title: sample 73 [1_2_5]

description:
1_2_5_CAATTAAC-CGAGATAT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_soldier_whole brain

value: worker

value: soldier

value: whole brain


title: HDL046, Lg, CD4, TEM

status: Public on May 09 2023

type: SRA

city: New York

first: Thomas

last: Connors

state: New York

address: 3595 Broadway CHN 10-24

country: USA

institute: Columbia University Medical Center

library_source: transcriptomic

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for each Sample
Supplementary files format and content: comma-delimited CSV file combined for all Samples

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
Total RNA was extracted from cells sorted in RLT lysis buffer (Qiagen) using RNeasy Plus Micro Kit (Qiagen, Germantown, MD, USA). RNA was quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with TapeStation (Agilent Technologies, Palo Alto, CA, USA).
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The final library was assessed with Agilent TapeStation.

treatment_protocol: Sorted CD69hi effector memory T cells

tag: tissue

value: Lung

tag: cell line

value: primary

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

tag: donor age_years


title: HiC, EV control replicate 2, library 2

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211, 6 Center Drive

institute: NICHD

description: Arima-HiC

library_source: genomic

data_processing:
Mouse genome (mm10) fragments were generated using the “digest_genome” tool in HiC-Pro utilities (Servant, Varoquaux et al. 2015) with restriction motifs “GATC” and “G^ANTC”. Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. HiC-Pro pipelines (v2.11.4) were then used with above genome fragments and the parameter “LIGATION_SITE = GATCGATC, GANTGATC, GANTANTC, GATCANTC” to generate valid interaction pairs and contact maps.
Pooled valid interaction pairs in EV control were used as input, and chromatin loops were detected from both 5 kb-resolution and 10 kb-resolution Hi-C maps using HiCCUPS in Juicer (v1.6) with the following parameters: “-r 5000,10000 -k KR -f .1,.1 -p 4,2 -i 7,5 -t 0.02,1.5,1.75,2 -d 20000,20000 --ignore-sparsity”. The loop anchors from 5 kb maps (where the length of anchors equaled 5 kb) were extended to 10 kb by extending 2.5 kb on each side.
Assembly: mm10
Supplementary files format and content: tab-delimited text files for valid interaction pairs (.allValidPairs.gz), hic file (.hic) and bedpe file for hiccups loops (.bedpe).

molecule: genomic DNA

organism: Mus musculus

source_name: R1 mESCs

growth_protocol: Cells were cultured in a 37 °C humidified incubator with 5% CO2.

extract_protocol:
Cells were crosslinked with 2% formaldehyde for 10 min and quenched using 0.4M glycine for 5 min.
Cells with approximately 4 μg of DNA were used as input to generate proximally ligated DNA using the Arima-HiC kit (Arima, A510008) according to the manufacturer’s protocol (Arima, A160134 v01). Briefly, crosslinked cells were digested using the Arima restriction enzyme cocktail, the 5’ overhangs were filled in and labeled with a biotinylated nucleotide, and the spatially proximal ends were ligated. The proximally ligated DNAs were purified and sonicated using the Covaris ME220 (8 microTube-130 AFA fiber strip V2: duration 42s, peak power 70w, duty factor 20%, cycle per burst 1000#). Then, size selection was performed on the resulting DNA Fragments (for size ranging from 200 to 600 bp). 2 μg of the resulting DNA fragments were used as input, and fragments labelled with biotin were bound to beads to construct Hi-C libraries using the KAPA HyperPrep Kit (Roche, KK8502) following the protocol provided by Arima (A160139 v00).

value: R1 mESCs

value: mouse embryonic stem cells

value: EV control


title: HiC, EV control replicate 2, library 1

description: Arima-HiC


title: sample 72 [12_4_4]

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

description:
12_4_4_GTCTACAC-GCCAAGGT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

data_processing:
fastq files were aligned to the honey bee genome (vHAv3.1) with STAR v2.7.3a
count files were generated using the "featureCounts" function in Subread v2.0.0
NOTE: Samples 1-96 are READ 1 ALIGNS TO ANTISENSE STRAND while 97-177 are READ 1 ALIGNS TO SENSE STRAND. This is just how the adaptors are made for such a big experiment. Because featureCounts requires strand orientation, I have noted on each counts file whether the "forward" and "reverse" command was used (prefix "f_" or "r_", respectively). If you realign and forget to do this, you will find that you get an excellent alignment to the genome but very few reads will be called as genes. This is totally artificial, so make sure you are sensitive to read orientation OR use a method that doesn't require strandedness information (e.g. Salmon).
Genome_build: HAv3.1
Supplementary_files_format_and_content: featureCounts output files

organism: Apis mellifera

source_name: Patillas2_forager_whole brain

growth_protocol: Honey bees were flash frozen in liquid nitrogen and stored at -80C until processing

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen) and assessed on a Nanodrop, Qubit, and Bioanalyzer
The libraries were quantitated by qPCR and sequenced on one lane for 151 cycles from each end of the fragments on a NovaSeq 6000  using a NovaSeq S4 reagent kit. Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used portion in bold font for adaptor trimming). Adaptor sequence in read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNNNN= 8 nt index). Adaptor sequence in read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTNNNNNNNNAGATCTCGGTGGTCGCCGTATCAT.

treatment_protocol: Frozen honey bee heads were freeze dried (~52 minutes) and dissected in a dry ice/ethanol bath.

tag: caste

tag: group

value: forager

tag: colony location

tag: colony latitude

tag: colony longitude


title: Mouse 2

city: Los Angeles

first: Olujimi

last: Ajijola

address: 100 Medical Plaza

department: Cardiovascular Center

institute: UCLA

description:
Mouse-2-2
10x Genomics
Chromium single cell

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1. scRNAseq analysis was done in Seurat (R) and Scanpy (python).
Assembly: mm10
Supplementary files format and content: neuron.dge.csv: Digital gene expression matrix.
Supplementary files format and content: neuron.metadata.csv: Cell type metadata containing the neuronal sub types.

source_name: Stellate ganglia

extract_protocol:
Bilateral stellate ganglia in C57BL/6 mice were identified, isolated, and collected in artificial cerebrospinal fluid (ACSF; Figure 1A). Next, 16 left and right stellate ganglia combined were incubated for an hour at 37°C in a digestion solution prepared with 500 μl TrypLE Express (ThermoFisher Scientific, Waltham, Massachusetts), 2000 μl Papain solution (Worthington Biochemical Corporation, Lakewood, New Jersey; 25 units/mL in ACSF), 100 μl Collagenase-Dispase (Millipore Sigma, Burlington, Massachusetts; 20 mg/mL in ACSF) and 270 μl DNase I (Worthington Biochemical Corporation, Lakewood, New Jersey; 200 units/mL in ACSF). After an hour, the cells were carefully triturated with fire-blown Pasteur pipettes every thirty minutes. Following the second trituration, 100 μl fresh Collagenase-Dispase (20 mg/mL in ACSF) was added to the solution and cells were incubated for another hour at 37°C, triturating every thirty minutes. Next, the suspension was filtered through a 40 um filter (ThermoFisher Scientific, Waltham, Massachusetts) and ACSF was added to halt enzymatic digestion. The suspension was spun down at 100g for four minutes at room temperature, and the pellet collected and resuspended in 500 μL ACSF and 500 μL supplemented Neurobasal-A medium (ThermoFisher Scientific, Waltham, Massachusetts; 250 μL B27, 250 μL Penicillin-streptomycin, 31.3 μL L-Glutamine). The cell suspension was transferred onto a density gradient (Millipore Sigma, Burlington, Massachusetts) and centrifuged at 100g for 10 minutes at room temperature. The supernatant was carefully removed until the solution was concentrated to 500 μL. Single cell RNA sequencing used microfluidic capture-based encapsulation, barcoding, and library preparation (10x Genomics Chromium scRNAseq system (10x Genomics, Pleasanton, California)). Cells were loaded into a Chromium Chip B along with partitioning oil, reverse transcription reagents, and a mix of hydrogel beads containing 3,500,000 unique 10X Barcodes. Paired end sequencing was performed on a Novaseq S4 system, using the v3 Illumina platform. Coverage depth was 20K per cell, and the read length was 2x50. Analysis including demultiplexing, reference-based mapping (GRCm38.98), and UMI identification, was performed according to the 10X Cell Ranger pipeline. We modified the reference by adding in the sequences for GFP to detect their transcripts in cells.
Chromium Single Cell Gene Expression Protocol V3 enables library preparation of hundreds to thousands of individual cells (500-10000 cells per sample) for 3’ digital gene expression profiling analysis simultaneously. Cells are loaded into a Chromium Chip B along with partitioning oil, reverse transcription reagents, and a mix of hydrogel beads containing 3,500,000 unique 10X Barcodes. After a 8 min run on the 10X Genomics Chromium Controller an emulsion is formed as the cells and reagents are passed through the microfluidic channels of the Chip. A fraction (1-10%) of the droplets within the emulsion will include a single cell in addition to a gel bead which releases its contents to deliver oligo(dT) primers containing a unique 10X Cell Barcode that is used to index the 3’ end of cDNA molecules during reverse transcription. Libraries are generated and sequenced starting from cDNA and 10X Barcodes enable the assignment of transcripts to individual cells during Illumina sequence analysis.

value: Neuron

value: Stellate ganglia

tag: strain

tag: age

value: 8-10 weeks


title: sample 71 [12_2_4]

description:
12_2_4_ACTCGTGT-ATTGGAAC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas2_soldier_whole brain


title: HiC, EV control replicate 1, library 2

description: Arima-HiC


title: p006, MLN, CD4, TEM

source_name: Gut Lymph Node

value: Gut Lymph Node


title: hdl042, MLN, CD8, TEM


title: sample 70 [11_4_6]

description:
11_4_6_ATTGTGAA-TGCATTGC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_forager_whole brain


title: PC-9GR shIGF2BP3_2

city: Guangzhou

first: Xiaolei

last: Zhang

state: Guangdong

address: 132 East Waihuan Road, Higher Education Mega Center, Panyu District

country: China

institute: Sun Yat-sen University

description: baseMeanA

data_processing:
sample1-8:Paired-end sequencing was performed with Illumina HiSeq 3000 (RiboBio Co, Ltd). TopHat2 and HTSeq were used for RNA-seq data analysis with GRCh38/hg19 as the reference genome. Differential analysis of the RNA-seq data was performed using DESeq2 analysis.
sample9-10:Raw data were generated after sequencing,  image analysis, base calling and quality filtering on Illumina NovaSeq 6000 sequencer. Firstly, Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality clean reads were generated. Then these clean reads were aligned to human reference genome  (UCSC hg19) using bowtie2 software  (v2.2.4) with default parameters. Peak calling was performed with MACS software (v1.4.3). Differentially enriched regions were identified by diffReps software (v1.55.4).The  enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Assembly: UCSC hg19
Supplementary files format and content: sample1-8:tab-delimited text files include TPM values for each Sample
Supplementary files format and content: sample9-10:bigWig, narrowPeak (except for Input sample)

