733LVM

city: Glasgow

first: Niranjan

last: Shirgaonkar

state: East Dunbartonshire

address: Switchback Rd, Garscube Estate

country: United Kingdom

institute: Cancer Research UK

description: Library name: CRC2733LVM

library_source: transcriptomic

data_processing:
Primary analysis of samples was performed using the bcbio-nextgen pipeline (version 1.0.9a)
RNASeq data were aligned with the RNASeq aligner STAR (version 2.5.4a)42 using 2-pass method, gene expression Transcript per Million (TPM) values were obtained from Salmon (version 0.9.1)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes TPM counts for each sample

extract_protocol:
RNA was extracted using the Rneasy Plus Mini Kit (Qiagen)
RNA libraries for RNA-Seq were prepared using the TruSeq Stranded Total RNA LT with Ribo-Zero Gold.

tag: cell line


title: Brain, CD3+ SS2 KO F11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F11


title: Untreated B (normal CD4) Gene Expression

description:
Library name: untreated_b_normal_cd4
Illumina HiSeq 2500 (rapid run)

source_name: Normal adjacent tissue

value: Normal adjacent tissue


title: CRC2580PRI

description: Library name: CRC2580PRI


title: Untreated B (blood CD8) Gene Expression

description:
Library name: untreated_b_blood_cd8
Illumina HiSeq 2500 (rapid run)

source_name: PBMC

value: PBMC


title: Brain, CD3+ SS2 KO F17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F17


title: Brain, CD3+ SS2 KO A10 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A10


title: Brain, CD3+ SS2 KO E8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_E8


title: mouse hindlimb field E9.75 H3K27ac ChIP rep1

city: Athens

first: Douglas

last: Menke

state: GA

address: 500 DW Brooks Drive

department: Genetics

institute: University of Georgia

description:
SE75 sequencing
mm_HF_E9.75_H3K27ac_naive_overlap.narrowPeak.gz
mm_HF_E9.75_H3K27ac_pooled.signal.bw

library_source: genomic

data_processing:
Libraries were sequenced by the Georgia Genomics and Bioinformatics Core (SE75) or by Genewiz (PE150). The GGBC provided pre-trimmed reads, while Genewiz reads were subsequently trimmed using cutadapt using the settings -O 1, -m 25
RNA-seq reads were aligned to mm10 using STAR (v. 2.7.3a). Transcripts were counted using HTSeq (v. 0.13.5). Differential gene expression was determined using DESeq2 (Galaxy v. 2.11.40.6).
ChIP-seq data were processed using the AQUAS Transcription Factor and Histone ChIP-seq pipeline. We used the pipeline's default bwa aligner to align mouse reads to mm10 (UCSC), chick to galGal6 (UCSC), alligator to allMis0.2/allMis1 (UCSC), turtle to CAS_Tse_1.0 NCBI RefSeq), and lizard to AnoSag2.0 (local genome build). Fragment size was set to 175 (-speak_spp 175, -extsize_macs2 175).
SPP was used to call IDR peaks using the default cutoff (0.05) in ISL1 ChIP-seq experiments performed in duplicate, while MACS2 peaks were used from individual experiments and from H3K27ac datasets. In H3K27ac datasets, the naive overlap peaks were used, while MACS2 peaks from ISL1 ChIP-seq in alligator, turtle, and lizard were filtered using a q-value cutoff of 0.01 and fold-enrichment cutoff of 4. bigWig files were generated using MACS2 and represent fold-enrichment values of ChIP vs control samples.
Mouse forelimb ISL1 ChIP-seq IDR peaks were used as a negative control to filter false-positive peaks from ISL1 peak sets, generating "FL_filtered" files
Assembly: varied by species (see above)
Supplementary files format and content: DESeq2 tabular files, SPP or MACS2 peak files, and MACS2 bigWig files

molecule: genomic DNA

source_name: hindlimb field

extract_protocol:
For RNA-seq, genital tubercle samples were placed in RNA-Later, which was then removed before freezing samples at -80C. For hindlimb field samples, both sides from each embryo were placed directly into mirVana Lysis/Binding buffer and frozen. RNA was extracted using the mirVana miRNA isolation kit. For ChIP-seq, tissues form multiple embryos were sonified using a probe sonifier followed by a bath sonifier. Lysates were then incubated with the antibody with a portion kept as input DNA.
RNA-seq libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina); ChIP-seq libraries were constructed using the NEBNext Ultra II Library Prep Kit

tag: developmental stage

value: ICR CD-1 outbred (Envigo)

value: WT

tag: chip antibody

value: H3K27ac (Millipore or Cosmo Bio, CMA309)


title: Brain, CD3+ SS2 KO A11 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A11


title: Brain, CD3+ SS2 KO E6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_E6


title: Untreated B (blood CD4) Gene Expression

description:
Library name: untreated_b_blood_cd4
Illumina HiSeq 2500 (rapid run)


title: CRC2552LVM

description: Library name: CRC2552LVM


title: CRC2552PRI

description: Library name: CRC2552PRI


title: Brain, CD3+ SS2 KO A17 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A17


title: mouse forelimb bud E10.5 ISL1 input

description: SE75 sequencing

source_name: forelimb bud


title: CRC2754PRI

description: Library name: CRC2754PRI


title: Untreated A (tumor CD8) Gene Expression

description:
Library name: untreated_a_tumor_cd8
Illumina HiSeq 2500 (rapid run)


title: CRC2476PRI

description: Library name: CRC2476PRI


title: Untreated B (normal CD8) Gene Expression

description:
Library name: untreated_b_normal_cd8
Illumina HiSeq 2500 (rapid run)


title: Brain, CD3+ SS2 KO E24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_E24


title: CRC2440PRI

description: Library name: CRC2440PRI


title: Untreated A (normal CD4) Gene Expression

description:
Library name: untreated_a_normal_cd4
Illumina HiSeq 2500 (rapid run)


title: CRC2423PRI

description: Library name: CRC2423PRI


title: Untreated A (tumor CD4) Gene Expression

description:
Library name: untreated_a_tumor_cd4
Illumina HiSeq 2500 (rapid run)


title: Brain, CD3+ SS2 KO E20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_E20


title: Brain, CD3+ SS2 KO E19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_E19


title: Untreated A (blood CD8) Gene Expression

description:
Library name: untreated_a_blood_cd8
Illumina HiSeq 2500 (rapid run)


title: mouse forelimb bud E10.5 ISL1 ChIP rep1

description:
SE75 sequencing
mm_FL_E10.5_ISL1_IDR.narrowPeak.gz


title: CRC2413PRI

description: Library name: CRC2413PRI


title: mouse genital tubercle E12.5 ISL1 input rep1

description: SE75 sequencing

source_name: genital tubercle


title: Brain, CD3+ SS2 KO E18 mouse 1 scRNAseq

description:
SmartSeq2
43_6_E18


title: mouse genital tubercle E12.5 ISL1 input rep2

description: SE75 sequencing


title: Brain, CD3+ SS2 KO F10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F10


title: Untreated A (blood CD4) Gene Expression

description:
Library name: untreated_a_blood_cd4
Illumina HiSeq 2500 (rapid run)


title: Brain, CD3+ SS2 KO E3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_E3


title: CRC2367PRI

description: Library name: CRC2367PRI


title: Healthy Blood (CD8 replicate 3) Gene Expression

description:
Library name: healthy_blood_cd8_replicate3
Illumina HiSeq 2500 (rapid run)

value: healthy


title: mouse genital tubercle E12.5 ISL1 ChIP rep2

description:
SE75 sequencing
mm_GT_E12.5_ISL1_IDR.narrowPeak.gz
mm_GT_E12.5_ISL1_IDR_FL_filtered.bed
mm_GT_E12.5_ISL1_pooled.bw


title: mouse forelimb bud E10.5 ISL1 ChIP rep2


title: Brain, CD3+ SS2 KO D9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D9


title: Healthy Blood (CD8 replicate 2) Gene Expression

description:
Library name: healthy_blood_cd8_replicate2
Illumina HiSeq 2500 (rapid run)


title: Brain, CD3+ SS2 KO E10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_E10


title: CRC2255PRI

description: Library name: CRC2255PRI


title: Brain, CD3+ SS2 KO D8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D8


title: CRC2135PRI

description: Library name: CRC2135PRI


title: mouse hindlimb field E9.75 ISL1 input rep2

description: SE75 sequencing


title: CRC2305LVM

description: Library name: CRC2305LVM


title: Healthy Blood (CD8 replicate 1) Gene Expression

description:
Library name: healthy_blood_cd8_replicate1
Illumina HiSeq 2500 (rapid run)


title: mouse hindlimb field E9.75 ISL1 input rep1

description: SE75 sequencing


title: Healthy Blood (CD4 replicate 3) Gene Expression

description:
Library name: healthy_blood_cd4_replicate3
Illumina HiSeq 2500 (rapid run)


title: CRC2130PRI

description: Library name: CRC2130PRI


title: mouse hindlimb field E9.75 ISL1 ChIP rep1

description:
SE75 sequencing
mm_HF_E9.75_ISL1_IDR.narrowPeak.gz
mm_HF_E9.75_ISL1_IDR_FL_filtered.bed
mm_HF_E9.75_ISL1_pooled.bw


title: Brain, CD3+ SS2 KO D6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D6


title: Healthy Blood (CD4 replicate 1) Gene Expression

description:
Library name: healthy_blood_cd4_replicate1
Illumina HiSeq 2500 (rapid run)


title: Brain, CD3+ SS2 KO D7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D7


title: Brain, CD3+ SS2 KO D4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D4


title: mouse hindlimb field E9.75 ISL1 ChIP rep2


title: mouse genital tubercle E12.5 ISL1 ChIP rep1


title: Brain, CD3+ SS2 KO D5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D5


title: CRC2001PRI

description: Library name: CRC2001PRI


title: mouse genital tubercle E12.5 RNA-seq control rep5

description:
SE75 sequencing
mm_GT_E12.5_DESeq2_result_file.tabular
mm_GT_E12.5_DESeq2_Normalized_counts_file.tabular


title: Chemo (tumor CD8) Gene Expression

description:
Library name: chemo_tumor_cd8
Illumina HiSeq 2500 (rapid run)

value: chemo

value: post-chemotherapy


title: CRC1924PRI

description: Library name: CRC1924PRI


title: Brain, CD3+ SS2 KO D24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D24


title: mouse genital tubercle E12.5 RNA-seq control rep4


title: CRC1846PRI

description: Library name: CRC1846PRI


title: mouse genital tubercle E12.5 RNA-seq control rep3


title: Chemo (normal CD8) Gene Expression

description:
Library name: chemo_normal_cd8
Illumina HiSeq 2500 (rapid run)


