title: E9_plate 1A_E8.5_foregut

description:
BSSE-QGF-59949
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F9_plate 1A_E8.5_foregut

status: Public on Jul 13 2021

type: SRA

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

description:
BSSE-QGF-59950
processed data file: E8.5-E14.5_AllCells_genes.csv

library_source: transcriptomic

data_processing:
Libraries were sequenced SR75 on an Illumina NextSeq 500 system (75 cycles High Output v2.5 kit).
Reads were uniquely aligned to mouse reference genome (GRCm38) using STAR (v.2.5.3.a).
Comparison of expression level between samples had been conducted with cufflinks.cuffdiff (2.2.1).
The gene expression matrices were generated employing GeneCounts as quantification type in STAR.
The gtf and fasta formatted annotations for mouse were retrieved from GENCODE project (released version v26, primary assembly).
Scater Package was used for filtering. All samples with at least 2000 genes and 500000 counts (visualised in log10 scale) were retained. These thresholds were calculated based on the average of library size and number of expressed genes in each library. We also applied a gene filtering step (transcript > 2 in at least 2 cells). Scran package was used for data normalization. For data visualization, we used t-SNE plot with a perplexity value of 20% of the total number of cells. Clustering of the cells was computed using SC3 package. Pseudo-time reconstruction was performed using Tscan package.
Genome_build: UCSC mm 10 (GRCm38)
Supplementary_files_format_and_content: E8.5-E14.5_AllCells_genes.csv: Comma-separated text file including a table of genes (rows) x cells (columns) showing logcounts (normalized counts) per single cell. Processed data file includes only samples that passed the QC check.

molecule: total RNA

organism: Mus musculus

source_name: Foregut endoderm

extract_protocol:
GFP+ ventral foregut (E8.5), pancreatic (E10.5, E14.5), and hepatic progenitors (E10.5) were dissected from Tg(Prox1-EGFP) transgenic mice and dissociated into single-cell suspensions. GFP+ cells were FACS sorted at 4°C using an Aria II or Aria III flow cytometer (BD) into 96-well plates containing cell lysis buffer. Plates containing FACS-sorted cells were then frozen and kept at -80°C until shipment to ETH Genomic Facility for library preparation and sequencing.
Libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina) protocols.

tag: tissue

value: Foregut

tag: developmental stage

tag: genotype


title: Wild-type sample4

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

country: USA

institute: Purdue University

description:
countMatrix.txt
WT_4

data_processing:
FastQC v.0.11.3 was used to observe read quality
Fastp was used to remove adapter sequences
STAR was used to map reads to the genome of mus_musculus
FeatureCounts on stranded mode was used to count reads mapping to genes
edgeR was used to identify differentially expressed genes
biomaRt was used to annotate genes using Ensembl annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix of raw counts in tab delimited format

source_name: neuron

growth_protocol: Mice were same-sex housed in mixed-genotype groups groups (3-5 mice per cage) on vented cage racks with 1/8" Bed-o-cobb bedding.  and > 8 g of nesting material as enrichment (shredded paper, crinkle-cut paper, and/or cotton nestles) on a 12hr light cycle. Food (2018S Teklad from Envigo) and reverse osmosis water were given ad-lib. Heterozygous (HET, Scn2aWT/gt) mice were used as breeding pairs to obtain homozygous (HOM, Scn2agt/gt) mice and WT littermates for study.

extract_protocol:
RNA isolated using Rnasy Qiagen kit
Tru-Seq stranded Illumina protocol, per manufacturer instructions
paired-end

treatment_protocol: To understand how a severe NaV1.2 deficiency affects the function of neurons, we utilized a NaV1.2-deficient mouse model generated using a gene-trap (gt) approach.

tag: strain

value: Wild-type

tag: cell type

value: neuron


title: s_GV_Mov10l_WT_F70_r1.SE

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Raw RNA-seq reads were mapped to golden hamster (mesAur1) and the newest golden hamster (PRJDB10770) genomes using STAR 2.7.3a with following parameters:  STAR --readFilesIn $ {FILE}.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 5000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --sjdbScore 2  For analysis of expression of protein coding genes, reads were mapped with maximum of 20 multimapping alignments allowed.
Reads mapped to mesAur1 were counted over exon features annotated by Ensembl (release 99) using featureCounts v2.0.0:  featureCounts -a $ {FILE}.gtf -o $ {FILE}.counts.txt $ {FILE}.bam -T 12 -F GTF -M -O –fraction
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: MesAur1.0
Supplementary_files_format_and_content: ensembl.99.MesAur1.0.Piwil3_Tex101.from_RefSeq.raw_counts.oocyte.txt: tab delimited table with counts of reads over exon coordinats from Ensembl Release 99 .gtf file with added Piwil3 and Tex101 annotated by RefSeq; samples are in columns, genes in rows
Supplementary_files_format_and_content: Coverage genome browser tracks files: bigWig format generated in a non-stranded mode, not normalized for library size

molecule: polyA RNA

organism: Mesocricetus auratus

source_name: GV oocyte_WT

growth_protocol: Fully-grown germinal vesicle-intact oocytes were collected from ovaries by puncturing antral follicles with a syringe needle in M2 medium (Sigma) containing 0.2 mM 3-isobutyl-1-methyl-xanthine (Sigma) to prevent resumption of meiosis.

extract_protocol:
Total RNA was extracted from 6 – 12 fully-grown oocytes using Arcturus Picopure RNA isolation kit (Thermo Fisher) according to the manufacturer’s protocol.
RNA-seq libraries were generated using the Ovation RNA-Seq system V2 (NuGEN) followed by Ovation Ultralow Library system (DR Multiplex System, NuGEN) according to the manufacturer’s protocol. cDNA fragmentation was performed on Bioruptor sonication device (Diagenode) with 30 s ON, 30 s OFF for 18 cycles on low intensity. Libraries were amplified by 9 cycles of PCR and sequenced by 100 nt single-end reading using the Illumina NovaSeq6000 platform.

treatment_protocol: Production of knock-out hamsters was carried out using an in vivo electroporation CRISPR/Cas9 system. Pairs of sgRNAs were designed to cleave Mov10l1 genomic sequence in intron 19 (sequence of DNA targets: 5´- gggtatcacatgacttgggg – 3´; 5´- ggtgttgggatcatagtgggg – 3´) and intron 20 (sequence of DNA targets: 5´-tctccactcttccatgtgggg - 3´; 5´- taccattacatttgtcagggg - 3´) in order to delete exon 20. Five animals were born of which one did not exhibit any deletion, two appeared homozygous for the deletion and were not used for breeding, and one male and one female showed modification of one allele. The male was fertile but did not transmit the allele (# of progeny = 13; 8 males + 5 females) while the female (#4) transmitted the allele into progeny (# of progeny = 10; 3 males + 4 females carried the mutant allele) when bred to a wild type animal. Subsequent breeding of heterozygotes for two generations with wild type outbred animals was performed in order to minimize possible off-targeting and inbreeding effects when heterozygotes were mated to produce homozygotes.

value: WT

value: GV oocyte

tag: age

value: 37 weeks


title: miR-145-5p_rep1

city: Seoul

first: Daehyun

last: Baek

address: Rm 402, Bldg 504, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: hsa-miR-145-5p-transfected mRNA-seq in HepG2

data_processing:
1. Base-calling by RTA(Real Time Analaysis) software within HiSeq 2500 (mRNA-Seq) or HiSeq 2000 (sRNA-Seq)
2. Quality trimming by the highest scoring path algorithm (hsptrim-1.2.6)
3. Adapter trimming by cutadapt-1.2.1
4. Remove tRNA, rRNA-derived reads by Bowtie2 alignment
5. Remove sequencing artifacts by fastx_artifacts_filter of fastx_toolkit
6. Alignment of filtered reads to human reference genome by Tophat2 (mRNA-Seq) or Bowtie2 (sRNA-Seq)
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Tab-delimited text file (*.quants.txt) contains expression levels for individual genes. Columns: (1) id: Gene identifier (e.g. NM_000000), (2) symbol: Gene symbol (e.g. GAPDH), (3) readcount: Number of mapped reads, (4) exlev: Expression level (RPM or RPKM), (5) expct: Expression percentile rank
Supplementary_files_format_and_content: BED file (*.dmscount.{plus,minus}.txt) contains RT truncation counts by DMS treatment in single nucleotide resolution

organism: Homo sapiens

source_name: liver hepatocellular carcinoma

extract_protocol:
For mRNA-seq, total RNA was extracted with Trizol reagent (Qiagen) according to the manufacturer's instructions. After total RNA extraction, mRNA was selected using Dynabead (Thermofisher). Isolated mRNA was then randomly fragmented using fragmentation reagent (Invitrogen). Size-selected RNA fragments (200-400nt) were used for library preparation.
poly(A)-selected RNA-seq
Total RNA was extracted using TRIzol (Invitrogen).
Both of the library preparations (mRNA-Seq and sRNA-Seq) were done based on the Illumina Truseq small RNA library preparation protocol (TruSeq Small RNA Library Prep Guide, Part # 15004197 Rev. G). DMS-seq libraries were prepared using adaptors from a previous study (PMID: 30605524) following procedures from Rouskin et al., 2014 (PMID: 24336214).
mRNA-seq, sRNA-seq, DMS-seq

tag: cell line

tag: treatment

value: hsa-miR-145-5p transfection

tag: concentration

tag: incubation


title: s_testis_Mov10l_WT_21dpp_F58-M1_r2.SE [small RNA-seq]

data_processing:
Small RNA-seq reads were trimmed in two rounds using bbduk.sh version 38.87 (https://jgi.doe.gov/data-and-tools/bbtools/). First, NEXTflex adapter were trimmed from right end:  bbduk.sh -Xmx20G threads=6 in=$ {FILE}.fastq.gz out=$ {FILE}.atrim.fastq.gz literal= TGGAATTCTCGGGTGCCAAGG stats=$ {FILE}.atrim.stats overwrite=t ktrim=r k=21 rcomp=f mink=10 hdist=1 minoverlap=8  Next, 4 random bases from both sides of reads were trimmed:  bbduk.sh -Xmx20G threads=6 in=$ {FILE}.atrim.fastq.gz out=$ {FILE}.trimmed.fastq.gz stats=$ {FILE}.ftrim.stats overwrite=t forcetrimright2=4 forcetrimleft=4 minlength=18
Trimmed reads were mapped to the genomes with following parameters:  STAR --readFilesIn $ {FILE}.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 1 --outFilterMismatchNoverReadLmax 1 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 5000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outFilterMultimapScoreRange 0 --alignIntronMax 1 --alignSJDBoverhangMin 999999999999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: MesAur1.0
Supplementary_files_format_and_content: coverage genome browser tracks files: bigWig format generated in a non-stranded mode, not normalized for library size

source_name: whole testis_WT

extract_protocol:
Total RNA was extracted from adult, 21dpp, 13dpp and 9dpp hamster testes using Sigma-Aldrich miR Premier micro RNA isolation kit according to the manufacturer´s protocol. Ribosomal RNA (rRNA) was depleted from RNA used for transcriptome analysis using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Epicentre) according to the manufacturer´s protocol. rRNA depletion was confirmed by 2100 Bioanalyzer (Agilent Technologies). For small RNA-seq analysis of testes, total RNA isolated from testes as described above was used for NextFlex Small RNA-seq v3 kit (Amplicon).
Libraries were prepared according to the manufacturer´s protocol with 3´ adapter ligation overnight at 16 °C, 15 cycles used for PCR amplification and NextFlex beads used for size selection. RNA-seq libraries were sequenced by 75 nt single-end reading using the Illumina NextSeq500/550 or 100 nt single-end reading using NovaSeq6000 platform.