source_name: Non-Small Cell Lung Cancer

extract_protocol:
sample1-8:Total RNA was isolated using TRIzol reagent according to the manufacturer’s instruction (15596026, Invitrogen, USA).
sample9-10:The RIP assay was performed using the Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (17-700, Merck Millipore, USA), according to the manufacturer’s protocol. Stable IGF2BP3-overexpressed PC-9/GR cells were collected, and RNA was obtained by re-suspending and dispersing the cell pellet in complete RIP Lysis Buffer. Antibodies against DYKDDDDK Tag Rabbit mAb (#14793S, CST, USA) and normal Rabbit IgG were added to the magnetic beads to pull down specific RNAs.
sample1-8: DNase I was used for column digestion to ensure RNA quality. RNA library preparation was performed using the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (E7420L). RNA libraries were prepared for paired-end sequencing using standard Illumina protocols.
sample9-10:The yield of ChIPed DNA was determined via Quant IT fluorescence assay (Life Technologies) and enrichment efficiencies of ChIP reactions were evaluated by qPCR. Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer’s manual. The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina Novaseq sequencer according to the manufacturer’s recommended protocol.
sample1-8:RNA-seq
sample9-10:RIP-seq

value: Non-Small Cell Lung Cancer


title: PC-9GR shIGF2BP3_1

description: baseMeanA


title: p006, LLN, CD8, TEM

source_name: Lung Lymph Node

value: Lung Lymph Node


title: PC-9/GR shCtrl_1

description: baseMeanB


title: TKI-resistant NSCLC patient2

description: MeanTPMA


title: TKI-sensitive NSCLC patient2

description: MeanTPMB


title: p006, LLN, CD4, TEM


title: TKI-resistant NSCLC patient1

description: MeanTPMA


title: HiC, ZFP661OE replicate 1, library 2

description: Arima-HiC

value: ZFP661-3HA OE


title: sample 67 [10_2_5]

description:
10_2_5_TTCCTGTT-AGTATCTT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel2_soldier_whole brain

value: worker

value: soldier


title: sample 68 [10_4_4]

description:
10_4_4_CCTTCACC-GACGCTCC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel2_forager_whole brain

value: whole brain


title: TKI-sensitive NSCLC patient1

description: MeanTPMB


title: PC-9/GR shCtrl_2

description: baseMeanB


title: sample 69 [11_2_4]

description:
11_2_4_GCCACAGG-CATGCCAT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_soldier_whole brain


title: p006, Lg, CD8, TEM

value: Lung

value: primary


title: p006, Lg, CD4, TEM

value: T cell

value: WT


title: ZFR-SMI-2

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

library_source: other

data_processing:
library strategy: eCLIP-seq
RNA-Seq data from eCLIP IP and input samples were analyzed using the ENCODE eCLIP-seq Processing Pipeline (Van Nostrand et al., 2018).
Raw fastq files were trimmed with Cutadapt as described (Martin, 2011), followed by removal of sequences derived from repetitive elements with STAR aligner, using human RepBase sequences (Bao et al., 2015; Dobin et al., 2013).
Remaining reads were mapped to the hg19 human genome release with STAR aligner.
ZFR eCLIP peaks were called with Clipper software and normalized vs the size-matched input control as described (Van Nostrand et al., 2016).
Round 1 trimming parameters: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A sequences corresponding to 15 nt tiling of X1A and X1B adapters
Round 2 trimming parameters:
cutadapt -f fastq
--match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A sequences corresponding to 15 nt tiling of X1A and X1B adapters
STAR mapping to repetitive elements, using hg19 Repbase sequences:
STAR --alignEndsType EndToEnd --outBAMcompression 10 --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1
--outFilterScoreMin 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --runMode alignReads
STAR mapping to Gencode release 19:
STAR --runMode alignReads --outStd BAM_Unsorted --outReadsUnmapped FastX --outSAMtype BAM Unsorted --outSAMattributes All --outSAMunmapped Within --outSAMattrRGline ID:foo --outFilterType BySJout --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3
PCR duplicates were removed with barcodecollapsepe.py provided by (Van Nostrand et al., 2018).
Samtools was used to generate bam files containing R2 only, using the following parameters:
samtools view -f 128 -b
Peaks were identified with and normalized vs the size-matched input control as described (Van Nostrand et al., 2016), with the following parameters:
clipper --species hg19 --save-pickle
samtools view -cF 4
Input normalization was preformed with the perl script provided by (Van Nostrand et al., 2018):
overlap_peakfi_with_bam_PE.pl
Assembly: hg19
Supplementary files format and content: Bed files of eCLIP peaks called by Clipper

molecule: other

source_name: HEK-293 Flp-In TREx cells

growth_protocol: Flp-In T-REx-293 cells (ThermoFisher Scientific) were maintained at 37°C in ambient oxygen and 5% CO2 in DMEM (Gibco #11965‐092) supplemented with 10% fetal bovine serum (Gibco) and a 1% penicillin, streptomycin, and L‐glutamine mixture (Gibco).

extract_protocol:
Samples were prepared according to the eCLIP protocol (Van Nostrand et al. 2016 Nat Methods.) For each sample, 2x10^7 cells were UV crosslinked at 400mJ/cm2 constant energy. Cells were lysed on ice for 15 min in 1 mL lysis buffer containing 50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, Halt protease inhibitor cocktail (ThermoFisher Scientific). Cells were passed through 27-gauge needles several times before sonication (Biorupter, Diagenode) for 3 min at low setting with 30 second on/30 second off duty cycle at 4°C.
eCLIP and size-matched input libraries were constructed according to the eCLIP protocol (Van Nostrand et al. 2016 Nat Methods.)

treatment_protocol: Polyclonal cells were treated with doxycyline hyclate (1 μg/mL final concentration, ThermoFisher Scientific) for 48-72 hours for induction of transgene expression.

value: HEK-293 Flp-In TREx cells

value: FLAG-ZFR stably integrated in FRT site

tag: sample type

value: size-matched input


title: ZFR-SMI-1


title: ZFR-eCLIP-2

value: eCLIP


title: siILF3-3

data_processing:
Reads were trimmed using fastp software, with options --detect_adapter_for_pe and --trim_poly_g.
Trimmed reads were aligned with HISAT2, using default parameters and the hg19/grch37 combined genome and transcriptome index provided by the authors.
Gene-level expression quantification was performed with featurecounts, using Ensembl GRCh37.75 transcript annotations.
Differential gene expression was quantified using voom and Topconfects, as implemented by the Degust web server.
Assembly: hg19
Supplementary files format and content: Tab-delimited file contains differential gene expression analysis, read counts, and CPM values for the indicated samples and comparisons.

source_name: HEK-293 cells

growth_protocol: HEK-293 cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml L-glutamine at 37°C and 5% CO2.

extract_protocol:
Qiagen RNeasy Plus Mini RNA isolation kit
2 μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq Stranded RNA Library Preparation Kit (Illumina).

treatment_protocol: HEK-293 cells were reverse-transfected with 40 nM of the indicated siRNA using Lipofectamine RNAiMAX. Seventy-two  hours post-siRNA transfection, cells were harvesed for total RNA.

value: HEK-293 cells

value: Transfected with anti-ILF3 siRNA (siILF3)


title: siILF3-2


title: ZFR-eCLIP-1

data_processing:
library strategy: eCLIP-seq
RNA-Seq data from eCLIP IP and input samples were analyzed using the ENCODE eCLIP-seq Processing Pipeline (Van Nostrand et al., 2018).
Raw fastq files were trimmed with Cutadapt as described (Martin, 2011), followed by removal of sequences derived from repetitive elements with STAR aligner, using human RepBase sequences (Bao et al., 2015; Dobin et al., 2013).
Remaining reads were mapped to the hg19 human genome release with STAR aligner.
ZFR eCLIP peaks were called with Clipper software and normalized vs the size-matched input control as described (Van Nostrand et al., 2016).
Round 1 trimming parameters: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A sequences corresponding to 15 nt tiling of X1A and X1B adapters
Round 2 trimming parameters:
cutadapt -f fastq
--match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A sequences corresponding to 15 nt tiling of X1A and X1B adapters
STAR mapping to repetitive elements, using hg19 Repbase sequences:
STAR --alignEndsType EndToEnd  --outBAMcompression 10 --outFilterMultimapNmax 30 --outFilterMultimapScoreRange  1
 --outFilterScoreMin 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline  ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --runMode alignReads
STAR mapping to Gencode release 19:
STAR   --runMode alignReads   --outStd BAM_Unsorted   --outReadsUnmapped FastX   --outSAMtype BAM   Unsorted      --outSAMattributes All      --outSAMunmapped Within      --outSAMattrRGline ID:foo      --outFilterType BySJout   --outFilterMultimapNmax 1   --outFilterMultimapScoreRange 1   --outFilterScoreMin 10   --outFilterScoreMinOverLread 0.3   --outFilterMatchNminOverLread 0.3
PCR duplicates were removed with barcodecollapsepe.py provided by (Van Nostrand et al., 2018).
Samtools was used to generate bam files containing R2 only, using the following parameters:
samtools view -f 128 -b
Peaks were identified with and normalized vs the size-matched input control as described (Van Nostrand et al., 2016), with the following parameters:
clipper --species  hg19 --save-pickle
samtools view -cF 4
Input normalization was preformed with the perl script provided by (Van Nostrand et al., 2018):
overlap_peakfi_with_bam_PE.pl
Assembly: hg19
Supplementary files format and content: Bed files of eCLIP peaks called by Clipper


title: sample 65 [9_2_4]

description:
9_2_4_ACACTAAG-ATCCATAT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_soldier_whole brain


title: p006, Jej, CD4, TEM

source_name: Jejunum

value: Jejunum


title: p006, Jej, CD8, TEM


title: sample 64 [7_4_5]

description:
7_4_5_CCATTCGA-GTTGTCCG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_forager_whole brain

value: forager

value: Comerio


title: sample 66 [9_4_4]

description:
9_4_4_GTGTCGGA-GCTTGCGC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_forager_whole brain


title: siILF3-1


title: siILF2-3

value: Transfected with anti-ILF2 siRNA (siILF2)


title: p006, Ile, CD8, TEM

source_name: Ileum

value: Ileum


title: siNS-3

value: Transfected with non-silencing siRNA (siNS)


title: sample 60 [4_4_5]

description:
4_4_5_AGCTCGCT-GCAGAATC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_forager_whole brain

value: worker

value: whole brain


title: siZFR-3

value: Transfected with anti-ZFR siRNA (siZFR)


title: siZFR-2


title: sample 62 [6_4_4]

description:
6_4_4_TAAGGTCA-TGTCGTAG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_forager_whole brain


title: sample 61 [6_2_4]

description:
6_2_4_CGGAACTG-CACTACGA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_soldier_whole brain

value: soldier


title: siILF2-2


title: siNS-2


title: HDL040, MLN, CD8, TEM

source_name: Gut Lymph Node

value: Gut Lymph Node

value: primary

value: T cell

value: WT


title: HDL040, LLN, CD8, TEM

value: Lung Lymph Node


title: siZFR-1

value: HEK-293 cells


title: HDL040, Lg, CD8, TEM

source_name: Lung

value: Lung


title: HDL040, MLN, CD4, TEM


title: L2C_Mdivi rep1

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
Assembly: mm10
Supplementary files format and content: DESeq result with normalized and raw gene counts for every gene and every sample