title: Chemo (tumor CD4) Gene Expression

description:
Library name: chemo_tumor_cd4
Illumina HiSeq 2500 (rapid run)

value: Tumor


title: Brain, CD3+ SS2 KO D23 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D23


title: Chemo (normal CD4) Gene Expression

description:
Library name: chemo_normal_cd4
Illumina HiSeq 2500 (rapid run)

value: bladder cancer


title: Healthy Blood (CD4 replicate 2) Gene Expression

description:
Library name: healthy_blood_cd4_replicate2
Illumina HiSeq 2500 (rapid run)

value: T cells


title: Brain, CD3+ SS2 KO D22 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D22


title: mouse genital tubercle E12.5 RNA-seq control rep2


title: CRC1826PRI

description: Library name: CRC1826PRI


title: mouse genital tubercle E12.5 RNA-seq control rep1


title: CRC2015MET

description: Library name: CRC2015MET


title: Brain, CD3+ SS2 KO D21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D21


title: Chemo (blood CD8) Gene Expression

description:
Library name: chemo_blood_cd8
Illumina HiSeq 2500 (rapid run)


title: mouse genital tubercle E12.5 RNA-seq Isl1 cKO rep5


title: Brain, CD3+ SS2 KO D20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D20


title: Chemo (blood CD4) Gene Expression

description:
Library name: chemo_blood_cd4
Illumina HiSeq 2500 (rapid run)


title: CRC1732PRI

description: Library name: CRC1732PRI


title: CRC1798LVM

description: Library name: CRC1798LVM


title: Anti-PD-L1 E (blood CD8 pre) Gene Expression

description:
Library name: anti_pdl1_e_blood_cd8_pre
Illumina HiSeq 2500 (rapid run)


title: mouse genital tubercle E12.5 RNA-seq Isl1 cKO rep3


title: Brain, CD3+ SS2 KO D18 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D18


title: Anti-PD-L1 E (blood CD8 post) Gene Expression

description:
Library name: anti_pdl1_e_blood_cd8_post
Illumina HiSeq 2500 (rapid run)

value: post-atezolizumab


title: CRC1707PRI-1

description: Library name: CRC1707PRI-1


title: mouse genital tubercle E12.5 RNA-seq Isl1 cKO rep1


title: CRC1837LVM

description: Library name: CRC1837LVM


title: mouse genital tubercle E12.5 RNA-seq Isl1 cKO rep2


title: Anti-PD-L1 E (blood CD4 pre) Gene Expression

description:
Library name: anti_pdl1_e_blood_cd4_pre
Illumina HiSeq 2500 (rapid run)

value: pre-treatment


title: Brain, CD3+ SS2 KO D17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D17

value: Brain


title: mouse hindlimb field E9.75 RNA-seq control rep6

description:
SE75 sequencing
mm_HF_E9.75_DESeq2_result_file.tabular
mm_HF_E9.75_DESeq2_Normalized_counts_file.tabular


title: CRC1707LVM

description: Library name: CRC1707LVM


title: Brain, CD3+ SS2 KO D16 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D16

value: male


title: Anti-PD-L1 D (tumor CD8) Gene Expression

description:
Library name: anti_pdl1_d_tumor_cd8
Illumina HiSeq 2500 (rapid run)


title: CRC1671PRI

description: Library name: CRC1671PRI


title: mouse genital tubercle E12.5 RNA-seq Isl1 cKO rep4


title: mouse hindlimb field E9.75 RNA-seq control rep5


title: Anti-PD-L1 E (blood CD4 post) Gene Expression

description:
Library name: anti_pdl1_e_blood_cd4_post
Illumina HiSeq 2500 (rapid run)


title: Brain, CD3+ SS2 KO D15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D15

value: KO


title: Brain, CD3+ SS2 KO D14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D14

value: 15 months


title: Brain, CD3+ SS2 KO D2 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D2


title: CRC1775PRI

description: Library name: CRC1775PRI


title: Anti-PD-L1 D (normal CD4) Gene Expression

description:
Library name: anti_pdl1_d_normal_cd4
Illumina HiSeq 2500 (rapid run)

value: Normal adjacent tissue


title: CRC1489PRI

description: Library name: CRC1489PRI


title: Brain, CD3+ SS2 KO D12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D12


title: Brain, CD3+ SS2 KO D13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D13


title: CRC1657PRI

description: Library name: CRC1657PRI


title: mouse hindlimb field E9.75 RNA-seq control rep3


title: CRC1685PRI

description: Library name: CRC1685PRI


title: mouse hindlimb field E9.75 RNA-seq control rep4


title: Anti-PD-L1 D (blood CD8 pre) Gene Expression

description:
Library name: anti_pdl1_d_blood_cd8_pre
Illumina HiSeq 2500 (rapid run)

value: PBMC


title: Anti-PD-L1 D (tumor CD4) Gene Expression

description:
Library name: anti_pdl1_d_tumor_cd4
Illumina HiSeq 2500 (rapid run)


title: Brain, CD3+ SS2 KO D1 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D1


title: mouse hindlimb field E9.75 RNA-seq Isl1 cKO rep6


title: Brain, CD3+ SS2 KO D10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_D10


title: CRC1481LVM

description: Library name: CRC1481LVM


title: Anti-PD-L1 D (blood CD8 post) Gene Expression

description:
Library name: anti_pdl1_d_blood_cd8_post
Illumina HiSeq 2500 (rapid run)


title: CRC1409MET

description: Library name: CRC1409MET


title: Anti-PD-L1 D (blood CD4 pre) Gene Expression

description:
Library name: anti_pdl1_d_blood_cd4_pre
Illumina HiSeq 2500 (rapid run)


title: mouse hindlimb field E9.75 RNA-seq control rep2


title: mouse hindlimb field E9.75 RNA-seq control rep1


title: CRC1414PRI

description: Library name: CRC1414PRI


title: CRC1463PRI

description: Library name: CRC1463PRI


title: mouse hindlimb field E9.75 RNA-seq Isl1 cKO rep4


title: Brain, CD3+ SS2 KO C5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C5


title: CRC1391PRI

description: Library name: CRC1391PRI


title: Anti-PD-L1 D (blood CD4 post) Gene Expression

description:
Library name: anti_pdl1_d_blood_cd4_post
Illumina HiSeq 2500 (rapid run)


title: Anti-PD-L1 C (tumor CD4) Gene Expression

description:
Library name: anti_pdl1_c_tumor_cd4
Illumina HiSeq 2500 (rapid run)


title: Brain, CD3+ SS2 KO C8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C8


title: Brain, CD3+ SS2 KO C6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C6


title: mouse hindlimb field E9.75 RNA-seq Isl1 cKO rep5


title: mouse hindlimb field E9.75 RNA-seq Isl1 cKO rep2


title: Brain, CD3+ SS2 KO C4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C4


title: Anti-PD-L1 C (tumor CD8) Gene Expression

description:
Library name: anti_pdl1_c_tumor_cd8
Illumina HiSeq 2500 (rapid run)


title: Anti-PD-L1 C (blood CD8 pre) Gene Expression

description:
Library name: anti_pdl1_c_blood_cd8_pre
Illumina HiSeq 2500 (rapid run)


title: Anti-PD-L1 C (blood CD8 post) Gene Expression

description:
Library name: anti_pdl1_c_blood_cd8_post
Illumina HiSeq 2500 (rapid run)


title: mouse hindlimb field E9.75 RNA-seq Isl1 cKO rep3


title: CRC1177PRI

description: Library name: CRC1177PRI


title: CRC1258LVM

description: Library name: CRC1258LVM


title: CRC1079LVM

description: Library name: CRC1079LVM


title: Brain, CD3+ SS2 KO C24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C24


title: Brain, CD3+ SS2 KO C21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C21


title: TIGK 24h-3

city: Chicago

first: Chen

last: Han

state: IL

address: 801 S. Paulina St.

department: Center for Wound healing and Tissue Regeneration

institute: University of Illinois Chicago

data_processing:
Clean data was obtained by using in-house perl scripts (Novogene America) to remove reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Hisat2 (v2.0.5) was used to index and map reads to the human reference genome. The reference genome and gene model annotation files were downloaded from the genome website directly.
The mapped reads were assembled with StringTie (v1.3.3b).
Read numbers mapped to each gene were then counted in R with FeatureCounts (v1.5.0-p3) and an FPKM of each gene was calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized FKPM values for each sample

source_name: Gingival

extract_protocol:
RNA was harvested at 0 h, 6 h, or 24 h post-scratch using Trizol and purified with an RNA Clean & Concentrator-25 kit. 1 ug of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared for by Novogene (Novogene America).

treatment_protocol: Cells were scratched or non-scratched (unwounded baseline - 0 h)

value: Gingival

value: TIGK

value: Gingival Keratinocytes

value: scratched (24 h)

tag: time

value: 24 hr


title: Anti-PD-L1 C (blood CD4 post) Gene Expression

description:
Library name: anti_pdl1_c_blood_cd4_post
Illumina HiSeq 2500 (rapid run)


title: mouse hindlimb field E9.75 RNA-seq Isl1 cKO rep1


title: Brain, CD3+ SS2 KO C19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C19


title: CRC1371PMET

description: Library name: CRC1371PMET


title: TIGK 24h-2


title: GSC G7 invitro model with CD8 ko

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: Library name: GSCG7_CD8KO

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and used a standard Illumina dual-index, paired-end constructs with the single Cell 14 bp barcode in the i7 index read (14 nt), sample index sequences in the i5 index read (8 nt), and Read 1 (98 nt) and Read 2 (10 nt) with standard Illumina sequencing primers in paired-end sequencing.
raw bcl files were processed using cellranger mkfastq and cellranger count
Assembly: hg38
Supplementary files format and content: barcodes.tsv, genes.tsv and matrix.mtx ( 3 files per sample, output from cellranger count) are submitted as processed files.

growth_protocol: GSC cell lines were grown on laminin-coated substrate in N2B27 media supplemented by EGF and FGF in subconfluent conditions.

extract_protocol:
5000 cells from subconfluent GSC827 (matched for density and media changes) were loaded on a a GemCode Single Cell Instrument (10x Genomics) to generate single-cell GEMs for library preparation using Single Cell Gel Bead Kit (P/N 120217) according to manufacturer's guidelines. G0/G1 cells were first sorted on an FACSAria II (BD Biosciences) for the cells postive only for mCherry-hCDT1(aa30/120).
RNA libraries were prepared for sequencing using Single Cell Library Kit from 10x Genomics (P/N 120218) according to manufacturer's guidelines.

treatment_protocol: CRISPR KO was performed through lentiviral transduction (lentiCRISPR v2 (Zhang lab)) and KO samples were collected at least 14 days post-selection.