value: whole testis

tag: molecule subtype

value: small RNA


title: Wild-type sample2

description:
countMatrix.txt
WT_2


title: s_testis_Mov10l_WT_21dpp_F17-M3_r1.SE [small RNA-seq]


title: C9_plate 1A_E8.5_foregut

description:
BSSE-QGF-59947
processed data file: E8.5-E14.5_AllCells_genes.csv


title: miR-489-3p_rep2

description: hsa-miR-489-3p-transfected mRNA-seq in HepG2

value: hsa-miR-489-3p transfection


title: D9_plate 1A_E8.5_foregut

description:
BSSE-QGF-59948
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Wild-type sample1

description:
countMatrix.txt
WT_1


title: miR-489-3p_rep1


title: miR-153-3p_rep2

description: hsa-miR-153-3p-transfected mRNA-seq in HepG2

value: hsa-miR-153-3p transfection


title: B9_plate 1A_E8.5_foregut

description:
BSSE-QGF-59946
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG Re-Stimuated 6h INPUT rep_02 ChIP-seq

city: La Jolla

first: Anjana

last: Rao

state: CA

address: 9420 Athena Circle

department: Signaling and Gene Epression

institute: La Jolla institute

library_source: genomic

data_processing:
Paired raw reads were aligned to the Mus Musculus genome (version mm10) using bwa mem (version 0.7.15-r1144- dirty).
Unmapped reads were trimmed to remove adapter sequences and clipped by 1 base pair with Trim_galore (version 0.4.3) before being aligned again.
Sorted alignments from the first and second alignments were merged together with samtools (version 1.8), followed by removal of reads aligned to the mitochondrial genome using a custom perl script (version v5.18.1).
Duplicated reads were removed with Picard tools' Mark Duplicates (version 1.94).
Reads aligning to the blacklisted regions (generated by Alan Boyle and Anshul Kundaje as part of the ENCODE and modENCODE's projects) were removed by using bedtools intersect (version v2.27.1).
Final mapping results were processed using HOMER's [HOMER] makeTagDirectory followed by makeMultiWigHub.pl programs (version v4.10.4) to produce normalized bigwig genome browser tracks.
All the peaks from all the different conditions and replicates were merged into a singularity table keeping track of which condition belonged to what region.
For the superset of peaks belonging to the IP aBATF, we kept peaks whose average RPM input signal (across the pMIG- BATF and HKE-Transfected samples’ INPUT) was lower than 0.75 times that of the BATF-aBATF RPM signal.
Similarly, for the IP aIRF4 superset, we kept peaks where said INPUT signal was lower than 0.75 times that of the pMIG-aIRF4 RPM signal.
All the restimulated analysis used these filtered supersets for subsequent analysis.
Genome_build: Mus Musculus genome (version mm10)
Supplementary_files_format_and_content: Table-Separated File with RPMs per sample. 4th column indicate what sample(s) called a given peak, i.e. peak's condition(s) of origin. 13 & 14 columns used in all the respective analysis as a positive filter.

molecule: genomic DNA

source_name: in vitro cultured CD8 T cells

extract_protocol:
ChiP was performed as described below. pMIG-, BATF- transduced ReStimulated CD8+ T cells (1x106 cells/ml in culture media) were fixed with 1% formaldehyde at room temperature for 10 minutes with nutation. To quench the fixation, 0.5 ml 2.5M glycine was added per 10 ml, the cells were incubated on ice for 5 minutes, and washed twice with cold PBS. Fixed cells were transferred to low-binding tubes with 1 ml cold PBS and spun down at 2000rpm at 4℃ for 10 min. Cells were pelleted, snap-frozen with liquid nitrogen, and stored at -80℃ until further processing. To isolate nuclei, cell pellets were thawed on ice and the pellets were resuspended in 1 ml Bioruptor lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X-100), and incubated for 10 min at 4℃ with nutation. After centrifugation at 1700g at 4℃ for 5min, the resulting nuclear pellets were washed twice with washing buffer (10 mM Tris-HCl pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). The pellets were resuspended in 100 l shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA. 1% SDS), and sonicated using a Bioruptor in 1.5 ml bioruptor tubes (10 cycles, 30 seconds on, 30 seconds off). After sonication, the supernatants were transferred to 1.5 ml lo-binding tubes, and insoluble debris was removed by centrifugation at 20,000g. Pellets were resuspended in 100 µl shearing buffer, and 9 volumes of conversion buffer (10 mM Tris-HCl pH 7.5, 255 mM NaCl, 1 mM EDTA, 0.55 mM EGTA. 0.11% Na Deoxycholate, 0.11 % Triton X-100) was added. Chromatin was precleared with washed protein A and protein G Dynabeads for 1 hour, and the chromatin concentration was measured by qubit. 5% of chromatin was saved as input, and chromatin was incubated with anti-BATF (Brookwood Biomedical, USA) or anti-IRF4 (clone D9P5H, Cell Signaling Technology, USA) antibodies and protein A and protein G Dynabeads overnight at 4℃ with rotation. The following day, bead-bound chromatin was washed twice with RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% NP40, 0.1% SDS, 0.5% Na Deoxycholate), and then with high salt buffer (50 mM Tris-HCl pH8.0, 500 mM NaCl, 1 mM EDTA, 1% NP40, 0.1% SDS), LiCl buffer (50 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na Deoxycholate), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was eluted with 100 l elution buffer (100 mM NaHCO3, 1% SDS, 1 mg/ml RNase A) twice for 30 minutes at 37℃ using a 1000 rpm shaking heat block. 5 l proteinase K (20 mg/ml, Ambion, USA) and 8 l of 5 M NaCl were added to the eluted DNA, and samples were incubated at 65℃ with shaking (1,200 rpm) for de-crosslinking. DNA was purified with Zymo ChIP DNA Clean & Concentrator (Zymo Research, USA).
Libraries were prepared using NEB Ultra II library Prep kits (NEB) following the manufacturer’s instructions
ChiP-seq, 2x50- cycle paired-end sequencing (illumina)

value: Spleen

value: in vitro cultured CD8 T cells

value: Re-stimulated for 6h CD8 T cells

tag: antibody


title: A9_plate 1A_E8.5_foregut

description:
BSSE-QGF-59945
processed data file: E8.5-E14.5_AllCells_genes.csv


title: s_testis_Mov10l_KO_adult_So780_r2.PE

data_processing:
Raw RNA-seq reads were mapped to golden hamster (mesAur1) and the newest golden hamster (PRJDB10770) genomes using STAR 2.7.3a with following parameters:  STAR --readFilesIn $ {FILE}.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 5000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --sjdbScore 2  For analysis of expression of protein coding genes, reads were mapped with maximum of 20 multimapping alignments allowed.
Reads mapped to mesAur1 were counted over exon features annotated by Ensembl (release 99) using featureCounts v2.0.0:  featureCounts -a $ {FILE}.gtf -o $ {FILE}.counts.txt $ {FILE}.bam -T 12 -F GTF -M -O –fraction  For the paired-end libraries -p flag was added. For the stranded libraries, -s 2 flag was added.
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: MesAur1.0
Supplementary_files_format_and_content: ensembl.99.MesAur1.0.Piwil3_Tex101.from_RefSeq.raw_counts.testis.txt: counts of reads over exon coordinats from Ensembl Release 99 .gtf file with added Piwil3 and Tex101 annotated by RefSeq, samples are in columns, genes in rows
Supplementary_files_format_and_content: Coverage genome browser tracks files: bigWig format generated in a non-stranded mode, not normalized for library size

source_name: whole testis_Mov10l1 KO

extract_protocol:
Total RNA was extracted from adult, 21dpp, 13dpp, 9dpp and 0dpp hamster testes using Sigma-Aldrich miR Premier micro RNA isolation kit according to the manufacturer´s protocol. Ribosomal RNA (rRNA) was depleted from RNA used for transcriptome analysis using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Epicentre) according to the manufacturer´s protocol. rRNA depletion was confirmed by 2100 Bioanalyzer (Agilent Technologies).
RNA-seq libraries were generated using NEBNext Ultra II directional RNA library Prep kit for Illumina (BioLabs, #E7765S) according to the manufacturer´s protocol. RNA-seq libraries from adult, 21dpp and 13dpp testes were sequenced by 150 nt pair-end reading. RNA-seq libraries from 9dpp and 0dpp testes were sequenced by 75 nt single-end reading using the Illumina NextSeq500/550 platform.

value: Mov10l1 KO

value: 53 weeks


title: miR-153-3p_rep1


title: miR-135b-5p_rep2

description: hsa-miR-135b-5p-transfected mRNA-seq in HepG2

value: hsa-miR-135b-5p transfection


title: s_testis_Mov10l_WT_adult_So808_r2.PE

value: 23 weeks


title: H8_plate 1A_E8.5_foregut

description:
BSSE-QGF-59944
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Foregut


title: s_testis_Mov10l_KO_adult_M68_r1.PE

value: 63 weeks


title: Wild-type sample3

description:
countMatrix.txt
WT_3

value: Wild-type

value: neuron


title: s_testis_Mov10l_WT_adult_M2_r1.PE

value: WT

value: 65 weeks


title: pMIG Re-Stimuated 6h INPUT rep_01 ChIP-seq


title: HKE Re-Stimuated 6h INPUT rep_02 ChIP-seq


title: G8_plate 1A_E8.5_foregut

description:
BSSE-QGF-59943
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HKE Re-Stimuated 6h INPUT rep_01 ChIP-seq


title: miR-135b-5p_rep1


title: s_testis_Mov10l_KO_21dpp_F58-M2_r1.PE

value: whole testis


title: BATF Re-Stimuated 6h INPUT rep_02 ChIP-seq


title: F8_plate 1A_E8.5_foregut

description:
BSSE-QGF-59942
processed data file: E8.5-E14.5_AllCells_genes.csv


title: s_testis_Mov10l_KO_21dpp_F43-M5_r2.PE


title: miR-126-3p_rep2

description: hsa-miR-126-3p-transfected mRNA-seq in HepG2

value: hsa-miR-126-3p transfection


title: E8_plate 1A_E8.5_foregut

description:
BSSE-QGF-59941
processed data file: E8.5-E14.5_AllCells_genes.csv


title: s_testis_Mov10l_WT_21dpp_F58-M1_r2.PE


title: miR-126-3p_rep1


title: D8_plate 1A_E8.5_foregut

description:
BSSE-QGF-59940
processed data file: E8.5-E14.5_AllCells_genes.csv


title: BATF Re-Stimuated 6h INPUT rep_01 ChIP-seq


title: C8_plate 1A_E8.5_foregut

description:
BSSE-QGF-59939
processed data file: E8.5-E14.5_AllCells_genes.csv


title: s_testis_Mov10l_WT_21dpp_F17-M3_r1.PE


title: pMIG Re-Stimuated 6h IP_aBATF rep_02 ChIP-seq

value: anti-BATF (Brookwood Biomedical, USA)


title: miR-7-5p_rep1

description: hsa-miR-7-5p-transfected mRNA-seq in HepG2

value: hsa-miR-7-5p transfection


title: s_testis_Mov10l_KO_13dpp_F64-M3_r2.PE


title: miR-24-3p_rep1

description: hsa-miR-24-3p-transfected mRNA-seq in HepG2

value: hsa-miR-24-3p transfection


title: s_testis_Mov10l_KO_13dpp_F60-M3_r1.PE


title: HKE Re-Stimuated 6h IP_aBATF rep_02 ChIP-seq

value: Spleen

value: in vitro cultured CD8 T cells


title: miR-24-3p_rep2


title: pMIG Re-Stimuated 6h IP_aBATF rep_01 ChIP-seq

value: Re-stimulated for 6h CD8 T cells


title: A8_plate 1A_E8.5_foregut

description:
BSSE-QGF-59937
processed data file: E8.5-E14.5_AllCells_genes.csv


title: BATF Re-Stimuated 6h IP_aBATF rep_02 ChIP-seq


title: H7_plate 1A_E8.5_foregut

description:
BSSE-QGF-59936
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HKE Re-Stimuated 6h IP_aBATF rep_01 ChIP-seq


title: miR-122-5p_rep2

description: hsa-miR-122-5p-transfected mRNA-seq in HepG2

value: hsa-miR-122-5p transfection


title: s_testis_Mov10l_WT_13dpp_F64-M2_r2.PE


title: miR-122-5p_rep1


title: G7_plate 1A_E8.5_foregut

description:
BSSE-QGF-59935
processed data file: E8.5-E14.5_AllCells_genes.csv


title: miR-138-5p_rep4

description: hsa-miR-138-5p-transfected mRNA-seq in HepG2

value: hsa-miR-138-5p transfection


title: miR-138-5p_rep3


title: F7_plate 1A_E8.5_foregut

description:
BSSE-QGF-59934
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG Re-Stimuated 6h IP_aIRF4 rep_02 ChIP-seq

