title: organ donor Right ear, replicate 1, scRNAseq

description: 10x Genomics

value: utricle (inner ear)

tag: individual

value: Organ Donor #5

value: female

tag: inner ear_analyzed

value: R

value: N


title: R ChIP, ATMi NAC, rep2

status: Public on Mar 01 2024

type: SRA

city: Austin

first: Tanya

middle: T.

last: Paull

state: TX

address: 2500 Speedway MBB 2.448

department: Molecular Biosciences

country: USA

institute: Univ. of Texas at Austin

library_source: genomic

data_processing:
Sequencing reads were cleaned using FASTP in paired end mode and mapped to the genome using STAR aligner and GRCh38 (hg38). Aligned reads were converted to bedgraph format via MACS2 (61). Output bedgraph files were processed again using MACS2’s bdgcmp command with the ppois flag to approximately remove the ChIP input influence from the ChIP bedgraph files. Finally, bedgraph output was read depth normalized to make files equivalent in total signal.
Sequencing reads were cleaned using FASTP in paired end mode, transcript abundance levels were determined using Salmon pseudoaligner and GRCh38 (hg38), and differentially abundant transcripts were quantified using Swish in the Gene mode. Statistically significant differences between density plots were determined using empirical cumulative distribution function tests via DTS R package with 5000 bootstraps. GSEA information was computed via the Fast Gene Set Enrichment Analysis (FGSEA) R package.
Assembly: HG38
Supplementary files format and content: bigwig, input adjusted and read depth normalized
Supplementary files format and content: text file showing read counts

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
PAR ChIP: The protocol was adapted from (16). Briefly, SH-SY5Y cells were differentiated as described above and two 15 cm dishes were used for each ChIP replicate (approximately 20M cells). Cells were removed from dishes using trypsin and then resuspended in media in a volume of 36 ml. Formaldehyde (37%, Sigma F1635) was added to 1% final concentration and incubated at 37°C for 7 min. with occasional inversion of the tube. 2.5M glycine was added to a final concentration of 0.125M. The tube was inverted several times and cells recovered by centrifugation at 550xg for 5 min. at 4°C. The pellet was washed twice with 10 ml cold PBS using 550xg centrifugation for 5 min. each time. The pellets were snap frozen using liquid nitrogen and stored at -80°C for later use. Each cell pellet was resuspended in 1mL cold PAR ChIP RIPA buffer (10 mM Tris-HCl, pH7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) containing protease inhibitor (Fisher, A32955). Samples were sonicated using a Diagenode Bioruptor UCD-200 instrument on high power with 15 sec on/ 15 sec off cycles for 45 min. at 4°C. Under these conditions, fragmented chromatin was 200 to 500 bp. Samples were centrifuged at 20,000xg for 10 minutes at 4°C. The supernatant was transferred to another tube; 50 μl were reserved as input DNA. 40 μl of Protein A/G magnetic beads was incubated with 5 μg anti-pan-ADP-ribose binding reagent (Millipore Sigma, MABE1016) per IP sample in 100 μl PBS for 30 min. then washed with 200μl PBS twice. The beads were then added to the supernatant and incubated at 4°C overnight. The following day, beads were washes for 10 min. at 4°C with the following sequence of buffers: 2x with 1 mL of RIPA buffer, 2x with 1 mL of RIPA buffer + 0.3M NaCl, 1x with 1 mL of TE pH 8 + 0.2% Triton X-100, 1x with 1 mL of TE pH 8. The beads were resuspended in 100μl TE; 3μl 10% SDS and 5μl 20 mg/ml proteinase K were added and the samples incubated at 65°C for 4 hrs while rocking. The tubes were vortexed every 30 to 50 min. The DNA was removed from beads using a magnetic stand; 100μl TE + 0.5M NaCl was added to the beads and then removed and combined with the first sample. 200 μl phenol/chloroform/isoamyl alcohol was added and samples were added to Phase Lock gel columns (VWR, 10847-802) and processed according to manufacturer instructions. Samples were then ethanol precipitated by adding 2μl glycogen (20 mg/ml), 20μl 3M NaOAc pH 5.2, and 500 μl cold ethanol (100%). After incubation on dry ice for 15 min., samples were centrifuged at 20,000xg for 15 min. at 4°C. Pellets were washed with 70% ethanol twice; the supernatant was removed and pellets dried at room temp. Pellets were resuspended in 22 μl 10 mM Tris-HCl pH 8.0, vortexed, and stored at -20°C.  R-ChIP  The protocol was adapted from (24). Briefly, SH-SY5Y cells were differentiated as described above and two 15 cm dishes were used for each ChIP replicate (approximately 20M cells). Cells were crosslinked in the dishes with the addition of formaldehyde to 1% final concentration and incubated for 7 min. while shaking (120 RPM). 2.5M glycine was added to a final concentration of 0.125M. Cells were removed by scraping and transferred to conical tubes with an additional 5 ml PBS to wash the dishes. Cells were centrifuged at 2187xg for 15 min. at 4°C, then washed with cold PBS and pelleted again. The pellets were snap frozen using liquid nitrogen and stored at -80°C for later use. Each cell pellet was resuspended in 2.3 mL cold R-ChIP RIPA buffer (50 mM Tris-HCl, pH 8.0, 0.15M NaCl, 2 mM EDTA, 0.1% SDS, 0.5% sodium deoxycholate, 0.1% Igepal CA-630 (NP40) containing protease inhibitor (Fisher, A32955) and incubated on ice for 10 min. Samples were sonicated using a Diagenode Bioruptor UCD-200 instrument on high power with 15 sec on/ 15 sec off cycles for 45 min. at 4°C. Samples were centrifuged at 3,889xg for 10 minutes at 4°C. The supernatant was transferred to another tube; 50 μl were reserved as input DNA. 25 μl of Protein A/G magnetic beads per IP sample were washed with 1 ml wash buffer (20 mM Tris-HCl pH 8.0, 0.15M NaCl, 2 mM EDTA, 1% Triton X-100) using a magnetic separator; this step was repeated for a total of 3 washes. Beads were resuspended in bead blocking buffer (0.2 μg/ml BSA, 0.2 mg/ml glycogen in PBS) and incubated for 1 hr at RT. Beads were then washed 3 times with antibody binding buffer (5 μg/ml BSA in PBS), resuspended in 250 μl antibody binding buffer and 2.5 μg FLAG M2 antibody (Sigma) per 25 μl of Protein A/G magnetic beads and incubated overnight at 4°C with rotation. After removal of unbound antibody, beads were resuspended in 1 ml sonicated lysate and incubated overnight at 4°C with rotation. The following day, beads were washed 3 times for 3 min. at room temperature with 1 ml wash buffer I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) containing protease inhibitor, then 3 times with wash buffer II (wash buffer I containing 0.5M NaCl), then once with wash buffer III (20 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP40, 0.25M LiCl), then once with TE. Samples were moved to a new tube and eluted with 100 μl elution buffer (0.1 M sodium bicarbonate, 1% SDS) at 30 °C for 30 min. Beads were removed, 1 μl RNase A (20 mg/ml) was added to each sample and supernatants were decrosslinked at 65°C for 22 hrs. 1 μl Proteinase K (20 mg/ml) was added to each sample and incubated for an additional 2 hrs at 65°C. Samples were purified using the nucleotide removal kit (Qiagen) according to manufacturer instructions.
RNA extraction from SH-SY5Y cells: Total RNA extraction was performed using NEB Monarch Total RNA Miniprep Kit (New England Biolabs Cat #T2010S). RNAseq library prep was performed using NEBNext Ultra II RNA Library Prep for Illumina (NEB Cat# E7770S). The NEB protocol was followed using the Poly(A) mRNA Magnetic Isolation Module and SPRIselect beads (Beckman Coulter Cat #B23317). Library adapter was diluted 5-fold. The additional SPRIselect cleanup step referred to at 1.11.3 in the NEB protocol was followed.RNA extraction from patient tissues: Fresh-frozen A-T patient and control tissues were obtained from the NIH Neurobiobank (Table S1). 50mg patient tissue RNA was extracted in an RNase free environment using RNA Extraction kit for Bioruptor Plus (Diagenode Cat# C20000010). The additional protocol listed for DNaseI treatment was followed for 10ug of extracted RNA per sample. DNaseI treated RNA was cleaned using RNeasy Mini Kit (Qiagen Cat# 74104).
ChIP library preparation and sequencing  For PAR and R-ChIP, the eluted DNA (2 biological replicates per condition) as well as input samples were used to make sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) with NEBNext Multiplex dual index primers using 12 amplification cycles and 2 additional AMPure XP clean-up steps at 0.8X. Libraries were sequenced by the UT Genomic Sequencing and Analysis Facility (RRID:SCR_021713) using the Illumina NovaSeq SP platform with PE150 runs.
RNAseq library prep was performed using NEBNext Ultra II RNA Library Prep for Illumina (NEB Cat# E7770S). The NEB protocol was followed using the Poly(A) mRNA Magnetic Isolation Module and SPRIselect beads (Beckman Coulter Cat #B23317). Library adapter was diluted 5-fold. The additional SPRIselect cleanup step referred to at 1.11.3 in the NEB protocol was followed.

tag: cell line

tag: chip antibody

value: expressed in SH-SY5Y cells:Flag-tagged human RNaseH(D210N)(R-ChIP)

tag: cell type

value: neuroblastoma, differentiated

tag: genotype

value: WT

tag: treatment

value: AZD1390 (ATMi) + N-acetyl cysteine (NAC)


title: AB6243

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
20181220_day16_tumor_CD45.2+_WT_2
MARSseq

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt

molecule: polyA RNA

organism: Mus musculus

source_name: tumor

growth_protocol: 8 to 10 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were sacrificed at various time points by cervical dislocation. Tumor, spleen, and tdLN were collected and put through a process of mechanical and enzymatic digestion. For single-cell suspensions, tumors were chopped into small pieces and suspended in RPMI supplemented with DNase (2mg/ml, Sigma-Aldrich) and collagenase IV (100mg/ml, Worthington). Tumors were homogenized by GentleMacs tissue homogenizer (Miltenyi Biotec) and incubated at 37oC for 30min, with frequent agitation. Following dissociation procedures, cells were washed with cold PBS, filtered through a 70-μm cell strainer, and centrifuged at 300g for 5 min at 4 °C. Spleen and tdLN were mashed through a 100uM cell strainer and washed with ice-cold MACS buffer (PBS supplemented with 0.2mM EDTA, pH 8, and 0.5% BSA). Cells were centrifuged at 300g, 5 min, and 4°C. Spleen was suspended in red blood lysis buffer (Sigma-Aldrich) and DNase (0.33U/ml, Sigma-Aldrich), incubated for 5min at room temperature, washed with cold PBS, passed through a 70μm mesh strainer, centrifuged at 300g, 5 min, 4°C and then resuspended in ice-cold MACS buffer.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol:
Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
mice were treated with 250ug of aPD1 or/and 200ug of a41BB.