value: CD8 ko


title: Brain, CD3+ SS2 KO C14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C14


title: TIGK 24h-1


title: Anti-PD-L1 B (tumor CD8) Gene Expression

description:
Library name: anti_pdl1_b_tumor_cd8
Illumina HiSeq 2500 (rapid run)

value: Tumor


title: GSC 578T invitro model with KAT5 ko

description: Library name: GSC578t_kat5KO

value: KAT5 ko


title: GSC 578T invitro model with CD8 ko

description: Library name: GSC578t_CD8KO


title: Anti-PD-L1 C (normal CD4) Gene Expression

description:
Library name: anti_pdl1_c_normal_cd4
Illumina HiSeq 2500 (rapid run)

value: bladder cancer

value: T cells


title: TIGK 6h-3

value: scratched (6 h)

value: 6 hr


title: Anti-PD-L1 C (blood CD4 pre) Gene Expression

description:
Library name: anti_pdl1_c_blood_cd4_pre
Illumina HiSeq 2500 (rapid run)

value: pre-treatment


title: Brain, CD3+ SS2 KO C12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C12

value: Brain

value: male

value: KO


title: TIGK 6h-2


title: GSC 464T invitro model with CD8 ko

description: Library name: GSC464T_CD8KO


title: Brain, CD3+ SS2 KO C2 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C2

value: 15 months


title: Brain, CD3+ SS2 KO C11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C11


title: Anti-PD-L1 B (blood CD8 pre) Gene Expression

description:
Library name: anti_pdl1_b_blood_cd8_pre
Illumina HiSeq 2500 (rapid run)

value: PBMC


title: Anti-PD-L1 B (tumor CD4) Gene Expression

description:
Library name: anti_pdl1_b_tumor_cd4
Illumina HiSeq 2500 (rapid run)

value: post-atezolizumab


title: Brain, CD3+ SS2 KO C13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_C13


title: Brain, CD3+ SS2 KO B9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B9


title: GSC 464T invitro model with KAT5 ko

description: Library name: GSC464T_kat5KO


title: Anti-PD-L1 B (blood CD8 post) Gene Expression

description:
Library name: anti_pdl1_b_blood_cd8_post
Illumina HiSeq 2500 (rapid run)


title: Anti-PD-L1 B (normal CD4) Gene Expression

description:
Library name: anti_pdl1_b_normal_cd4
Illumina HiSeq 2500 (rapid run)

value: Normal adjacent tissue


title: Brain, CD3+ SS2 KO B8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B8


title: GSC 448T invitro model with KAT5 ko

description: Library name: GSC448T_kat5KO


title: GSC G7 invitro model with KAT5 ko

description: Library name: GSCG7_kat5KO


title: TIGK 0 h-3

value: Gingival

value: TIGK

value: Gingival Keratinocytes

value: non-scratched (0 h)

value: 0 hr


title: Anti-PD-L1 B (blood CD4 pre) Gene Expression

description:
Library name: anti_pdl1_b_blood_cd4_pre
Illumina HiSeq 2500 (rapid run)

value: bladder cancer


title: GSC 308 invitro model with CD8 ko

description: Library name: GSC308_CD8KO

value: CD8 ko


title: GSC 308 invitro model with KAT5 ko

description: Library name: GSC308_KAT5KO

value: KAT5 ko


title: Anti-PD-L1 B (blood CD4 post) Gene Expression

description:
Library name: anti_pdl1_b_blood_cd4_post
Illumina HiSeq 2500 (rapid run)

value: T cells


title: Brain, CD3+ SS2 KO B7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B7


title: Brain, CD3+ SS2 KO B6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B6


title: Brain, CD3+ SS2 KO B5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B5


title: GSC 448T invitro model with CD8 ko

description: Library name: GSC448T_CD8KO


title: TIGK 0 h-2


title: Anti-PD-L1 A (tumor CD8) Gene Expression

description:
Library name: anti_pdl1_a_tumor_cd8
Illumina HiSeq 2500 (rapid run)

value: Tumor


title: HaCaT 24h-3

source_name: Skin

value: Skin

value: HaCaT

value: Skin Keratinocytes

value: scratched (24 h)

value: 24 hr


title: GSC 1406 invitro model with KAT5 ko

description: Library name: GSC1406_kat5KO.


title: Anti-PD-L1 A (tumor CD4) Gene Expression

description:
Library name: anti_pdl1_a_tumor_cd4
Illumina HiSeq 2500 (rapid run)

value: post-atezolizumab


title: TIGK 6h-1

value: scratched (6 h)

value: 6 hr


title: Brain, CD3+ SS2 KO B4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B4

value: Brain

value: male

value: KO

value: 15 months


title: SRA01/04 DHN-A3

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

country: China

institute: Tongji University

description: Library name: DHN-A3

data_processing:
The fastq data were cleaned with the Fastx-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with the default protocol by the manufacturer. The Blastn (http://blast.ncbi.nlm.nih.gov/) was used to annotated the mRNA. The Bowtie ( http://bowtie-bio.sourceforge.net/index.shtml ) was used to mapped the sequences to reference gennome.
Assembly: hg38
Supplementary files format and content: Raw counts

source_name: cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using AccuNext Stranded RNA-Seq Library Kit following manufacturer's protocols.

value: cell line

value: Immortalized human lens epithelial cell line


title: GSC 1406 invitro model with CD8 ko

description: Library name: GSC1406_CD8KO

value: CD8 ko


title: Brain, CD3+ SS2 KO B3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B3


title: GSC 131 invitro model with CD8 ko

description: Library name: GSC131_CD8KO


title: Brain, CD3+ SS2 KO B24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B24


title: SRA01/04 DHN-A1

description: Library name: DHN-A1


title: SRA01/04 DHN-A2

description: Library name: DHN-A2


title: HaCaT 24h-1


title: TIGK 0 h-1

value: Gingival

value: TIGK

value: Gingival Keratinocytes

value: non-scratched (0 h)

value: 0 hr


title: HaCaT 6h-2

value: Skin

value: HaCaT

value: Skin Keratinocytes


title: GSC 131 invitro model with KAT5 ko

description: Library name: GSC131_KAT5KO.

value: KAT5 ko


title: HaCaT 6h-1

value: scratched (6 h)

value: 6 hr


title: HaCaT 6h-3


title: Brain, CD3+ SS2 KO B23 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B23

value: Brain

value: male


title: GSC 025T invitro model with CD8 ko

description: Library name: GSC025T_CD8KO


title: SRA01/04 DHN3

description: Library name: DHN3


title: HaCaT 0 h-3


title: SRA01/04 DHN2

description: Library name: DHN2


title: Brain, CD3+ SS2 KO B21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B21

value: KO

value: 15 months


title: Brain, CD3+ SS2 KO B22 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B22


title: HaCaT 24h-2

value: scratched (24 h)

value: 24 hr


title: GSC 025T invitro model with KAT5 ko

description: Library name: GSC025T_kat5KO


title: Brain, CD3+ SS2 KO B20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B20


title: HaCaT 0 h-2


title: SRA01/04 DHN1

description: Library name: DHN1

value: cell line

value: Immortalized human lens epithelial cell line


title: PBMC_Critical_Patient3

first: Anastasia

last: Kotanidou

address: 45 Ipsilantou Str

department: 1st Department of Critical Care Medicine and Pulmonary Services

country: Greece

institute: Evangelismos Hospital, National and Kapodistrian University of Athens

description: Library name: CI3

data_processing:
The quality of the FASTQ files was assessed with the fastqc software. Reads werealigned to the GRCh38 genome were performed with the Hisat2 aligner. FeatureCounts was utilized for the step of read summarization at the gene level. Differential expression analysis was conducted by DESeq2.
Assembly: GRCh38
Supplementary files format and content: Raw processed counts

source_name: blood cells

extract_protocol:
RNA was extracted using the Rneasy mini kit (Qiagen).
RnNA libraries were prepared using   the 3′ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to the manufacturer’s instructions.

value: blood cells


title: SRA01/04 NC-A3

description: Library name: NC-A3


title: HaCaT 0 h-1

value: non-scratched (0 h)


title: PBMC_Critical_Patient2

description: Library name: CI2


title: Brain, CD3+ SS2 KO B2 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B2


title: SRA01/04 NC-A2

description: Library name: NC-A2


title: PBMC_Critical_Patient1

description: Library name: CI1


title: Stable-cell, Unsorted control (live cell input), rep 2

city: Seoul

first: Myeonghwan

last: Kim

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
CRISPR screen
stbl_un_2

data_processing:
Before alignment, 20-nt sgRNA sequence per read was extracted from demultiplexed FASTQ files using cutadapt. sgRNA-extracted reads were aligned to sgRNA library index using Bowtie2 with unique alignment and no mismatch options. Aligned reads were RPM-normalized
Assembly: Bowtie2 index building using Brunello sgRNA pooled library (Addgene #73179)
Supplementary files format and content: RPM-normalized count is listed in normed-count.txt (row - sgRNA, column - sample abbreviation)
Library strategy: PCR amplicon-seq for gDNA region of sgRNA integration

extract_protocol:
HCT116 cells were transduced by CRISPR lentivirus generated from Brunello sgRNA pooled library (Addgene #73179) and transduced cells were selected by puromycin. After puromycin selection, LNP-formulated EGFP-encoding mRNA with or without base modification was transfected to pooled KO cells, and cells with different GFP intensity was FACS sorted for subsequent library preparation.
sgRNA sequence-containing region of gDNA from FACS sorted cells were PCR-amplified with TruSeq adaptor, purified using SPRI beads, then sequenced


title: Brain, CD3+ SS2 KO B19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B19


title: SRA01/04 NC-A1

description: Library name: NC-A1


title: Stable-cell, Bottom 0-2.5% (GFP Low), rep 2

description:
CRISPR screen
stbl_dim_2_5_2


title: SRA01/04 NC3

description: Library name: NC3


title: Brain, CD3+ SS2 KO B18 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B18


title: PBMC_Severe_Patient4

description: Library name: CS4


title: Stable-cell, Bottom 2.5-5% (GFP 2nd Low), rep 2

description:
CRISPR screen
stbl_dim_5_2


title: Stable-cell, Top 2.5-5% (GFP 2nd High), rep 2

description:
CRISPR screen
stbl_bri_5_2


title: PBMC_Severe_Patient3

description: Library name: CS3


title: Brain, CD3+ SS2 KO B17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B17


title: Stable-cell, Top 0-2.5% (GFP High), rep 2

description:
CRISPR screen
stbl_bri_2_5_2


title: PBMC_Critical_Patient4

description: Library name: CI4


title: BM7

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: Column BM7 within deSeq2_counts.txt

data_processing:
Data Formatting: bcltofastq-2.19.0
Data Cleaning: fastp 0.20.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment: STAR_2.7.6a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification: subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Assembly: hg38 + Gencode-36 Annotation
Supplementary files format and content: raw gene counts

source_name: Apheresis buffy coat

growth_protocol: N/A, primary samples from human subjects

extract_protocol:
Total RNA was purified with Qiagen Rneasy PLUS kit per manufacturer recommendations. Eluted in nuclease-free water
The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample using Illumina’s HiSeq2500v4.

