title: X430 day 2 after CHMI [X5172571]

description:
430_G3_V06A
BSPZV1-34-038

value: NO


title: Mock - 4dpi - Rep2 [M4B RNA-seq]

status: Public on Feb 04 2022

type: SRA

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

library_source: transcriptomic

data_processing:
Raw 100nt strand-specific single-end reads were quality checked with FASTQC. As many samples presented undetermined nucleotides (“N”) and decreased quality after 76th position, all reads from all samples were truncated to the first 75 nucleotides.
Truncated (75nt) reads were aligned against mouse genome sequence (GRCm38) with TopHat2 (Kim et al. 2013) allowing intron sizes up to 100.000 nt and using default settings for single-end alignments.
Htseq-count function of HTSeq package (Anders et al., 2014) was used for assigning reads to each mouse gene and lncRNA. Genomic feature coordinates were obtained from mouse annotation version GRCm38.76 (ENSEMBL).
To evaluate differential expression of features between SARS-CoV-∆E (2dpi) and WildType (2dpi) samples, DESeq2 (Love et al., 2014) was used. Default parameters were used except detection of outlier counts by Cook’s distance that was not applied (cooksCutoff=FALSE). Three biological replicates per sample were included in the analysis and p.values obtained were adjusted by FDR (Benjamini and Hochberg, 1995).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include raw read count values for all samples

molecule: total RNA

organism: Mus musculus

growth_protocol: Specific-pathogen-free 8 week-old BALB/c OlaHsd female mice were purchased from Harlan. Mice were maintained for 8 additional weeks in the animal care facility at the National Center of Biotechnology (CNB-CSIC, Madrid).

extract_protocol:
To isolate long and small RNAs separately, one-half of the right lung was homogenized in 2 mL of Lysis/Binding Solution (mirVana miRNA Isolation Kit, Ambion) using a MACS homogenizer (Miltenyi Biotec), according to manufacturer’s protocols. Small and long RNAs were extracted separately from total RNA samples using mirVana miRNA Isolation protocol.
.6 µg of the long RNA fraction were treated to eliminate ribosomal RNA (RiboZero rRNA Removal Kit, Epicentre) and libraries were constructed (NEBNext Ultra directional Library prep A, Illumina) and subjected to 100SE sequencing on a Hiseq 2000 sequencer (Illumina, Parque Científico de Madrid, PCM), resulting in 20 million reads per sample.

treatment_protocol: 16-week-old mice were inoculated with rSARS-CoV wt or rSARS-CoV-ΔE in 50 μl of DMEM containing 2% fetal bovine serum (FBS, Biowhittaker). Mice were sacrificed at days 2 and 4 post infection and lung and serum samples were collected.

tag: strain

value: BALB/c OlaHsd

tag: age

tag: infected with

value: mock

tag: time point

tag: tissue

value: lung


title: X430 before CHMI [X7172501]

city: Seattle

first: Raphael

last: Gottardo

state: WA

address: 1100 Fairview Ave N

department: VIDD

country: USA

institute: Fred Hutch

description:
430_G3_V05C
BSPZV1-34-038

data_processing:
Reads were aligned to the human hg19 genome using STAR.
htseq-count using the intersection-strict option was used to convert mapped reads into a gene count table.
Genes were filtered to retain only genes with >10 read counts in at least 5% of samples.
Counts were then normalized using the R limma and voom packages to account for sequencing depth and log2 transformed for all downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Whole Blood

extract_protocol:
Whole blood samples taken from participants via venipuncture and collected into PaxGene tubes. Total RNA was extracted using PAXgene Blood Kit (PreAnalytiX) and globin mRNA removed using GLOBINclear Human Kit (Ambion).
RNA libraries were generated using standard manufacturers’ protocols for Illumina’s HiSeq 4000