tag: tissue

value: tumor

value: endogenous CD8+

tag: experiment id

tag: days post_adoptive_transfer

tag: mouse number


title: CRC-404 Patient, rep3

city: Durham

first: Ergang

last: Wang

state: NC

address: C215, LSRC

department: PCB

institute: Duke University

data_processing:
ATAC seq data was processed using the pipeline developed for ENCODE to perform quality control filtering of low0quality reads and PCR duplicates analysis of reproducibility, reference genome alignment, peaks calling, and fold-enrichment or p-value signal tracks generation.
Reads were aligned to reference genome hg19 using Bowtie2. Duplicate an mitochondrial reads were removed, and peaks were called by MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig for genome track visualization

extract_protocol:
The nuclei were extracted from samples (PT, PDO, PDX and PDOX). For each sample type in one PT-PDO-PDX/PDOX set, three replciates were included. Intact nuclei (5x10^4) were used for each replicate. Transposase, digitonin, and Tween-20 were added, and the mixture was incubated at 37C for 30 minutes. The tranposed fragments were amplified.
The Omni-ATAC protocol was utilized for ATAC library preparations.

tag: replicate

value: Patient


title: R ChIP, ATMi NAC, rep1


title: CRC-404 PDO, rep1

value: PDO


title: 62-6t2_S19

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

country: Netherlands

institute: Erasmus MC

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
62-6t2_S19_L001

data_processing:
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive IGH repertoire for each sample was downloaded in .csv format and processed in R (R Core Team, 2020) during further analysis.
Assembly: GRCh38
Supplementary files format and content: Tab delimited tekst file containing: sample,QC.status,scenario,rearrangements,raw.count,w.junction.count,w.junction.percent,artefacts.count,artefacts.percent,usable.count,usable.percent,w.most.pop.cln.s..count,w.most.pop.cln.s..percent,uniq.usable.seq.count,clonotypes.count,diversity..norm.ed..count,effective.species.count,R1.Q.mean.stdev.count,R2.Q.mean.stdev.count,joined.normally.count,joined.normally.percent,joined.loosely.count,joined.loosely.percent,total.joined.count,total.joined.percent,saved.from.unjoined.count,saved.from.unjoined.percent,low.quality..ee.nt...0.01..count,low.quality..ee.nt...0.01..percent,short...50nt..count,short...50nt..percent,annotated.count,annotated.percent,w.TR.receptor.count,w.TR.receptor.percent,w.B.chain.count,w.B.chain.percent,w.VJ.Vb..Db..Jb.count,w.VJ.Vb..Db..Jb.percent,w.VJ.Vb..Db..Jb.cln

source_name: PBMCs

extract_protocol:
gDNA was available from the HOVON-139/GIVE trial. 2-12 ug DNA was amplified through multiplex PCR of IGHV-IGHD-IGHJ gene rearrangements following the EC-NGS leader primer protocol. After amplification, PCR products were purified on Agencourt AMPURE beads (Beckman Coulter, Brea, CA, USA) and eluted using H2O. The purified product was checked for primer dimers using the Agilent Tapestation (Agilent,Santa Clara, CA, USA).
The intitial multiplex PCR already attached the indexes to the PCR products, so library construction was simply pooling the purified PCR product in equilmolar fashion.

value: PBMCs

tag: sample type

value: HOVON139/GIVE post-Tx

tag: patient number

tag: timepoint

value: 6 months after randomization


title: AB6241

description:
20181220_day16_tumor_CD45.1+_OT1_1
MARSseq

value: OT1 CD8+


title: CRC-404 Patient, rep2


title: 62-5_S18

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
62-5_S18_L001

value: End of induction treatment


title: R ChIP input, ATMi, rep2

value: AZD1390 (ATMi)


title: AB6240

description:
20181220_day16_spleen_CD45.2+_WT_1
MARSseq

source_name: spleen

value: spleen


title: R ChIP, NAC, rep2

value: N-acetyl cysteine (NAC)


title: 62-3t4_S18

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
62-3t4_S18_L001

value: Venetoclax ramp-up


title: CRC-404 Patient, rep1


title: 61-6t4_S18

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
61-6t4_S18_L001

value: 12 months after randomization


title: AB6239

description:
20181220_day16_spleen_CD45.1+_OT1_1
MARSseq


title: R ChIP, NAC, rep1

value: expressed in SH-SY5Y cells:Flag-tagged human RNaseH(D210N)(R-ChIP)

value: neuroblastoma, differentiated


title: 61-6t3_S17

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
61-6t3_S17_L001

value: 9 months after randomization


title: CRC-404 PDOX, rep1

value: PDOX


title: AB6238

description:
20181214_day10_tumor_CD45.2+_WT_2
MARSseq

value: tumor

value: endogenous CD8+


title: R ChIP, ATMi, rep1

value: WT


title: R ChIP, ATMi, rep2


title: 61-5_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
61-5_S11_L001

value: PBMCs


title: AB6237

description:
20181214_day10_tumor_CD45.2+_WT_1
MARSseq


title: AB6242

description:
20181220_day16_tumor_CD45.2+_WT_1
MARSseq


title: R ChIP, DMSO, rep2


title: 60-6t4_S20

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
60-6t4_S20_L001

value: HOVON139/GIVE post-Tx


title: AB6236

description:
20181214_day10_tumor_CD45.1+_OT1_2
MARSseq


title: R ChIP, DMSO, rep1


title: AB6235

description:
20181214_day10_tumor_CD45.1+_OT1_1
MARSseq


title: CRC-403 PDOX, rep2


title: CRC-403 PDOX, rep1


title: PAR ChIP input, ATMi, rep2

value: anti-pan-ADP-ribose binding reagent (Millipore Sigma, MABE1016)


title: 60-5_S14

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
60-5_S14_L001


title: 60-6t2_S17

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
60-6t2_S17_L001

value: 6 months after randomization


title: AB6233

description:
20181214_day10_spleen_CD45.1+_OT1_1
MARSseq

value: OT1 CD8+


title: CRC-403 PDO, rep2

value: PDO


title: PAR ChIP input, ATMi, rep1

value: AZD1390 (ATMi)


title: CRC-403 Patient, rep3

value: Patient


title: 60-3t4_S16

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
60-3t4_S16_L001

value: Venetoclax ramp-up


title: AB6234

description:
20181214_day10_spleen_CD45.2+_WT_1
MARSseq

value: spleen


title: CRC-403 PDO, rep1


title: CRC-403 PDOX, rep3


title: PAR ChIP input, DMSO, rep2


title: AB6232

description:
20181210_day6_tumor_CD45.2+_WT_2
MARSseq


title: 59-6t4_S16

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
59-6t4_S16_L001

value: 12 months after randomization


title: PAR ChIP input, DMSO, rep1

value: neuroblastoma, differentiated


title: 59-6t2_S15

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
59-6t2_S15_L001


title: CRC-403 Patient, rep2


title: CRC-403 Patient, rep1


title: CRC-403 PDO, rep3


title: PAR ChIP, ATMi, rep2


title: 59-5_S13

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
59-5_S13_L001

value: End of induction treatment


title: AB6230

description:
20181210_day6_tumor_CD45.1+_OT1_2
MARSseq


title: 19-106 PDOX, rep3

value: PDOX


title: PAR ChIP, ATMi, rep1


title: 57-t5_S15

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
57-t5_S15_L001

value: -End of induction treatment


title: AB6229

description:
20181210_day6_tumor_CD45.1+_OT1_1
MARSseq

value: tumor


title: PAR ChIP, DMSO, rep2

value: WT


title: 57-6t4A_S13

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
57-6t4A_S13_L001

value: PBMCs


title: 19-106 PDOX, rep2


title: AB6228

description:
20181210_day6_spleen_CD45.2+_WT_1
MARSseq

value: endogenous CD8+


title: 57-6t4A_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
57-6t4A_S12_L001

value: HOVON139/GIVE post-Tx


title: AB6227

description:
20181210_day6_spleen_CD45.1+_OT1_1
MARSseq


title: AB6226

description:
20181207_day3_tumor_CD45.2+_WT_1
MARSseq


title: 19-106 PDO, rep3


title: Raji_Mut1

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

library_source: transcriptomic

data_processing:
SLAM-Seq datasets were analyzed using the T>C conversion-aware SLAM-DUNK (Digital Unmasking of Nucleotide conversion-containing k-mers) pipeline utilizing the default parameters (DOI: 10.1038/nmeth.4435, DOI: 10.1186/s12859-019-2849-7). Briefly, nucleotide conversion-aware read mapping of adapter- and poly(A)-trimmed sequences to the human GRCh38/hg38 reference genome assembly was performed with NextGenMap (DOI:10.1093/bioinformatics/btt468). Alignments were filtered for those with a minimum identity of 95% and minimum of 50% of the read bases mapped. For multi-mappers, ambiguous reads and non-3' UTR alignments were discarded, while one read was randomly selected from multimappers aligned to the same 3’ UTR. SNP calling (coverage cut-off of 10X and variant fraction cut-off of 0.8) with VarScan2 (DOI: 10.1101/gr.129684.111) was performed in order to mask actual T>C SNPs. Non-SNP T>C conversion events were then counted and the fraction of labeled transcripts determined. All output is contained in tcount files.
Assembly: GRCh38/hg38
Supplementary files format and content: The processed data is contained in the tcount file, which are the central output of slamdunk. These contain all results, conversion rates, and other statistics for each UTR. Tcount files are comma-separated text files containing one line entry per annotated 3’ UTR. Each entry contains the following columns:  chromosome, start, end, name, length, strand, conversionRate, readsCPM, Tcontent, coverageOnTs, conversionsOnTs, readCount, tcReadCount, and multimapCount.
Library strategy: SLAM-seq

molecule: total RNA

source_name: Raji

growth_protocol: BCBL-1 and Raji cell lines were cultured in RPMI 1640 medium supplemented with 15% FBS, L-glutamine, and antibiotics. The BC3 cell line was cultured in IMDM supplemented with 15% FBS, L-glutamine, and antibiotics.The cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA, USA)
Total RNA was isolated from cells following incubation with 4-Thiouridine (s4U; 300 uM). Subsequently, the 4-thiol groups in the s4Uracil-labeled transcripts were alkylated with iodoacetamide (IAA). QuantSeq 3’ mRNA-Seq (FWD) (Lexogen, Inc.) Illumina-compatible, indexed sequencing libraries were then prepared from the alkylated RNA samples (100 ng) according to the manufacturer’s protocol for oligo(dT)-primed first strand cDNA synthesis, random-primed second strand synthesis, and library amplification.