treatment_protocol: N/A, no treatment was perforrmed

value: Apheresis buffy coat

value: mononuclear cells

tag: group

value: BM


title: Brain, CD3+ SS2 KO B15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B15


title: PBMC_Severe_Patient1

description: Library name: CS1


title: Brain, CD3+ SS2 KO B14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B14


title: Stable-cell, Unsorted control (live cell input), rep 1

description:
CRISPR screen
stbl_un_1


title: BM6

description: Column BM6 within deSeq2_counts.txt


title: Stable-cell, Bottom 0-2.5% (GFP Low), rep 1

description:
CRISPR screen
stbl_dim_2_5_1


title: PBMC_Mild_Patient4

description: Library name: CM4


title: Brain, CD3+ SS2 KO B13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B13


title: Stable-cell, Bottom 2.5-5% (GFP 2nd Low), rep 1

description:
CRISPR screen
stbl_dim_5_1


title: Brain, CD3+ SS2 KO B12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B12


title: PBMC_Mild_Patient3

description: Library name: CM3


title: Stable-cell, Top 2.5-5% (GFP 2nd High), rep 1

description:
CRISPR screen
stbl_bri_5_1


title: BM4

description: Column BM4 within deSeq2_counts.txt


title: Brain, CD3+ SS2 KO B11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B11


title: PBMC_Mild_Patient2

description: Library name: CM2


title: PBMC_Mild_Patient1

description: Library name: CM1


title: SRA01/04 NC2

description: Library name: NC2


title: BM3

description: Column BM3 within deSeq2_counts.txt


title: Stable-cell, Top 0-2.5% (GFP High), rep 1

description:
CRISPR screen
stbl_bri_2_5_1


title: SRA01/04 NC1

description: Library name: NC1


title: Brain, CD3+ SS2 KO B16 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B16


title: PBMC_Severe_Patient2

description: Library name: CS2


title: UTP, Unsorted control (live cell input), rep 2

description:
CRISPR screen
utp_un_2


title: BM2

description: Column BM2 within deSeq2_counts.txt


title: PBMC_Healthy_Patient3

description: Library name: H3

value: Healthy


title: Brain, CD3+ SS2 KO B1 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B1


title: Brain, CD3+ SS2 KO B10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_B10


title: BM1

description: Column BM1 within deSeq2_counts.txt


title: UTP, Bottom 0-2.5% (GFP Low), rep 2

description:
CRISPR screen
utp_dim_2_5_2


title: Brain, CD3+ SS2 KO A9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A9


title: bcCML9

description: Column bcCML9 within deSeq2_counts.txt

value: bcCML


title: UTP, Bottom 2.5-5% (GFP 2nd Low), rep 2

description:
CRISPR screen
utp_dim_5_2


title: PBMC_Healthy_Patient2

description: Library name: H2


title: BM5

description: Column BM5 within deSeq2_counts.txt


title: PBMC_Healthy_Patient1

description: Library name: H1


title: Brain, CD3+ SS2 KO A8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A8


title: bcCML8

description: Column bcCML8 within deSeq2_counts.txt


title: UTP, Top 0-2.5% (GFP High), rep 2

description:
CRISPR screen
utp_bri_2_5_2


title: Brain, CD3+ SS2 KO A7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A7


title: Brain, CD3+ SS2 KO A6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A6


title: PBMC_Healthy_Patient4

description: Library name: H4


title: bcCML5

description: Column bcCML5 within deSeq2_counts.txt


title: UTP, Bottom 0-2.5% (GFP Low), rep 1

description:
CRISPR screen
utp_dim_2_5_1


title: bcCML6

description: Column bcCML6 within deSeq2_counts.txt


title: bcCML7

description: Column bcCML7 within deSeq2_counts.txt


title: UTP, Unsorted control (live cell input), rep 1

description:
CRISPR screen
utp_un_1


title: bcCML4

description: Column bcCML4 within deSeq2_counts.txt


title: Brain, CD3+ SS2 KO A5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A5


title: hFOB cells, Day10, replicate 1

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

description: Library name: D10_rep1

data_processing:
Raw sequencing read quality was assessed using FastQC and RSeQC.
Reads were aligned to the human reference genome (GENCODE v34) using HISAT2.
Read counts in genes were quantified using StringTie.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: hFOB 1.19

growth_protocol: hFOB 1.19 cells (ATCC #CRL-11372) were cultured at 34°C in minimal essential media (MEM; Gibco #10370‐021) supplemented with 10% fetal bovine serum (FBS; Atlantic Biologicals #S12450), 1% Glutamax (Gibco #35050‐061), and 1% Pen Strep (Gibco #15140‐122), following ATCC recommendations.

extract_protocol:
Total RNA was extracted from ~0.5 × 106 cells at days 0, 2, 4, 6, 8, and 10 of differentiation using the RNeasy Mini Kit (QIAGEN #74106) according to the manufacturer's protocol.
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Osteogenic differentiation was induced (Day 0) by culturing hFOB 1.19 cells at 39.5°C in MEM alpha (Gibco #12571‐063) supplemented with 10% FBS, 1% Glutamax, 1% Peni Strep, 50 μg/μL Ascorbic Acid (Sigma‐Aldrich #A4544‐25G), 10mM beta‐Glycerophosphate (Sigma‐Aldrich #G9422‐100G), and 10nM Dexamethasone (Sigma‐Aldrich #D4902‐25MG).

value: hFOB 1.19

value: human fetal osteoblasts

value: Day 10

value: osteogenic differentiation

tag: replicate


title: hFOB cells, Day8, replicate 3

description: Library name: D8_rep3

value: Day 8


title: hFOB cells, Day10, replicate 2

description: Library name: D10_rep2


title: Brain, CD3+ SS2 KO A24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A24

value: Brain

value: male

value: KO

value: 15 months


title: hFOB cells, Day8, replicate 2

description: Library name: D8_rep2


title: UTP, Top 2.5-5% (GFP 2nd High), rep 1

description:
CRISPR screen
utp_bri_5_1


title: UTP, Bottom 2.5-5% (GFP 2nd Low), rep 1

description:
CRISPR screen
utp_dim_5_1


title: bcCML3

description: Column bcCML3 within deSeq2_counts.txt


title: bcCML2

description: Column bcCML2 within deSeq2_counts.txt


title: hFOB cells, Day8, replicate 1

description: Library name: D8_rep1


title: Brain, CD3+ SS2 KO A22 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A22


title: hFOB cells, Day10, replicate 3

description: Library name: D10_rep3


title: hFOB cells, Day6, replicate 3

description: Library name: D6_rep3

value: Day 6


title: bcCML1

description: Column bcCML1 within deSeq2_counts.txt


title: UTP, Top 0-2.5% (GFP High), rep 1

description:
CRISPR screen
utp_bri_2_5_1


title: N1m, Unsorted control (live cell input), rep 2

description:
CRISPR screen
n1m_un_2


title: Brain, CD3+ SS2 KO A23 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A23


title: hFOB cells, Day6, replicate 2

description: Library name: D6_rep2


title: UTP, Top 2.5-5% (GFP 2nd High), rep 2

description:
CRISPR screen
utp_bri_5_2


title: Brain, CD3+ SS2 KO A21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A21


title: Brain, CD3+ SS2 KO A3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A3


title: hFOB cells, Day6, repliacte 1

description: Library name: D6_rep1


title: N1m, Bottom 0-2.5% (GFP Low), rep 2

description:
CRISPR screen
n1m_dim_2_5_2


title: Brain, CD3+ SS2 KO A20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A20


title: AML9

description: Column AML9 within deSeq2_counts.txt

value: AML


title: N1m, Bottom 2.5-5% (GFP 2nd Low), rep 2

description:
CRISPR screen
n1m_dim_5_2


title: hFOB cells, Day4, replicate 3

description: Library name: D4_rep3

value: Day 4


title: Brain, CD3+ SS2 KO A19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A19


title: hFOB cells, Day4, replicate 2

description: Library name: D4_rep2


title: AML7

description: Column AML7 within deSeq2_counts.txt

value: Apheresis buffy coat


title: Brain, CD3+ SS2 KO A17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A17


title: AML5

description: Column AML5 within deSeq2_counts.txt

value: mononuclear cells


title: AML3

description: Column AML3 within deSeq2_counts.txt


title: N1m, Bottom 0-2.5% (GFP Low), rep 1

description:
CRISPR screen
n1m_dim_2_5_1


title: AML4

description: Column AML4 within deSeq2_counts.txt


title: hFOB cells, Day2, replicate 2

description: Library name: D2_rep2

value: Day 2


title: hFOB cells, Day4, replicate 1

description: Library name: D4_rep1


title: Brain, CD3+ SS2 KO A13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A13


title: N1m, Top 2.5-5% (GFP 2nd High), rep 2

description:
CRISPR screen
n1m_bri_5_2


title: N1m, Top 0-2.5% (GFP High), rep 2

description:
CRISPR screen
n1m_bri_2_5_2


title: Brain, CD3+ SS2 KO A14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A14


title: N1m, Top 0-2.5% (GFP High), rep 1

description:
CRISPR screen
n1m_bri_2_5_1


title: hFOB cells, Day2, replicate 3

description: Library name: D2_rep3


title: Brain, CD3+ SS2 KO A15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A15


title: AML2

description: Column AML2 within deSeq2_counts.txt


title: AML6

description: Column AML6 within deSeq2_counts.txt


title: hFOB cells, Day0, replicate 2

description: Library name: D0_rep2

value: Day 0


title: N1m, Bottom 2.5-5% (GFP 2nd Low), rep 1

description:
CRISPR screen
n1m_dim_5_1


title: Brain, CD3+ SS2 KO A12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A12


title: bcCML10

description: Column bcCML10 within deSeq2_counts.txt

value: bcCML


title: hFOB cells, Day0, replicate 3

description: Library name: D0_rep3

value: hFOB 1.19


title: AML8

description: Column AML8 within deSeq2_counts.txt


title: Brain, CD3+ SS2 KO A11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A11


title: Brain, CD3+ SS2 KO A2 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A2