source_name: embryo

extract_protocol:
Embryos were collected in tubes with lysis component, then amplification was carried out by the Smart-Seq2 methodlibraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: embryo

value: Mdivi


title: L2C_Con rep2

value: Control


title: siILF2-1

value: Transfected with anti-ILF2 siRNA (siILF2)


title: p006, Ile, CD4, TEM

value: Ileum


title: sample 63 [7_2_4]

description:
7_2_4_TTGCCTAG-ACCACTTA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_soldier_whole brain

value: worker

value: Comerio


title: sample 59 [4_2_6]

description:
4_2_6_GATCTATC-ATGAGGCT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_soldier_whole brain

value: whole brain


title: siNS-1

value: Transfected with non-silencing siRNA (siNS)


title: L2C_Con rep1


title: sample 57 [2_2_4]

description:
2_2_4_TGCGGCGT-CCTCGGTA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas2_soldier_whole brain

value: soldier


title: HiC, EV control replicate 1, library 1

description: Arima-HiC

source_name: R1 mESCs

value: R1 mESCs

value: mouse embryonic stem cells

value: EV control


title: HDL040, Jej, CD8, TEM

value: Jejunum

value: primary

value: T cell

value: WT


title: HDL040, Lg, CD4, TEM

value: Lung


title: EV control mESCs (replicate 2), RAD21 ChIP

description: ChIP-seq

data_processing:
Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. The resulting clean reads were mapped onto the mouse genome (mm10) using BWA with default parameters, and only uniquely mapped reads (with tag X0:i:1) were retained for downstream analyses.
MACS2 (v2.2.7.1) was used to call peaks with one duplicated tag kept, fragment length 200bp for single-end reads, and the threshold q ≤ 0.01. Peaks that overlapped (overlap represents any bases of a peak sharing with other peaks/regions) with the regions on ENCODE blacklist (Amemiya et al. 2019) were filtered out. During peak calling, ChIP inputs were used as controls for all factors except for ZFP661. For ZFP661 in ZFP661-3HA OE mESCs, ChIP input and the corresponding ChIP in EV control mESCs using anti-HA antibodies (referred to as HA-ChIP) were used as controls to detect peaks (referred to as input-peaks and HA-peaks), respectively. Only HA-peaks that overlapped with input-peaks were retained as reliable peaks for downstream analyses. For ZFP661 in endogenous tagged ZFP661-3HA mESCs, HA-ChIP in un-tagged mESCs were used as ChIP input to detect peaks. For H3K9me3, the peak regions from MACS2 output were used directly. For other factors, the 50 bp flanking regions of ChIP summits (i.e., summits ± 50 bp) were used as refined peak regions for downstream analyses.
To generate high-quality and consistent ChIP peak lists, peaks from two biological replicates in the same condition (i.e., WT or Zfp661 KO, EV control or ZFP661-3HA OE) were combined by retaining peaks in replicate 1 that overlapped with peaks in replicate 2. As ZFP661 expressed at low level in mESCs, the following steps were employed to generate a high-quality peak list for ZFP661 in ZFP661-3HA mESC: ZFP661 peaks in ZFP661-3HA mESCs were detected using a relatively loose threshold (q ≤ 0.1), and only peaks that overlapped with consistent ZFP661 peaks in ZFP661-3HA OE mESCs were retained. To generate consistent ChIP signal (i.e., bigwig) files, deepTools (v3.5.1) was used with the parameters “--normalizeUsing CPM --binSize 10 –extendReads” (CPM represents counts per million) and with chrM and regions on ENCODE blacklist excluded. The ChIP signals were normalized by subtracting the ChIP input in each biological replicate (for ZFP661, subtracted by HA-ChIP), and then the two biological replicates were averaged to generate a consistent bigwig file for each factor.
Assembly: mm10
Supplementary files format and content: bigwig signal files (.bw), MACS2 peak files (.NarrowPeak), tar of consistent bigwig files (.tar), and tar of consistent peak files (.tar).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.4M glycine for 5 min.
ChIP assays were performed according to the ENCODE protocol with modifications. 20M cells/ChIP were used for ZFP661-3HA (anti-HA: Abcam, ab9110), CTCF (anti-CTCF: Millipore, 07-729), RAD21 (Anti-RAD21: Abcam, ab992) and KAP1 (anti-KAP1: Abcam, ab22553), and 10M cells/ChIP were used for H3K9me3 (anti-H3K9me3: Abcam, ab8898). 5 μg of antibodies were used for each ChIP. ChIP DNA was purified, and 10 μl (or up to 50 ng) of ChIP DNA was used as input to construct ChIP library using ThruPLEX DNA-Seq Kit (Takara, R400676). The ChIP inputs from the same biological replicate were evenly sampled and pooled together to construct the corresponding ChIP input library.

tag: chip antibody

value: RAD21 (Abcam, ab992)


title: sample 58 [2_4_4]

description:
2_4_4_CATAATAC-TTCTAACG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas2_forager_whole brain

value: forager


title: sample 56 [1_4_4]

description:
1_4_4_GAATGAGA-GAGGCATT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_forager_whole brain


title: PTBP1-80 nM

data_processing:
library strategy: RNA Bind-n-Seq
RBNS data were analyzed using rbns_pipeline software (https://github.com/alexrson/rbns_pipeline).
Supplementary files format and content: Comma-delimited files contain B values generated by the RBNS analysis pipeline for the indicated 6-mer sequences.

organism: synthetic construct

source_name: Protein-bound RNA

extract_protocol:
The DNA template for T7 transcription of the RBNS library containing 40 random nucleotides was synthesized by Integrated DNA Technologies and transcribed with the MEGAshortscript T7 transcription kit (ThermoFisher Scientific).  Four concentrations of each  ZFRDZF/ILF2, ZFRlong/ILF2 (5, 20, 80, and 320 nM) or two concentrations of control protein PTBP1 (20 and 80 nM) were equilibrated in 45 µl binding buffer (20 mM HEPES pH 7.5, 150 mM potassium acetate, 3 mM magnesium acetate, 0.01% Tween-20, 1 mM DTT, 1 mM zinc sulfate, 0.5 mg/ml BSA) for 30 minutes at RT, and 90 µl 1 µM RBNS RNA library supplemented with 20 units of SUPERaseIn (ThermoFisher Scientific) was added and rotated for 1 hr at RT. Pre-washed 25 µl His-Tag Dynabeads (ThermoFisher Scientific) were added, rotated for 1 hour at RT, and washed three times with wash buffer (20 mM HEPES pH 7.5, 150 mM potassium acetate, 0.01% Tween, 0.5 mM EDTA, 0.5 mg/ml BSA). Bound RNA was eluted with 100 µl elution buffer (10 mM Tris, pH 7.0, 1 mM EDTA, 1% SDS) by heating at 70°C for 10 min.
Eluted RNA was purified with Zymo RNA Clean & Concentrator-5 columns (Zymo Research), reverse-transcribed with SuperScript IV (ThermoFisher Scientific), PCR amplified with AccuPrime PFX SuperMix (ThermoFisher Scientific), and sequenced on the Illumina HiSeq 3000 platform.

value: synthetic sequence library

value: PTBP1-80 nM

tag: molecule subtype

value: Protein-bound RNA


title: L2C_Mdivi rep2

value: ICR

value: embryo

value: Mdivi


title: HDL040, Jej, CD4, TEM

source_name: Jejunum


title: sample 54 [12_4_3]

description:
12_4_3_TGGTGGCA-TCCTGTAA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas2_forager_whole brain

value: worker

value: whole brain


title: PTBP1-20 nM

value: PTBP1-20 nM


title: EV control mESCs (replicate 2), ZFP661-3HA ChIP

description: ChIP-seq

value: R1 mESCs

value: mouse embryonic stem cells

value: EV control

value: HA (Abcam, ab9110)


title: EV control mESCs (replicate 2), ChIP Input

description: ChIP-seq

value: Input control


title: sample 55 [1_2_4]

description:
1_2_4_AGGCAGAG-AGAATGCC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_soldier_whole brain

value: soldier


title: ZFRlong/ILF2-80 nM

value: ZFRlong/ILF2-80 nM


title: sample 53 [12_2_3]

description:
12_2_3_CAACAATG-CTTCACGG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas2_soldier_whole brain


title: EV control mESCs (replicate 2), KAP1 ChIP

description: ChIP-seq

value: KAP1 (Abcam, ab22553)


title: NS_Unt_PolII_1

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

description: PolII CUT&Tag from MB135 myoblasts with inducibile DUX4-aa154-424, Untreated

data_processing:
Sequencing data was processed with Illumina Pipeline software (Casava version 1.9)
Reads quality and adapter trimmed using Trimmomatic v0.39 with the following arguments: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Using Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to GRCh38 patch 13 Homo sapiens genome.
Properly paired reads were extracted and used to generate bedgraph files via bedtools v. 2.3.0
Assembly: GRCh38, patch 13
Supplementary files format and content: Bedgraphs
Library strategy: CUT&TAG

source_name: DUX4_aa154-424 PolII CUT&Tag, Untreated

growth_protocol: Myoblasts were cultured in F-10 media supplemented with 15% Fetal Bovine Serum, 10ng/mL rhFGF Basic, 1uM dexamethasone, and 2ug/mL puromycin. Cells were passaged at ~70% confluence with a 1:5 split ratio.

extract_protocol:
Chromatin was isolated following the Benchtop CUT&Tag v.2 protocol from Kaya-Okur & Henikoff (2020)
Benchtop Cut&Tag v.2 protocol from Kaya-Okur & Henikoff (2020)

treatment_protocol: IFNg treated samples were 200ng/mL interferon gamma for 16 hours, DOX+IFNg samples were pre-treated with 1ug/mL doxicycline for 4 hours and then 200ng/mL interferon gamma for 16 hours (20 hours total treatment)

value: MB135 myoblasts

value: with inducibile DUX4-aa154-424

tag: passages

value: Untreated

tag: antibody

value: phospho-RpB1 CTD (Ser5) (D9N51)


title: HDL040, Ile, CD8, TEM

source_name: Ileum

tag: tissue

value: Ileum

tag: cell line

value: primary

value: T cell

value: WT


title: ZFRlong/ILF2-320 nM

value: synthetic sequence library

value: ZFRlong/ILF2-320 nM

value: Protein-bound RNA


title: sample 51 [11_2_3]

description:
11_2_3_AACAGGTT-ATACCAAG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_soldier_whole brain

value: worker

value: whole brain


title: ZFRlong/ILF2-5 nM

value: ZFRlong/ILF2-5 nM


title: sample 50 [10_4_3]

description:
10_4_3_GCGCTCTA-GCTCCGAC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel2_forager_whole brain

value: forager


title: NS_Unt_PolII_2

tag: cell type

tag: genotype


title: ZFRlong/ILF2-20 nM

tag: treatment

value: ZFRlong/ILF2-20 nM


title: NS_IFNg_PolII_1

description: PolII CUT&Tag from MB135 myoblasts with inducibile DUX4-aa154-424, treated with IFNg