treatment_protocol: BC3, BCBL-1, and Raji  cell cultures (two cultures per treatment) were incubated with wild type peptide (at the IC50 for each cell line), mutant peptide (at the equivalent concentrations to the IC50 of wild type peptide for each cell line), or vehicle control for 30 minutes. Subsequently, 4-Thiouridine (s4U; 300 uM) was added to the culture media and the cells treated for 1.5 hours in order to label newly synthesized RNA.

value: Raji

value: Burkitt's lymphoma

tag: treatment group

value: Mutant peptide

tag: peptide treatment_and_duration

value: No treatment for 30 minutes

tag: labeling treatment

value: 4-Thiouridine (s4U; 300 uM) for 1.5 hours


title: 19-106 PDO, rep2

value: PDO


title: Raji_Wt2


title: 57-3t2_S14

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
57-3t2_S14_L001

value: Venetoclax ramp-up


title: 19-106 PDO, rep1


title: AB6231

description:
20181210_day6_tumor_CD45.2+_WT_1
MARSseq


title: Raji_Ctrl2

value: Control


title: 5-6t4_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
5-6t4_S5_L001

value: 12 months after randomization


title: 19-106 Patient, rep3

value: Patient


title: BCBL1_Mut1

value: primary effusion lymphoma


title: AB6224

description:
20181207_day3_spleen_CD45.2+_WT_1
MARSseq

value: spleen


title: 5-6t2_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
5-6t2_S4_L001

value: 6 months after randomization


title: BC3_Mut1


title: 19-106 PDOX, rep1

value: PDOX


title: 55-t5_S14

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
55-t5_S14_L001

value: PBMCs

value: -End of induction treatment


title: PAR ChIP, DMSO, rep1

value: anti-pan-ADP-ribose binding reagent (Millipore Sigma, MABE1016)

value: neuroblastoma, differentiated

value: WT


title: 19-106 Patient, rep2


title: 19-106 Patient, rep1


title: BC3_Wt1


title: AB6134

description:
20180925_day15_tumor_GFP-_AND_CD45.1-_CD8+_1
MARSseq

value: tumor

value: endogenous CD8+


title: AB6098

description:
20180916_day6_spleen_GFP-_AND_CD45.1+_CD8+_1
MARSseq

value: OT1 CD8+


title: 55-6t4_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
55-6t4_S12_L001

value: HOVON139/GIVE post-Tx


title: 19-192 PDX, rep3

value: PDX


title: 57-6t2_S19

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
57-6t2_S19_L001


title: 55-6t4_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
55-6t4_S11_L001


title: BC3_Ctrl2

value: Control

value: No treatment for 30 minutes

value: 4-Thiouridine (s4U; 300 uM) for 1.5 hours


title: 19-192 PDX, rep2


title: AB6094

description:
20181024_day45_spleen_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: AB6093

description:
20181024_day45_tumor_GFP-_AND_CD45.1-_CD8+_2
MARSseq


title: 55-6t2_S18

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
55-6t2_S18_L001


title: AB6225

description:
20181207_day3_tumor_CD45.1+_OT1_1
MARSseq


title: 19-192 PDX, rep1


title: 55-3t2_S13

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
55-3t2_S13_L001

value: Venetoclax ramp-up


title: 19-192 PDOX, rep3


title: AB6091

description:
20181009_day29_spleen2_GFP-_AND_CD45.1-_CD8+_1
MARSseq

value: spleen


title: AB6135

description:
20180925_day15_spleen_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: 5-3t4_S13

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
5-3t4_S13_L001


title: 19-192 PDOX, rep2


title: 53-6t4_S17

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
53-6t4_S17_L001

value: 12 months after randomization


title: AB6090

description:
20181009_day29_tumor2_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: 19-192 PDOX, rep1

value: PDOX


title: 53-6t2_S13

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
53-6t2_S13_L001

value: PBMCs

value: 6 months after randomization


title: AB6089

description:
20181009_day29_tumor2_GFP-_AND_CD45.1+_CD8+_2
MARSseq


title: AB6088

description:
20181009_day29_tumor2_GFP-_AND_CD45.1+_CD8+_1
MARSseq


title: 19-192 PDO, rep2

value: PDO


title: 53-5_S3

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
53-5_S3_L001

value: End of induction treatment


title: 19-192 PDO, rep1


title: AB6087

description:
20181009_day29_spleen1_GFP-_AND_CD45.1+_CD8+_1
MARSseq


title: 53-3t4_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
53-3t4_S12_L001


title: AB6085

description:
20181009_day29_tumor1_GFP-_AND_CD45.1-_CD8+_2
MARSseq


title: AB6086

description:
20181009_day29_spleen1_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: 52-6t4_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
52-6t4_S12_L001


title: 19-192 Patient, rep3

value: Patient


title: AB6092

description:
20181024_day45_tumor_GFP-_AND_CD45.1-_CD8+_1
MARSseq

value: tumor


title: 19-192 Patient, rep1


title: 52-5_S16

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
52-5_S16_L001


title: AB6084

description:
20181009_day29_tumor1_GFP-_AND_CD45.1-_CD8+_1
MARSseq

value: endogenous CD8+


title: 19-192 Patient, rep2


title: AB6083

description:
20181009_day29_tumor1_GFP-_AND_CD45.1+_CD8+_2
MARSseq

value: OT1 CD8+


title: AB6082

description:
20181009_day29_tumor1_GFP-_AND_CD45.1+_CD8+_1
MARSseq


title: 19-245 PDX, rep3


title: 51-6t4_S16

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
51-6t4_S16_L001

value: HOVON139/GIVE post-Tx


title: 51-6t2_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
51-6t2_S11_L001


title: 19-245 PDX, rep2

value: PDX


title: AB6081

description:
20180916_day6_spleen_GFP+_AND_CD45.1-_CD8+_1
MARSseq

value: bystander CD8+


title: 51-5_S21

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
51-5_S21_L001


title: AB6080

description:
20180916_day6_spleen_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: 19-192 PDO, rep3


title: 19-245 PDX, rep1


title: 51-3t4_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
51-3t4_S10_L001


title: 19-245 PDOX, rep3


title: AB6079

description:
20180913_day3_spleen_GFP-_AND_CD45.1+_CD8+_1
MARSseq


title: 50-6t4_S15

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
50-6t4_S15_L001


title: 19-245 PDOX, rep2


title: 50-6t2_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
50-6t2_S9_L001


title: 19-245 PDOX, rep1


title: 50-5_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
50-5_S6_L001


title: AB6075

description:
20180913_day3_tumor_GFP-_AND_CD45.1+_CD8+_1
MARSseq


title: 19-245 PDO, rep2


title: AB6078

description:
20180913_day3_spleen_GFP+_AND_CD45.1-_CD8+_1
MARSseq


title: 19-245 PDO, rep3


title: AB6077

description:
20180913_day3_spleen_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: 19-245 PDO, rep1


title: AB6074

description:
20180913_day3_tumor_GFP+_OR_CD45.1+_CD8+_3
MARSseq

value: OT1 CD8+_or_bystander CD8+


title: AB6073

description:
20180913_day3_tumor_GFP+_OR_CD45.1+_CD8+_2
MARSseq


title: 19-245 Patient, rep3


title: 49-6t2_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
49-6t2_S10_L001


title: 52-6t2_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
52-6t2_S11_L001


title: AB6076

description:
20180913_day3_tumor_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: 19-245 Patient, rep2


title: 49-6t4_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
49-6t4_S9_L001


title: 49-6t2_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
49-6t2_S11_L001


title: 49-5_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
49-5_S4_L001


title: AB6072

description:
20180913_day3_tumor_GFP+_OR_CD45.1+_CD8+_1
MARSseq


title: 19-245 Patient, rep1


title: 50-3t4A_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
50-3t4A_S10_L001


title: 49-3t4_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
49-3t4_S8_L001


title: AB5847

description:
20180920_day10_spleen_GFP+_OR_CD45.1+_CD8+_1
MARSseq


title: 47-6t4_S14

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
47-6t4_S14_L001


title: AB5845

description:
20180920_day10_tumor_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: AB5846

description:
20180920_day10_spleen_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: 47-6t2_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
47-6t2_S7_L001


title: 19-187 PDX, rep1


title: AB5844

description:
20180920_day10_tumor_GFP-_AND_CD45.1+_CD8+_2
MARSseq


title: 47-5_S19

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
47-5_S19_L001


title: 19-187 PDOX, rep3


title: AB5843

description:
20180920_day10_tumor_GFP-_AND_CD45.1+_CD8+_1
MARSseq


title: AB5842

description:
20180920_day10_tumor_GFP+_AND_CD45.1-_CD8+_1
MARSseq


title: 19-187 PDOX, rep2


title: 19-187 PDOX, rep1


title: 19-187 PDO, rep3


title: AB5840

description:
20180916_day6_tumor_GFP-_AND_CD45.1+_CD8+_2
MARSseq


title: 19-187 PDO, rep2


title: 4-6t2_S3

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
4-6t2_S3_L001


title: AB5838

description:
20180916_day6_tumor_GFP+_AND_CD45.1-_CD8+_2
MARSseq


title: AB5841

description:
20180916_day6_tumor_GFP-_AND_CD45.1-_CD8+_1
MARSseq


title: 4-6t4_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
4-6t4_S10_L001


title: 19-187 PDX, rep3


title: AB5839

description:
20180916_day6_tumor_GFP-_AND_CD45.1+_CD8+_1
MARSseq


title: 46-6t4_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
46-6t4_S6_L001


title: AB5837

description:
20180916_day6_tumor_GFP+_AND_CD45.1-_CD8+_1
MARSseq


title: 4-5PB_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
4-5PB_S12_L001


title: 19-187 PDX, rep2


title: 45-6t4_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
45-6t4_S7_L001


title: 19-187 Patient, rep3


title: 19-187 PDO, rep1


title: 45-6t2_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
45-6t2_S5_L001