title: N1m, Top 2.5-5% (GFP 2nd High), rep 1

description:
CRISPR screen
n1m_bri_5_1


title: N1m, Unsorted control (live cell input), rep 1

description:
CRISPR screen
n1m_un_1


title: hFOB cells, Day0, replicate 1

description: Library name: D0_rep1

value: human fetal osteoblasts


title: RNAseq_HDP2_Day4_WT_rep2

city: Boston

first: Stuart

last: Orkin

state: MA

address: 1 Blackfan Circle

department: Hematology and Oncology

institute: Boston Childrens Hospital

description:
D4WT_2
readcount.txt
readcount_genename.txt

data_processing:
CUT&RUN analysis and normalization: We used CUT&RUNTools (Zhu et al) to process BCL11A, NF-Y and MTA2 CUT&RUN experiments from raw fastq reads. This process included reads trimming, alignment to the reference genome (hg19), BAM file duplicate marking, and fragment filtering based on fragment size. Next, we performed background-based data normalization on the group of experiments to be normalized together. For experiment in each group, we pooled all the BAM files and performed MACS2 peak calling to get initial set of peaks. Peak-flanking regions were obtained and stored for the purpose of normalization. Bamliquidator was called to compute the number of reads in each peak-flanking region in each experiment. DESeq2’s estimateSizeFactor was called on the matrix of peak-flanking region reads over all reads to calculate a scale factor per experiment. With the scale factor computed, the original BAM file was subsampled at a rate equal to the scale factor to get a normalized BAM file. Finally, MACS2 was called to generate peaks from the normalized BAM file based on fragments of 120bp or less. A normalized bigwig file was used for visualization. ATAC-seq analysis and normalization: ATAC-Seq data were processed using a procedure similar to CUT&RUN described above, which included reads trimming, alignment to the reference genome, BAM duplicate marking, and fragment size filtering. A special note is that we kept paired-end fragments that are <150 bp instead of <120 bp setting for TF CUT&RUN. For ATAC-Seq data normalization, we adopted the same background-based data normalization as used in CUT&RUN. RNA-seq and DE analysis: We aligned raw cDNA reads, quantified exonic expression, and finally gene abundances using the HISAT pipeline. Afterward with gene expression count matrix, we proceeded with differential expression analysis with DESeq2.
Assembly: hg19
Supplementary files format and content: Bigwig - normalized bigwig files for visualization
Supplementary files format and content: TXT - gene expression matrix (counts)
Supplementary files format and content: NarrowPeak - narrow peak calls from MACS2
Supplementary files format and content: .txt - gene counts for RNAseq
Supplementary files format and content: .de_files.txt - differentially expressed genes for RNAseq

growth_protocol: ATACseq: HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies, 09650) supplemented with Penicillin-Streptomycin solution (2%), SCF (50 ng/mL), EPO (3 IU/mL), dexamethasone (10-6 M), and doxycycline (1 ug/mL). Erythroid differentiation was carried out by replacing the medium to EDM-II: Iscove’s modified Dulbecco’s medium (IMDM, Corning, 15-016-CV) supplemented with Penicillin-Streptomycin solution (2%), L-Glutamine (1%), holo-human transferrin (330 ug/mL), recombinant human insulin solution (10 ug/mL), heparin (2 IU/mL), inactivated human plasma (5%), EPO (3 IU/mL), SCF (100 ng/mL), doxycycline (1 ug/mL). Cells were cultured in EDM-II for 4 days, followed by 3 more days in medium without SCF. CUT&RUN: HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies, 09650) supplemented with Penicillin-Streptomycin solution (2%), SCF (50 ng/mL), EPO (3 IU/mL), dexamethasone (10-6 M), and doxycycline (1 ug/mL). Erythroid differentiation was carried out by replacing the medium to EDM-II: Iscove’s modified Dulbecco’s medium (IMDM, Corning, 15-016-CV) supplemented with Penicillin-Streptomycin solution (2%), L-Glutamine (1%), holo-human transferrin (330 ug/mL), recombinant human insulin solution (10 ug/mL), heparin (2 IU/mL), inactivated human plasma (5%), EPO (3 IU/mL), SCF (100 ng/mL), doxycycline (1 ug/mL). Cells were cultured in EDM-II for 4 days, followed by 3 more days in medium without SCF. RNASeq: HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies, 09650) supplemented with Penicillin-Streptomycin solution (2%), SCF (50 ng/mL), EPO (3 IU/mL), dexamethasone (10-6 M), and doxycycline (1 ug/mL). Erythroid differentiation was carried out by replacing the medium to EDM-II: Iscove’s modified Dulbecco’s medium (IMDM, Corning, 15-016-CV) supplemented with Penicillin-Streptomycin solution (2%), L-Glutamine (1%), holo-human transferrin (330 ug/mL), recombinant human insulin solution (10 ug/mL), heparin (2 IU/mL), inactivated human plasma (5%), EPO (3 IU/mL), SCF (100 ng/mL), doxycycline (1 ug/mL). Cells were cultured in EDM-II for 4 days, followed by 3 more days in medium without SCF.

extract_protocol:
ATAC-seq: ATAC-seq was performed with the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit, as previously described (Buenrostro et al., 2015). 50,000 cells were collected and washed once with cold PBS. Cells were then permeabilized with 50 μL ice-cold lysis buffer containing10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-360 for 10 minutes. The transposition reaction was carried out at 37°C for 90 minutes in 50 μL volume containing 25 μL TD Buffer and 2.5 μL TDE1 Tagment DNA Enzyme. Immediately following transposition incubation, DNA was purified with the MinElute PCR Purification Kit (Qiagen).  CUT&RUN was performed as previously described (Liu et al., 2021). Briefly, 1x106 cells were freshly collected for each sample. Cells were washed once with cold PBS and processed according to the following steps: (1) 800 μL of NE buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol and protease inhibitor (Roche)) was added to the pellet for nuclear isolation. Nuclei were pelleted at 600g for 3 min and resuspended in 200 μL of NE buffer. (2) 30 μL of BioMagPlus Concanavalin A bead slurry was washed twice and resuspended in 100 μL of binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2). Beads were then added to the nuclear suspension. The mixture was thoroughly mixed on a rocker for 10 min at RT to allow binding of nuclei to the beads. The nuclei were pelleted with a magnet stand and blocked with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% BSA and protease inhibitor (Roche)) supplemented with 2 mM EDTA for 5 min on ice. (4) After washing once with wash buffer, nuclei were resuspended in 200 μL of wash buffer containing 1 μg of antibody and incubated overnight at 4°C. (5) The next day, nuclei were washed twice on a magnet stand with wash buffer and incubated with 1:1000 Protein A-micrococcal nuclease fusion protein (pA-MNase) in 200 μL of wash buffer for 1 hr at 4°C. The nuclei were then washed twice with wash buffer to remove unbound pA-MNase. (6) Nuclei were resuspended in 150 μL of wash buffer and chilled on a metal block at 0°C in a water-ice mixture. 3 μL of 100 mM CaCl2 was added to the nuclei to activate pA-MNase with incubation at 0°C for 60 min. (7) The reaction was stopped by the addition of 150 μL of 2x STOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A and 40 μg/mL glycogen). The protein-DNA complex was released by centrifugation and then digested by proteinase K at 50°C overnight. DNA was extracted by ethanol precipitation, followed by Qubit fluorometry and bioanalyzer quality control. The antibodies used for CUT&RUN were BCL11A (Sigma, ZRB1518), NF-YA (Abcam, ab139402) and MTA2 (Abcam, ab8106). RNA: Total RNA was isolated from cells using the RNeasy Plus Mini Kit (Qiagen).
ATACseq: Transposed DNA fragments were amplified using NEBNext® Ultra™ II Q5 Master Mix and PCR reaction was carried out as follows: 72°C for 5 min; 98°C for 30 s; 8 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The resulting libraries were purified using the QIAquick PCR Purification Kit (Qiagen), quantified with Qubit fluorometer and TapeStation, and then sequenced using the NextSeq 500 platform. Paired-end sequencing was performed with read length of 42 bp and index of 8 bp. CUT&RUN: Library preparation of CUT&RUN was performed using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina, as previously described (Liu et al., 2021). Briefly, 6 ng of DNA was used as input. End preparation was performed at 20 °C for 30 min and then 50 °C for 60 min. 0.6 pmol adapter was added and ligated to end-preparation products at 20 °C for 15 min. USER enzyme was then added to cleave the uracil in the loop at 37°C for 15 min. 1.7x volume of AMPure XP beads was used to purify the ligation product for efficient recovery of short fragments. To amplify the library, the ligation product was mixed with 2x NEBNext® Ultra™ II Q5 Master Mix, universal primer and index primers. PCR reaction was carried out as follows: 98°C for 30 s; 12 cycles of 98°C for 10 s and 65°C for 10 s; and a final extension at 65°C for 5 min. The PCR product was subjected to double-size selection, first with 0.8x and then with 1.2x AMPure XP beads. The purified library was quantified by Qubit fluorometer and TapeStation. Libraries were pooled in equimolar ratios and sequenced using the NextSeq500 platform. Paired-end sequencing was performed with read length of 42 bp and index of 6 bp. RNAseq: RNA sequencing libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche) from 200 ng of purified total RNA. The finished dsDNA libraries were quantified by Qubit fluorometer, TapeStation, and RT-qPCR using the KAPA Library Quantification Kit (Roche). Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina NextSeq500 with single-end 75bp reads.
ATACseq and CUT&RUN: read length 42
RNAseq: read length 75

value: erythroid

value: WT

tag: antibody

tag: batch

value: Novogen


title: hFOB cells, Day2, replicate 1

description: Library name: D2_rep1

value: osteogenic differentiation


title: AML11

description: Column AML11 within deSeq2_counts.txt

tag: tissue


title: Brain, CD3+ SS2 KO A10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_A10