value: anti-IRF4 (clone D9P5H, Cell Signaling Technology, USA)


title: miR-138-5p_rep2


title: BATF Re-Stimuated 6h IP_aBATF rep_01 ChIP-seq


title: E7_plate 1A_E8.5_foregut

description:
BSSE-QGF-59933
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Foregut


title: B8_plate 1A_E8.5_foregut

description:
BSSE-QGF-59938
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D7_plate 1A_E8.5_foregut

description:
BSSE-QGF-59932
processed data file: E8.5-E14.5_AllCells_genes.csv


title: miR-138-5p_rep1


title: HKE Re-Stimuated 6h IP_aIRF4 rep_02 ChIP-seq


title: pMIG Re-Stimuated 6h IP_aIRF4 rep_01 ChIP-seq


title: miR-142-3p_rep5

description: hsa-miR-142-3p-transfected mRNA-seq in HepG2

value: hsa-miR-142-3p transfection


title: miR-142-3p_rep6


title: C7_plate 1A_E8.5_foregut

description:
BSSE-QGF-59931
processed data file: E8.5-E14.5_AllCells_genes.csv


title: miR-218-5p_rep6

description: hsa-miR-218-5p-transfected mRNA-seq in HepG2

value: hsa-miR-218-5p transfection


title: B7_plate 1A_E8.5_foregut

description:
BSSE-QGF-59930
processed data file: E8.5-E14.5_AllCells_genes.csv


title: s_testis_Mov10l_WT_13dpp_F60-M2_r1.PE


title: A7_plate 1A_E8.5_foregut

description:
BSSE-QGF-59929
processed data file: E8.5-E14.5_AllCells_genes.csv


title: miR-218-5p_rep5


title: HKE Re-Stimuated 6h IP_aIRF4 rep_01 ChIP-seq


title: H6_plate 1A_E8.5_foregut

description:
BSSE-QGF-59928
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG Re-Stimuated 6h CD8 T cells_rep3 RNA-seq

data_processing:
Paired reads were mapped to STAR using the parameters (--outFilterMultimapNmax 30 --outReadsUnmapped Fastx --outSAMattributes All --outSAMprimaryFlag OneBestScore --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts).
Mapping results were processed using HOMER's makeTagDirectory twice, once for the individual replicates and a subsequent one merging them (for a less crowded genome browser session), followed by makeMultiWigHub.pl programs (version v4.10.4) to produce normalized bigwig genome browser tracks.
Counts per gene were obtained from STAR’s “STAR_gene_counts” (version subread-2.0.0-source) Differential Gene Expression was done with R (version 3.5.2) and these packages: IRdisplay, limma, edgeR, Glimma, Mus.musculus, RColorBrewer, gplots.
In brief, count reads from STAR were read and voom-normalized after both CPM conversion and removal of genes whose CPM was lower than 1 across less than a third of total samples.
After limma-voom normalization performed in the gene’s signal, and a linear model fitter to each gene, computation of significance statistics for differential gene expression (DGE) was done by empirical Bayes moderation of the standard errors, with intervals for the null hypothesis ([-log2(1.2), log2(1.2)] lfc).
A gene was considered DGE if both the absolute Log2FC was ≥ 2 and a adj.pvalue (FDR) ≤0.05 threshold was met.
Genome_build: Mus Musculus genome (version mm10)
Supplementary_files_format_and_content: Table-Separated File with Voom-Normalized and log2 scaled gene expression signal per sample.

source_name: pMIG Re-Stimuated 6h CD8 T cells

extract_protocol:
GFP+CD8+Thy1.1+ CAR T cells were sorted from Stimluated CD8 T cells (either 0h or 6h after Re-Stimulation with CD3 & CD28). And  total RNA were extracted using Qiagen RNeasy plus micro kit
Libraries were constructed by Smart2seq protocol
50x50bp pair end sequencing

tag: age/cell type

value: pMIG transduced


title: mock_rep17

description: mock-transfected mRNA-seq in HepG2

value: mock transfection


title: pMIG Re-Stimuated 6h CD8 T cells_rep2 RNA-seq


title: mock_rep16

description: mock-transfected mRNA-seq in HepG2


title: BATF Re-Stimuated 6h IP_aIRF4 rep_02 ChIP-seq


title: F6_plate 1A_E8.5_foregut

description:
BSSE-QGF-59926
processed data file: E8.5-E14.5_AllCells_genes.csv


title: mock_rep15

description: mock-transfected mRNA-seq in HepG2


title: pMIG Re-Stimuated 6h CD8 T cells_rep1 RNA-seq


title: BATF Re-Stimuated 6h IP_aIRF4 rep_01 ChIP-seq


title: mock_rep14

description: mock-transfected mRNA-seq in HepG2


title: D6_plate 1A_E8.5_foregut

description:
BSSE-QGF-59924
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HKE Re-Stimuated 6h CD8 T cells_rep3 RNA-seq

source_name: HKE Re-Stimuated 6h CD8 T cells

value: HKE transduced


title: C6_plate 1A_E8.5_foregut

description:
BSSE-QGF-59923
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HKE Re-Stimuated 6h CD8 T cells_rep1 RNA-seq


title: mock_rep13

description: mock-transfected mRNA-seq in HepG2


title: G6_plate 1A_E8.5_foregut

description:
BSSE-QGF-59927
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B6_plate 1A_E8.5_foregut

description:
BSSE-QGF-59922
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E6_plate 1A_E8.5_foregut

description:
BSSE-QGF-59925
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A6_plate 1A_E8.5_foregut

description:
BSSE-QGF-59921
processed data file: E8.5-E14.5_AllCells_genes.csv


title: BATF Re-Stimuated 6h CD8 T cells_rep3 RNA-seq

source_name: BATF Re-Stimuated 6h CD8 T cells

value: Batf transduced


title: HKE Re-Stimuated 6h CD8 T cells_rep2 RNA-seq


title: mock_rep12

description: mock-transfected mRNA-seq in HepG2


title: BATF Re-Stimuated 6h CD8 T cells_rep2 RNA-seq


title: H5_plate 1A_E8.5_foregut

description:
BSSE-QGF-59920
processed data file: E8.5-E14.5_AllCells_genes.csv


title: BATF Re-Stimuated 6h CD8 T cells_rep1 RNA-seq


title: GC B cells from RagC Q119L/+ mice [YRC00693]

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
RNA-seq processing:
Eightysix-base-pair single-end sequenced reads followed adapter and polyA tail removal as indicated by Lexogen. UMI tags were extracted with umi_tools as indicated by Lexogen. The resulting reads were analysed with the nextpresso pipeline (http://www.eurekaselect.com/154865/article) as follows: sequencing quality was checked with FastQC v0.11.0 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse genome (GRCm38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19, allowing 3 mismatches and 20 multihits. The Gencode vM25 gene annotation for GRCm38 was used. Read counts were obtained with HTSeq. Differential expression and normalization was performed with DESeq2, keeping only those genes where the normalized count value was higher than 2 in at least 10% of the samples, and those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis for selected gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

source_name: Germinal centre B cells sorted from spleen of SRBC immunized mice

extract_protocol:
Germinal Centre B cells (B220+, CD95+,CD38−) were sorted from RagCQ119L/+ and RagC+/+ splenocytes after 12 d of SRBC immunization in a BD FACSAria Ilu (Becton Dickinson) and InFlux (Cytopeia-Becton Dickinson) cell sorters. Total RNA was extracted using TRIzol and PicoPure RNA Isolation kit (Arcturus, #12204-01) following the manufacturer’s instructions.
Total RNA samples were processed into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. A UMI Second Strand Synthesis module was used whereby random primers featured a 6 nt long Unique Molecular Identifier 5' tag. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols. {This library preparation kit generates directional libraries stranded in the sense orientation: the read1 (the only read in single read format) has the sense orientation}

treatment_protocol: Sheep red blood cells to immunize the mice

value: germinal centre B cells

value: 12d SRBC

value: RagC Q119L/+


title: GC B cells from RagC +/+ mice [YRC00696]

value: RagC +/+


title: G5_plate 1A_E8.5_foregut

description:
BSSE-QGF-59919
processed data file: E8.5-E14.5_AllCells_genes.csv


title: GC B cells from RagC Q119L/+ mice [YRC00692]


title: pMIG Re-Stimuated 0h CD8 T cells_rep3 RNA-seq

source_name: pMIG Re-Stimuated 0h CD8 T cells

value: Spleen

value: 5 days after in vitro culture


title: GC B cells from RagC Q119L/+ mice [YRC00691]


title: F5_plate 1A_E8.5_foregut

description:
BSSE-QGF-59918
processed data file: E8.5-E14.5_AllCells_genes.csv


title: GC B cells from RagC +/+ mice [YRC00690]


title: E5_plate 1A_E8.5_foregut

description:
BSSE-QGF-59917
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG Re-Stimuated 0h CD8 T cells_rep1 RNA-seq


title: D5_plate 1A_E8.5_foregut

description:
BSSE-QGF-59916
processed data file: E8.5-E14.5_AllCells_genes.csv


title: GC B cells from RagC Q119L/+ mice [YRC00685]


title: pMIG Re-Stimuated 0h CD8 T cells_rep2 RNA-seq


title: A5_plate 1A_E8.5_foregut

description:
BSSE-QGF-59913
processed data file: E8.5-E14.5_AllCells_genes.csv


title: GC B cells from RagC +/+ mice [YRC00684]


title: HKE Re-Stimuated 0h CD8 T cells_rep2 RNA-seq

source_name: HKE Re-Stimuated 0h CD8 T cells


title: GC B cells from RagC +/+ mice [YRC00689]


title: A9_plate 4A_E14.5_PA

description:
BSSE-QGF-60041
processed data file: E8.5-E14.5_AllCells_genes.csv

source_name: Pancreatic epithelium

value: Pancreas


title: HKE Re-Stimuated 0h CD8 T cells_rep1 RNA-seq


title: B220+ sorted cells from VavPBcl2/RagC Q119L/+ lymphoma [YCX00166]

data_processing:
RNA-seq processing:
Eightysix-base-pair single-end sequenced reads followed adapter and polyA tail removal as indicated by Lexogen. The resulting reads were analysed with the nextpresso pipeline (http://www.eurekaselect.com/154865/article) as follows: sequencing quality was checked with FastQC v0.11.0 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse genome (GRCm38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19, allowing 3 mismatches and 20 multihits. The Gencode vM25 gene annotation for GRCm38 was used. Read counts were obtained with HTSeq. Differential expression and normalization was performed with DESeq2, keeping only those genes where the normalized count value was higher than 2 in at least 10% of the samples, and those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis for selected gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

source_name: B220+ cells sorted from spleen

extract_protocol:
B220+ were isolated from mouse lymphoma tumours by immunomagnetic enrichment with CD45R (B220) microbeads (Miltenyi Biotech, #130-049-501). Total RNA was extracted using TRIzol and PicoPure RNA Isolation kit (Arcturus, #12204-01) following the manufacturer’s instructions
Total RNA samples were processed into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols. {This library preparation kit generates directional libraries stranded in the sense orientation: the read1 (the only read in single read format) has the sense orientation}

value: VavPBcl2/RagC Q119L/+

value: lymphoma


title: H4_plate 1A_E8.5_foregut

description:
BSSE-QGF-59912
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B220+ sorted cells from VavPBcl2/RagC +/+ lymphoma [YCX00077]

value: VavPBcl2/RagC +/+


title: BATF Re-Stimuated 0h CD8 T cells_rep3 RNA-seq

source_name: BATF Re-Stimuated 0h CD8 T cells


title: G4_plate 1A_E8.5_foregut

description:
BSSE-QGF-59911
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Foregut


title: cell line [MCCL13]

type: genomic

city: Los Angeles

first: Gangning

last: Liang

address: 1441 Eastlake Ave. NOR7344

department: Urology

institute: University f Southern California

description:
FFPE
203060700072_R02C01

hyb_protocol: standard protocol

scan_protocol: BeadArrays were scanned using Illumina iScan scanners

data_processing:
minfi
The signal_intensities.txt' contains Unmethylated and methylated signal intensities

extract_protocol: Following bisulfite treatment (ZYMO research EZ DNA Methylation kit), DNA methylation data were generated using the Illumina Infinium MethylationEPIC BeadChip array at the USC Norris Molecular Genomics Core Facility).