title: AB10120

description:
20200724_D6_T1_aPD1_Tim3+PD1+CD25+
MARSseq


title: 19-187 Patient, rep1


title: 45-5_S15

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
45-5_S15_L001


title: 46-t5_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
46-t5_S9_L001

value: -End of induction treatment


title: 19-187 Patient, rep2


title: 46-t5_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
46-t5_S10_L001


title: 12-day-old SPCHΔ49, b2 seedlings [D3]

city: Shenyang

first: Wang

middle: Ming

last: Lin

address: 120 Dongling Road

country: China

institute: shenyang agricultural university

data_processing:
Raw reads were trimmed and filtered by removing adapters sequence and bases with low quality score (Q30 score < 15) using Trimmomatic v0.38
Clean reads were mapped to Arabidopsis thaliana (version 11) primary transcript sequences (https://phytozome.jgi.doe.gov) to calculate the gene expression in transcript per million (TPM) using Kallisto v 0.44.0 (Bray, et.al., Nat Biotechnol, 2016).
Candidates with TPM ≥10  in all biological replicates of any group, and with parameters |b| ≥ 0.692 and q-value < 0.05 were identified differentially expressed genes (DEGs) using Sleuth program (Pimentel, et.al., Nat Methods, 2017).
Assembly: Arabidopsis thaliana (version 11) primary transcript sequences
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: After 3-day imbibition at 4 °C, seeds were sown on ½ MS medium, grown under 16 h light/8 h dark cycle with 100µmol m-2 s-1 light density at 22 °C

extract_protocol:
Total RNA was isolated from 12-day-old Arabidopsis seedlings by the Plant RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample Prep Kit v2 LS protocol (Illumina, San Diego, CA, USA)

value: whole seedling

value: 35S:SPCH{delta}49, basl-2


title: 42-t5_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
42-t5_S6_L001


title: RNA-seq_Young_rep4

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

description: Primary pro-B cells by CD19+ selection

data_processing:
Hi-C and capture Hi-C raw reads were processed to the mouse reference genome mm10 by HiCUP (v0.7.2) with the settings of Arima. High-quality and unique paired-end tags (PETs) from HiCUP were further processed to the HIC file through Juicer (v1.6.0) for visualization with Juicebox. These PETs were also processed with cLoops2 (v0.0.2) for quantifications. Chromosome X was excluded from the analysis. Compartment analysis of eigenvectors (PC1) were obtained by hicPCA in HiCExplorer3 package (v3.6) with parameters of -noe 1 at the resolution of 100 kb. Hi-C TADs were called by Juicer arrowhead with parameters of -r 25000 -k KR and quantified by cLoops2. Hi-C or capture Hi-C virtual 4C tracks were generated by the cLoops2 dump module.
CTCF and Rad21 ChIP-seq raw reads were mapped to the mouse reference genome mm10 by Bowtie2 (v2.3.5). Only non-redundant reads with MAPQ >=10 were used for the following analysis. BigWig tracks were generated by bamCoverage in deepTools (v3.3.0) with parameters of --ignoreDuplicates --minMappingQuality 10 --normalizeUsing CPM for visualization and quantification aggregation analysis.
RNA-seq raw reads were mapped to mm10 by STAR (v2.7.3a) and quantified into RPKM with Cufflinks (v2.2.1). BigWig tracks were also generated by STAR as signal quantified as RPKM.
Assembly: mm10
Supplementary files format and content: BEDPE files for Hi-C and capture Hi-C samples were provided for valid interactions.
Supplementary files format and content: BED files for single-end ChIP-seq samples were provided for processed high quality unique reads.
Supplementary files format and content: TEXT files for processed gene expression in FPKM from RNA-seq data were also provided.

source_name: progenitor B cells

growth_protocol:
For Rag2-/- mice, total bone marrow was extracted from tibia and femurs and erythrocytes are lysed. Pro-B cells were purified by combining positive selection using CD19+ selective beads (Stem Cell Technology, Cat #18954) and sorting by CD19+ and B220+ markers.
Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+ and Rag2-/-Ebf1+/−Pax5+/− pro-B cell lines are cultured as previous described (Ramamoorthy et al., 2020).

extract_protocol:
For the capture Hi-C libraries, whole genome Hi-C libraries were first generated as previously described. To enrich the IgH locus (mm10, chr12: 113,201,001 - 116,030,000), SureSelect Target Enrichment probes (Table S3) with 2× tiling density were designed and manufactured by Agilent (Agilent Technologies Inc.). Hi-C libraries were hybridized to probes as specified by the manufacturer. Enriched libraries were sequenced using Illumina NextSeq sequencer to generate paired-end 150-bp reads.
Genome-wide in situ Hi-C was performed with Rag2-/- young and old primary pro-B cells, and Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+ and Rag2-/-Ebf1+/−Pax5+/− pro-B cell lines using the Arima Hi-C Kit (Arima Genomics), including KAPA Hyper Prep indexing and library amplification (catalog no. KK8500, Roche Molecular Systems Inc) according to the manufacturer’s instructions. For each assay, 1X10^6 cells to be used as the input materials and two biological replicates were performed for each group. Samples were sequenced 2×150 bp on an Illumina NovaSeq instrument.
For the ChIP-seq libraries, Young and old primary Rag2-/- pro-B cells were crosslinked with 1% formaldehyde (Sigma) for 10 min, quenched with 125 mM of glycine and lysed in lysis buffer containing 1% SDS. Chromatin was sheared by Bioruptor (Diagenode) and followed by immunoprecipitation with specific antibodies. For each immunoprecipitation assay, 1×10^6 cells was used. Antibody information anti-H3K27ac (Active Motif, # 39133; 1:500), anti-H3K27me3 (Diagonode, #C1541005; 1:500), anti-CTCF (Abcam, # ab70303; 1:250), anti-Rad21 (Abcam, # ab992; 1:500).
Total RNA was prepared using the Direct-zol RNA Miniprep Kit (# R2051, Zymo Research) according to manufacturer’s instructions. RNA libraries for Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+ and Rag2-/-Ebf1+/−Pax5+/− pro-B cell lines (two replicates for each group) were prepared using SMARTer Stranded Total RNA-Seq Kit v2 (# 634412, Takara Bio USA, Inc.) and sequenced 1×100 bp on an Illumina NovaSeq instrument.
Total RNA was prepared using the Direct-zol RNA Miniprep Kit (# R2051, Zymo Research) according to manufacturer’s instructions. The RNA libraries for young and old Rag2-/- primary pro-B cells (four biological replicates for each group) were prepared using the NEXTFLEX Rapid Directional RNA-Seq Kit (NOVA-5138-07, PerkinElmer) and sequenced 2×75 bp on an Illumina NovaSeq instrument.

tag: strain

value: progenitor B cells

value: Bone marrow

tag: age

value: young


title: SC286_1_G0+T_APCmin

city: Houston

first: Jiexi

last: Li

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Count matrices were generated and analyzed in Seurat. Next, low-quality cells, potential doublets, and multiplets were removed. Batch effect was corrected using canonical correlation analysis in Seurat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Distal colon adenoma

extract_protocol:
Freshly collected distal colon adenomas were harvested from mice and single cell isolation was performed following (Gao et al 2021, Nature Biotechnology). In brief, fresh tumors of 1–3 cm3 were placed in a 10-cm dish with 5 ml of dissociation solution, minced with scalpels into pieces of 1 mm3, transferred to a 50-ml conical tube with 30 ml dissociation solution and incubated at 37 °C in a rotating hybridization oven for 15 min to 1 h. For trypsinization, the tissue suspension was centrifuged at 450g for 5 min to remove the supernatant, and the pellet was resuspended in 5 ml trypsin (Corning, 25053CI) and incubated at 37 °C in a rotating hybridization oven for 5 min. Trypsin was neutralized by adding 10 ml DMEM (Sigma, D5796) containing 10% FBS (Sigma, F0926). The tissue suspension was filtered through a 70-μm strainer by using a syringe plunger flange to grind the leftover, unfiltered tissue. The strainer was rinsed and ground with DMEM to ensure any remaining single cells were filtered. The flow-through was centrifuged at 450g for 5 min and the supernatant was removed. If red blood cells (RBCs) were present in the pellet, 10–20 ml of 1× MACS RBC lysis buffer (1:10 dilution of 10× MACS RBC lysis buffer (MACS, 130-094-183) in Milli-Q water) was applied by nutating at room temperature for 10 min. To stop RBC lysis, 20 ml DMEM was added and the mixture was centrifuged at 450g for 5 min. The supernatant was discarded and the cell pellet was washed with 10 ml of 4 °C DMEM. After centrifuging at 450g for 5 min, the supernatant was discarded and cells were resuspended in cold PBS (Sigma, D8537) + 0.04% BSA solution (Ambion, AM2616) and passed through a 40-μm flowmi cell strainer (Bel-Art, h13680-0040). To make dissociation solution, collagenase A (Sigma, 11088793001) was dissolved in 75% (vol/vol) DMEM F12/HEPES medium (Gibco, 113300) and 25% (vol/vol) BSA fraction V (Gibco, 15260037) to prepare a concentration of 1 mg ml–1
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Libraries were prepared by the SINGLE CORE at MD Anderson Cancer Center.