source_name: DUX4_aa154-424 PolII CUT&Tag, IFNg treated

value: IFNg treated


title: EV control mESCs (replicate 2), H3K9me3 ChIP

description: ChIP-seq

value: R1 mESCs

value: mouse embryonic stem cells

value: EV control

value: H3K9me3 (Abcam, ab8898)


title: EV control mESCs (replicate 2), CTCF ChIP

description: ChIP-seq

value: CTCF (Millipore, 07-729)


title: sample 49 [10_2_4]

description:
10_2_4_ATATCTCG-ATCTTAGT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel2_soldier_whole brain

tag: caste

value: soldier


title: NS_IFNg_PolII_2

value: MB135 myoblasts

value: with inducibile DUX4-aa154-424

value: phospho-RpB1 CTD (Ser5) (D9N51)


title: sample 52 [11_4_5]

description:
11_4_5_GGTGAACC-GCGTTGGA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_forager_whole brain

tag: group


title: ZFRDZF/ILF2-320 nM

value: synthetic sequence library

value: ZFRDZF/ILF2-320 nM


title: EV control mESCs (replicate 1), KAP1 ChIP

description: ChIP-seq

value: KAP1 (Abcam, ab22553)


title: ZFRDZF/ILF2-80 nM

value: ZFRDZF/ILF2-80 nM

value: Protein-bound RNA


title: EV control mESCs (replicate 1), RAD21 ChIP

description: ChIP-seq

value: RAD21 (Abcam, ab992)


title: NS_DoxIFNg_PolII_1

description: PolII CUT&Tag from MB135 myoblasts with inducibile DUX4-aa154-424, treated with IFNg and Dox

source_name: DUX4_aa154-424 PolII CUT&Tag, Dox + IFNg treated

value: Dox + IFNg treated


title: NS_DoxIFNg_PolII_2


title: EV control mESCs (replicate 1), ChIP Input

description: ChIP-seq

value: Input control


title: sample 48 [9_4_3]

description:
9_4_3_ACCTTGGC-GGCCTCAT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_forager_whole brain

value: worker

value: forager

tag: colony location

value: whole brain


title: AS_Unt_PolII_2

value: Untreated


title: EV control mESCs (replicate 1), ZFP661-3HA ChIP

description: ChIP-seq

source_name: R1 mESCs

value: R1 mESCs

value: mouse embryonic stem cells

value: EV control

value: HA (Abcam, ab9110)


title: No_Protein control

description:
ZFR_DZF_ILF2_RBNS.csv
PTBP1_RBNS.csv
ZFR_long_ILF2_RBNS.csv

source_name: Without protein control


title: AS_IFNg_PolII_2

value: MB135 myoblasts

value: with inducibile DUX4-aa154-424

value: IFNg treated

value: phospho-RpB1 CTD (Ser5) (D9N51)


title: ZFRDZF/ILF2-5 nM

value: synthetic sequence library

value: ZFRDZF/ILF2-5 nM


title: AS_Unt_PolII_1


title: EV control mESCs (replicate 1), H3K9me3 ChIP

description: ChIP-seq

value: H3K9me3 (Abcam, ab8898)


title: sample 46 [7_4_4]

description:
7_4_4_GCAATGCA-GGAACGTT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_forager_whole brain

value: Comerio

tag: colony latitude


title: RBNS Input RNA library

source_name: Synthetic RNA


title: sample 47 [9_2_3]

description:
9_2_3_GTTCCAAT-AATTCTGC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_soldier_whole brain

value: soldier

tag: colony longitude


title: sample 44 [6_4_3]

description:
6_4_3_GGAGCGTC-GTCCGTGC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_forager_whole brain

value: worker


title: ZFP661-3HA OE mESCs (replicate 2), KAP1 ChIP

description: ChIP-seq

value: ZFP661-3HA OE

value: KAP1 (Abcam, ab22553)


title: AS_IFNg_PolII_1


title: ZFP661-3HA OE mESCs (replicate 2), RAD21 ChIP

description: ChIP-seq

value: RAD21 (Abcam, ab992)


title: EV control mESCs (replicate 1), CTCF ChIP

description: ChIP-seq

value: R1 mESCs

value: CTCF (Millipore, 07-729)


title: ZFP661-3HA OE mESCs (replicate 2), ChIP Input

description: ChIP-seq

value: mouse embryonic stem cells

value: Input control


title: PR-Y-018_PD_WTS

city: Seoul

first: Yeon Hee

last: Park

address: 81 Ilwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description: paired-end sequence reads

data_processing:
After trimming poor quality bases from the FASTQ files, reads were aligned to the human reference genome (hg19) with STAR v2.5.2b.
Alignment quality was verified with SAMTOOLS (v 0.1.19).
Estimated gene expression was calculated in terms of Transcripts Per Million (TPM) using RSEM v1.3.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for for every gene and every sample

source_name: breast tissue of breast cancer patients

extract_protocol:
Total RNA from fresh-frozen tumor tissues was extracted with an RNeasy Mini Kit (Qiagen) and from FFPE tissues using ReliaPrep™ FFPE Total RNA Miniprep System (Promega) according to the manufacturer’s instructions.
Seqeuncing libraries were prepared using the TruSeq RNA Access Library Prep Kit (Illumina, Inc.) using standard Illumina protocols.

value: breast

tag: gender

value: female

tag: disease state

value: breast cancer

tag: time

value: PD


title: AS_DoxIFNG_PolII_2

value: MB135 myoblasts

value: with inducibile DUX4-aa154-424

value: Dox + IFNg treated

value: phospho-RpB1 CTD (Ser5) (D9N51)


title: ced-3(-) with FASN-CTF Tunicamycin Biol Rep 3 (CtOE)

city: Dallas

first: Benjamin

last: Weaver

address: 6001 Forest Park Rd

department: Pharmacology

institute: University of Texas Southwestern Medical Center

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to C elegans genome using STAR (v2.5.3a)
Duplicate alignments were removed using picard-tools(v2.10)
Read counts were generated using featureCounts (subread) for coding genes from igenomes (Refseq)
Normalized read counts generated using edgeR
Assembly: ce10
Supplementary files format and content: glmLRT.txt: Files with Diﬀerential expressed gene list

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: BPW317 animals were maintained on OP50 with K-NAA supplement to supress transgene expression prior to experiment

extract_protocol:
RNA was extracted using Trizol. Total RNA was treated with DNAse prior to library construction
Illumina NextSeq 500 Kits

treatment_protocol: Synchronized L1 animals were placed on either mock_RNAi/K-NAA plates to suppress transgene expression or on At-tir-1_RNAi plates to allow transgene expression. When animals reached L4 stage, 4µg/ml tunicamycin was added to induce ER stress for 12 hours prior to RNA collection.

value: whole organism

value: Tunicamycin (4microg/mL)


title: ced-3(-) with FASN-CTF Tunicamycin Biol Rep 1 (CtOE)


title: sample 41 [4_2_5]

description:
4_2_5_ATATGGAT-CTGTATTA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_soldier_whole brain

value: worker

value: soldier

value: whole brain


title: ced-3(-) with FASN-CTF Tunicamycin Biol Rep 2 (CtOE)


title: sample 42 [4_4_4]

description:
4_4_4_GCGCAAGC-TCACGCCG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_forager_whole brain

value: forager


title: ced-3(-) Tunicamycin Biol Rep 3  (CtrL)

value: K-NAA + Tunicamycin (4microg/mL)


title: ZFP661 3HA OE mESCs (replicate 2), ZFP661-3HA ChIP

description: ChIP-seq

value: R1 mESCs

value: mouse embryonic stem cells

value: ZFP661-3HA OE

tag: chip antibody

value: HA (Abcam, ab9110)


title: ZFRDZF/ILF2-20 nM

source_name: Protein-bound RNA

tag: sample type

value: synthetic sequence library

value: ZFRDZF/ILF2-20 nM

tag: molecule subtype

value: Protein-bound RNA


title: sample 45 [7_2_3]

description:
7_2_3_ATGGCATG-AAGGTACC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_soldier_whole brain

value: Comerio


title: ZFP661-3HA OE mESCs (replicate 2), H3K9me3 ChIP

description: ChIP-seq

value: H3K9me3 (Abcam, ab8898)


title: sample 40 [2_4_3]

description:
2_4_3_CGGACAAC-TCCGGATT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas2_forager_whole brain


title: ced-3(-) Tunicamycin Biol Rep 2  (CtrL)


title: sample 43 [6_2_3]

description:
6_2_3_AAGATACT-ACTTACAT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_soldier_whole brain


title: PR-Y-010_Baseline_WTS

description: paired-end sequence reads

value: breast

value: female

value: breast cancer

value: Baseline


title: AS_DoxIFNG_PolII_1

value: MB135 myoblasts

value: with inducibile DUX4-aa154-424

tag: passages

value: Dox + IFNg treated

tag: antibody

value: phospho-RpB1 CTD (Ser5) (D9N51)


title: ced-3(-) Tunicamycin Biol Rep 1  (CtrL)

tag: tissue

value: whole organism

value: K-NAA + Tunicamycin (4microg/mL)


title: PR-Y-006_Baseline_WTS

description: paired-end sequence reads


title: sample 38 [1_4_3]

description:
1_4_3_CTACGACA-GAGTCCAA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_forager_whole brain

value: worker

value: forager

value: whole brain


title: 20230217_hpap_8_Pool_Well8_RNA, RNA derived cDNA

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

data_processing:
Raw BCL files were converted to fastq files using either cellranger mkfastq (for RNA) or bcl2fastq (for ADT/HTO)
For RNA, fastq files were aligned to hg38, counted, and filtered for QC using cellranger count.
For ADT/HTO, fastq files were aligned to ADT or HTO catalog references. Alignments were barcode corrected and counted as part of the kallisto bustools pipeline (KITE; see https://github.com/betts-lab/scc-proc for snakemake pipeline).
Assembly: hg38
Supplementary files format and content: RNA: tar.gz archive of cellranger output (matrix.tsv.gz, features.tsv.gz, barcodes.tsv.gz). ADT/HTO: tar.gz archive of kallisto bustools output (output.genes.txt, output.mtx, output.barcodes.txt)
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: polyA RNA

source_name: tail, spleen, head

extract_protocol:
Pooled samples were placed through the 3' scRNAseq v3.1 pipeline (10X Genomics) to generate single cell partitions sharing cDNA, antibody derived tag, and hashing antibody barcodes. Each well of a 10X chip was superloaded with ~1.75X manufacturer's recommended maximum cell count. cDNA extract protocol followed manufacturer's instructions. To extract antibody derived tag and hashing tag sequences, the supernatant from cDNA Cleanup - SPRIselect (Step 2.3d in Protocol CG000315 Rev C, or equivalent step) was saved for further processing following the standard CITEseq protocol (https://cite-seq.com/protocols/).
Dual indexed cDNA libraries were generated following manufacturer's instructions (10X Genomics Protocol CG000315 Rev C, or equivalent for high-throughput protocols). Dual indexed antibody derived tag and hashing tag libraries were generated following standard CITEseq protocol (https://cite-seq.com/protocols/) using primers recommended from Biolegend. Antibody derived tag and hashing tag sequences were enriched in the initial cDNA amplification step of the 3' scRNAseq v3.1 protocol via addition of additive primers (https://cite-seq.com/protocols/).