value: Brain

tag: strain

value: male


title: RNAseq_HDP2_Day4_WT_rep1

description:
D4WT_1
readcount.txt
readcount_genename.txt


title: RNAseq_HDP2_Day4_delN_rep2

description:
D4DelN_2
readcount.txt
readcount_genename.txt

value: delN


title: AML10

description: Column AML10 within deSeq2_counts.txt


title: NFY_CR_HDP2_Day6_WT_rep2

data_processing:
CUT&RUN analysis and normalization: We used CUT&RUNTools (Zhu et al) to process BCL11A, NF-Y and MTA2 CUT&RUN experiments from raw fastq reads. This process included reads trimming, alignment to the reference genome (hg19), BAM file duplicate marking, and fragment filtering based on fragment size. Next, we performed background-based data normalization on the group of experiments to be normalized together. For experiment in each group, we pooled all the BAM files and performed MACS2 peak calling to get initial set of peaks. Peak-flanking regions were obtained and stored for the purpose of normalization. Bamliquidator was called to compute the number of reads in each peak-flanking region in each experiment. DESeq2’s estimateSizeFactor was called on the matrix of peak-flanking region reads over all reads to calculate a scale factor per experiment. With the scale factor computed, the original BAM file was subsampled at a rate equal to the scale factor to get a normalized BAM file. Finally, MACS2 was called to generate peaks from the normalized BAM file based on fragments of 120bp or less. A normalized bigwig file was used for visualization. ATAC-seq analysis and normalization: ATAC-Seq data were processed using a procedure similar to CUT&RUN described above, which included reads trimming, alignment to the reference genome, BAM duplicate marking, and fragment size filtering. A special note is that we kept paired-end fragments that are <150 bp instead of <120 bp setting for TF CUT&RUN. For ATAC-Seq data normalization, we adopted the same background-based data normalization as used in CUT&RUN. RNA-seq and DE analysis: We aligned raw cDNA reads, quantified exonic expression, and finally gene abundances using the HISAT pipeline. Afterward with gene expression count matrix, we proceeded with differential expression analysis with DESeq2.
Assembly: hg19
Supplementary files format and content: Bigwig - normalized bigwig files for visualization
Supplementary files format and content: TXT - gene expression matrix (counts)
Supplementary files format and content: NarrowPeak - narrow peak calls from MACS2
Supplementary files format and content: .txt - gene counts for RNAseq
Supplementary files format and content: .de_files.txt - differentially expressed genes for RNAseq
Library strategy: CUT&RUN

value: Day 6

value: NFY


title: 165_H

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

data_processing:
The sequencing reads generated were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK).
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genome was assessed using bamutils (from ngsutils v.0.5.9)
Uniquely mapped reads were used to quantify the gene level expression employing featureCounts (subread v.1.5.1) with the following parameters: “-s 2 -Q 10”.
The data was normalized using TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.3.12.1). False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: The sequence data were next mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.5) with the following parameter: “--outSAMmapqUnique 60”
Supplementary files format and content: .xlsx file format was used for processed files - raw counts
Supplementary files format and content: .xlsx file format was used for processed files - log2FPKM counts

source_name: KPC+GnP

extract_protocol:
Total RNA was isolated using the miRNeasy kit (217004, Qiagen)
100 nanograms of total RNA was used for library preparation with the KAPA mRNA Hyperprep Kit (KK8581) (Roche). Each resulting uniquely dual-indexed library was quantified and quality accessed by Qubit and TapeStation. The libraries pooled in equal molarity were sequenced with 2×100bp paired-end configuration on an Illumina NovaSeq 6000 sequencer using thev1.0 reagent kit.

value: Heart

tag: Sex

value: Male

value: Gemcitabine plus nab paclitaxel


title: NFY_CR_HDP2_Day6_WT_rep3

tag: genotype


title: 164_H


title: RNAseq_HDP2_Day4_delN_rep1

description:
D4DelN_1
readcount.txt
readcount_genename.txt

value: Day 4


title: 162_H


title: RNAseq_HDP2_Day0_WT_rep1

description:
D0WT_1
readcount.txt
readcount_genename.txt

value: Day 0


title: c184_CART19_Only

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

institute: Mayo Clinic

data_processing:
Binary base call data converted to fastq using Illumina bcl2fastq software
Check quality with FastQC, trim adapters with trimmomatic, and re-check quality with FastQC
Latest human reference genome GRCh38 was downloaded from NCBI and indexed using STAR
Paired end reads were mapped to the genome, and HTSeq was used to generate expression counts for each gene
DeSeq2 was used to calculate differential expression
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files contain the gene expression counts for each sample or DeSeq2 dataset

source_name: T cell

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
TruSeq RNA Library Prep Kit v2
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CART19 alone, CART19 and GM-CSFRA Ab, or CART19 and GM-CSF Ab were produced on 3 biological replicates of normal donor T cells and total RNA was isolated.

value: No Treatment


title: RNAseq_HDP2_Day0_WT_rep2

description:
D0WT_2
readcount.txt
readcount_genename.txt


title: RNAseq_HDP2_Day0_delN_rep2

description:
D0DelN_2
readcount.txt
readcount_genename.txt


title: 148_H

source_name: KPC

value: Vehicle


title: NFY_CR_HDP2_Day6_WT_rep1


title: AML1

description: Column AML1 within deSeq2_counts.txt

value: Apheresis buffy coat

value: mononuclear cells

value: AML


title: c179_CSF2RA_Ab

value: CSF2RA Ab Treatment


title: 141_H


title: NFY_CR_HDP2_Day6_delZnF1_rep3

value: erythroid


title: c184_GMCSF_Ab

value: GM-CSF Ab Treatment


title: RNAseq_HDP2_Day0_delN_rep1

description:
D0DelN_1
readcount.txt
readcount_genename.txt

value: Novogen


title: NFY_CR_HDP2_Day6_delZnF1_rep1


title: 163_H


title: NFY_CR_HDP2_Day6_delZnF0_rep3


title: NFY_CR_HDP2_Day6_delZnF1_rep2


title: 144_H


title: RNAseq_HDP2_Day7_WT_rep2

description:
D7_WT_2
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt

value: WT

value: Day 7


title: c179_CART19_Only


title: 142_H


title: c184_CSF2RA_Ab


title: c154_CSF2RA_Ab


title: 176_H

source_name: Control

value: No treatment


title: NFY_CR_HDP2_Day6_delZnF0_rep1

value: Day 6

value: NFY


title: c154_GMCSF_Ab


title: 146_H

value: Heart

value: Male


title: RNAseq_HDP2_Day7_WT_rep1

description:
D7_WT_1
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: RNAseq_HDP2_Day7_delZnF1_rep3

description:
D7_delZnF1_3
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: 166_H


title: NFY_CR_HDP2_Day6_delZnF01_rep2


title: NFY_CR_HDP2_Day6_delZnF0_rep2


title: NFY_CR_HDP2_Day6_delZnF01_rep3


title: NFY_CR_HDP2_Day6_delZnF01_rep1


title: RNAseq_HDP2_Day7_delZnF1_rep2

description:
D7_delZnF1_2
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: c154_CART19_Only


title: 181_H


title: 170_M

value: Skeletal muscle

value: Gemcitabine plus nab paclitaxel


title: MC38 tumor tissue, BMS-986408+aPD1 treated, replicate 4

city: Cambridge

first: Siqi

last: Liu

address: 250 WATER STREET

department: Oncology

institute: BMS

description: Library name: BMS986408+AntiPD1_4

data_processing:
Paired-end reads were analyzed using the Seven Bridges platform (Seven Bridges Genomics).  FASTQ reads were aligned to reference genome GRCm38 using STAR with default parameters
Transcriptome gene-level abundance estimated through RSEM v1.1.13 with Ensembl GRCm38 v91 gene annotation
Downstream differential expression analysis was performed in R using limma and voom R packages
Assembly: GRCm38
Supplementary files format and content: CSV file includes raw counts for each sample

source_name: tumor tissue

growth_protocol: The MC38 cell line was maintained in DMEM (Gibco) supplemented with 10% FBS in T175 flasks. Approximately twice a week, cells contained in a single T175 flask were divided and expanded to multiple T175 flasks at a 1:8 dilutions until a sufficient number of cells were obtained for tumor implantation into the required number of mice as per study design. The cells were harvested near 85% confluence, washed in FBS-free medium 3-times, and re-suspended in Dulbecco’s phosphate buffer saline (DPBS, Gibco /Life Technologies) prior to implantation. Cell preparations with ≥ 90% viability were used for implantation. At the time of tumor cell implantation (day 0), female C57BL/6 mice were injected subcutaneously in the right flank with 1.0×106 of MC38 tumor cells in 0.1 mL using a 1 mL syringe and 26-gauge needle. To ensure a uniform suspension of injected cells, loaded syringes were inverted several times prior to subcutaneous injection into the right flank of each animal. At mean tumor volume of ~100 mm3 animals were randomized into various treatment groups typically on day 6 or 7 post implant and treatment was initiated.

extract_protocol:
Tumors were collected seven days after the start of treatment and prepared as single cell suspensions using the Mouse Tumor Dissociation Kit by Miltenyi Biotec (#130-096-730), according to the manufacturer’s recommendations. Briefly, tumors were weighed and minced, then combined with the enzyme mixture in RPMI for enzymatic digestion and loaded onto a gentleMACS Dissociator for mechanical dissociation. Following dissociation, the samples were filtered through 70-micron and 40-micron cell strainers to remove any remaining large particles and cell clumps and washed with media.
Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragments for 15 minutes at 94 ºC. First strand and second strand cDNA are subsequently synthesized. cDNA fragmetns are end repaired and adenylated at 3’ ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR.

treatment_protocol: At the time of tumor cell implantation (day 0), female C57BL/6 mice were injected subcutaneously in the right flank with 1.0 ×106 of CT26 tumor cells in 0.1 mL using a 1 mL syringe and 26-gauge needle. To ensure a uniform suspension of injected cells, loaded syringes were inverted several times prior to subcutaneous injection into the right flank of each animal. At mean tumor volume of ~100 mm3 animals were randomized into various treatment groups typically on day 9 or 10 post implant and treatment was initiated. All compounds were formulated in a vehicle consisting of ethanol/polyethylene glycol 400 (PEG400)/tocopheryl polyethylene glycol succinate (TPGS) (5:90:5, v/v/v) for oral (PO) administration at 10 mL/kg dose volume. BMS-986408 was administered QD at a final doses of 0.3 mg/kg. An anti-mPD-1 and anti- CTLA-4 mAbs (BMS) were dosed intraperitoneally Q4D×3 at 10 mg/kg in a 10 mL/kg volume of phosphate-buffered saline (PBS). The isotype controls for anti-PD-1, a mouse IgG1 monoclonal antibody (clone MOPC-21, Bio X Cell) was dosed IP at 10 mg/kg in a volume of 10 mL/kg PBS. Treatment groups were terminated when the mean tumor weight reached a target size of ≥1000 mm3 for two consecutive measurements. If the mean tumor volume did not reach the target size, the treatment group was monitored for 10-times tumor volume doubling time.