tag: gender

value: F


title: Patient-Metastatic-lymph node [MCC_s20]

description:
FFPE
203490650051_R08C01

value: M

value: lymph node

tag: tumor stage

value: III

tag: race

value: WHITE

tag: recurrence

tag: immunosuppressed?

value: NO

tag: tumor location

value: UNK

tag: surgery

value: LND

tag: radiation

value: YES

tag: systemic

tag: date of dx

tag: date of relapse

tag: date of last follow-up

tag: status

value: ALIVE

tag: patient


title: BATF Re-Stimuated 0h CD8 T cells_rep2 RNA-seq

tag: strain

tag: tissue

value: Spleen

tag: treatment

value: Batf transduced


title: B220+ sorted cells from VavPBcl2/RagC Q119L/+ lymphoma [YCX00073]

tag: cell type

tag: genotype


title: F4_plate 1A_E8.5_foregut

description:
BSSE-QGF-59910
processed data file: E8.5-E14.5_AllCells_genes.csv

tag: developmental stage


title: B5_plate 1A_E8.5_foregut

description:
BSSE-QGF-59914
processed data file: E8.5-E14.5_AllCells_genes.csv


title: cell line [MS1]

description:
FFPE
203060700072_R01C01

tag: gender

tag: age


title: Patient-adjacent normal [MCC_s18]

description:
FFPE
203490650051_R06C01

source_name: Normal

value: skin

tag: tumor stage

tag: race

tag: recurrence

tag: immunosuppressed?

tag: tumor location


title: B220+ sorted cells from VavPBcl2/RagC +/+ lymphoma [YCX00060]


title: E4_plate 1A_E8.5_foregut

description:
BSSE-QGF-59909
processed data file: E8.5-E14.5_AllCells_genes.csv

source_name: Foregut endoderm


title: Patient-Metastatic-lymph node [MCC_s13]

description:
FFPE
203490650051_R01C01

value: IIII

value: HISP

value: H/N

tag: surgery

value: WLE + LND

tag: radiation

tag: systemic

value: chemo

tag: date of dx

tag: date of relapse


title: Patient-Primary [MCC_s16]

description:
FFPE
203490650051_R04C01

source_name: Primary

value: M

tag: tissue

value: II

value: LE

tag: date of last follow-up

tag: status

value: DEAD

tag: additional info

value: UNKNOWN COD

tag: patient


title: HKE Re-Stimuated 0h CD8 T cells_rep3 RNA-seq

tag: strain

tag: age/cell type

value: 5 days after in vitro culture

tag: treatment

value: HKE transduced


title: SST+ cSNAIL ATAC-seq Y2Spos [Y2Spos_CKDL190142778-1a-N707-N506_HMHTYDSXX_L4]

city: Pittsburgh

first: BaDoi

middle: Nguyen

last: Phan

state: PA

address: 5000 Forbes Ave

department: Computational Biology

institute: Carnegie Mellon University

description:
unmerged fastq from lane L4
processed data file: Y2Spos_Cpu_SST.bw
Y2Spos_CKDL190142778-1a-N707-N506_HMHTYDSXX_L4
processed data file:
Pfenning_SSTpos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

data_processing:
We processed raw FASTQ files of ATAC-seq experiments with the official ENCODE ATAC-seq pipeline (Landt et al., 2012) accessed by https://github.com/ENCODE-DCC/atac-seq-pipeline. We ran this pipeline using the mm10 genome assembly for mouse and the hg38 genome for human with the following settings: smooth_win = 150, multimapping = 0, idr_thresh = 0.1, cap_num_peak = 300,000, keep_irregular_chr_in_bfilt_peak = true. We grouped biological replicates when processing data to obtain individual de-duplicated, filtered bam files and reproducible (IDR) peaks for each condition. Unless otherwise stated, we used the optimal reproducible set of peaks for downstream analyses. We removed samples that had low periodicity indicated by ENCODE quality control metrics and reprocessed the remaining replicates with the pipeline.
We created a consensus set of non-overlapping IDR peaks from the ATAC-seq pipeline for cSNAIL ATAC-seq and Mo et al. INTACT samples (Tissue: Ctx, Cpu, and NAc ; Celltype: EXC, PV, SST, VIP, D1, D2). We extended the peak set 200bp up- and down-stream, count overlapping fragments with Rsubread v2.0.1 using the de-duplicated BAM files from the pipeline(Liao et al., 2014). This is the raw counts matrix including experiments published with this work and
We used Deeptools v3.5.0 to convert the deduplicated BAM files to normalized bigWig files (Ramírez et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: peak: optimal IDR peaks from ENCODE pipeline. bigWig = normalized bigWig files from BAM alignment. counts= featurecounts summarized rangedExperiment of consensus IDR peaks across celltypes/tissues

source_name: Striatum

extract_protocol:
We performed bulk and cSNAIL ATAC-seq from cortex (CTX) and dorsal striatum/nucleus accumbens C57Bl/6J mice  as described in Buenrostro et al., 2015(Buenrostro et al., 2015) with the following minor differences in buffers and reagents. We euthanized mice with isoflurane, rapidly decapitated to extract the brain, and sectioned it in ice-cold oxygenated aCSF (119mM NaCl, 2.5 mM KCl, 1mM NaH2PO4(monobasic), 26.2mM NaHCO3, 11mM glucose) at 200-micron sections on a vibratome (Leica VT1200). We further micro-dissected sections for cortex and dorsal striatum on a stereo microscope and transferred dissected regions into chilled lysis buffer (Buenrostro et al., 2015). We dounce homogenized the dissected brains in 5mL of lysis buffer with the loose pestle (pestle A) in a 15mL glass dounce homogenizer (Pyrex #7722-15). We washed nuclei lysate off the pestle with 5mL of lysis buffer and filtered the nuclei through a 70-micron cell strainer into a 50mL conical tube. We washed the dounce homogenizer again with 10mL of BL buffer and transferred the lysate through the 70-micron filter (Foxx 1170C02). We pelleted the 20 mL of nuclei lysate at 2,000 x g for 10 minutes in a refrigerated centrifuge at 4°C. We discarded the supernatant and resuspended the nuclei in 100-300 microliters of water to approximate a concentration of 1-2 million nuclei/ mL. We filtered the nuclei suspension through a 40-micron cell strainer. We stained a sample of nuclei with DAPI (Invitrogen #D1206) and counted the sample to measure 50k nuclei per ATAC-seq transposition reaction. On the day of the ATAC-seq experiments, we dissected brain regions from fresh tissue and extracted nuclei in the same manner as described for bulk tissue experiments. Then, we sorted the nuclei suspension into Sun1GFP+ (Cre+) and Sun1GFP- (Cre-) fractions using affinity purification with Protein G Dynabeads (Thermo Fisher, cat. 10004D). A pre-clearing incubation with beads and nuclei for 10-15 minutes removes effects from non-specific binding events. Next, we incubated the remaining free nuclei with anti-GFP antibody (Invitrogen, #G10362) for 30 minutes to bind Sun1GFP. Finally, we added new beads to the solution to conjugate with the antibody and incubated the reaction for an additional 20 minutes. The pre-clear step and all incubations took place in wash buffer (0.25M Sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine with KOH to pH 7.8, and 0.4% IGEPAL) at 4°C with end-to-end rotation. After the binding process, we separated bead-bound nuclei on a magnet, washed three times with wash buffer, and filtered through a 20µM filter to ensure purity. We resuspended nuclei in nuclease-free water for input into the ATAC-seq tagmentation reaction. We performed nuclei quantification and tagmentation in the same manner described for bulk tissue ATAC-seq above. We list in the table below the number of animals, the genotypes, and which regions collected for ATAC-seq experiments in this study. N=2 Pvalb-cre samples from CPU/NAc region had received a sham surgery with saline injection into the external globus pallidus 5 days before they were sacrificed (Lawler et al, 2020 in press J. Neuro.) N=2 Drd1-cre samples from both CPU and NAc regions had received headcap surgeries 3 weeks before they were sacrificed. Both Pvalb-cre and Drd1-cre were overall healthy at time of sacrifice.
The remaining steps follow the Buenrostro et al., 2015(Buenrostro et al., 2015) protocol for tagmentation and library amplification.
We shallowly sequenced barcoded ATAC-seq libraries at 1-5 million reads per sample on an Illumina MiSeq and processed individual samples through the ENCODE pipeline for initial quality control. We used these QC measures (clear periodicity, library complexity, and minimal bottlenecking) to filter out low-quality samples and re-pooled a balanced library for paired-end deep sequencing on an Illumina NextSeq to target 30 million uniquely mapped fragments per sample after mitochondrial DNA and PCR duplicate removal. These raw sequencing files entered processing through the ENCODE ATAC-seq pipeline as above by merging technical replicates and grouping biological replicates by brain region for each pipeline run.

treatment_protocol: For cSNAIL, cell type-specific ATAC-seq, we used the following treatment protocol on C57 mice. The cSNAIL genome (pAAV-Ef1a-DIO-Sun1-Gfp-WPRE-pA) contains loxP sites to invert the Sun1-Gfp fusion gene and integrate into the nuclear membrane of cells expressing the Cre gene, allowing these cell populations to be profiled for various genomic assays (Lawler et al, 2020 in press J. Neuro).  We packaged the cSNAIL genome with AAV variant PHP.eB (pUCmini-iCAP-PHP.eB) in AAVpro(R) 293T cells (Takara, cat #632273). Viviana Gradinaru provided us with the pUCmini-iCAP-PHP.eB (http://n2t.net/addgene:103005; RRID: Addgene 103005)(Chan et al., 2017). We precipitated viral particles with polyethylene glycol, isolated with ultracentrifugation on an iodixanol density gradient, and purified in PBS with centrifugation washes and 0.2µM syringe filtration. We injected each mouse with 4.0 x 1011vg into the retro-orbital cavity under isoflurane anesthesia. We allowed the virus to incubate in the animal for 3-4 weeks to reach peak expression. We closely monitored the health of the animals throughout the length of the virus incubation and did not note any concerns.

tag: animal

tag: assay

value: cSNAIL ATAC-seq

value: retro-orbital AAV injection

tag: virus

tag: genotype

value: Sst-cre

tag: project

value: Aging ATAC-seq

tag: cell type

value: SST+


title: B220+ sorted cells from VavPBcl2/RagC +/+ lymphoma [YCX00051]

value: VavPBcl2/RagC +/+

value: lymphoma


title: Patient-Primary [MCC_s17]

description:
FFPE
203490650051_R05C01

tag: gender

value: F

value: skin

tag: tumor stage

tag: race

value: WHITE

tag: age

tag: recurrence

tag: immunosuppressed?

value: NO

tag: tumor location

value: H/N

tag: surgery

value: WLE

tag: radiation

value: YES

tag: systemic

value: ALIVE


title: Patient-Primary [MCC_s14]

description:
FFPE
203490650051_R02C01

value: M

tag: tissue

value: III

value: WLE + LND

tag: date of dx

tag: date of relapse

tag: date of last follow-up

tag: status

value: LOST

tag: patient


title: RD-18-629 Eplilepsy treated patient

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

description: FCD I

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research.  After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification.  The amplified DNA is then enzymatically fragmented using end-point fragmentation.  The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer.  The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization.  The DNA hybridizes with the array overnight in an oven at 48⁰C.  After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: minfi- R package was used to analyze the data. Arrays were combined to 450K probes using minfi combineArray() function. Data was preprocessed, quantile normalized and poor probes were removed based on mean detection Pvalues per sample.