treatment_protocol: All samples were thawed from -150℃ cryopreservation. Individual tubes were gently shaken in a 37℃ water bath until the frozen cells were partially thawed. Cells were then quickly resuspended in at least 14 mL cold R10 + DNAse (RPMI-1640 supplemented with 10% fetal bovine serum, 1% L-glutamine, and 1% penicillin/streptomycin in the presence of 10 U/mL DNAse I) and spun down at 500 xg to pellet. The cell pellet was resuspended in R10 + DNase I and counted. Cells were then rested at 2E6 cells/mL in R10 + DNAse I for 2 hours. After resting, cells were washed in cold Cell Staining Buffer (Biolegend) 2 times, filtered through a 70 um filter, and counted. 5E5 cells from each sample were incubated with Human TruStain FcX (Biolegend) at 4℃ for 10 min at the manufacturer's recommended concentration of 10E6 cells/mL. Then, each individual sample was incubated with a unique TotalSeq-A compatible Hashing Antibody (Biolegend) at 0.5 ug antibody at 11.8E6 cells/mL. Then, samples were incubated with the TotalSeq-A Universal cocktail (Biolegend #399907) according to manufacturer's instructions. Samples were washed 3X with Cell Staining Buffer and counted. Cells from each sample were then pooled, concentrated to 2000 cells/uL, and filtered through a 40 um FlowMi filter (Bel-Art).

tag: cell type

value: mononuclear cells

tag: individual id

value: tail, spleen, head

tag: run number


title: ZFP661-3HA OE mESCs (replicate 1), RAD21 ChIP

description: ChIP-seq

tag: cell line

value: R1 mESCs

value: mouse embryonic stem cells

tag: genotype

value: ZFP661-3HA OE

value: RAD21 (Abcam, ab992)


title: ZFP661-3HA OE mESCs (replicate 2), CTCF ChIP

description: ChIP-seq

value: CTCF (Millipore, 07-729)


title: PR-Y-004_PD_WTS

description: paired-end sequence reads

value: breast

value: female

value: breast cancer

value: PD


title: PR-Y-004_Baseline_WTS

description: paired-end sequence reads

value: Baseline


title: 20230217_hpap_8_Pool_Well7_RNA, RNA derived cDNA


title: ZFP661-3HA OE mESCs (replicate 1), ChIP Input

description: ChIP-seq

value: Input control


title: ZFP661-3HA OE mESCs (replicate 1), KAP1 ChIP

description: ChIP-seq

value: KAP1 (Abcam, ab22553)


title: sample 37 [1_2_3]

description:
1_2_3_TCGTAGTG-AGACTTGG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_soldier_whole brain

tag: caste

value: worker

tag: group

value: soldier

tag: colony location


title: PR-Y-003_PD_WTS

description: paired-end sequence reads

tag: gender


title: 20230217_hpap_8_Pool_Well6_RNA, RNA derived cDNA


title: sample 36 [12_4_2]

description:
12_4_2_GATTCTGC-GACGAGAG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas2_forager_whole brain

value: forager

tag: colony latitude

tag: colony longitude

value: whole brain


title: PR-Y-003_Baseline_WTS

description: paired-end sequence reads

tag: disease state

tag: time


title: sample 35 [12_2_2]

description:
12_2_2_AGCCTCAT-AGTAGAGA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas2_soldier_whole brain


title: 20230217_hpap_8_Pool_Well5_RNA, RNA derived cDNA

value: mononuclear cells

value: tail, spleen, head


title: sample 34 [11_4_4]

description:
11_4_4_CGTTAGAA-TTCAGGTC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_forager_whole brain


title: PR-Y-018_Baseline_WTS

description: paired-end sequence reads


title: sample 39 [2_2_3]

description:
2_2_3_TAAGTGGT-CTTAAGCC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas2_soldier_whole brain


title: PR-L-095_PD_WTS

description: paired-end sequence reads


title: sample 33 [11_2_2]

description:
11_2_2_TACCGAGG-CCTGAACT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_soldier_whole brain


title: 20230217_hpap_8_Pool_Well4_RNA, RNA derived cDNA


title: PR-L-095_Baseline_WTS

description: paired-end sequence reads


title: 20230217_hpap_8_Pool_Well3_RNA, RNA derived cDNA


title: ZFP661-3HA OE mESC (replicate 2), ChIP-reChIP, 2nd ChIP anti-CTCF

description: 1st ChIP anti-HA; 2nd ChIP anti-CTCF

data_processing:
The raw fastq reads from the 2nd ChIP (anti-CTCF and anti-IgG in two biological replicates) were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. The resulting clean reads were mapped onto the mouse genome (mm10) using BWA with default parameters, and only uniquely mapped reads (with tag X0:i:1) were retained for downstream analyses.
The top 1000 CTCF-only peaks (CTCF peaks that did not overlap with ZFP661 peaks), the top 1000 ZFP661&CTCF peaks (ZFP661 peaks that were co-occupied with CTCF peaks), and all ZFP661-only peaks (ZFP661 peaks that did not overlap with CTCF peaks) were used for following analysis. Uniquely mapped reads in the 1kb flanking regions of the ChIP summits of these peaks were extracted, and duplicated reads were removed using Samtools. The resulting reads from the two biological replicates were pooled together. DeepTools was used to generate the “CTCF - IgG” bigwig file (anti-CTCF signals subtracted by anti-IgG signals) with parameters “-normalizeUsing CPM --binSize 10 –extendReads” and excluding chrM and the regions on ENCODE blacklist (Amemiya et al. 2019).
Assembly: mm10
Supplementary files format and content: bigwig signal files (.bw).

source_name: R1 mESCs

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.4M glycine for 5 min.
ChIP-reChIP was performed on two biological replicates of ZFP661-3HA OE mESCs. For each replicate, 40M cells were used and divided into two ChIP assays for the 1st ChIP. In the 1st ChIP, 5 μg of anti-HA antibodies per ChIP were used by following the ChIP protocol until finishing the beads washing after IP. Then, the beads of two ChIP assays from the same biological replicate were pooled and resuspended in 50 μl of re-ChIP elution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2% SDS, and 15 mM DTT) with 1X fresh protease inhibitor cocktail (PIC) (Roche, 11836145001), and incubated 30 min at 37°C to elute chromatin and denature antibodies. The beads were then removed, and the chromatin supernatant was diluted to normal IP conditions by adding 950 μl of re-ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris–HCl pH 8.0, and 167 mM NaCl) with 1X fresh PIC. To remove any remnant anti-HA antibodies, chromatin was further precleared with 25 μl of Dynabeads Protein A by incubation for 2 hours, while 2.5 μg of anti-CTCF and anti-IgG antibodies were coupled onto 15 μl of Dynabeads Protein A, respectively. Then, chromatin from each biological replicate was divided into two parts (one for anti-CTCF and the other one for anti-IgG), and ChIP procedure of IP and beads washing after IP were performed for the 2nd ChIP. ChIP DNA was purified, and 10 μl of ChIP DNA was used as input to construct ChIP library using ThruPLEX DNA-Seq Kit (Takara, R400676).

value: R1 mESCs

value: mouse embryonic stem cells

tag: chip antibody


title: PR-L-085_PD_WTS

description: paired-end sequence reads

source_name: breast tissue of breast cancer patients


title: sample 32 [10_4_2]

description:
10_4_2_AATGCCTC-TCGATCCA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel2_forager_whole brain


title: ZFP661-3HA OE mESCs (replicate 1), CTCF ChIP

description: ChIP-seq

value: ZFP661-3HA OE


title: PR-L-085_Baseline_WTS

description: paired-end sequence reads


title: 20230217_hpap_8_Pool_Well1_RNA, RNA derived cDNA


title: 20230217_hpap_8_Pool_Well2_RNA, RNA derived cDNA


title: ZFP661-3HA OE mESC (replicate 2), ChIP-reChIP, 2nd ChIP anti-IgG

description: 1st ChIP anti-HA; 2nd ChIP anti-IgG

value: IgG (Invitrogen, 02-6102)


title: sample 31 [10_2_3]

description:
10_2_3_GGCATTCT-CTAGCTTG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel2_soldier_whole brain


title: ZFP661 3HA OE mESCs (replicate 1), ZFP661-3HA ChIP

description: ChIP-seq

value: HA (Abcam, ab9110)


title: ZFP661-3HA OE mESC (replicate 1), ChIP-reChIP, 2nd ChIP anti-CTCF

description: 1st ChIP anti-HA; 2nd ChIP anti-CTCF

value: CTCF (Millipore, 07-729)


title: ZFP661-3HA OE mESCs (replicate 1), H3K9me3 ChIP

description: ChIP-seq

value: H3K9me3 (Abcam, ab8898)


title: sample 30 [9_4_2]

description:
9_4_2_TTACAGGA-TGACAAGC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_forager_whole brain


title: PR-L-076_PD_WTS

description: paired-end sequence reads

value: breast

value: female

value: breast cancer

value: PD


title: PR-L-076_Baseline_WTS

description: paired-end sequence reads

value: Baseline


title: sample 28 [7_4_2]

description:
7_4_2_TCCAACGC-TTGGACTT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_forager_whole brain

value: worker

value: Comerio


title: E16.5 forebrain, Capture HiC, Zfp661 KO replicate 3

description: Arima-HiC followed by Capture

data_processing:
Mouse genome (mm10) fragments were generated using the “digest_genome” tool in HiC-Pro utilities with restriction motifs “GATC” and “G^ANTC”. Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. HiC-Pro pipelines (v2.11.4) were then used with above genome fragments and the parameter “LIGATION_SITE = GATCGATC, GANTGATC, GANTANTC, GATCANTC” to generate valid interaction pairs and contact maps.
Assembly: mm10
Supplementary files format and content: tab-delimited text files for valid interaction pairs (.allValidPairs.gz).

source_name: forebrain

extract_protocol:
Embryonic forebrains were dissociated into a single-cell suspension using the Papain Dissociation System (Worthington LK003150) by incubating 45 min at 37°C. Both the Cells from E16.5 forebrains and mESCs were crosslinked with 2% formaldehyde for 10 min and quenched using 0.4M glycine for 5 min.
Hi-C libraries were constructed using the Arima-HiC kit (Arima, A510008) according to the manufacturer’s protocol (Arima, A160134 v01). Probes were designed to cover the Pcdh locus and nearby genomic regions (mm10, chr18: 36,630,000-38,080,000) using the SureSelect DNA tool of Agilent SureDesign with the following settings: 2X tiling density, moderately stringent masking, and optimized performance for HS2/XT. The Capture Hi-C libraries were obtained by fast hybridization for 90 min with probes, followed by capture, washes and post-capture amplification using the SureSelect XT HS2 DNA Target Enrichment Kit (Agilent, G9987A) according to the protocol (Agilent, G9983-90000).