value: Adenoma cells

value: Distal colon adenoma

value: Apcmin;LSL-mTERT

value: 25 weeks old


title: 42-6t2_S13

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
42-6t2_S13_L001

value: PBMCs

value: 6 months after randomization


title: 12-day-old SPCHΔ49, b2 seedlings [D1]


title: RNA-seq_Young_rep3

description: Primary pro-B cells by CD19+ selection


title: 42-3t4_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
42-3t4_S4_L001

value: Venetoclax ramp-up


title: 41-t5_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
41-t5_S5_L001

value: HOVON139/GIVE post-Tx

value: End of induction treatment


title: 12-day-old SPCHΔ49 seedlings [C2]


title: RNA-seq_Young_rep2

description: Primary pro-B cells by CD19+ selection


title: RNA-seq_Young_rep1

description: Primary pro-B cells by CD19+ selection


title: 41-6t4_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
41-6t4_S9_L001

value: 12 months after randomization


title: 12-day-old SPCHΔ49 seedlings [C1]


title: RNA-seq_Old_rep4

description: Primary pro-B cells by CD19+ selection

value: old


title: 41-6t2_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
41-6t2_S12_L001


title: 12-day-old WT seedlings [A2]

value: WT


title: RNA-seq_Old_rep3

description: Primary pro-B cells by CD19+ selection


title: SC286_2_G4+T_APCmin

description: 10x Genomics


title: 12-day-old WT seedlings [A1]

value: whole seedling


title: RNA-seq_Old_rep2

description: Primary pro-B cells by CD19+ selection


title: RNA-seq_Old_rep1

description: Primary pro-B cells by CD19+ selection


title: 40-6t4_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
40-6t4_S4_L001


title: 41-3t4_S3

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
41-3t4_S3_L001


title: Scer, optimal growth, RNA, rep3

city: Canberra

first: Erin

middle: Elizabeth

last: Hahn

state: ACT

address: Clunies Ross

department: National Research Collections Australia

country: Australia

institute: CSIRO

data_processing:
Genome preparation : We performed repeat masking with RepeatMasker v.4.1.0 (http://www.repeatmasker.org) through two rounds of masking, first with default settings and with standard Illumina adapters using -e rmblast enabled.
Alignment: We aligned RNA-Seq reads with kalign (ngskit4b tool suite version 200218) with options -c25 -l25 -d50 -U4. We removed PCR and optical duplicates using MarkDuplicates (PICARD) enabling REMOVE_DUPLICATES=TRUE.
FPKM: We calculated FPKM using the Tuxedo pipeline. We then z-transformed the FPKM values using the R package zFPKM.
edgeR: For the differential expression analyses, we used the Trinity edgeR pipeline to calculate log2FC between treatments.
Assembly: S288C R64/sacCer3
Supplementary files format and content: tab-delimited text file including FPKM for all samples
Supplementary files format and content: tab-delimited text file output from edgeR including logFC between treatments for each gene

organism: Saccharomyces cerevisiae

source_name: BJ5464 (delta-URA3)

growth_protocol: We grew Saccharomyces cerevisiae strain BJ5464 auxotroph ΔURA3 in 500 mL Yeast Extract-Peptone-Dextrose (YPD) medium to OD600 = 0.75 at 28°C.

extract_protocol:
We resuspended three 2 mL aliquots per culture in 450 mL RLT Buffer and followed the manufacturer’s instructions for the Qiagen RNeasy plant mini kit, eluting in 30 mL nuclease-free water.
Illumina stranded mRNA library prep

treatment_protocol: Splitting the culture into equal volumes, one underwent 37°C heat stress for 20 minutes.

value: BJ5464 (delta-URA3)

value: Optimal growth


title: 12-day-old SPCHΔ49, b2 seedlings [D2]

value: 35S:SPCH{delta}49, basl-2


title: ChIP-seq_Young_H3K27me3_rep2

description: Primary pro-B cells by CD19+ selection

value: progenitor B cells

value: Bone marrow

value: young

tag: chip antibody


title: 40-6t2_S2

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
40-6t2_S2_L001


title: Scer, optimal growth, RNA, rep2


title: Scer, optimal growth, RNA, rep1


title: ChIP-seq_Young_H3K27me3_rep1

description: Primary pro-B cells by CD19+ selection

tag: cell type


title: 12-day-old SPCHΔ49 seedlings [C3]

tag: genotype


title: 40-5_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
40-5_S6_L001


title: Scer, heatshock, RNA, rep3

tag: treatment

value: Heatshocked


title: Raji_Mut2

data_processing:
SLAM-Seq datasets were analyzed using the T>C conversion-aware SLAM-DUNK (Digital Unmasking of Nucleotide conversion-containing k-mers) pipeline utilizing the default parameters (DOI: 10.1038/nmeth.4435, DOI: 10.1186/s12859-019-2849-7). Briefly, nucleotide conversion-aware read mapping of adapter- and poly(A)-trimmed sequences to the human GRCh38/hg38 reference genome assembly was performed with NextGenMap (DOI:10.1093/bioinformatics/btt468). Alignments were filtered for those with a minimum identity of 95% and minimum of 50% of the read bases mapped. For multi-mappers, ambiguous reads and non-3' UTR alignments were discarded, while one read was randomly selected from multimappers aligned to the same 3’ UTR. SNP calling (coverage cut-off of 10X and variant fraction cut-off of 0.8) with VarScan2 (DOI: 10.1101/gr.129684.111) was performed in order to mask actual T>C SNPs. Non-SNP T>C conversion events were then counted and the fraction of labeled transcripts determined. All output is contained in tcount files.
Assembly: GRCh38/hg38
Supplementary files format and content: The processed data is contained in the tcount file, which are the central output of slamdunk. These contain all results, conversion rates, and other statistics for each UTR. Tcount files are comma-separated text files containing one line entry per annotated 3’ UTR. Each entry contains the following columns:  chromosome, start, end, name, length, strand, conversionRate, readsCPM, Tcontent, coverageOnTs, conversionsOnTs, readCount, tcReadCount, and multimapCount.

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA, USA)
Total RNA was isolated from cells following incubation with 4-Thiouridine (s4U; 300 uM). Subsequently, the 4-thiol groups in the s4Uracil-labeled transcripts were alkylated with iodoacetamide (IAA). QuantSeq 3’ mRNA-Seq (FWD) (Lexogen, Inc.) Illumina-compatible, indexed sequencing libraries were then prepared from the alkylated RNA samples (100 ng) according to the manufacturer’s protocol for oligo(dT)-primed first strand cDNA synthesis, random-primed second strand synthesis, and library amplification.
SLAM-seq

treatment_protocol: BC3, BCBL-1, and Raji  cell cultures (three cultures per treatment) were incubated with wild type peptide (at the IC50 for each cell line), mutant peptide (at the equivalent concentrations to the IC50 of wild type peptide for each cell line), or vehicle control for 30 minutes. Subsequently, 4-Thiouridine (s4U; 300 uM) was added to the culture media and the cells treated for 1.5 hours in order to label newly synthesized RNA.

tag: cell line

value: Raji

value: Burkitt's lymphoma

value: Mutant peptide

value: Mutant peptide (9.6 uM) for 30 minutes

value: 4-Thiouridine (s4U; 300 uM) for 1.5 hours


title: ChIP-seq_Young_H3K27ac_rep2

description: Primary pro-B cells by CD19+ selection

tag: tissue


title: 41-6t4_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
41-6t4_S8_L001

value: PBMCs

value: HOVON139/GIVE post-Tx


title: Scer, heatshock, RNA, rep2


title: Raji_Wt1

value: Wild type peptide (9.6 uM) for 30 minutes


title: 37-t5_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
37-t5_S11_L001

value: -End of induction treatment


title: 37-6t4_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
37-6t4_S8_L001

value: 12 months after randomization


title: Scer, heatshock, RNA, rep1

value: BJ5464 (delta-URA3)


title: ChIP-seq_Young_H3K27ac_rep1

description: Primary pro-B cells by CD19+ selection


title: Scer, 24hr fixation, heatshock, MNase rep 3

data_processing:
Genome preparation : We performed repeat masking with RepeatMasker v.4.1.0 (http://www.repeatmasker.org) through two rounds of masking, first with default settings and with standard Illumina adapters using -e rmblast enabled.
Alignment: For deduplication with the IDT library unique molecular identifiers (UMIs), we converted the Fastq files to BAM format using FastqToSam (PICARD v 2.9.2), extracted the UMIs with ExtractUmisFromBam (FGBio v. 1.3.0) and restored the files to FastQ format with SamToFastq (PICARD). We aligned raw reads using kalign (ngskit4b tool suite version 200218) with options -c25 -l25 -d50 -U4. We removed PCR and optical duplicates using MarkDuplicates (PICARD) enabling REMOVE_DUPLICATES=TRUE and utilising UMIs. We computed and corrected for GC-bias with deepTools version 3.5.1 using an effective genome size of 12,157,105 bp.
Peak analysis: We analysed regional occupancy after quantile normalisation of sequencing depth differences between treatment and control to calculate differential occupancy values with the dtriple function in DANPOS3. We analysed all alignments both as individual samples and as pools of three replicates. For profiling the effect of FAIRE and MNase treatment, we used a corresponding input control. For differential peak analyses, we ran pooled heat-shocked cultures versus pooled optimal growth conditions as input control.
Assembly: S288C R64/sacCer3
Supplementary files format and content: WIG files are provided for all individual samples and DANPOS3 comparions with input controls and between conditions