label: Cy5 and Cy3

source_name: Brain

label_protocol: Standard Illumina Protocol

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit

value: Brain


title: D4_plate 1A_E8.5_foregut

description:
BSSE-QGF-59908
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Foregut

tag: developmental stage

tag: genotype


title: B220+ sorted cells from VavPBcl2/RagC +/+ lymphoma [YCX00043]

tag: cell type


title: SST+ cSNAIL ATAC-seq Y2Spos [Y2Spos_CKDL190142778-1a-N707-N506_HMHTYDSXX_L3]

description:
unmerged fastq from lane L3
processed data file: Y2Spos_Cpu_SST.bw
Y2Spos_CKDL190142778-1a-N707-N506_HMHTYDSXX_L3
processed data file:
Pfenning_SSTpos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

tag: animal

tag: assay

value: cSNAIL ATAC-seq

value: retro-orbital AAV injection

tag: virus

value: Sst-cre

tag: project

value: Aging ATAC-seq

value: SST+


title: B4_plate 1A_E8.5_foregut

description:
BSSE-QGF-59906
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SST+ cSNAIL ATAC-seq Y2Spos [Y2Spos_CKDL190142778-1a-N707-N506_HMHTYDSXX_L2]

description:
unmerged fastq from lane L2
processed data file: Y2Spos_Cpu_SST.bw
Y2Spos_CKDL190142778-1a-N707-N506_HMHTYDSXX_L2
processed data file:
Pfenning_SSTpos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: B220+ sorted cells from VavPBcl2/RagC Q119L/+ lymphoma [YCX00026]

value: VavPBcl2/RagC Q119L/+

value: lymphoma


title: Patient-Primary [MCC_s12]

description:
FFPE
203490650039_R08C01

tag: gender

value: skin

tag: tumor stage

value: I

tag: race

value: HISP

tag: age

tag: recurrence

tag: immunosuppressed?

value: YES (TRANSPLANT)

tag: tumor location

value: H/N

value: NO

value: HOSPICE

tag: additional info

value: mCSCC, CHF


title: Patient-Metastatic-skin [MCC_s11]

description:
FFPE
203490650039_R07C01

value: M

tag: tissue

value: III

tag: surgery

value: WLE + LND

tag: radiation

value: YES

tag: systemic

tag: date of dx

tag: date of relapse

tag: date of last follow-up

tag: status

value: ALIVE


title: Patient-Metastatic-skin [MCC_s5]

description:
FFPE
203490650039_R01C01

value: WHITE

value: LE

value: chemo, PD-1, CTLA-4, TVEC

tag: patient


title: G3_plate 1A_E8.5_foregut

description:
BSSE-QGF-59903
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Foregut

tag: developmental stage

tag: genotype


title: B220+ sorted cells from VavPBcl2/RagC Q119L/+ lymphoma [YCX00021]

tag: cell type

value: VavPBcl2/RagC Q119L/+

value: lymphoma


title: Patient-Metastatic-lymph node [MCC_s19]

description:
FFPE
203490650051_R07C01

tag: gender

value: lymph node

tag: tumor stage

tag: race

tag: age

value: UNK

value: LND


title: RD-18-679 Eplilepsy treated patient

description: FCD II

value: Brain


title: SST+ cSNAIL ATAC-seq Y2Cpos [Y2Cpos_CKDL190142778-1a-N705-N506_HMHTYDSXX_L3]

description:
unmerged fastq from lane L3
processed data file: Y2Cpos_Ctx_SST.bw
Y2Cpos_CKDL190142778-1a-N705-N506_HMHTYDSXX_L3
processed data file:
Pfenning_SSTpos_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

source_name: Cortex

tag: animal

tag: assay

value: cSNAIL ATAC-seq

value: retro-orbital AAV injection

tag: virus

value: Sst-cre

tag: project

value: Aging ATAC-seq

value: SST+


title: B220+ sorted cells from VavPBcl2/RagC Q119L/+ lymphoma [YCX00009]

tag: tissue


title: RD-18-646 Eplilepsy treated patient

description: FCD III


title: Patient-adjacent normal [MCC_s8]

description:
FFPE
203490650039_R04C01

value: M

value: skin

tag: recurrence


title: BATF Re-Stimuated 0h CD8 T cells_rep1 RNA-seq

tag: strain

value: Spleen

tag: age/cell type

value: 5 days after in vitro culture

tag: treatment

value: Batf transduced


title: F3_plate 1A_E8.5_foregut

description:
BSSE-QGF-59902
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Foregut


title: Patient-adjacent normal [MCC_s10]

description:
FFPE
203490650039_R06C01

value: III

value: HISP

tag: immunosuppressed?

value: NO

tag: tumor location

value: H/N

tag: surgery

value: WLE + LND

tag: radiation

value: YES

tag: systemic

tag: date of dx

tag: date of relapse

tag: date of last follow-up

tag: status

value: ALIVE

tag: patient


title: E3_plate 1A_E8.5_foregut

description:
BSSE-QGF-59901
processed data file: E8.5-E14.5_AllCells_genes.csv

tag: developmental stage

tag: genotype


title: H3_plate 1A_E8.5_foregut

description:
BSSE-QGF-59904
processed data file: E8.5-E14.5_AllCells_genes.csv

tag: tissue


title: D3_plate 1A_E8.5_foregut

description:
BSSE-QGF-59900
processed data file: E8.5-E14.5_AllCells_genes.csv


title: RNA_P3_Tumor_1_0023

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

data_processing:
Adapter trimming and quality filtering of sequencing data were performed using cutadapt v1.18. Filtered reads were mapped to hg38 Refseq RNA using Bowtie2-3.4.2 with the following parameters: -t -N 1 -D 200 -R 20 -L 20 -i S,1,0.50 --nofw. Tag numbers of each gene were quantified as the expression level of each gene.
Between-sample normalization was performed against raw count data using Microsoft R open 3.6.1 (https://mran.microsoft.com/open/) and TCC package (DDD-D method). Genes with fold change ≥4 and maximum expression ≥20 were identified as differentially expressed genes.
Co-expressed gene modules among differentially expressed genes were detected using the WGCNA package. For WGCNA, the power value was 19, the merge threshold value was 0.1, the threshold value for the output of co-expression interactions was 0.25, and other calculation settings were set to defaults. The genes in PR associated gene modules detected using WGCNA were further clustered into upregulated and downregulated genes in PR patients using hclust function of stats package.
Among genes upregulated in PR (1,606 genes), genes included in the term “T cell activation” in GO biological processes (GO) was extracted using Cytoscape 3.7.2 with ClueGO plugin (v2.5.5). We used versions of the GO term database and KEGG pathway term database that were current on Feb 27, 2019. If multiple biopsies are obtained at the same time point in patient, RNAseq and subsequent data processing were performed separately.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw tag-count values for each sample

source_name: tumor biopsy

extract_protocol:
Tumor biopsy was conducted on before (day0) and after the treatment (day39-day55). Presence or absence of tumor tissue in biopsies was determined pathologically. Tumor biopsies were homogenized in TRIzol (Ambion, Carlsbad, CA, USA). RNA was extracted from each sample using the RNeasy mini kit (QIAGEN, Hilden, Germany, # 74106) and amounts and purity measured with the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Five-micrograms of total RNA was diluted with 1 mL of cell lysis buffer and used for RNA sequencing.
PolyA RNAs were isolated according to a previous report with some modifications (GSE110711). Beads with containing cDNA was resuspended with whole transcript amplification mixture comprised 2 μL of 10 μM primer mix (trP1 and 3’WTA), 10.5 μL of dH2O, and 12.5 μL of KAPA Hifi Hotstart ReadyMix (KAPA Biosystems). The thermal cycling conditions were programmed as follows: denaturation at 95°C for 3 min, 12 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 5 min at 72°C, followed by a final extension at 72°C for 5 min. Next, 25 μL of the first-PCR products were used for purification with an Agencort AM Pure XP kit (Bexkman-Coulter) at a 0.7:1 ratio of beads to sample, and eluted with 15 μL of DW. Fragmentasion and adaptor ligation were performed using 10-60ng of second-PCR product as a template with NEBNext FS DNA Library Prep Kit (New England Biolabs) with some modifications; NEBNext Adaptor for Illumina in “Adaptor Ligation” step was substituted by 1.5uM CS1 adaptor, and the reaction volume was 1/4 of the recommended in all steps. Adaptor-ligated DNA was added with 7.125 uL of 10x TE, then purified using Agencort AM Pure XP kit (Bexkman-Coulter) at a 0.4:1 ratio of beads to sample to remove large fragments, a 0.7:1 ratio of beads to sample to remove smaller fragments, and eluted with 20 μL of Tris-HCl (pH 8.0). The second PCR was carried out using barcoded primers to enrich the TCR cDNA flanked with sequencing adapters. The second PCR mixture consisted of 2.5 μL of 10 μM trP1 primer, 2.5 μL of 10 μM IonA-BC primer, 7.5 μL of template and 12.5 μL of NEBNext Ultra II Q5 Master Mix (accessory of NEBNext FS DNA Library Prep Kit). The thermal cycling conditions were programmed as follows: denaturation at 98°C for 30 sec, 11 cycles of denaturation for 10 sec at 98°C, annealing and extension for 1min 15 sec at 65°C, followed by a final extension at 65°C for 5 min. The PCR product was purified and subjected to size selection using Agencort AM Pure XP kit (Bexkman-Coulter) at a 0.7:1 ratio of beads to sample, and eluted with 20 μL of Tris-HCl (pH 8.0). Amplified TCR libraries were quantified using a KAPA SYBR Fast qPCR Kit (KAPA Biosystems, #KK4621) and size distribution was analyzed by agarose electrophoresis and SYBR Gold staining (Thermo Fisher Scientific, #S11494).   Final RNAseq libraries, whose lengths were 200–300 base pairs, were pooled and sequenced using an Ion 540 Kit Chef, an Ion 540 Chip kit, and an Ion Genestudio S5 Sequencer (Thermo Fisher Scientific, # A27759, #A27766, # A38194) according to the manufacturer’s instructions, except the input library concentration (65 pM) and flow number (550).

treatment_protocol: Patients with advanced gastrointestinal cancers with high TMB confirmed by Guardant360 (Guardant Health, Inc. Redwood City, CA), a 74-gene sequencing circulating tumor DNA assay, received intravenous nivolumab monotherapy of 360 mg every 3 weeks.

tag: age

tag: Sex

value: female

tag: cancer type

value: colorectal

value: tumor biopsy

tag: date


title: Patient-Primary [MCC_s15]

description:
FFPE
203490650051_R03C01

tag: gender

tag: tumor stage

tag: race

value: WHITE

tag: recurrence

tag: immunosuppressed?

value: LOST


title: RNA_P3_Tumor_2_0023


title: SST+ cSNAIL ATAC-seq Y2Cpos [Y2Cpos_CKDL190142778-1a-N705-N506_HMHTYDSXX_L2]

description:
unmerged fastq from lane L2
processed data file: Y2Cpos_Ctx_SST.bw
Y2Cpos_CKDL190142778-1a-N705-N506_HMHTYDSXX_L2
processed data file:
Pfenning_SSTpos_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

tag: animal

tag: assay

value: cSNAIL ATAC-seq

tag: surgery

value: retro-orbital AAV injection

tag: virus

value: Sst-cre

tag: project

value: Aging ATAC-seq

tag: cell type

value: SST+


title: SST+ cSNAIL ATAC-seq Y1Spos [Y1Spos_CKDL190142778-1a-N711-N506_HMHTYDSXX_L3]

description:
unmerged fastq from lane L3
processed data file: Y1Spos_Cpu_SST.bw
Y1Spos_CKDL190142778-1a-N711-N506_HMHTYDSXX_L3
processed data file:
Pfenning_SSTpos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

tag: genotype


title: Patient-Primary [MCC_s9]

description:
FFPE
203490650039_R05C01

value: M

tag: tissue

value: skin

tag: patient


title: Patient-Metastatic-lymph node [MCC_s2]

description:
FFPE
203490650035_R06C01

value: lymph node

value: III

value: HISP

tag: age

value: NO

tag: tumor location

value: chest

tag: radiation

tag: systemic

tag: date of dx

tag: date of relapse

tag: date of last follow-up

tag: status


title: SST+ cSNAIL ATAC-seq Y1Spos [Y1Spos_CKDL190142778-1a-N711-N506_HMHTYDSXX_L4]

description:
unmerged fastq from lane L4
processed data file: Y1Spos_Cpu_SST.bw
Y1Spos_CKDL190142778-1a-N711-N506_HMHTYDSXX_L4
processed data file:
Pfenning_SSTpos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

tag: animal


title: RD-18-581 Eplilepsy treated patient

description: FCD II

value: Brain


title: RD-19-235 Eplilepsy treated patient

description: FCD II


title: RD-19-236 Eplilepsy treated patient

description: FCD II


title: Patient-Metastatic-skin [MCC_s7]

description:
FFPE
203490650039_R03C01

tag: gender

tag: tumor stage

tag: race

tag: recurrence

tag: immunosuppressed?