value: mouse embryonic brain

value: forebrain

tag: developmental stage

tag: strain

value: mixture of C57BL/6J and B6D2F1/J

value: Zfp661 KO


title: sample 29 [9_2_2]

description:
9_2_2_CCGTGAAG-CAGTGGAT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_soldier_whole brain

value: soldier

tag: tissue

value: whole brain


title: ZFP661-3HA OE mESC (replicate 1), ChIP-reChIP, 2nd ChIP anti-IgG

description: 1st ChIP anti-HA; 2nd ChIP anti-IgG

value: R1 mESCs

tag: cell type

value: mouse embryonic stem cells

value: IgG (Invitrogen, 02-6102)


title: IGF2BP3-RIP

source_name: Non-Small Cell Lung Cancer

value: Non-Small Cell Lung Cancer


title: PR-L-057_Baseline_WTS

description: paired-end sequence reads

value: breast


title: E16.5 forebrain, Capture HiC, Zfp661 KO replicate 2

description: Arima-HiC followed by Capture


title: PR-L-056_Baseline_WTS

description: paired-end sequence reads

value: female


title: sample 27 [7_2_2]

description:
7_2_2_CTTGGTAT-CCAAGTCC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_soldier_whole brain


title: E16.5 forebrain, Capture HiC, Zfp661 KO replicate 1

description: Arima-HiC followed by Capture


title: HaCaT cells, KO Clone 1, rep1

city: Nicosia

first: Katerina

last: Strati

state: Nicosia

address: 1 Panepistimiou Avenue - Aglantzia

department: Biological Sciences

country: Cyprus

institute: University of Cyprus

data_processing:
Trimmed for adapter sequences and poor quality bases using Trimmomatic v.0.36
Alignment using Bowtie2 v.2.2.6. against GRCh38
Hit counts for each sample calculated using featureCounts from the Subread package v.1.5.2.
Assembly: GRCh38
Supplementary files format and content: Raw count table, ENSEMBL transcript ID in column 1, sample read counts in columns 2-7 and Gene Symbol in column 8

source_name: Skin

extract_protocol:
Total RNA was isolated from the cells using RNeasy Maxi Kit (QIAGEN, 75162)
NEBNext Ultra II RNA Library Prep Kit for Illumina

value: Skin

value: HaCaT immortalized keratinocyte cell line from male adult human skin (CLS, 300493)

value: OCT4 knockout


title: sample 26 [6_4_2]

description:
6_4_2_GTCGGAGC-GGTTATAA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_forager_whole brain

value: worker

value: forager


title: HaCaT cells, KO Clone 1, rep2


title: E16.5 forebrain, Capture HiC, WT replicate 2

description: Arima-HiC followed by Capture

value: mouse embryonic brain

value: WT


title: IgG-RIP


title: PR-L-055_Baseline_WTS

description: paired-end sequence reads

value: breast cancer

value: Baseline


title: E16.5 forebrain, Capture HiC, WT replicate 1

description: Arima-HiC followed by Capture

value: forebrain

value: mixture of C57BL/6J and B6D2F1/J


title: sample 25 [6_2_2]

description:
6_2_2_ACTAAGAT-AACCGCGG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_soldier_whole brain

value: soldier

value: whole brain


title: E16.5 forebrain, Capture HiC, WT replicate 3

description: Arima-HiC followed by Capture


title: PR-L-046_Baseline_WTS

description: paired-end sequence reads


title: sample 24 [4_4_3]

description:
4_4_3_ATGAGGCC-GTTAATTG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_forager_whole brain


title: HC_B_cells_GEX

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

description: 10x Genomics

data_processing:
Sequences from scRNA-seq and scCITE-seq were processed using 10x Genomics Cellranger v 6.0.1 software (Zheng et al., 2017) with the cellranger GRCh38-2020-A genome and gtf file. Raw data generated by Cellranger were then read into R (v4.1.2) using the Seurat (Hao et al., 2021) v4.1.0 R package with at least 200 genes per cell and at least 3 cells. Cells were further filtered based on the number of genes per cell (between 500 and 4000), the number of ADT reads (less than 2000) and the percent of mitochondrial reads per cell (less than 10%). After filtering, 10737 were used for downstream analysis. The data were normalized by using 'NormalizeData'. For each sample, variable genes were found by using 'FindVariableFeatures' and data was scaled using 'ScaleData'. Doublets were removed using 'DoubletFinder' (McGinnis et al., 2019) using the default values except for pK, nExp, and PCs (pk = 0.14, nExp 32, PCs = 1:10). After doublet removal, 9910 cells were used for downstream analysis. CITE-seq antibodies were normalized using 'DSBNormalizeProtein' from the dsb package (v0.3.0) (Mule 2022)
Dimensionality reduction and clustering were performed using 'RunPCA', 'FindNeighbors', 'FindClusters', and 'RunUMAP'. 'RunPCA' was run using the default values except all variable features were used for the features argument. 'FindNeighbors' was run with default parameters except for the dims argument (dims=1:14). 'FindClusters' was run with default parameters except for the resolution argument (resolution=0.8). 'RunUMAP' was run with default parameters except for the dims and metric arguments (dims=1:14, metric=""correlation""), which were adjusted based on
We made a first pass at naming clusters using a bulk RNA high-quality dataset(Calderon et al., 2019) as a reference and determining cluster identity using 'clustifyr (Fu et al., 2020). To generate the reference, we downloaded the RNA_gene_abundance file from GEO GSE118165 and mapped the Ensembl IDs to gene IDs. We then used this matrix as in 'clustify' from 'clustifyr' as the 'ref_mat' argument. We used the top 2000 variable genes as the 'query_genes' and the clusters identified by 'FindClusters' as the 'cluster_col'. The top correlated cell type to each cluster was used as the first determination of cell type."
After naming cell types, we found a small number of T cells (195), Monocytes (23), and undetermined cells (27). We removed these cells and only kept cells identified as B cells (9665). Following subsetting, we repeated finding variable genes and scaling the data ('FindVariableFeatures' and 'ScaleData'). We repeated dimensionality reduction and clustering on the subset of cells. 'RunPCA' was run using the default values except all variable features were used for the features argument. 'FindNeighbors' was run with default parameters except for the dims argument (dims=1:14). 'FindClusters' was run with default parameters except for the resolution argument (resolution=0.6). 'RunUMAP' was run with default parameters except for the dims and metric arguments (dims=1:14, metric=""correlation""). To identify markers of each cluster, 'FindAllMarkers' was run using default settings except we set only.pos to TRUE. Genes were called differentially expressed if the adjusted p-value was less than 0.05 and the log fold change was greater than 0.5. To generate a heatmap of markers, the average expression of all genes within each cluster was determined using 'AverageExpression' from Seurat. Next, the top 10 markers based on log fold change were selected for each cluster and the average expression matrix was subset to only those genes. Finally, a z-score was computed, and the plot was generated with 'pheatmap' (https://cran.r-project.org/web/packages/pheatmap/index.html).
To locate the clustering that contained the BND2 cells, we used our ClTE-seq antibodies to locate cells that were lgD positive (the top 50% of lgD expression), lgM low (the bottom 95% of lgM expression) and CD21 negative (bottom 10% of cells). Many of the cells matching these cutoffs were in cluster 6 (10% of total cells in the cluster). To gain better resolution of thiscluster, we subset the data to only cluster 6 and reprocessed. Following subsetting, we repeated finding variable genes and scaling the data ('FindVariableFeatures' and 'scaleData'). We repeated dimensionality reduction and clustering on the subset of cells. 'RunPCA' was run using the default values except all variable features were used for the features argument. 'FindNeighbors' was run with default parameters except for the dims argument (dims=1:7). 'FindClusters' was run with default parameters except for the resolution argument (resolution=0.4). 'RunUMAP' was run with default parameters except for the dims and metric arguments (dims=1:7, metric=""correlation""). Three clusters were identified by this analysis (early memory, BND2, and DN2). We added these three clusters to the full dataset in place of cluster 6.
To compare the DN2 and BND2 populations we also used the 'FindMarkers' function from Seurat and kept genes with an adjusted p-value less than 0.05. To compare BND1 to BND2 cells, BND2 cells were found as described above (IgD positive, lgM low, and CD21 negative). BND1 cells were similarly identified but were lgD positive, lgMlo, and CD21 positive (top 25% of cells). We performed differential expression between these two populations using the 'FindMarkers' function from Seurat and kept genes with an adjusted p-value less than 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMCs

extract_protocol:
B cells from fresh PBMCs were isolated using the Miltenyi No Touch B cell Enrichment Kit.   Cells   were   then   divided   in   half,   one   for   scRNA-sequencing   and   one   for   flow verification/comparison.   Samples   for   scRNA-seq   were   stained   with   Total-Seq   antibodies (Biolegend) at 1ug/ 106 cells for the following surface markers: lgD, lgM, CD27, CXCR5, and CD21 for 20 minutes on ice, washed twice with FACS buffer, and then resuspended in 1X PBS. Cells were then prepared for scRNA-seq using the 10X Genomics platform per manufacturer's instructions  (see  below).  For  the  flow  cytometry  parallel  samples,  B  cells  were  stained  with antibodies  of  the  same  clone  as  Total-Seq  antibodies  using  the  following  panel:  anti-CD27-BUV563,  anti-CD19-BV510,  anti-lgM-BV650,  anti-lgD-FlTC,  anti-CXCR5-PE/Dazzle594,  and anti-CD21-PE/Cy7 (all Biolegend) for 15 minutes on ice, washed twice with FACS buffer, and then fixed in 2% PFA in preparation for flow cytometry.
A single cell suspension of B cells previously stained with Total-Seq antibodies was prepared at 1000 cells/ul for a capture of 10,000 cells on the Chromium Next GEM Chip G for 5' capture gel beads. Following single cell capture and GEM-RT Cleanup, as described in the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 User Guide Rev F, a cDNA amplification reaction was prepared  with  the  addition  of  an  appropriate  primer  to  amplify  the  Total-Seq  antibody  oligo (feature  barcode)  sequences  in  addition  to  captured  mRNA.  After  cDNA  amplification,  the supernatant  from  the  0.6X  SPRIselect  size  selection  was  saved  and  used  downstream  for analysis of the feature barcodes contained in that smaller size fraction. The 5' Gene Expression (GEX) Library Construction was done as described in the previously mentioned User Guide for the  mRNA  GEX  Library.  For  the  Feature  Barcode  (ADT)  Library  preparation,  the  CITE-seq protocol from the New York Genome Center Technology Innovation  Lab Version: 2019-02-13 was  followed  using  the  retained  supernatant  from  the  cDNA  cleanup.  Unique  indexes  were added to the 3' and 5' ends of the ADT library molecules with 2X PCR NEB High Fidelity with Q5 Polymerase Master Mix for downstream demultiplexing and data analysis.