extract_protocol:
We pelleted the fixed cells (4,000 × g, 5 min, 4°C), washed twice with Phosphate Buffered Saline, pH 7.4 (PBS), then resuspended in 10 mL cold Glycine Tris EDTA (GTE; 100 mM glycine, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA) buffer and incubated at 4°C with rocking for 24 hr.    We isolated nuclei by harvesting fixed cells (4,000 × g, 5 min, 4°C), washed twice with cold milliQ water, and resuspended in 2 mL Spheroplast Buffer (SB; 1M Sorbitol, 50 mM Tris, pH 7.5 with freshly added 10 mM b-mercaptoethanol).We obtained spheroplasts by adding Zymolase 20T (MP Biomedicals) to 0.25 mg/mL and incubating at 28°C for 2 hr. We harvested fixed spheroplasts (1,500 × g, 10 min, 4°C), washed twice with cold SB and resuspended in 10 mL. We aliquoted spheroplasts such that each aliquot contained a volume of cells from 4 mL and 10 mL of original culture for the short (15 min and 1 hr) and long (6 hr and 24 hr) cultures, respectively. We collected more cells from longer fixation timepoints to account for lower expected DNA recovery due to heavy fixation. We pelleted spheroplasts (1,500 × g, 10 min, 4°C), removed the supernatant and froze the tubes at -80°C.  gDNA and RNA extraction from unfixed yeast   We extracted gDNA and RNA from unfixed cells frozen at -80°C. For gDNA, we resuspended cells in 200 mL SB, added Zymolase 20T to 0.25 mg/mL and 1 mL RNase A and incubated at 37°C for 30 min. We harvested spheroplasts (3,000 × g, 10 min, 4°C), resuspended in 100 mL PBS plus 0.01 M EDTA, added 2 mL of proteinase K (20 mg/mL) and incubated at 56°C for 45 min in a thermal mixer with agitation at full speed (1,400 rpm). We purified gDNA using phenol:chloroform:isoamyl alcohol (25:24:1) extraction and concentrated the gDNA on beads as described in Small fragment-optimised bead purification of DNA, eluting in 20 mL 10 mM Tris, pH 8.0. For RNA, we resuspended three aliquots per culture in 450 mL RLT Buffer and followed the manufacturer’s instructions for the Qiagen RNeasy plant mini kit, eluting in 30 mL nuclease-free water.   MNase treatment:  We resuspended triplicate aliquots of each fixation timepoint (heat shock and optimal growth) in 200 mL MNase Digestion Buffer (DB; 0.5 mM spermidine, 0.075% Nonidet P40, 50 mM NaCl, 10 mM Tris pH 8.0, 5 mM MgCl2, 5 mM CaCl2 plus freshly added cOmplete EDTA-free protease inhibitor cocktail (Merck)), added 0.5 U of micrococcal nuclease (Worthington Biochemical Corporation) and incubated the tubes for 7 min in a 37°C water bath. We quenched the reaction with 50 μL Quenching Solution (QS; 4% Triton X-100, 1.2% SDS, 600 mM NaCl, 12 mM EDTA) and incubated the tubes on ice for 10 min. We collected digested chromatin by centrifuging (14,000 × g, 10 min, 4°C) and removing the supernatant to a new tube. We digested the supernatant with proteinase K at a final concentration of 0.1 mg/mL and incubated at 56°C for 2 hr. We purified DNA with two phenol:chloroform:isoamyl alcohol (25:24:1) extractions, RNase treatment (1 μL RNase A and incubation at room temperature for 30 min) between extractions one and two followed by Small fragment-optimised bead purification of DNA, resuspending in 20 mL 10 mM Tris, pH 8.0 and fully de-crosslinking at 65°C overnight.    FAIRE treatment: We resuspended four aliquots from each fixation timepoint ( heat shock and optimal growth) in 1 mL Chromatin Shearing Buffer (CSB; 10 mM Tris-HCl pH 8.0, 0.1% SDS, 1 mM EDTA) and transferred each to a 1 mL Covaris milliTUBE. We sonicated the tubes in a Covaris E220 focused-ultrasonicator on settings PIP 420, duty factor 30%, cycles per burst 200 for 7 min (short fixation time points) or 12 min (long fixation time points). After clarifying the lysate by centrifugation (5,500 × g, 15 min, 4°C), we set aside one tube per sample type at this point as an input control. With the remaining tubes, we performed phenol:chloroform:isoamyl alcohol (25:24:1) extraction with back-extraction of the organic phase with addition of 150 mL 10 mM Tris, pH 8.0 followed by an additional extraction. To the aqueous and input control tubes, we added 10 mL RNase A and incubated at room temperature for 30 min followed by addition of 2 mL proteinase K and incubation at 55°C for 1 hr. We de-crosslinked overnight with incubation at 65°C and concentrated the DNA via Small fragment-optimised bead purification of DNA, resuspending in 20 mL 10 mM Tris, pH 8.0.
xGen cfDNA & FFPE DNA Library Prep Kit (IDT)

treatment_protocol: Splitting the culture into equal volumes, one underwent 37°C heat stress for 20 minutes. We added formaldehyde (1%) to both optimal and heat shock flasks and incubated with slow shaking at room temperature. At 15 min, 1 hr, 6 hr and 24 hr we collected aliquots and quenched fixation with addition of glycine to 0.125 M followed by gentle shaking at room temperature for 15 min.

tag: fixation time

value: 24 hr


title: 37-6t4_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
37-6t4_S7_L001


title: Raji_Ctrl1

value: Control

value: No treatment for 30 minutes


title: ChIP-seq_Old_H3K27me3_rep2

description: Primary pro-B cells by CD19+ selection

value: progenitor B cells

value: Bone marrow

value: old


title: BCBL1_Mut2

value: primary effusion lymphoma

value: Mutant peptide (13.1 uM) for 30 minutes


title: Scer, 24hr fixation, heatshock, MNase rep 2

value: Heatshocked


title: BCBL1_Wt2

value: Wild type peptide (13.1 uM) for 30 minutes


title: ChIP-seq_Old_H3K27me3_rep1

description: Primary pro-B cells by CD19+ selection


title: ChIP-seq_Old_H3K27ac_rep2

description: Primary pro-B cells by CD19+ selection


title: Scer, 24hr fixation, heatshock, MNase rep 1


title: 37-6-2_S3

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
37-6-2_S3_L001

value: 6 months after randomization


title: Scer, 6hr fixation, heatshock, MNase rep 3

value: 6 hr


title: ChIP-seq_Old_H3K27ac_rep1

description: Primary pro-B cells by CD19+ selection


title: BCBL1_Wt1

value: 4-Thiouridine (s4U; 300 uM) for 1.5 hours


title: 3-6t4_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
3-6t4_S9_L001

value: PBMCs

value: HOVON139/GIVE post-Tx


title: 36-6t4_S2

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
36-6t4_S2_L001

value: 12 months after randomization


title: HiC_old_rep2

description: Primary pro-B cells by CD19+ selection


title: BCBL1_Ctrl2


title: HiC_old_rep1

description: Primary pro-B cells by CD19+ selection


title: 36-6t2_S15

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
36-6t2_S15_L001


title: Scer, 6hr fixation, heatshock, MNase rep 1

value: BJ5464 (delta-URA3)


title: 36-5_S2

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
36-5_S2_L001

value: End of induction treatment


title: HiC_young_rep2

description: Primary pro-B cells by CD19+ selection

value: young


title: Scer, 6hr fixation, heatshock, MNase rep 2


title: Scer, 1hr fixation, heatshock, MNase rep 3

value: 1 hr


title: Scer, 1hr fixation, heatshock, MNase rep 2


title: 35-t5_S23

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
35-t5_S23_L001


title: BC3_Ctrl1

value: Control

value: No treatment for 30 minutes


title: HiC_young_rep1

description: Primary pro-B cells by CD19+ selection

value: progenitor B cells

value: Bone marrow


title: Scer, 1hr fixation, heatshock, MNase rep 1


title: CaptureHiC_Young

description: Primary pro-B cells by CD19+ selection


title: 35-6t4_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
35-6t4_S7_L001


title: 3-6t4_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
3-6t4_S11_L001


title: 35-6t4_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
35-6t4_S6_L001


title: Scer, 15 min fixation, heatshock, MNase rep 3

value: 15 min


title: BCBL1_Ctrl1

value: primary effusion lymphoma


title: 35-6t2_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
35-6t2_S8_L001


title: Scer, 15 min fixation, heatshock, MNase rep 2

value: Heatshocked


title: CaptureHiC_Old

description: Primary pro-B cells by CD19+ selection

value: old


title: Caerulein_20

city: Charleston

first: Heehwa

last: Son

state: MA

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

data_processing:
The raw files were aligned to mouse genome/GRCm38 using STAR-2.5.3.
Sequences located at transcripts were quantified by using RSEM-1.3.1.
Differentially expressed genes (DEG) analysis was performed using DESeq2-1.24.0.
Assembly: Mouse genome/GRCm38
Supplementary files format and content: tab-delimited text files containing read counts estimated by using RSEM

source_name: Pancreas

extract_protocol:
Lysis buffer
Modified SMART-Seq2 cDNA and Illumina NexteraXT library construction. Protocol based on preparation of Single-Cell RNA-Seq libraries for next generation sequencing -Trombetta et al 2017

value: Pancreas

value: WT

value: Caerulein


title: PMA_VGN8_1

data_processing:
RNA-Seq data was analyzed using a STAR-HTSeq pipeline. Raw sequence reads (FASTQ format) were mapped with STAR to the reference human genome assembly (GRCh38/hg38, GENCODE release 36) and gene-level read counts were quantified with HTSeq (htseq-count).
Processed data are gene-level read counts generated from the output of STAR alignment and quantified with HTSeq (htseq-count) for each sample.
Assembly: GRCh38/hg38
Supplementary files format and content: Individual files in tab-separated text format. Each file contains Ensembl ID (column 1), gene name (column 2), and gene-level counts (column 3) for each gene.

growth_protocol: U937 cells were cultured in RPMI 1640 medium supplemented with 15% FBS, L-glutamine, and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA, USA)
Indexed, stranded mRNA-seq libraries were prepared from total RNA (100 ng) using the KAPA Stranded mRNA-Seq (Roche) according to the manufacturer’s standard protocol.

treatment_protocol: U937 cells were pretreated with VGN73 (4 or 8 μM) for 24 hours, and then stimulated with PMA (10 ng/ml final concentration) for an additional 24 hours. Controls groups were stimulated with PMA (10 ng/ml, 24 hrs)  without pretreatment or treated with VGN alone (4 μM, 48 hrs).

value: monocyte-macrophage

tag: pretreatment

value: VGN73 (8 uM, 24 hrs) pretreatment

value: PMA (10 ng/ml, 24 hrs)


title: Scer, 15 min fixation, heatshock, MNase rep 1

value: BJ5464 (delta-URA3)


title: BC3_Mut2

value: Mutant peptide

value: Mutant peptide (18.1 uM) for 30 minutes

value: 4-Thiouridine (s4U; 300 uM) for 1.5 hours


title: Caerulein_19


title: 34-t5_S22

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
34-t5_S22_L001

value: PBMCs

value: HOVON139/GIVE post-Tx

value: End of induction treatment


title: PMA_VGN4_3

value: VGN73 (4 uM, 24 hrs) pretreatment


title: Caerulein_18


title: BC3_Wt2

value: primary effusion lymphoma

value: Wild type peptide (18.1 uM) for 30 minutes


title: Scer, 24hr fixation, optimal growth, MNase rep 3

value: Optimal growth

value: 24 hr


title: PMA_VGN4_2


title: Caerulein_10

value: Pancreas

value: WT


title: 34-6t4_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
34-6t4_S9_L001

value: 12 months after randomization


title: Scer, 24hr fixation, optimal growth, MNase rep 2


title: PMA_VGN4_1

value: monocyte-macrophage


title: Caerulein_9

value: Caerulein


title: PMA_VGN8_3

value: VGN73 (8 uM, 24 hrs) pretreatment

value: PMA (10 ng/ml, 24 hrs)


title: PMA_VGN8_2


title: 34-6t2_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
34-6t2_S9_L001

value: 6 months after randomization


title: VGN73_3

value: VGN73 (4 uM, 24 hrs)


title: Scer, 24hr fixation, optimal growth, MNase rep 1

value: BJ5464 (delta-URA3)


title: 33-6t4_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
33-6t4_S8_L001

value: PBMCs

value: HOVON139/GIVE post-Tx


title: Scer, 6hr fixation, optimal growth, MNase rep 3

value: 6 hr


title: 35-3t4_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
35-3t4_S10_L001