value: LE

value: WLE + LND

value: YES

value: chemo


title: SST+ cSNAIL ATAC-seq Y2Cpos [Y2Cpos_CKDL190142778-1a-N705-N506_HMHTYDSXX_L4]

description:
unmerged fastq from lane L4
processed data file: Y2Cpos_Ctx_SST.bw
Y2Cpos_CKDL190142778-1a-N705-N506_HMHTYDSXX_L4
processed data file:
Pfenning_SSTpos_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

tag: assay

value: cSNAIL ATAC-seq

tag: surgery

tag: virus

tag: genotype

tag: project

tag: cell type


title: C3_plate 1A_E8.5_foregut

description:
BSSE-QGF-59899
processed data file: E8.5-E14.5_AllCells_genes.csv

tag: tissue

value: Foregut

tag: developmental stage


title: RD-19-233 Eplilepsy treated patient

description: FCD II


title: SST+ cSNAIL ATAC-seq Y1Spos [Y1Spos_CKDL190142778-1a-N711-N506_HMHTYDSXX_L2]

description:
unmerged fastq from lane L2
processed data file: Y1Spos_Cpu_SST.bw
Y1Spos_CKDL190142778-1a-N711-N506_HMHTYDSXX_L2
processed data file:
Pfenning_SSTpos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

value: retro-orbital AAV injection

value: Sst-cre


title: B3_plate 1A_E8.5_foregut

description:
BSSE-QGF-59898
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient-Primary [MCC_s6]

description:
FFPE
203490650039_R02C01

value: WHITE

tag: age

tag: patient


title: SST+ cSNAIL ATAC-seq Y1Cpos [CKDL190142778-1a-N709-N506_HMHTYDSXX_L4]

description:
unmerged fastq from lane L4
processed data file: Y1Cpos_Ctx_SST.bw
Y1Cpos_CKDL190142778-1a-N709-N506_HMHTYDSXX_L4
processed data file:
Pfenning_SSTpos_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

value: Aging ATAC-seq

value: SST+


title: Patient-adjacent normal [MCC_s1]

description:
FFPE
203490650035_R05C01

value: M

value: skin

tag: tumor location

tag: radiation

tag: systemic

tag: date of dx

tag: date of relapse

tag: date of last follow-up

tag: status

value: LOST


title: RD-19-232 Eplilepsy treated patient

description: FCD II


title: RD-19-234 Eplilepsy treated patient

description: FCD II


title: RNA_P1_Tumor_1_0023

tag: Sex

value: female

tag: cancer type

value: colorectal

value: tumor biopsy

tag: date


title: RNA_P1_Tumor_1_0013

value: male

value: esophageal


title: E2_plate 1A_E8.5_foregut

description:
BSSE-QGF-59893
processed data file: E8.5-E14.5_AllCells_genes.csv

tag: genotype


title: EY1341 Cpu D2+ [YD3B]

description:
this sample recieved no headcap
YD3B
processed data file:
Pfenning_D2pos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

source_name: Dorsal striatum

tag: animal

tag: assay

tag: surgery

value: no headcap, retro-orbital AAV injection

tag: virus

tag: project

value: Motor Learning ATAC-seq


title: RNA_P3_Tumor_1_0013

tag: age

tag: tissue


title: RD-19-230 Eplilepsy treated patient

description: FCD II

value: Brain


title: A3_plate 1A_E8.5_foregut

description:
BSSE-QGF-59897
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Foregut

tag: developmental stage


title: RNA_P1_Tumor_2_0013


title: G2_plate 1A_E8.5_foregut

description:
BSSE-QGF-59895
processed data file: E8.5-E14.5_AllCells_genes.csv


title: EY1341 NAcc D2+ [YD1B]

description:
this sample recieved no headcap
YD1B
processed data file:
Pfenning_D2pos_Nac.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

source_name: Nucleus accumbens

value: cSNAIL ATAC-seq

tag: cell type


title: SST+ cSNAIL ATAC-seq Y1Cpos [CKDL190142778-1a-N709-N506_HMHTYDSXX_L2]

description:
unmerged fastq from lane L2
processed data file: Y1Cpos_Ctx_SST.bw
Y1Cpos_CKDL190142778-1a-N709-N506_HMHTYDSXX_L2
processed data file:
Pfenning_SSTpos_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

value: retro-orbital AAV injection

value: Sst-cre


title: RNA_P1_Tumor_2_0011


title: SST+ cSNAIL ATAC-seq Y1Cpos [CKDL190142778-1a-N709-N506_HMHTYDSXX_L3]

description:
unmerged fastq from lane L3
processed data file: Y1Cpos_Ctx_SST.bw
Y1Cpos_CKDL190142778-1a-N709-N506_HMHTYDSXX_L3
processed data file:
Pfenning_SSTpos_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

value: Aging ATAC-seq


title: EY1340 Cpu D2+ [YD3A]

description:
this sample recieved no headcap
YD3A
processed data file:
Pfenning_D2pos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: RNA_P3_Tumor_1_0011


title: D2_plate 1A_E8.5_foregut

description:
BSSE-QGF-59892
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C2_plate 1A_E8.5_foregut

description:
BSSE-QGF-59891
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B2_plate 1A_E8.5_foregut

description:
BSSE-QGF-59890
processed data file: E8.5-E14.5_AllCells_genes.csv


title: RD-19-231 Eplilepsy treated patient

description: FCD II


title: EY1340 NAcc D2+ [YD1A]

description:
this sample recieved no headcap
YD1A
processed data file:
Pfenning_D2pos_Nac.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: RD-19-229 Eplilepsy treated patient

description: FCD II


title: RNA_P1_Tumor_1_0011


title: E1_plate 1A_E8.5_foregut

description:
BSSE-QGF-59885
processed data file: E8.5-E14.5_AllCells_genes.csv


title: RNA_P1_Tumor_1_0007


title: D1_plate 1A_E8.5_foregut

description:
BSSE-QGF-59884
processed data file: E8.5-E14.5_AllCells_genes.csv


title: RNA_P3_Tumor_1_0005

value: gastric


title: C1_plate 1A_E8.5_foregut

description:
BSSE-QGF-59883
processed data file: E8.5-E14.5_AllCells_genes.csv


title: RNA_P1_Tumor_2_0005


title: RNA_P1_Tumor_1_0005


title: EY1166 Cpu D1+ [YN3B]

description:
this sample recieved headcap
YN3B
processed data file:
Pfenning_D1pos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

value: headcap, retro-orbital AAV injection


title: EY1311 Cpu D1+ [YN3A]

description:
this sample recieved headcap
YN3A
processed data file:
Pfenning_D1pos_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: EY1166 NAcc D1+ [YN1B]

description:
this sample recieved headcap
YN1B
processed data file:
Pfenning_D1pos_Nac.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: RD-19-226 Eplilepsy treated patient

description: FCD II


title: EY1311 NAcc D1+ [YN1A]

description:
this sample recieved headcap
YN1A
processed data file:
Pfenning_D1pos_Nac.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: RNA_P3_Tumor_1_0003


title: RD-19-228 Eplilepsy treated patient

description: FCD II


title: litterCtr_Input_r1

city: Daejeon

first: Seung-Kyoon

last: Kim

address: 99 Daehak-ro, Yuseong-gu,

department: Convergent Bioscience and Informatics

institute: Chungnam National University

description: CHIPSEQ

data_processing:
The sequencing reads were mapped to the mm10 UCSC annotation using TOPHAT (Trapnell, et al., 2009) with the parameters (-a 8 -m 0 -I 500000 -p 8 -g 20 --library-type fr-firststrand --no-novel-indels  --segment-mismatches 2 for RNA-Seq.
For GRO-Seq, the raw fastq reads were trimmed using cutadapt with parameters -a AAAAAAAAAAAAAAAAAAAA -z -e 0.10 -f fastq -m 32 (Chae et al., 2015).
The CHIPSEQ FASTQ reads were aligned to UCSC's mm10 genome using Bowtie2 with default parameters (Langmead, et al., 2012). Reads with mapping quality less than 10 were removed using SAMtools (Li, et al., 2009) for ChIP-seq. To normalize the differences induced from sequencing depths, the mapped reads were “down sampled” to the lowest number of the uniquely mapped reads with duplicates followed by duplicate reads removal using our inhouse perl scripts. The downsampled, duplicates removed mapped reads were extended to the fragment estimate from MACS using inhouse perl and R scripts. Wig files followed by bigWig files were generated through perl scripts for visualization on UCSC using these extended reads. The coverage values in bigWig files were normalized to 10million.
RPKM calculations were done using the HOMER package by normalizing to 10 million reads
Tracks for visualization on UCSC browser are generated using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Strand specific bigWig files for visualizing expression levels on a genome browser.

growth_protocol: Primary cortical neurons from E16/18 mice were cultured in Neurobasal media with B-27 and Glutamax until DIV7

extract_protocol:
RNA was extracted using Trizol reagent for mRNA- or GRO-seq. Protein was crosslinked with DNA, cross-linked samples incubated with antibodies, and genomic DNA was purified for ChIP-seq.
mRNA-seq libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturer's instructions. GRO-seq libraries was prepared as previously described (C. G. Danko, Molecular cell 50, 212-222, 2013). ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set (NEB).

treatment_protocol: DIV7 Neurons neurons were made quiescent overnight in 1 μM tetrodotoxin (TTX). In the BDNF experiment, neurons were incubated with BDNF (10 ng/ml) for different length of time. For JQ1 experiment, TTX treated neurons were pre-treated with -/+ JQ1 (0.5 µM) for 5 min, then followed by treating with 55 mM KCl for different length of time. For C646 experiment, TTX treated neurons were pre-treated with C646 (20 µM) for 48 hr, then followed by treating with 55 mM KCl for 30 min.

tag: strain

value: Cortex

value: 60 days


title: RNA_P1_Tumor_2_0023

value: female


title: Patient-Primary [MCC_s3]

description:
FFPE
203490650035_R07C01

tag: gender

value: F

value: skin

tag: tumor stage

value: I

tag: race

value: WHITE

tag: recurrence

tag: immunosuppressed?

value: NO

tag: tumor location

value: H/N

value: WLE

tag: radiation

tag: systemic

tag: date of dx

tag: date of relapse

value: LOST

tag: additional info

value: Metastatic Breast CA

tag: patient


title: CD45+ cells sorted from B16 tumor after treatment with anti-PD1-IL15 protein fusion

city: San Diego

first: Wenjing

last: Yanf

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

data_processing:
Data were processed using the Cell Ranger v2.1.1 (10x Genomics) to generate count-level cell by gene matrix for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output files

source_name: CD45+ cells sorted from B16 tumor

growth_protocol: 5x10^5 B16-F10 tumor cells were implanted s.c into mice and  tumor resected 11 days post s.c. implantation.

extract_protocol:
TILs were isolated by digesting tumor fragments using Mylteni mouse tumor disassociation kit with enzyme R at 1:10 per manufacturer's guidelines. 1 to 5 × 106 cells were stained using fluorescently labeled mouse CD45 antibody (clone 30F11) and Fixable Viability Dye eFluor 506 (Thermo Fisher Scientific; Waltham, MA) to sort for live CD45+ and CD45- cells using the FACSAria II cell sorter.
approximately 1.6x10^4 cells were onto Chromium Single Cell A chips and library construction performed using the Chromium Single Cell 5’ Library and Gel Bead Kit protocol (10x Genomics)
Libraries were sequenced using the NovaSeq 6000 platform (Illumina; San Diego, CA)

treatment_protocol: Following resection mice were treated with five different treatments.