value: B cells

value: PBMCs

value: Non-diabetic control

tag: age

value: Adult


title: HaCaT cells, Control, rep2

value: Skin


title: PR-L-037_Baseline_WTS

description: paired-end sequence reads

value: breast

value: female


title: HaCaT cells, KO Clone 4, rep1

value: HaCaT immortalized keratinocyte cell line from male adult human skin (CLS, 300493)

value: OCT4 knockout


title: HaCaT cells, KO Clone 4, rep2


title: sample 21 [2_2_2]

description:
2_2_2_GGTACCTT-AAGACGTC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

data_processing:
fastq files were aligned to the honey bee genome (vHAv3.1) with STAR v2.7.3a
count files were generated using the "featureCounts" function in Subread v2.0.0
NOTE: Samples 1-96 are READ 1 ALIGNS TO ANTISENSE STRAND while 97-177 are READ 1 ALIGNS TO SENSE STRAND. This is just how the adaptors are made for such a big experiment. Because featureCounts requires strand orientation, I have noted on each counts file whether the "forward" and "reverse" command was used (prefix "f_" or "r_", respectively). If you realign and forget to do this, you will find that you get an excellent alignment to the genome but very few reads will be called as genes. This is totally artificial, so make sure you are sensitive to read orientation OR use a method that doesn't require strandedness information (e.g. Salmon).
Genome_build: HAv3.1
Supplementary_files_format_and_content: featureCounts output files

source_name: Salinas2_soldier_whole brain

value: worker


title: Capture_HiC, ZFP661OE replicate 2, library 2

description: Arima-HiC followed by Capture

value: R1 mESCs

value: mouse embryonic stem cells

value: mixture of 129S1/SvImJ and 129X1/SvJ

value: ZFP661-3HA OE


title: HaCaT cells, Control, rep1

value: WT


title: sample 22 [2_4_2]

description:
2_4_2_AACGTTCC-GGAGTACT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas2_forager_whole brain

value: forager


title: PR-L-036_Baseline_WTS

description: paired-end sequence reads

value: breast cancer

value: Baseline


title: PR-L-035_Baseline_WTS

description: paired-end sequence reads


title: Capture_HiC, ZFP661OE replicate 2, library 1

description: Arima-HiC followed by Capture

source_name: R1 mESCs


title: PR-L-033_Baseline_WTS

description: paired-end sequence reads

source_name: breast tissue of breast cancer patients


title: HC_B_cells_ADT

description: 10x Genomics

value: B cells

value: PBMCs


title: PR-L-027_Baseline_WTS

description: paired-end sequence reads


title: Capture_HiC, EV control replicate 2, library 2

description: Arima-HiC followed by Capture

value: EV control


title: Capture_HiC, ZFP661OE replicate 1, library 2

description: Arima-HiC followed by Capture


title: sample 20 [1_4_2]

description:
1_4_2_GCACGGAC-GTCTCGCA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_forager_whole brain

value: whole brain


title: PR-L-027_PD_WTS

description: paired-end sequence reads

value: breast

value: PD


title: iPSC-derived hepatocytes in mono-culture (24h) [C_7]

city: San Francisco

first: Marko

last: Groeger

state: CA

address: 35 Medical Center Way

institute: University of California San Francisco

data_processing:
Homo sapiens fastq files were aligned to Homo sapiens.GRCh38.96 using STAR_2.7.2b.
Read counts per gene were used as input to DESeq2 .
Assembly: Homo sapiens.GRCh38.96
Supplementary files format and content: counts.STAR.HUMAN.txt - Counting number of reads per gene

growth_protocol: Undifferentiated iPSCs were cultured in mTeSR1 in 6-well plates coated with Cultrex Reduced Growth Factor Basement Membrane Extract (RGF-BME) at 1:30 dilution in Knockout DMEM at 37°C in 5% CO2 and 5% O2.

extract_protocol:
PureLink RNA Mini Kit (Invitrogen)
RNAseq was performed at Novogene. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra TM RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5x). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150-200 bp in length, the library fragments were purified with AMPure XP system. Then 3 µl USER Enzyme was used with size-selected, adaptor-ligated cDNA at 37°C for 15 minutes followed by 5 minutes at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Finally, PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 2100 system.

treatment_protocol: Differentiation was performed at 37°C in 5% CO2 and 5% O2 unless stated otherwise. iPSCs were differentiated into iPSC-Heps using a refined version of a protocol previously published by Si-Tayeb et al. At 70 to 80% confluency, colonies of iPSCs were detached using Accutase and 100,000 cells/cm² diluted in mTeSR1 including 10 mM Y-27632 were seeded in RGF-BME-coated 6-well plates. After 24 hours, medium was changed to endoderm-induction medium (EIM), consisting of RPMI 1640 containing 2% Gem21 without insulin, 1% Glutamax, 1% non-essential amino acids solution (NEAA), 0.5 mM sodium butyrate and 100 ng/ml activin A, for 7 days in 20% O2. The following compounds were added to EIM during the first 3 days: 3 mM CHIR on day 1, 20 ng/ml basic fibroblast growth factor (FGFb) and 10 ng/ml bone morphogenetic protein 4 (BMP4) on days 1 and 2, 50 nM PI103 on days 1 to 3, knockout serum replacement (KSR) at 2% on day 1, 1% on day 2 and 0.2% on day 3. On days 8 to 17, cells were cultured in hepatic induction medium (HIM), consisting of IMDM containing 1% Glutamax, 1% NEAA, 100 nM dexamethasone, 100 nM insulin and 0.5 mM 1-thioglycerol. The following compounds were added to HIM between days 8 and 17: 10 ng/ml FGFb and 20 ng/ml BMP4 between days 8 to 17, 20 ng/ml hepatocyte growth factor (HGF) between days 12 to 17. On day 10, cells were detached using 0.25% trypsin-EDTA and split 1:2 into RGF-BME-coated 12 or 24-well plates. On days 18 to 22, cells were cultured in Hepatocyte Culture Medium BulletKit (HCM) without epidermal growth factor, including 20 ng/ml oncostatin M and 20 ng/ml HGF in 20% O2. After day 22 (end of differentiation), iPSC-Heps were used within 7 days for experiments. Medium was changed daily during differentiation and maintenance. iPSC-derived macrophages for co-culture were differentiated using a protocol by Matsuo et al. 2021.

value: skin

value: induced pluripotent stem cells

tag: treatment

value: hepatocyte differentiation

tag: biomaterial provider


title: iPSC-derived hepatocytes in mono-culture (24h) [C_12]

tag: cell line

tag: genotype


title: iPSC-derived hepatocytes in mono-culture (24h) [C_11]


title: sample 19 [1_2_2]

description:
1_2_2_ATGTAAGT-ACTCTATG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_soldier_whole brain

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen) and assessed on a Nanodrop, Qubit, and Bioanalyzer
The libraries were quantitated by qPCR and sequenced on one lane for 151 cycles from each end of the fragments on a NovaSeq 6000  using a NovaSeq S4 reagent kit. Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used portion in bold font for adaptor trimming). Adaptor sequence in read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNNNN= 8 nt index). Adaptor sequence in read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTNNNNNNNNAGATCTCGGTGGTCGCCGTATCAT.

tag: caste

value: worker

tag: group

value: soldier


title: sample 23 [4_2_4]

description:
4_2_4_GCAGAATT-ACCGGCCA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_soldier_whole brain

tag: colony location


title: PR-L-024_PD_WTS

description: paired-end sequence reads

tag: gender

value: female


title: iPSC-derived hepatocytes co-cultured with M0 iPSC-derived macrophages (24h) [M0_7]

value: hepatocyte differentiation and susequent co-culture


title: PR-L-017_Baseline_WTS

description: paired-end sequence reads


title: sample 18 [12_4_1]

description:
12_4_1_CGGCGTGA-GCGCCTGT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas2_forager_whole brain

tag: colony latitude

tag: colony longitude


title: iPSC-derived hepatocytes co-cultured with M0 iPSC-derived macrophages (24h) [M0_12]

value: WT


title: Capture_HiC, EV control replicate 1, library 1

description: Arima-HiC followed by Capture

value: R1 mESCs

value: mouse embryonic stem cells

value: mixture of 129S1/SvImJ and 129X1/SvJ


title: Capture_HiC, EV control replicate 2, library 1

description: Arima-HiC followed by Capture


title: Capture_HiC, EV control replicate 1, library 2

description: Arima-HiC followed by Capture


title: sample 15 [11_2_1]

description:
11_2_1_GGCTTAAG-TCGTGACC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_soldier_whole brain


title: sample 14 [10_4_1]

description:
10_4_1_TTGGACTC-GGAAGCAG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel2_forager_whole brain

value: forager


title: Capture_HiC, ZFP661OE replicate 1, library 1

description: Arima-HiC followed by Capture

value: ZFP661-3HA OE


title: iPSC-derived hepatocytes co-cultured with M0 iPSC-derived macrophages (24h) [M0_11]


title: PR-L-011_PD_WTS

description: paired-end sequence reads

tag: disease state

value: breast cancer

tag: time


title: K49A-24 dot dot_2-cell

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

description:
Smart-seq2
Sample_5056-LM-48

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011).
Alignment options followed ENCODE standards for RNA-seq (Dobin).
Assembly: mm10
Supplementary files format and content: Tab-delimited gene expression matrix

source_name: embryo

extract_protocol:
Two-cell embryos were collected between 26 and 28 hours post fertilization. Each embryo was immediately placed into a single well of a plexWell Rapid Single Cell plate (SmartSeq Platform), which was then frozen until sample prep.
Libraries were generated from 2 cell embryos using Smart Seq2 platform.
Single-embryo RNA sequencing using NovaSeq 6000 Illumina platform

value: embryo

value: 26 - 28 hours post fertilization


title: sample 17 [12_2_1]

description:
12_2_1_TAATACAG-ATATTCAC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas2_soldier_whole brain

value: whole brain


title: iPSC-derived hepatocytes co-cultured with M1 iPSC-derived macrophages (24h) [M1_12]

value: skin


title: PR-L-011_Baseline_WTS

description: paired-end sequence reads

value: breast

value: Baseline


title: K49A-12_2-cell

description:
Smart-seq2
Sample_5056-LM-46


title: iPSC-derived hepatocytes co-cultured with M1 iPSC-derived macrophages (24h) [M1_11]

value: induced pluripotent stem cells


title: sample 12 [9_4_1]

description:
9_4_1_CTCTCGTC-TATAACCT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_forager_whole brain

value: worker


title: PR-L-008_PD_WTS

description: paired-end sequence reads

value: female

value: PD


title: K49A-6_2-cell

description:
Smart-seq2
Sample_5056-LM-45


title: PR-L-017_PD_WTS

description: paired-end sequence reads


title: sample 16 [11_4_1]

description:
11_4_1_AATCCGGA-CTACAGTT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_forager_whole brain


title: sample 10 [7_4_1]

description:
7_4_1_GACCTGAA-TTGGTGAG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_forager_whole brain

value: Comerio


title: PR-L-008_Baseline_WTS

description: paired-end sequence reads


title: GBM_GSK715_D32(EXP7)