value: tumor tissue


title: MC38 tumor tissue, BMS-986408+aPD1 treated, replicate 3

description: Library name: BMS986408+AntiPD1_3


title: MTA2_CR_HDP2_Day7_delN

value: delN


title: RNAseq_HDP2_Day7_delZnF1_rep1

description:
D7_delZnF1_1
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: MC38 tumor tissue, BMS-986408+aPD1 treated, replicate 5

description: Library name: BMS986408+AntiPD1_5


title: RNAseq_HDP2_Day7_delZnF01_rep3

description:
D7_delZnF01_3
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: 169_M


title: RNAseq_HDP2_Day7_WT_rep3

description:
D7_WT_3
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: RNAseq_HDP2_Day7_delZnF01_rep2

description:
D7_delZnF01_2
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: MC38 tumor tissue, BMS-986408+aPD1 treated, replicate 2

description: Library name: BMS986408+AntiPD1_2


title: MTA2_CR_HDP2_Day7_delZnF01


title: RNAseq_HDP2_Day7_delZnF01_rep1

description:
D7_delZnF01_1
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: 163_M


title: MC38 tumor tissue, BMS-986408+aPD1 treated, replicate 1

description: Library name: BMS986408+AntiPD1_1


title: MTA2_CR_HDP2_Day7_delZnF1


title: MC38 tumor tissue, BMS-986408 treated, replicate 5

description: Library name: AntiPD1_5


title: MTA2_CR_HDP2_Day7_delZnF0


title: MC38 tumor tissue, BMS-986408 treated, replicate 4

description: Library name: AntiPD1_4


title: 148_M

value: Vehicle


title: RNAseq_HDP2_Day0_WT_rep2_gz11316

description:
D0_WT_2
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt

value: Day 0


title: 144_M


title: MC38 tumor tissue, BMS-986408 treated, replicate 3

description: Library name: AntiPD1_3


title: MTA2_CR_HDP2_Day7_WT


title: 149_M


title: RNAseq_HDP2_Day0_delZnF1_rep3

description:
D0_delZnF1_3
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: BCL11A_CR_HDP2_Day7_WT


title: 141_M


title: MC38 tumor tissue, BMS-986408 treated, replicate 2

description: Library name: AntiPD1_2


title: BCL11A_CR_HDP2_Day7_delZnF01_clone1


title: 176_M


title: BCL11A_CR_HDP2_Day7_delZnF01_clone2


title: RNAseq_HDP2_Day0_delZnF1_rep2

description:
D0_delZnF1_2
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: RNAseq_HDP2_Day0_delZnF1_rep1

description:
D0_delZnF1_1
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: 162_M


title: MC38 tumor tissue, aPD1 treated, replicate 4

description: Library name: BMS986408_4


title: atac_HDP2_Day0_delZnF01_clone1_rep3


title: MC38 tumor tissue, aPD1 treated, replicate 5

description: Library name: BMS986408_5


title: 156_M


title: RNAseq_HDP2_Day0_WT_rep3_gz11316

description:
D0_WT_3
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: RNAseq_HDP2_Day0_delZnF01_rep3

description:
D0_delZnF01_3
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: 146_M


title: MTA2_CR_HDP2_Day7_WT_gz11179


title: atac_HDP2_Day0_delZnF01_clone1_rep2


title: MC38 tumor tissue, aPD1 treated, replicate 3

description: Library name: BMS986408_3


title: RNAseq_HDP2_Day0_WT_rep1_gz11316

description:
D0_WT_1
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: MC38 tumor tissue, aPD1 treated, replicate 2

description: Library name: BMS986408_2


title: 181_M


title: atac_HDP2_Day0_delZnF01_clone1_rep1


title: RNAseq_HDP2_Day0_delZnF01_rep2

description:
D0_delZnF01_2
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: RNAseq_HDP2_Day0_delZnF01_rep1

description:
D0_delZnF01_1
salmon_genes_count.csv
salmon_genes_tpm.csv
salmon.de_files.txt


title: atac_HDP2_Day0_delZnF1_rep3


title: bcMicroenv_D9

data_processing:
demultiplexing: cellranger 4.0.0 mkfastq ran using default parameters
cell and gene counting: cellranger 4.0.0 count ran using default parameters
Assembly: 10X provided mm10-2020-A reference
Supplementary files format and content: compressed folders containing barcode, feature, and matrix files for each sample. Generated as part of the outputs via cellranger count

source_name: Bone/Bone marrow

extract_protocol:
Extraction is included within the 10X genomics scRNA protocol
Cell suspensions were processed to generate single-cell RNA-Seq libraries using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction.  Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Sequence data was generated using Illumina’s NovaSeq 6000.

treatment_protocol: Treated mice were transplanted with 100,000 BCR-ABL+NUP98-HOXA9+ primary leukemia cells

value: Bone/Bone marrow

value: C57BL/6J Wildtype

value: bcCML leukemia


title: MC38 tumor tissue, aPD1 treated, replicate 1

description: Library name: BMS986408_1


title: MC38 tumor tissue, BMS-986408 treated, replicate 1

description: Library name: AntiPD1_1


title: atac_HDP2_Day0_delZnF1_rep2

value: erythroid


title: Donor_20

city: Panania

first: Benjamin

middle: John

last: Hunter

state: NSW

address: 118 Horsley Rd

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

data_processing:
The quality of each RNA sequence (reversely stranded) was assessed using ShortRead. The raw sequences were aligned on hg38 genome assembly (UCSC) with Rsubread version 2.2.1. The alignment was performed on pair-end sequences without trimming. Rsubread was also used for generating the gene count matrix. The gene counts were converted in Count Per Million (CPM), log2 transformed, and then normalised using Voom.
Assembly: The raw sequences were aligned on hg38 genome assembly (UCSC) with Rsubread version 2.2.1.
Supplementary files format and content: Microsoft Exel Worksheet. De-itdentified patient details (study ID, disease phenotype, sex, age, BMI), Normalised log2 transformed data with associated Entrez and Gene Symbol IDs.

source_name: Pre-mortem

extract_protocol:
Cryopreserved human myocardium was powderised as described in the proteomic MS methods and weighed to approximately 30mg. Powderised myocardium was lysed and homogenised in 500 µL TRIzol (Invitrogen) using steel balls in the TissueLyser LT (Qiagen) and kept on dry ice between cycles (3-5 x 1 minute). 1-bromo-3-chloropopane (50 µL) was added to each sample and left to incubate for 5 minutes at RT, then spun at 14,000 x g at 4°C for 15 minutes to induce phase separation. RNA-containing aqueous phase was transferred to a sterile tube and an equal volume of isopropanol was added, mixed by inverting, and left for 1 hour at RT. RNA was pelleted at 14,000 x g at 18°C for 15 minutes, supernatant discarded. RNA was then washed in 4°C 70% ethanol twice discarding supernatant after spinning at 14,000 x g at 4°C for 10 minutes and left to dry at RT. RNA was DNase treated for 30 minutes at 37°C and washed again. Pelleted RNA was reconstituted in 15 µL 4°C nuclease free diethyl pyrocarbonate (DEPC). Concentration and quality were tested on NanoDrop (Thermo Fisher Scientific) to a standard of 260nm/280nm = 1.8-2.0 and 260nm/230nm 1.7-2.2. RNA integrity was assessed using an RNA Nano Chip on an Bioanalyzer (Agilent).
RNA-seq libraries were prepared with Illumina Stranded Total RNA prep Ligation with Ribo Zero Plus (100ng input and 11 PCR cycles) according to manufacturer’s instructions. Quality checks were performed using the Qubit dsDNA High Sensitivity Assay Kit and the Revvity LabChip GX Touch. The final sequencing pool was quantified using the Qubit dsDNA High Sensitivity Assay Kit after pooling all libraries equimolar into a single library pool. Sizing was checked using the Agilent High Sensitivity D1000 Tapestation system. The RNA-seq libraries were sequenced using a paired-end 250bp kit on a S4 flow cell of the Illumina NovaSeq 6000 with a final run concentration of 58pM and 1% PhiX.

value: Left ventricular myocardium

tag: condition

value: Donor


title: MC38 tumor tissue, vehicle treated, replicate 5

description: Library name: Vehicle_5

value: WT


title: bcMicroenv_D7


title: atac_HDP2_Day0_delZnF1_rep1


title: Donor_18


title: bcMicroenv_D4


title: MC38 tumor tissue, vehicle treated, replicate 3

description: Library name: Vehicle_3


title: atac_HDP2_Day0_WT_rep3_gz11363


title: Donor_17


title: bcMicroenv_D2


title: bcMicroenv_D14


title: MC38 tumor tissue, vehicle treated, replicate 4

description: Library name: Vehicle_4


title: MC38 tumor tissue, vehicle treated, replicate 2

description: Library name: Vehicle_2


title: Donor_15


title: atac_HDP2_Day0_WT_rep2_gz11363


title: Donor_16


title: MC38 tumor tissue, vehicle treated, replicate 1

description: Library name: Vehicle_1


title: bcMicroenv_D11


title: bcMicroenv_CTL


title: Donor_12


title: atac_HDP2_Day7_delZnF01_clone2_rep2

value: Day 7


title: cMafcKO_cMafcKOset, scRNAseq

first: Isle

last: Bastille

address: 220 Longwood Avenue

department: Neurobiology

institute: Harvard University

description: 10X Genomics v3.1

data_processing:
Cell Ranger (10X Genomics) was used for de-multiplexing and initial processing; subsequent analysis using count matrix was performed in Seurat. After preliminary clusteriing analysis that identified SGN-specific clusters, cells with high mitochondrial content were discarded before further analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole cochlea

extract_protocol:
Freshly collected cochlea were dissociated with collagenase followed by papain
10X Genomics 3' assay v3.1 Dual-indexed single-cell transcriptomic libraries were created using the 10X Genomics Chromium Single Cell 3' GEM library and Gel Bead Kit v3.1. Libraries were sequenced using the NovaSeq SP6000 100 cyles (Illumina)
Library prep was performed according to manufacturers instructions (single cell 3' v3.1)

value: whole cochlea


title: chick hindlimb bud HH25 H3K27ac input rep2

description: SE75 sequencing

organism: Gallus gallus

source_name: hindlimb bud


title: atac_HDP2_Day7_delZnF01_clone2_rep1


title: ICMNoDM_16

value: ICM


title: chick hindlimb bud HH25 H3K27ac input rep1

description: SE75 sequencing


title: atac_HDP2_Day7_delZnF01_clone1_rep3


title: ICMNoDM_15


title: chick hindlimb bud HH25 H3K27ac ChIP rep2

description:
SE75 sequencing
gg_HL_HH25_H3K27ac_naive_overlap.narrowPeak.gz
gg_HL_HH25_H3K27ac_pooled.bw

value: H3K27ac (Abcam ab4729)


title: Skeletal Muscle D2-HG female rep1

city: Los Angeles

first: Anja

last: Karlstaedt

state: California

address: 127 San Vincente Blvd

department: Cardiology

institute: Cedars Sinai Medical Center

data_processing:
Raw reads from the sequencer were demultiplexed and converted to fastq format using bcl2fastq v2.19.1.403, optioned to allow for zero mismatch in the barcodes.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat2 -p 8 –GTF “$GTF_file” –transcriptome-index “$transcriptome” -o thout $Bowtie2Index *R1_001_paired.fastq *R2_001_paired.fastq; cufflinks -p 8 –GTF “$GTF_file” –multi-read-correct -o clout thout/accepted_hits.bam; cuffmerge -g “$GTF_file” -s “$transcriptome.fa” -p 8 assemblies.txt; htseq-count -f bam -r name -i gene_id -t exon thout/accepted_hits.bam “$GTF_file” > count.txt
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: M. gastrocnemius