value: B16-F10 tumor bearing mice

tag: treatment

value: anti-PD1-IL15 protein fusion

value: CD45+ cells sorted from B16 tumor


title: Fmr1KO_Input_r1

description: CHIPSEQ


title: RNA_P1_Tumor_1_0003

tag: age

tag: Sex

value: male

tag: cancer type

value: esophageal

tag: tissue

value: tumor biopsy

tag: date


title: RNA_P4_Tumor_2_0002

value: colorectal


title: Fmr1KO_BRD4_r1

description: CHIPSEQ

tag: strain

tag: cell type

value: Cortex

tag: developmental stage

value: 60 days


title: CD45+ cells sorted from B16 tumor after treatment with IL15 superagonist and anti-PD1 combination

value: IL15 and anti-PD1 combination


title: litterCtr_BRD4_r1

description: CHIPSEQ


title: RNA_P4_Tumor_1_0002

value: female


title: CD45+ cells sorted from B16 tumor after treatment with IL15 superagonist

value: IL15 superagonist


title: RNA_P3_Tumor_2_0002


title: Fmr1KO_BRD3_r1

description: CHIPSEQ


title: CD45+ cells sorted from B16 tumor after treatment with PBS

value: PBS


title: Fmr1KO_BRD2_r1

description: CHIPSEQ


title: RNA_P3_Tumor_1_0002


title: litterCtr_BRD3_r1

description: CHIPSEQ


title: CD45+ cells sorted from B16 tumor after treatment with anti-PD1


title: Week 3 Replicate 1 (3-1)

first: Megan

middle: Laura

last: McCain

state: California

address: 1042 Downey Way

department: Biomedical Engineering

institute: University of Southern California

data_processing:
Illumina software on NovaSeq 6000 system used for basecalling and generation fo quality scores (Q-scores).
Sequenced reads were trimmed based on read length and minimum Q-score and then mapped to galGal6 whole genome using STAR 2.7.3a index.
Fragments per kilobase of transcript per million mapped reads with upper quartile normalization (FPKM-UQ) was calculated for each gene using Partek Flow analysis software
Genome_build: galGal6 (GRCg6a)
Supplementary_files_format_and_content: FPKM-UQ values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Gallus gallus

source_name: skeletal muscle myotubes

growth_protocol: Myoblasts from chicken thighs were isolated from E10 chick embryos and seeded on gelatin-transglutaminase hydrogels. After reaching confluence, myoblasts were induced to differentiate by lowering serum content in differentation media.

extract_protocol:
Myotubes were lysed with TRIzol reagent and chloroform phase separation. RNA (≥ 0.4 μg) was precipitated with isopropyl alcohol, washed with 75% ethanol and resuspended in 10 mM Trizma-HCl (pH = 8.0).
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Co., Ltd.

value: myotube

value: post differentiation day 21


title: RD-19-225 Eplilepsy treated patient

description: FCD II

value: Brain


title: ChIP-seq_input_OFF_inverted

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institute of Pathology

country: Germany

institute: University Medical Centre Göttingen

description: cell population

data_processing:
Two mates of paired-end reads were aligned individually using the Bowtie~2 software version 2.3.4.1 with the parameter “--reorder –local”.
ChIP-seq data were processed with ENCODE chip-seq-pipeline2
Genome_build: hg19 for Hi-C; hg38 for ChIP-seq
Supplementary_files_format_and_content: cool: contact matrix; bed: conservative idr peaks

source_name: “OFF” HBECs

growth_protocol: HBEC-CDC6 Tet-ON cells were maintained in Keratinocyte-Serum-Free Medium (#17005-075, Invitrogen) supplemented with 50μg/ml Bovine Pituitary Extract and 5ng/ml hEGF (#17005-075, Invitrogen) at 37οC and 5% CO2 [Komseli et al., 2018]. CDC6 induction was conducted by treatment of the cell culture with 1 μg/ml doxycycline (DOX) (Applichem) [Komseli et al., 2018].

extract_protocol:
In situ Hi-C on HBECs of different states and genotypes was performed and controlled for quality using the Arima Hi-C kit as per manufacturer’s instructions. All resulting libraries that met the QC criteria set by the manufacturer were paired-end sequenced on a NovoSeq6000 platform (Illumina) to at least 0.5 billion reads.
Standard Hi-C library construction on the basis of the Mate-pair kit (Illumina); 100bp single-end sequencing

treatment_protocol: "Bypass" cells are under constant doxycycline treatment to overexpress the CDC6 transgene. "OFF" cells are untreated.

value: human bronchial epithelial cells

tag: sample type

value: OFF

tag: chip antibody

value: none (input)


title: RD-19-227 Eplilepsy treated patient

description: FCD II


title: RD-19-222 Eplilepsy treated patient

description: FCD II


title: Week 3 Replicate 2 (3-2)


title: ChIP-seq_bHLHE40_OFF_inverted

description: cell population

value: anti-DEC1 (Novus Biologicals, catalog number NB100-1800)


title: RD-19-224 Eplilepsy treated patient

description: FCD II


title: RD-18-740 Eplilepsy treated patient

description: FCD I


title: litterCtr_BRD2_r1

description: CHIPSEQ


title: untreated_SUZ12_rep2

city: Aurora

first: Joshua

middle: C

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

data_processing:
Library strategy: CUT&RUN
CUT&RUN experiments were adaptor trimmed using BBtools bbduk (version 38.87) using supplied adaptor reference file adapters.fa with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo
Samples were then aligned to a custom genome combining human hg38 and E. coli mg1655 genomes using Bowtie2 (2.3.4.1). Sam files were transformed into bam files, mapped reads with insert size greater than or equal to 150 bp were isolated, sorted and indexed using samtools (version 1.8)
Bedgraphs were binned and normalized by RPM and mitochondrial reads using a custom R script
CUT&RUN alignment coverage bigwig files were created with deeptools bamCoverage (version 3.1.3) using CPM with 50 bp binning.
Biological replicates were averaged at the bin level using WiggleTools (version 1.2) using the mean operation and the resulting wig file was converted to bigwig using wigToBigWig command.
Genome_build: HG38
Supplementary_files_format_and_content: bigwig

source_name: Untreated control

growth_protocol: MDA-MB-231 female breast cancer cell lines were maintained at 37°C in Dulbecco’s Modified Essential Medium (DMEM) with 10% FB essence (VWR), 1% penicillin/streptomycin, and L-glutamine.

extract_protocol:
CUT&RUN experiments were carried out following Epicypher CUT&RUN protocol (version 1.6, August 2020) with minor modifications. Briefly, nuclei from 5x105 cells were isolated with wash buffer (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1x protease inhibitor cocktails from Sigma), captured with Concanavalin A conjugated paramagnetic beads (Bangs Laboratory Inc.) and incubated while nutating with 0.5 µl primary antibody for EZH2 (Cell Signaling Technology), or SUZ12 (Cell Signaling Technology) in antibody buffer (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.02% digitonin, 2 mM EDTA and 1x protease inhibitor cocktails from Sigma) overnight. After washing with digitonin buffer (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.02% digitonin and 1x protease inhibitor cocktails from Sigma), pAG-MNase (Epicypher Inc) was added at a 1:20 ratio and incubated for 10 min at RT. The nuclei were washed again and placed on ice. To activate pAG-MNase, CaCl2 was added to a final concentration of 2 mM. The reaction was inubated for 2 hours while nutating at 4°C and stopped by addition of STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 mg/mL RNase A and 40 mg/mL glycogen). The protein-DNA complex was released by incubating for 10 min at 37°C. DNA was extracted using Qiagen Minelute PCR purification kit. Purified DNA was used for library preparation.
CUT&RUN libraries were prepared using the Illumina NEBNext Ultra II ChIP-Seq sample kit, according to the manufacturer’s protocol. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer

treatment_protocol: Cadmium-resistant cell (MDA-MB-231cadR) cell lines were selected by passage in medium containing CdSO4. The CdSO4 concentration was increased by increments of 5-25 μM after 10 passages at the current concentration and when cell count increased at least 1.8 times average daily over at least four passages consistently. Cells used in this study were adapted to CdSO4 containing medium for 7 months up to 10 μM CdSO4.

value: Untreated control

tag: chip target

tag: cell line


title: ChIP_shScr_K30_Input_r1

description: CHIPSEQ

source_name: Cortical neurons

value: Cortical neurons

tag: knockdown

value: shScrambled Ctr


title: RNA_P1_Tumor_3_0002

value: colorectal

value: tumor biopsy


title: RNA_P1_Tumor_2_0002


title: RD-18-741 Eplilepsy treated patient

description: FCD I


title: RNA_P1_Tumor_1_0002


title: RD-18-739 Eplilepsy treated patient

description: FCD I


title: RD-18-738 Eplilepsy treated patient

description: FCD I


title: RD-18-737 Eplilepsy treated patient

description: FCD I


title: shBRD4_K30_BRD4_r1

description: CHIPSEQ


title: RD-19-223 Eplilepsy treated patient

description: FCD II


title: Week 3 Replicate 3 (3-3)


title: Week 1 Replicate 3 (1-3)

value: post differentiation day 7


title: untreated_SUZ12_rep1


title: untreated_EZH2_rep2


title: RNA_P3_Tumor_1_0001

value: male

value: esophageal


title: Week 1 Replicate 1 (1-1)


title: Week 1 Replicate 4 (1-4)


title: untreated_EZH2_rep1


title: RD-18-735 Eplilepsy treated patient

description: FCD I


title: 10umCad_SUZ12_rep2

source_name: 10uM cadmium resistance

value: 10uM cadmium resistance


title: Week 1 Replicate 2 (1-2)


title: 10umCad_SUZ12_rep1


title: P3_Tumor_0023

data_processing:
Library strategy: TCR-seq
Adapter trimming and quality filtering of sequencing data were performed by using Cutadapt and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5. In MiXCR, Filtered reads were aligned to reference human TCR V/D/J sequences with the following parameters: -vParameters.geneFeatureToAlign = VTranscript -vjAlignmentOrder = JThenV, then identical sequences were assembled and grouped in clones with PCR and sequencing error correlation with the following parameters: -badQualityThreshold=10, –separateByV=true, --only-productive=true, –region-of-interest=CDR3. The Variable (V) and Joining (J) segment of TCRs were represented in IMGT gene nomenclature.
List of final clones were analyzed by VDJtools-1.2.1. Then, the sequencing reads of sample was normalized to the cell count in each sample for PBMC, and 50,000 reads in tumor biopsy samples by “DownSample” command of VDJtools. T-cell clones were determined as TCR reads with the same TCR Variable (V) segment, Joining (J) segment and CDR3 nucleotide sequence.
If multiple biopsies are obtained at the same time point in patient, TCRseq and subsequent data processing were performed separately, then clonotype tables are pooled by “PoolSamples” command of VDJtools.
Genome_build: IMGT reference sequences of human TRB
Supplementary_files_format_and_content: text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