value: Venetoclax ramp-up


title: PBS_16

value: PBS


title: Scer, 6hr fixation, optimal growth, MNase rep 2

value: Optimal growth


title: 32-3t4_S21

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
32-3t4_S21_L001


title: Scer, 6hr fixation, optimal growth, MNase rep 1


title: PBS_17


title: PBS_15


title: PMA_3

value: No pretreatment


title: VGN73_1

value: VGN73 (4 uM, 24 hrs) pretreatment


title: PBS_8

value: Pancreas

value: WT


title: 31-6t2_S16

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
31-6t2_S16_L001


title: Scer, 1hr fixation, optimal growth, MNase rep 3

value: 1 hr


title: PBS_7


title: 33-6t2_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
33-6t2_S10_L001


title: DNFB_14

source_name: Epithelial skin

value: Epithelial skin

value: DNFB


title: PMA_2

value: monocyte-macrophage

value: PMA (10 ng/ml, 24 hrs)


title: Scer, 1hr fixation, optimal growth, MNase rep 2


title: 30-6t4_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
30-6t4_S6_L001

value: 12 months after randomization


title: Scer, 15 min fixation, optimal growth, MNase rep 3

value: BJ5464 (delta-URA3)

value: 15 min


title: 30-6t2_S13

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
30-6t2_S13_L001

value: PBMCs

value: HOVON139/GIVE post-Tx

value: 6 months after randomization


title: 30-6t4_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
30-6t4_S5_L001


title: ATAC_NC_3

city: Beijing

first: Wenxue

last: Zhao

address: Yiheyuan Road

institute: Peking University

data_processing:
Sequencing adaptors were removed from the raw ATAC-seq reads using TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and the clean data were mapped to the human reference genome (hg19) using Bowtie2 (v.2.4.1) (Langmead and Salzberg, 2012). Picard (https://broadinstitute.github.io/picard/) was used to remove PCR duplicates. The nuclear repeat length (NRL) was calculated using NRLfinder as previous publication (Willcockson et al., 2020).
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak

source_name: colon cancer

extract_protocol:
Each sample containes 100,000 cells and the cell pellet was collected using moderately cold lysis buffer.
Each sample (containing 500,000 cells) was centrifuged with 500 g, 4°C for 5 min to collect cell pellet. The cell pellet was resuspended with moderately cold lysis buffer, and library construction used the TruePrep DNA Library Prep Kit V2 for Illumina (TD501) (Vazyme Biotech Co., Ltd). DNA libraries were produced after 12 cycles of PCR amplification using the TruePrep library prep kit. After purification, the paired-end sequencing was performed on the Illumina Novaseq 6000 platform.

value: colon cancer

value: human colon cancer cell line

value: wild type


title: ATAC_NC_2


title: Scer, 1hr fixation, optimal growth, MNase rep 1

value: Optimal growth


title: Scer, 15 min fixation, optimal growth, MNase rep 2


title: VGN73_2

value: VGN73 (4 uM, 24 hrs) pretreatment

value: VGN73 (4 uM, 24 hrs)


title: DNFB_13

value: WT


title: Scer, 15 min fixation, optimal growth, MNase rep 1


title: 30-3t4_S20

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
30-3t4_S20_L001

value: Venetoclax ramp-up


title: ATAC_NC_1


title: DNFB_5

value: Epithelial skin

value: DNFB


title: 29-3t4_S19

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
29-3t4_S19_L001


title: DNFB_4


title: 30-t5_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
30-t5_S7_L001

value: End of induction treatment


title: ATAC_AID_2

value: NuMA depletion


title: Scer, 24hr fixation, heatshock, FAIRE rep 3

value: BJ5464 (delta-URA3)

value: Heatshocked

value: 24 hr


title: 28-t5_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
28-t5_S6_L001

value: PBMCs

value: HOVON139/GIVE post-Tx


title: ATAC_AID_3

value: colon cancer


title: PMA_1

value: monocyte-macrophage

value: No pretreatment

value: PMA (10 ng/ml, 24 hrs)


title: Acetone_12

value: Acetone


title: ATAC_AID_1

value: human colon cancer cell line


title: Scer, 24hr fixation, heatshock, FAIRE rep 1


title: NuMA-N_terminal

data_processing:
TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to cut adapters, and then trimmed reads were aligned to the human genome (hg19) using Bowtie2. Reads were sorted and converted to BAM format and duplicates were marked using Picard (https://broadinstitute.github.io/picard/). After normalizing the samples to the same sequencing depth, deepTools2 (v 3.3.1) software was used to plot the heat maps to show signals around peak regions with default parameters. Peaks were called using Macs2 with a relaxed q-value threshold of 0.001.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Target genomic DNA was extracted using the NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit (NovoProtein, N259-YH01).
The CUT&Tag assay was performed using the NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit (NovoProtein, N259-YH01). 10,000 cells were washed twice with 1.5 mL of wash buffer and then mixed with activated concanavalin A beads. After successive incubations with the primary antibody (RT, 2h) and secondary antibody (RT, 1.5 h), the cells were washed and incubated with pAG-Tn5 for 1.5 h. Then, tagmentation buffer was added to activate tagmentation for 1 h. The tagment DNA fragments were purified using tagment DNA extract beads and washed by 80% ethanol. Then, the libraries were sequenced using the Illumina NovaSeq 6000 platform.

value: wild type


title: Acetone_3

value: WT


title: Acetone_11

value: Epithelial skin


title: 28-3t4_S18

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
28-3t4_S18_L001

value: Venetoclax ramp-up


title: Scer, 6hr fixation, heatshock, FAIRE rep 3

value: 6 hr


title: 28-6t2_S11

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
28-6t2_S11_L001

value: 6 months after randomization


title: DNFB_6

value: DNFB


title: Acetone_2


title: NuMA-C_terminal


title: Scer, 6hr fixation, heatshock, FAIRE rep 2

value: BJ5464 (delta-URA3)

value: Heatshocked


title: Acetone_1


title: NuMA-IgG


title: 27-t5_S17

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
27-t5_S17_L001

value: PBMCs

value: End of induction treatment


title: 27-6t4_S23

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
27-6t4_S23_L001

value: HOVON139/GIVE post-Tx

value: 12 months after randomization


title: Scer, 24hr fixation, heatshock, FAIRE rep 2

value: 24 hr


title: histoneH1_NC_2

value: colon cancer


title: 27-6t2_S12

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
27-6t2_S12_L001


title: Scer, 6hr fixation, heatshock, FAIRE rep 1


title: TCR library_Vax C_CD3+cells

city: Dallas

first: Jiahui

last: Chen

state: TEXAS

address: 5323 Harry Hines Blvd

department: SCCC

institute: UTSW

data_processing:
The Cell Ranger (4.0.0) Software Suite was used to process the raw sequence data into gene expression profiles. The fastq files for each sample were processed with Cell Ranger count, which was used to align to mm10-2020-A reference genome, filter and quantify.
The output files of Cell Ranger for each sample included surface protein and gene expression (in UMI count). Merged surface protein and gene expression data were obtained using the cellranger aggr, which performed an inter-sample normalization and merged the results of all samples into one file, to remove the potential technique variability of samples.
For scTCR-seq data, TCR reads were aligned to the vdj_GRCm38_alts_ensembl-4.0.0 reference genome and TCR annotation was performed using the 10x cellranger vdj pipeline.
The Cd45 expression was defined as the average UMI counts of Ptprc, and those cells with Ptprc expression > 0 were kept for subsequent analysis.  The Cd3 expression was defined as the average UMI counts of Cd3d, Cd3e, Cd3g, and those cells with Cd3 expression > 0 were kept for subsequent analysis.
The Seurat pipeline was applied to the combined expression data. Principle component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and Uniform Manifold Approximation and Projection (UMAP) were  was performed on the scaled data of all genes.
Clusters were identified using shared nearest neighbor (SNN)-based clustering based on the same principal components. We used the function FindClusters for clustering with resolution from 0.1 to 1.5. For each resolution, the silhouette values were calculated. Such value was used to determine the optimaloptional cluster number k.
Assembly: mm10-2020-A
Supplementary files format and content: matrix.mtx file, features.tsv file, and a barcodes.tsv file with rawcounts from CellRanger Count

source_name: TC-1 mouse tumor infiltrated immune cell

extract_protocol:
TC-1 tumors harvested at day 17, 22 and day 27 post inoculation. Tumor tissues were cut into approximately 1 mm3 pieces in the RPMI-1640 medium (Invitrogen) with 2% fetal bovine serum (FBS), and enzymatically digested with MACS tumor Dissociation Kit (Miltenyi Biotec) for 40 min on gentleMACS™ Dissociator according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 70 μm cell strainer and centrifuged at 500 g for 10 min.
As described in Single Cell V(D)J Reagent Kits with Feature Barcode technology for Cell Surface Protein User maual (10x Genomics, CG000186).

treatment_protocol: A total of 1.5x105 TC-1 were inoculated subcutaneously into right dorsal flanks of the mice in 100 μl phosphate buffered saline (PBS). Tumor-bearing mice were randomly grouped into treatment groups when tumors grew to around 30-60mm3. For E7-vaccine treatment, 0.5 μg of peptide and 30 μg of PC7a was mixed in 100 μl of PBS, subcutaneously injected on day 6-9 post tumor inoculation. For cGAMP treatment, the antibody was diluted in 200 μl of PBS and intraperitoneally injected on day 6, 9, 12 post tumor inoculation.