extract_protocol:
Skeletal muscle were removed, flash frozen in liquid nitrogen, and RNA was extracted from 20 to 30 mg skeletal  muscle  tissue  using  the QIAGEN  RNeasy  Fibrous  Tissue  Mini  Kit (Qiagen, Hilden, Germany; CAT#74704). RNA concentration was determined using a Qubit 4.0 fluorometer (Life Technologies) and Qubit™ RNA HS Assay Kit (ThermoFisher Scientific, Waltham, MA; CAT#Q32852) according to the manufacturer’s instructions. The quality of each RNA sample was checked using an Agilent 4200 Tape Station with Agilent High Sensitivity RNA ScreenTape (Agilent Technologies, Santa Clara, CA, USA; CAT#5067-5579) according to the manufacturer’s instructions. For library preparation, poly-A RNA was purified from mRNA using oligo-dT magnetic beads. mRNA was fragmented, and cDNA synthesized. A-tailing was conducted to enable subsequent ligation of paired-end sequencing adapters. Library quality was determined using an Agilent 4200 Tape Station with Agilent High Sensitivity D5000 DNA ScreenTape (CAT#5067-5592, Agilent Technologies, Santa Clara, CA, USA) to ensure correct fragment sizes between 250 and 300 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: M. gastrocnemius

tag: age

value: Week 14

value: wild type


title: Skeletal Muscle D2-HG female rep2


title: atac_HDP2_Day7_delZnF01_clone1_rep2

tag: cell type


title: chick hindlimb bud HH25 H3K27ac ChIP rep1

data_processing:
Libraries were sequenced by the Georgia Genomics and Bioinformatics Core (SE75) or by Genewiz (PE150). The GGBC provided pre-trimmed reads, while Genewiz reads were subsequently trimmed using cutadapt using the settings -O 1, -m 25
RNA-seq reads were aligned to mm10 using STAR (v. 2.7.3a). Transcripts were counted using HTSeq (v. 0.13.5). Differential gene expression was determined using DESeq2 (Galaxy v. 2.11.40.6).
ChIP-seq data were processed using the AQUAS Transcription Factor and Histone ChIP-seq pipeline. We used the pipeline's default bwa aligner to align mouse reads to mm10 (UCSC), chick to galGal6 (UCSC), alligator to allMis0.2/allMis1 (UCSC), turtle to CAS_Tse_1.0 NCBI RefSeq), and lizard to AnoSag2.0 (local genome build). Fragment size was set to 175 (-speak_spp 175, -extsize_macs2 175).
SPP was used to call IDR peaks using the default cutoff (0.05) in ISL1 ChIP-seq experiments performed in duplicate, while MACS2 peaks were used from individual experiments and from H3K27ac datasets. In H3K27ac datasets, the naive overlap peaks were used, while MACS2 peaks from ISL1 ChIP-seq in alligator, turtle, and lizard were filtered using a q-value cutoff of 0.01 and fold-enrichment cutoff of 4. bigWig files were generated using MACS2 and represent fold-enrichment values of ChIP vs control samples.
Mouse forelimb ISL1 ChIP-seq IDR peaks were used as a negative control to filter false-positive peaks from ISL1 peak sets, generating "FL_filtered" files
Assembly: varied by species (see above)
Supplementary files format and content: DESeq2 tabular files, SPP or MACS2 peak files, and MACS2 bigWig files


title: atac_HDP2_Day7_delZnF01_clone2_rep3


title: atac_HDP2_Day0_WT_rep1_gz11363


title: ICMNoDM_13


title: chick forelimb bud HH25 H3K27ac input rep2

description: SE75 sequencing

source_name: forelimb bud


title: ICMNoDM_14


title: atac_HDP2_Day7_delZnF01_clone1_rep1


title: atac_HDP2_Day7_delZnF1_rep3


title: Donor_14


title: ICMNoDM_11


title: Skeletal Muscle D2-HG male rep2

tag: treatment


title: chick forelimb bud HH25 H3K27ac input rep1

description: SE75 sequencing


title: Skeletal Muscle D2-HG male rep1


title: ICMNoDM_10


title: atac_HDP2_Day7_delZnF1_rep2


title: Skeletal Muscle Cnt female rep3

value: Phosphate buffered saline


title: atac_HDP2_Day7_delZnF1_rep1


title: Skeletal Muscle D2-HG female rep3


title: Skeletal Muscle Cnt female rep2


title: Skeletal Muscle D2-HG male rep3


title: chick forelimb bud HH25 H3K27ac ChIP rep1

description:
SE75 sequencing
gg_FL_HH25_H3K27ac_naive_overlap.narrowPeak.gz
gg_FL_HH25_H3K27ac_pooled.bw


title: ICMDM_14

value: ICM-DM


title: ICMNoDM_8


title: chick genital tubercle HH28 H3K27ac input rep2

description: SE75 sequencing

source_name: genital tubercle


title: ICMDM_13


title: Skeletal Muscle Cnt female rep1


title: ICMDM_10


title: chick forelimb bud HH25 H3K27ac ChIP rep2


title: atac_HDP2_Day7_WT_rep2_gz11363


title: chick genital tubercle HH28 H3K27ac ChIP rep2

description:
SE75 sequencing
gg_GT_HH28_H3K27ac_naive_overlap.narrowPeak.gz
gg_GT_HH28_H3K27ac_pooled.bw

value: H3K27ac (Millipore or Cosmo Bio, CMA309)


title: chick genital tubercle HH28 H3K27ac input rep1

description: SE75 sequencing


title: Skeletal Muscle Cnt male rep3


title: atac_HDP2_Day0_delZnF01_clone2_rep2

value: Day 0


title: atac_HDP2_Day0_delZnF01_clone2_rep3


title: chick genital tubercle HH28 ISL1 input rep2

description: SE75 sequencing


title: Skeletal Muscle Cnt male rep1


title: ICMDM_9


title: Skeletal Muscle Cnt male rep2


title: ICMDM_11


title: WT3

description: Column WT3 within counts file

data_processing:
Data Formatting: bcltofastq-2.19.1
Data Cleaning: fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment: STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification: subread-2.0.1, featurecounts, -s 0 -t exon -g gene_name
Assembly: m38 + Gencode-M27 Annotation
Supplementary files format and content: raw gene counts

source_name: Spleen

extract_protocol:
Rneasy Plus Micro Kit (Qiagen, Valencia, CA)
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina flow cell and sequenced using the llumina NextSeq 550 (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample.

treatment_protocol: Treated mice were transplanted BCR-ABL and NUP98-HOXA9 primary leukemia cells

value: Spleen

value: leukemia

value: SLC6A6 WT


title: chick genital tubercle HH28 H3K27ac ChIP rep1

extract_protocol:
For RNA-seq, genital tubercle samples were placed in RNA-Later, which was then removed before freezing samples at -80C. For hindlimb field samples, both sides from each embryo were placed directly into mirVana Lysis/Binding buffer and frozen. RNA was extracted using the mirVana miRNA isolation kit. For ChIP-seq, tissues form multiple embryos were sonified using a probe sonifier followed by a bath sonifier. Lysates were then incubated with the antibody with a portion kept as input DNA.
RNA-seq libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina); ChIP-seq libraries were constructed using the NEBNext Ultra II Library Prep Kit


title: ICMDM_8

value: Left ventricular myocardium


title: c179_GMCSF_Ab

value: GM-CSF Ab Treatment


title: WT2

description: Column WT2 within counts file


title: atac_HDP2_Day7_WT_rep3_gz11363

value: erythroid

value: WT


title: atac_HDP2_Day0_delZnF01_clone2_rep1


title: chick genital tubercle HH28 ISL1 ChIP rep2

description:
SE75 sequencing
gg_GT_HH28_ISL1_IDR.narrowPeak.gz
gg_GT_HH28_ISL1_IDR_mouse_FL_filtered.bed
gg_GT_HH28_ISL1_pooled.bw


title: ICMDM_7


title: chick genital tubercle HH28 ISL1 input rep1

description: SE75 sequencing


title: WT1

description: Column WT1 within counts file


title: chick genital tubercle HH28 ISL1 ChIP rep1


title: Guided differentiation cell culture

first: Erik

last: McIntire

address: 920 E. 58th Street, CLSC 317

department: Department of Human Genetics

institute: University of Chicago

description:
cell lines: 19114, 19130, 19152
sex: female, male, female

data_processing:
Aligned samples to the human genome (GRCh38) using Cell Ranger17 v6.1.2 and assigned cells to individuals using Vireo v0.5.6.
Aligned UMI count data was loaded into R (v4.2.0) / RStudio (v2022.02.3+492).
Removed cells classified by Virero (v0.5.6) as doublets or unassigned; also, filtered out cells expressing less than 1,500 unique genes.
Performed sctransform-based normalization (v0.3.5) then analyzed using Seurat v4.3.0.
Performed unsupervised clustering followed by differential expression analysis; annotated cell clusters based on canonical marker gene expression.
Assembly: GRCh38
Supplementary files format and content: The matrix.mtx file contains UMI counts for every gene and cell.
Supplementary files format and content: The features.tsv file contains row names (genes) for the counts matrix.
Supplementary files format and content: The barcodes.tsv file contains column names (cell barcodes) for the counts matrix.
Supplementary files format and content: The metadata.csv file contains cell type annotation.

growth_protocol: Maintained 3 iPSC lines on Matrigel with Essential 8™ (E8) medium. At roughly 80% confluency, passaged cultures using EDTA and seeded iPSCs in the new culture with ROCK inhibitor Y-27632.

extract_protocol:
Collected day 10 aggregates from the 3 iPSC lines and disassociated them by treating with room temperature AccuMax™. Then processed cells for scRNA-seq using the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index).
3' gene expression dual index library construction (10x Genomics).

treatment_protocol: Performed guided differentiation of 3 iPSC lines by forming three-dimensional cell aggregates and subjecting aggregates to temporal Wnt modulation over the course of 10 days.

value: mixed sample (non-demultiplexed)

value: iPSC-derived cells

value: Day 10

value: guided differentiation


title: atac_HDP2_Day7_WT_rep2

value: Day 7


title: KO3

description: Column KO3 within counts file

value: SLC6A6 KO


title: atac_HDP2_Day7_WT_rep1_gz11363


title: alligator hindlimb bud st13 H3K27ac input rep2

description: PE150 sequencing

organism: Alligator mississippiensis


title: KO2

description: Column KO2 within counts file


title: chick hindlimb bud HH18-20 ISL1 input rep2

description: SE75 sequencing