city: Hull

first: Pedro

last: Beltran-Alvarez

address: University of Hull, Cottingham Road

department: HYMS Centre for Biomedicine

country: United Kingdom

institute: University of Hull

data_processing:
HISAT2 algorithm was used for read alignment and FPKM was used to normalise gene expression61.
Differential gene expression was determined from read counts using the DESeq2 R package62.
Gene expression change in either treated tissues on-chip, compared to 1uM GSK3368715-treated tissues on-chip, respectively, was log2 transformed, and the calculated p-values were adjusted using the Benjamini-Hochberg correction for false discovery rate (padj).
Genes significantly (padj ≤ 0.05) up- or down-regulated at least 1.5- fold (log2 fold change FC = ± 0.585) with a gene symbol/ID annotation were used in subsequent analysis.
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: gene_count.xls=gene_id, sample readconts, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, tf_family
Supplementary files format and content: gene_fkpm.xls=gene_id, sample readconts, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, tf_family
Supplementary files format and content: gene_fkpm_group.xls=gene_id, sample readconts, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, tf_family
Supplementary files format and content: EXP4vsCTRL4_deg.xls=gene_id, normalised readcounts of sample and group, log2foldchange, pvalue, padj, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_descripton, tf_family, sampleID_count, sampleID_fpkm
Supplementary files format and content: EXP5vsCTRL5_deg.xls=gene_id, normalised readcounts of sample and group, log2foldchange, pvalue, padj, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_descripton, tf_family, sampleID_count, sampleID_fpkm
Supplementary files format and content: EXP6vsCTRL6_deg.xls=gene_id, normalised readcounts of sample and group, log2foldchange, pvalue, padj, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_descripton, tf_family, sampleID_count, sampleID_fpkm
Supplementary files format and content: EXP7vsCTRL7_deg.xls=gene_id, normalised readcounts of sample and group, log2foldchange, pvalue, padj, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_descripton, tf_family, sampleID_count, sampleID_fpkm

source_name: Glioblastoma

extract_protocol:
GBM samples were pooled so that there were 2-3 chips (~40-60mg) of GBM tissue, per treatment condition, per each of the 4 patients for RNA extraction. TRIzol™ (ThermoFisherScientific) was added to the tissue biopsies and samples were homogenised using a douncer. Chloroform was added 1:5 to the lysate, tubes inverted gently for 15 seconds and then incubated for 3 minutes on ice. Samples were centrifuged at 12,000 x g for 15 minutes at 4°C. Isopropanol was added 1:2 to the upper, colourless, aqueous phase and samples were incubated overnight at -80°C before centrifuging at 12,000 x g for 10 minutes at 4°C. The RNA pellet was washed twice in 75% ethanol before centrifuging for 5 minutes, at 7500 x g at 4°C and the supernatant discarded each time. The RNA pellet was air dried before resuspending in RNase-free water through incubation at 55°C. Total RNA was then analysed to yield the transcriptomic profile of the tissues in the two different conditions (DMSO control and 1uM GSK3368715 treated.)
Library preparation and RNA sequencing were done by Novogene Co. Ltd. (Cambridge, UK) using the Illumina NovaSeq 6000 platform at a depth of 34-60 million reads

treatment_protocol: Four glioblastoma patient samples were microdissected into ~20mg pieces and put 'on-chip' into a microfluidics device, within an hour of resection. Samples were left on-chip for 8 days, at a flow rate of 3ul/min, with a media change at day 4. Samples were treated with 1 uM GSK3368715, or DMSO control via the media supplying the microfluidics system. At the end of the 8 days, tissues were removed from the chips, snap frozen in liquid nitrogen and stored at -80°C until a time when RNA could be extracted.

value: Glioblastoma

value: 1uM GSK3368715 8 days post-chip


title: sample 11 [9_2_1]

description:
9_2_1_TCTCTACT-CGCGGTTC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_soldier_whole brain

value: soldier


title: WT-18_2-cell

description:
Smart-seq2
Sample_5056-LM-43


title: GBM_GSK715_D32(EXP6)


title: PR-L-016_Baseline_WTS

description: paired-end sequence reads


title: PR-F-009_PD_WTS

description: paired-end sequence reads


title: WT-12_2-cell

description:
Smart-seq2
Sample_5056-LM-42


title: sample 8 [6_4_1]

description:
6_4_1_TGGATCGA-GTGCGATA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_forager_whole brain

value: forager


title: sample 9 [7_2_1]

description:
7_2_1_AGTTCAGG-CCAACAGA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_soldier_whole brain


title: PR-F-008_Baseline_WTS

description: paired-end sequence reads


title: PR-F-002_PD_WTS

description: paired-end sequence reads


title: GBM_CTRL_D32(CTRL7)

value: DMSO 8 days post-chip


title: iPSC-derived hepatocytes co-cultured with M1 iPSC-derived macrophages (24h) [M1_7]

value: WT

value: hepatocyte differentiation and susequent co-culture


title: K49A-18_2-cell

description:
Smart-seq2
Sample_5056-LM-47

value: embryo

value: 26 - 28 hours post fertilization


title: sample 13 [10_2_1]

description:
10_2_1_CCAAGTCT-AAGGATGA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel2_soldier_whole brain

value: whole brain


title: WT-6_2-cell

description:
Smart-seq2
Sample_5056-LM-41


title: PR-F-002_Baseline_WTS

description: paired-end sequence reads

source_name: breast tissue of breast cancer patients

value: breast

value: breast cancer


title: GBM_CTRL_D32(CTRL6)


title: GBM_GSK715_D32(EXP5)


title: WT-24_2-cell

description:
Smart-seq2
Sample_5056-LM-44


title: GBM_CTRL_D32(CTRL5)


title: sample 7 [6_2_1]

description:
6_2_1_CAAGCTAG-ACATAGCG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_soldier_whole brain


title: PR-F-001_Baseline_WTS

description: paired-end sequence reads

value: Baseline


title: sample 6 [4_4_2]

description:
4_4_2_GCTTGTCA-GAACATAC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_forager_whole brain

value: worker


title: K49A-17_2-cell

description:
Smart-seq2
Sample_5056-LM-39


title: sample 5 [4_2_1]

description:
4_2_1_ATCCACTG-AGGTGCGT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_soldier_whole brain


title: GBM_GSK715_D31(EXP4)


title: BRO7F-093_PD_WTS

description: paired-end sequence reads

value: female


title: BRO7F-093_Baseline_WTS

description: paired-end sequence reads


title: sample 4 [2_4_1]

description:
2_4_1_AAGTCCAA-TATGAGTA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas2_forager_whole brain


title: sample 3 [2_2_1]

description:
2_2_1_GGACTTGG-CGCAGACG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas2_soldier_whole brain


title: BRO7F-091_Baseline_WTS

description: paired-end sequence reads


title: WT-23_2-cell

description:
Smart-seq2
Sample_5056-LM-36


title: GBM_CTRL_D31(CTRL4)


title: control mito-monosome longer fragments

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

data_processing:
Reads where trimmed from adapter sequence using cutadapt (version: 3.5; options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30) and quality filtered using fastx_toolkit (version: 0.0.14; options: -Q33 -q 24 -p 90)
UMIs were extracted from each read with UMItools (options: extract --extract-method string --bc-pattern NNNNNNNNCCCCC --3prime --filter-cell-barcode –error-correct-cell).
Reads where size-selected for single ribosome using two sizes: 26 to 35 (usual monosome fragments) and 35 to 50 for longer read monosome samples. To estimate rRNA and tRNA contamination, reads were mapped to human and human cytosolic rRNA and tRNA databases using bowtie2 (options: -p 2 -L 15 -k 20 --trim5 2). Reads that failed to map to these, where then mapped to the mitochondrial genome (Ensembl database v. 107).
Assembly: Ensembl genome v107
Supplementary files format and content: BigWig (.bw): mitochondrial genome coverage files separated in plus and minus strand mapping reads
Library strategy: Ribo-seq

source_name: HEK293 EBNA

growth_protocol: HEK293 EBNA cells were grown as suspension culture in serum-free EX-CELL 293 medium (Sigma-Aldrich) at 37° C and 4.5% CO2. For transfection, 1.2 x 109 cells were pelleted at 500 x g for 5 min and resuspended in 60 ml RPMI 1640 medium (Gibco) supplemented with 0.6 ml 10% Pluronic F-68. Next, 1.8 mg plasmid DNA and 3.6 mg PEI Max 40kDa (Polysciences) were added to the cells. After 1h incubation in the shaker the cells were diluted to 1.2 l with EX-CELL 293 medium. The cells were incubated for two days before being harvested by centrifugation at 1,000 x g for 10 min at 4° C. Control cells were not transfected.

extract_protocol:
For ribosome profiling of isolated mitochondria, freshly harvested cells were rinsed with ice-cold 1X PBS pH 7.4. All steps were performed at 4° C or on ice roughly following previously published methods (Aibara et al. 2018; Clayton and Shadel 2014). Cells were resuspended in a hypotonic buffer (10 mM HEPES KOH pH 7.5, 10 mM NaCl, and 1.5 mM MgCl2) left to swell for 10 min and lysed using glass dounce homogenizer. Cell lysate was mixed with 1 volume of 2x MS homogenization buffer (20 mM HEPES KOH pH 7.5, 420 mM mannitol, 140 mM sucrose, 2 mM EDTA), cleared by centrifugation at 1,300 x g for 5 min, with supernatant cleared again at 3,000 x g for 5 min. Mitochondria were pelleted by centrifugation at 9,500 x g for 20 min, resuspended in resuspension buffer (20 mM HEPES KOH pH 7.5, 250 mM sucrose, 1 mM EDTA). Sucrose step gradients were prepared in SW32.1 tubes by layering different concentration of sucrose in gradient buffer (20 mM HEPES KOH pH 7.5, 1 mM EDTA): 1.5 ml 60% (w/v) sucrose on the bottom, 4.5 ml 32% (w/v) sucrose in the middle and 3 ml 23% (w/v) on top. The mitochondria suspension was loaded onto the sucrose step gradients and centrifuged using a SW32.1 rotor (Beckman-Coulter) at 22,000 x g for 70 min. Mitochondria were harvested from the interface between the 32- and 60% sucrose layer and flash-frozen in liquid N2. Mitochondria were lysed in 5 volumes of polysome buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, 100 µg/ ml cycloheximide, complete EDTA-free protease inhibitors (Roche) and 40 U/ml RNasin plus (Promega)) supplemented with 1% Triton X-100 and 0.5% Sodium deoxycholate. Lysates were incubated on ice for 10 min and cleared by centrifugation at 10000g, 4° C for 10 min.
Ribosome footpritnting and library construction was performed as described earlier (Arpat et al. 2020, McGlisny and Ingolia 2017) with few modifications. Libraries were generated from 24-36 nt (monosome footprints) and 36-69 nt (extended range that includes disome footprints) without ribosomal RNA depletion.

value: HEK293 EBNA


title: sample 1 [1_2_1]

description:
1_2_1_CCGCGGTT-AGCGCTAG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_soldier_whole brain


title: Pulled-down_mtRF1-AAQ_RP

value: untreated


title: BRO7F-088_Baseline_WTS

description: paired-end sequence reads


title: sample 2 [1_4_1]

description:
1_4_1_TTATAACC-GATATCGA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_forager_whole brain


title: WT-17_2-cell

description:
Smart-seq2
Sample_5056-LM-35

source_name: embryo


title: K49A-23 dot_2-cell

description:
Smart-seq2
Sample_5056-LM-40


title: BRO7F-087_Baseline_WTS

description: paired-end sequence reads


title: mtRF1-AAQ mito-monosomes longer fragments

value: Overexpressed mtRF1-AAQ


title: control mito-monosomes