extract_protocol:
10 ml of patient’s blood was taken at four time point (P1; day0, P2; day21-27, P3; day39-55, P4; disease progression). PBMCs were prepared by density gradient centrifugation by Ficoll®-Paque Plus (GE Healthcare Japan). The PBMCs were separated in two samples, then CD8+ T cell and CD4+ T cell were enriched by using CD8 Microbeads or CD4 Microbeads for human (Milteny Biotec Inc., Bergisch Gladbach, Germany). The purity was checked by FACSCanto II (BD Biosciences) with staining with CD8a-APC (clone RPA-T8, TONMO Biosciences, San Diego, CA, USA ), CD3-FITC (clone UCHT1, TONBO Biosciences, San Diego, CA, USA), CD4-PE (clone SK3, BioLegend), and Ghost Dye Red780 (TONBO Biosciences). The purity of enriched cells was routinely more than 95%.
Tumor biopsy was conducted on before (day0) and after the treatment (day39-day55). Presence or absence of tumor tissue in biopsies was determined pathologically. Tumor biopsies were homogenized in TRIzol (Ambion, Carlsbad, CA, USA). RNA was extracted from each sample using the RNeasy mini kit (QIAGEN, Hilden, Germany, # 74106) and amounts and purity measured with the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Five-micrograms of total RNA was diluted with 1 mL of cell lysis buffer and used for TCR sequencing.
TCR sequencing libraries for next-generation sequencing were prepared according to the previous report (GSE115425) with some modifications. PolyA RNAs were isolated according to a previous report with some modifications (GSE110711). To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. Beads with containing cDNA was resuspended with the first PCR mixture comprised 0.8 μL of 10 μM primer mix (trP1, Trac_ex and Trbc_ex), 4.2 μL of dH2O, and 5 μL of KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, USA, #KK2602). The thermal cycling conditions were programmed as follows: denaturation at 95°C for 3 min, 5 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min. Next, 10 μL of the first-PCR products were used for purification with an Agencort AM Pure XP kit (Bexkman-Coulter, CA, USA, #A63881) at a 0.7:1 ratio of beads to sample, and eluted with 15 μL of DW. The second PCR mixture consisted of 1.75 μL of 10 μM primer mix (5’ WTA, Trac_in-Bio, and Trbc_in-Bio), 10.75 μL of the template and 12.5 μL of KAPA Hifi Hotstart ReadyMix. The thermal cycling conditions were the same as the first PCR except for the cycle number; 21 cycles. Next, 25 μL of the second-PCR products were purified using Agencort AM Pure XP kit (Bexkman-Coulter) at a 0.7:1 ratio of beads to sample, and eluted in 18 μL of DW. Fragmentasion and adaptor ligation were performed using 10-20ng of second-PCR product as a template with NEBNext FS DNA Library Prep Kit (New England Biolabs, #E7805) with some modifications; NEBNext Adaptor for Illumina in “Adaptor Ligation” step was substituted by 5uM Adaptor P1, and the reaction volume was 1/4 of the recommended in all steps. Adaptor-ligated DNA was purified using Agencort AM Pure XP kit (Bexkman-Coulter) at a 0.8:1 ratio of beads to sample, and eluted in 20 μL of DW. The third PCR was carried out using barcoded primers to enrich the TCR cDNA flanked with sequencing adapters. The third PCR mixture consisted of 1 μL of 10 μM trP1 primer, 1 μL of 10 μM IonA-BC-Trbc primer, 3 μL of template and 5 μL of NEBNext Ultra II Q5 Master Mix (accessory of NEBNext FS DNA Library Prep Kit). The thermal cycling conditions were programmed as follows: denaturation at 98°C for 30 sec, 10 cycles of denaturation for 10 sec at 98°C, annealing and extension for 1min 15 sec at 65°C, followed by a final extension at 65°C for 5 min. The PCR product was purified and subjected to size selection using Agencort AM Pure XP kit (Bexkman-Coulter) at a 1.0:1 ratio of beads to sample, and eluted with 20 μL of Tris-HCl (pH 8.0). Amplified TCR libraries were quantified using a KAPA SYBR Fast qPCR Kit (KAPA Biosystems, #KK4621) and size distribution was analyzed by agarose electrophoresis and SYBR Gold staining (Thermo Fisher Scientific, #S11494).   Final TCR libraries, whose lengths were 200–300 base pairs, were pooled and sequenced using an Ion 540 Kit Chef, an Ion 540 Chip kit, and an Ion Genestudio S5 Sequencer (Thermo Fisher Scientific, # A27759, #A27766, # A38194) according to the manufacturer’s instructions, except the input library concentration (65 pM) and flow number (500).

value: female


title: Week 1 Replicate 5 (1-5)

value: myotube


title: RD-18-734 Eplilepsy treated patient

description: FCD I


title: P3_Blood_CD8_0023

source_name: peripheral blood

value: CD4- CD8+ T cells

value: peripheral blood


title: 10umCad_EZH2_rep2


title: shScr_K30_BRD4_r1

description: CHIPSEQ


title: shBRD3_K30_BRD4_r1

description: CHIPSEQ


title: shBRD4_K30_BRD3_r1

description: CHIPSEQ


title: shBRD2_K30_BRD4_r1

description: CHIPSEQ


title: shBRD3_K30_BRD3_r1

description: CHIPSEQ


title: RD-18-407 Eplilepsy treated patient

description: FCD II

value: Brain


title: RNA_P1_Tumor_1_0001


title: RD-18-733 Eplilepsy treated patient

description: FCD I


title: P3_Blood_CD4_0023

value: CD4+ CD8- T cells


title: shBRD2_K30_BRD3_r1

description: CHIPSEQ


title: 10umCad_EZH2_rep1


title: P2_Blood_CD8_0023


title: untreatedControl_H3K27me3_rep3

data_processing:
ChIP-seq experiments were aligned to a custom genome combining human hg38 and drosophila dr3 genomes using Bowtie2 (2.3.4.1).
Sam files were transformed into bam files and sorted using samtools (version 1.8).
Reads aligned to chr1-22 and chrX were isolated and an equal number of reads were randomly selected from each biological replicate for H3K27me3 and Input.
Replicates were merged and indexed using samtools (version 1.8).
Alignment coverage bigwig files were created with deeptools bamCoverage (version 3.1.3) using CPM with 50 bp binning.
Genome_build: HG38
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were crosslinked by adding 1% formaldehyde to media for 10 minutes at 37°C. Crosslinking was stopped by addition of Glycine to 0.125M and incubating for 5 minutes at room temperature. Cells were washed with PBS and collected and centrifuged. Cells were resuspended in cellular lysis buffer (5mM PIPES pH 8, 85 mM KCl, 0.5% NP40), incubated on ice for 5 minutes and centrifuged. Samples were resuspended in nuclear lysis buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 1% SDS) and sonicated for 45 minutes using 30 second on/off cycle repeats at 70% intensity (using a Qsonica Q800R). 10 g crosslinked DNA and 2 g crosslinked Drosophila control spike-in chromatin was used per immunoprecipitation. Chromatin was pulled down overnight using Invitrogen Protein A Dynabeads with antibodies for H3 (Cell Signaling Technology), H3K27me3 (Abcam) or IgG (Cell Signaling Technology). Beads were washed twice with IP buffer (16.7 mM Tris pH 8, 1.2 mM EDTA pH 8, 167 mM NaCl, 0.1% SDS, 1.84% Triton X100), once with TSE buffer (20 mM Tris pH 8, 2 mM EDTA pH 8, 500 mM NaCl, 1% Triton X100, 0.1% SDS) and LiCl buffer (100mM Tris pH 8, 500 mM LiCl, 1% deoxycholic acid, 1% NP40), and twice with TE (10mM Tris pH 8, 1 mM EDTA pH 8). DNA was eluted from beads with proteinase K and purified with Promega Wizard SV PCR clean up kit. DNA was analyzed with qPCR and compared to 10% input collected prior to pulldown.
ChIP-seq libraries were prepared using the Illumina NEBNext Ultra II ChIP-Seq sample kit, according to the manufacturer’s protocol. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer.


title: untreatedControl_H3K27me3_rep2


title: shScr_K30_BRD3_r1

description: CHIPSEQ


title: shBRD3_K30_BRD2_r1

description: CHIPSEQ


title: untreatedControl_H3K27me3_rep1


title: untreatedControl_input_rep3

value: input


title: shBRD2_K30_BRD2_r1

description: CHIPSEQ


title: shScr_K30_BRD2_r1

description: CHIPSEQ


title: untreatedControl_input_rep2


title: P1_Blood_CD4_0023


title: tot_30m-yafo1

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

data_processing:
The inline barcode was clipped from read 2 and used to separate reads into their source samples using cutadapt (v3.2). Adapter sequences were also trimmed at this stage – the provided fastq files are both demultiplexed and trimmed.
Reads were mapped to the MG1655 genome using bowtie2 (v2.4.1) using the --very-sensitive argument set.
For processed files ending in “5_prime_ends”: for each proper pair, 1 count was added to the 5’-end of the fragment (corresponding to a free RNA 5’-end). For processed files ending in “density”: for each proper pair, 1 count was added to every position aligning to and between the two reads.
Genome_build: U00096.3
Supplementary_files_format_and_content: Processed files are gzipped csv files. The first column corresponds to the forward strand and the second two the reverse strand. Each row corresponds to the counts at a genomic position from 1 to len(genome). Counts are defined in the data processing steps. Integer counts are raw and not normalized to library depth.

organism: Escherichia coli

source_name: bacterial liquid culture

growth_protocol: Escherichia coli was grown in M9 (10x stock made with 64 g/L Na2HPO4-7H2O, 15 g/L KH2PO4, 2.5 g/L NaCl, 5.0 g/L NH4Cl) medium supplemented with 0.1% casamino acids, 0.4% glycerol, 2 mM MgSO4, and 0.1 mM CaCl2. Single colonies on an LB + 0.4% glucose plate were picked and grown overnight in M9 media + 0.4% glucose on a roller drum then grown at 37°C on a Synergy H1 plate reader (BioTek) in 24-well plates using double orbital rotation at 307 CPM for the course of the experiment. Overnight cultures grown with 0.4% glucose were back-diluted to 0.02 OD600 in 1.5 mL of M9 media with added glucose and grown to OD 0.2 – 0.35 in 24-well plates. Cultures were pelleted by spinning 5 minutes on a benchtop centrifuge at 4000 G. Pellets were washed once with M9 media lacking glucose, respun, and resuspended in M9 media lacking glucose. On a fresh 24-well plate, individual cultures were back-diluted to 0.1 and returned to the plate reader. After 30 minutes of growth, toxin was induced by adding arabinose to 0.2% and cells were returned to the plate reader. After induction for either 5 or 30 minutes, 1 mL of the culture was mixed with 110 uL of stop solution (95% ethanol and 5% phenol), spun for 30 seconds at 13k RPM to pellet cells, and flash frozen in liquid nitrogen.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
See publication for complete details. For samples with rRNA depletion, rRNA was removed by hybridization to custom biotinylated oligos. Next, if samples were fragmented, RNA was mixed with reverse transcription buffer and heated to 95°C for 3 minutes before placing on ice. All samples were then reverse transcribed using reverse transcription primers with a 5’-overhang with a PCR amplification handle and 1 of 24 inline barcodes. As cDNA now contained a barcode, samples were pooled and those with a tRNA size selection step were loaded onto a denaturing TBE urea gel and the tRNA region of the gel was extracted for cDNA purification. For all other samples, pools were cleaned up with a modified AMPure XP bead protocol to remove leftover primers. Next, all samples were subjected to a second round of reverse transcription with a template switching oligo to add a second PCR amplification handle to the 3’-end of the cDNA. After a bead cleanup, samples were PCR amplified with primers adding the i5 and i7 handles for Illumina sequencing. PCR reactions were size selected with a 2-sided bead cut and sequenced using a custom read 1 primer on a NovaSeq instrument. The combination of the i7 index and the inline read 2 barcode were used to separate out biological samples into their own fastq files using cutadapt.

value: MG1655 pBAD30-yafo

tag: induction time

value: 30 minutes

tag: rrna depletion

value: No

tag: trna size selection

tag: fragmentation time

value: 0 minutes


title: tot_30m-yhav1

value: MG1655 pBAD30-yhav


title: tot_30m-yafo2


title: tot_30m-yoeb1

value: MG1655 pBAD30-yoeb


title: P4_Blood_CD8_0013

tag: age


title: tot_30m-yhav2


title: tot_30m-yoeb2


title: shBRD4_K30_BRD2_r1

description: CHIPSEQ

value: Cortical neurons


title: P2_Blood_CD4_0023

tag: Sex

value: colorectal


title: untreatedControl_input_rep1

tag: treatment

value: Untreated control


title: WT_Input_r2

description: CHIPSEQ

value: Vehicle


title: P1_Tumor_0023

value: tumor biopsy

value: female

tag: cancer type

tag: tissue


title: P4_Blood_CD4_0013

value: male

value: esophageal

tag: date


title: P3_Tumor_0013

tag: cell type


title: 10umCad_input_rep2

value: 10uM cadmium resistance


title: tot_30m-rele1

tag: strain

value: MG1655 pBAD30-rele


title: 10umCad_input_rep3

value: input