value: tumor

value: Vaccine


title: TCR library_Vax B_CD3+cells


title: TCR library_Ctrl A_CD3+cells

value: PBS


title: Scer, 1hr fixation, heatshock, FAIRE rep 3

value: 1 hr


title: 27-3t4_S16

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
27-3t4_S16_L001


title: Scer, 1hr fixation, heatshock, FAIRE rep 1


title: Scer, 1hr fixation, heatshock, FAIRE rep 2


title: 27-3t4_S13

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
27-3t4_S13_L001


title: histoneH1_AID_2

value: human colon cancer cell line

value: NuMA depletion


title: histoneH1_AID_1


title: Scer, 15 min fixation, heatshock, FAIRE rep 3

value: 15 min


title: TCR library_Vax A_CD3+cells


title: C1 kidney, AKI,  visium

city: Birmingham

first: James

middle: F

last: George

state: Alabama

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0, samples were analyzed using Seurat v4.3.0. Kidney resident macrophages were identified via expression of C1QA
Assembly: human GRCh38 (GCA_000001405.28)

source_name: kidney

extract_protocol:
Freshly collected immune cells were isolated from human kidneys. Cross sections of kidney were digested in the commercially available collagenase, Liberase, for 30 minutes at 37 degrees Celsius. Red blood cells were lysed and the samples were resuspended in PBS. Samples were stained for Viability and resuspended in FACS Buffer (PBS, 5% FBS, 5% EDTA) and stained with CD45-FITC antibody. Samples were identified as being FITC positive using FACS (Aria, BD) and unstained samples were used as a negative control.
RNA was isolated according to manufacturer's instructions for 3' Chromium gene expression and Visium spatial transcriptomics kits

value: kidney

tag: gender

value: male

tag: disease state

value: Acute Kidney Injury


title: 26-3t4_S31

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
26-3t4_S31_L001

tag: sample type

tag: patient number

value: Venetoclax ramp-up


title: gene expression library_Ctrl C_CD3+cells

description:
E8GEXW3
W3_matrix.mtx.gz
W3_barcodes.tsv.gz
W3_features.tsv.gz


title: B15 kidney, AKI,  visium

description: 10X Genomics


title: H1 kidney, AKI, scRNAseq

description: 10X Genomics


title: Scer, 15 min fixation, heatshock, FAIRE rep 2

value: BJ5464 (delta-URA3)

value: Heatshocked


title: gene expression library_Ctrl C_CD45+CD3- cells

description:
E7GEXW45
W45_matrix.mtx.gz
W45_barcodes.tsv.gz
W45_features.tsv.gz


title: 26-3t4_S10

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
26-3t4_S10_L001

value: PBMCs

value: HOVON139/GIVE post-Tx

tag: timepoint


title: gene expression library_Vax C_CD45+CD3- cells

description:
D10GXC45
C45_matrix.mtx.gz
C45_barcodes.tsv.gz
C45_features.tsv.gz


title: 25-6t4_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
25-6t4_S4_L001

value: 12 months after randomization


title: histoneH1_NC_1

value: colon cancer

value: wild type


title: PS3P9

city: Hong Kong

first: Mingxi

last: WENG

state: Not Applicable

address: L408A, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

country: Hong Kong

institute: School of Biomedical Sciences, The University of Hong Kong

data_processing:
Raw reads in fastq format were aligned to the hg38 transcriptome using RSEM and bowtie 2.0 (with options: rsem-calculate-expression --bowtie2 --bowtie2-sensitivity-level very_sensitive --no-bam-output --estimate-rspd --paired-end).
Gene level alignment results of samples were merged and annotated using glbase3.
Read counts per genes were calculated using RSEM and normalized to GC content using EDAseq. GC-normalized read counts no less than 20 in at least two samples were kept, leading to a final read count table.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files. The first column is the ensemble gene ID(ensg). The second column contains the official gene names (name). The rest of the columns contain the normalized read counts for each sample.

source_name: Pluripotent stem cells

growth_protocol: Human naive PSCs (NPSCs), including those reprogrammed from dermal fibroblasts and iEPSCs, were propagated in different naïve culture condition: EPSCM, PXGLM and HENSM on mitomycin C-treated ICR MEF feeders. Human iEPSCs were propagated in EPSCM. ROCK inhibitor (Y-27632, #) were added to culture medium at the day of cell-replating onto feeders. Human NPSCs and EPSCs were cultured in a humidified incubator at 37 ℃.

extract_protocol:
NPSCs and iEPSCs were incubated onto gelatin for 60 min at 37 degree to remove MEFs. Total RNA was extracted using TRIzol reagent (Invitrogen, #15596018) following the user guide quantified using a Nanodrop One spectrophotometer (Thermo Scientific).
mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. ffective concentration of library was determined by Q-PCR. Finally, the qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

value: Pluripotent stem cells

value: hiEPSC

value: PXGLM


title: gene expression library_Vax C_CD3+cells

description:
D11GEXC3
C3_matrix.mtx.gz
C3_barcodes.tsv.gz
C3_features.tsv.gz

value: tumor

value: Vaccine


title: gene expression library_Vax B_CD3+cells

description:
D9GEXB3
B3_matrix.mtx.gz
B3_barcodes.tsv.gz
B3_features.tsv.gz


title: 25-6t4_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
25-6t4_S5_L001


title: Scer, 15 min fixation, heatshock, FAIRE rep 1

value: 15 min


title: H2 kidney, AKI, scRNAseq

description: 10X Genomics

value: kidney


title: Scer, 24hr fixation, optimal growth, FAIRE rep 3

value: Optimal growth

value: 24 hr


title: 26-6t2_S16

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
26-6t2_S16_L001

value: 6 months after randomization


title: 25-6t2A_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
25-6t2A_S7_L001


title: Scer, 6hr fixation, optimal growth, FAIRE rep 3

value: BJ5464 (delta-URA3)

value: 6 hr


title: 25-3t4B-echt_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
25-3t4B-echt_S5_L001

value: PBMCs

value: Venetoclax ramp-up


title: PF2P10


title: gene expression library_Vax B_CD45+CD3- cells

description:
D8GEXB45
B45_matrix.mtx.gz
B45_barcodes.tsv.gz
B45_features.tsv.gz


title: gene expression library_Vax A_CD3+cells

description:
D5GEXA3
A3_matrix.mtx.gz
A3_barcodes.tsv.gz
A3_features.tsv.gz


title: H9PXP18

value: ESC


title: ES3P27

value: EPSCM


title: Scer, 24hr fixation, optimal growth, FAIRE rep 2


title: Scer, 6hr fixation, optimal growth, FAIRE rep 2


title: gene expression library_Vax A_CD45+CD3- cells

description:
D4GEXA45
A45_matrix.mtx.gz
A45_barcodes.tsv.gz
A45_features.tsv.gz


title: Scer, 6hr fixation, optimal growth, FAIRE rep 1


title: surface protein library_Vax C_CD3+cells

description:
A11_SC3
C3_matrix.mtx.gz
C3_barcodes.tsv.gz
C3_features.tsv.gz


title: S1_9


title: Scer, 24hr fixation, optimal growth, FAIRE rep 1


title: Scer, 1hr fixation, optimal growth, FAIRE rep 3

value: 1 hr


title: PF1P13

value: Pluripotent stem cells


title: surface protein library_Vax C_CD45+CD3- cells

description:
A10_SC45
C45_matrix.mtx.gz
C45_barcodes.tsv.gz
C45_features.tsv.gz


title: HS5P5

value: hiEPSC

value: HENSM


title: 24-3t4_S3

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
24-3t4_S3_L001

value: HOVON139/GIVE post-Tx


title: 22-6t4_S20

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
22-6t4_S20_L001

value: 12 months after randomization


title: surface protein library_Vax B_CD3+cells

description:
A9_SB3
B3_matrix.mtx.gz
B3_barcodes.tsv.gz
B3_features.tsv.gz

value: tumor

value: Vaccine


title: HS3P5


title: Scer, 1hr fixation, optimal growth, FAIRE rep 2

value: Optimal growth


title: surface protein library_Vax B_CD45+CD3- cells

description:
A8_SB45
B45_matrix.mtx.gz
B45_barcodes.tsv.gz
B45_features.tsv.gz


title: Scer, 1hr fixation, optimal growth, FAIRE rep 1


title: 22-6t2_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
22-6t2_S4_L001


title: 22-5PB_S29

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
22-5PB_S29_L001

value: End of induction treatment


title: Scer, 15 min fixation, optimal growth, FAIRE rep 2

value: 15 min


title: HF5P5


title: 25-3t4_S15

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
25-3t4_S15_L001


title: surface protein library_Ctrl A_CD3+cells

description:
A5_SW3
W3_matrix.mtx.gz
W3_barcodes.tsv.gz
W3_features.tsv.gz

value: PBS


title: HF2P5


title: 24-t5A_S14

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
24-t5A_S14_L001

value: End of induction treatmentA


title: surface protein library_Ctrl A_CD45+CD3- cells

description:
A4_SW45
W45_matrix.mtx.gz
W45_barcodes.tsv.gz
W45_features.tsv.gz


title: 24-3t4_S30

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
24-3t4_S30_L001

value: PBMCs


title: Scer, 15 min fixation, optimal growth, FAIRE rep 1

value: BJ5464 (delta-URA3)


title: ES2P5


title: surface protein library_Vax A_CD3+cells

description:
A3_SA3
A3_matrix.mtx.gz
A3_barcodes.tsv.gz
A3_features.tsv.gz


title: 21-6t2_S8

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
21-6t2_S8_L001

value: 6 months after randomization


title: 21-6t4_S19

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
21-6t4_S19_L001


title: Scer, 24 hr fixation, heatshock, FAIRE Input

value: Heatshocked

value: 24 hr


title: ES1P5

value: Pluripotent stem cells

value: EPSCM


title: Scer, 6 hr fixation, heatshock, FAIRE Input

value: 6 hr


title: 21-3t4_S28

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
21-3t4_S28_L001

value: HOVON139/GIVE post-Tx

value: Venetoclax ramp-up


title: EF3P5

value: hiEPSC


title: surface protein library_Vax A_CD45+CD3- cells

description:
A2_SA45
A45_matrix.mtx.gz
A45_barcodes.tsv.gz
A45_features.tsv.gz

value: tumor

value: Vaccine


title: Scer, 15 min fixation, optimal growth, FAIRE rep 3

value: Optimal growth


title: 20-6t4_S17

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
20-6t4_S17_L001

value: 12 months after randomization


title: Seq04_SingleCell

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

country: Germany

institute: University Hospital Bonn

data_processing:
Raw sequencing bcl files were demultiplexed using the Bcl2fastq2 V2.20
Sequencing adapters were trimmed and sequencing reads with a PHRED score >20 were filtered using Cutadapt 1.16
STAR aligner1 was used to align reads against GENCODE vM16 mouse reference genome
Drop-seq tools 2.0.0 were used to generate a UMI-corrected gene expression count matrix
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited list of Barcodes
Supplementary_files_format_and_content: Tab-delimited list of genes
Supplementary_files_format_and_content: UMI-corrected gene expression count matrix

source_name: activated murine CD4 T cells in vitro

growth_protocol: Isolated naive CD4 cells were cultured in cRPMI for indicated periods

extract_protocol:
Cells were stained for flow cytometry and and sorted. The sorted cells were pooled, spun down and resuspend in sample buffer. Cell counting was performed using an INCYTO hemocytometer, and a total of 58,000 cells were loaded on a BD Rhapsody cartridge.
Libraries were prepared using the BD Rhapsody mRNA Whole Transcriptome Analysis and Sample Tag Library Preparation Protocol, as per the manufacturer’s recommendations (BD Biosciences).

treatment_protocol: The cell culture are activated with plate-bound anti-CD3 and anti-CD28 and differentiated in the Tfh(2) conditions

value: CD4 T cell

tag: condition