tag: visit

tag: day

tag: protection

value: NP

tag: immunization

tag: group

tag: sample id

value: Whole Blood


title: Mock - 2dpi - Rep2 [M2B RNA-seq]


title: X411 day 7 after 1st vac [X1170020]

description:
411_G3_V01B
BSPZV1-34-081

value: P

value: YES


title: Infected (deltaE) - 4dpi - Rep3 [E4D RNA-seq]

source_name: Infected (deltaE)_4dpi_lung

value: rSARS-CoV-ΔE


title: Mock - 2dpi - Rep1 [M2A RNA-seq]


title: X411 day 2 after CHMI [X1172531]

description:
411_G3_V06A
BSPZV1-34-081


title: X430 day 9 after CHMI [X3172011]

description:
430_G3_V07T0
BSPZV1-34-038


title: Infected (deltaE) - 4dpi - Rep2 [E4B RNA-seq]


title: X411 day 7 after 2nd vac [X4170563]

description:
411_G3_V02B
BSPZV1-34-081


title: Infected (deltaE) - 4dpi - Rep1 [E4A RNA-seq]


title: X411 day 2 after 1st vac [X7170467]

description:
411_G3_V01A
BSPZV1-34-081


title: X411 day 0 [X7169963]

description:
411_G3_PreVAC
BSPZV1-34-081

value: Screen 3


title: X360 day 9 after CHMI [X1172018]

description:
360_G3_V07T0
BSPZV1-34-031


title: Infected (deltaE) - 2dpi - Rep1 [E2A RNA-seq]

source_name: Infected (deltaE)_2dpi_lung


title: Infected (deltaE) - 2dpi - Rep3 [E2D RNA-seq]


title: X360 before CHMI [X8172484]

description:
360_G3_V05C
BSPZV1-34-031


title: A23

city: Framingham

first: herve

last: husson

state: ma

address: 49 New York Avenue

department: genomics medicine unit

institute: Sanofi

data_processing:
Using Array Studio version 9.0 (Omicsoft Corporation, a Qiagen Company), reads were filtered  according to the following protocol: Trimming  /Mode=TrimByQuality /ReadTrimQuality=20;  FilterSource IlluminaAdapters,Ercc /CustomFile="";  Options  /FileFormat=AUTO /QualityEncoding=Automatic /WriteFilterFiles=False /EnableLengthCutoff=True /LengthCutoff=25 /EnableMaxQualityCutoff=False /MaxQualityCutoff=15 /EnableAverageQualityCutoff=True /AverageQualityCutoff=15 /EnablePolyRateCutoff=True /PolyRateCutoff=75 /OutputFolder="/site/ne/data/bi/omicsoft/FtpRootCR/Users/soka01/wax.1055_test/wax1057_test" /CompressionMethod=Gzip /Gzip=True /PairedEnd=True /FilterPairByBothEnds=True /ParallelJobNumber=32;  End;
Using Array Studio version 9.0 Mapping to the reference was as follows: Reference Mouse.B38;  GeneModel Ensembl.R83;  Trimming  /Mode=TrimByQuality /ReadTrimQuality=20;  Options  /ParallelJobNumber=32 /PairedEnd=True /FileFormat=AUTO /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=True /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /OutputFolder="/site/ne/data/bi/omicsoft/FtpRootCR/Users/soka01/Alport_kidney_RNAseq/Study13-04182_April2016/B38_R83_mapped" /ThreadNumber=8 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=200 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=True /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;  Output Alport kidney 4.16;  End;
Using Array Studio version 9.0 counts & FPKM values were generated using the following parameters: Begin ReportGeneTranscriptCounts /Namespace=NgsLib /RunOnServer=True;  Project alport.kidney.study13-04182;  Data "alport.kidney.study13-04182.exu09sep2016.ricbr01\\Alport kidney 4.16";  GeneModel Ensembl.R83;  Options  /ExpressionMeasurement=RPKM+Count /ParallelJobNumber=32 /Add1=False /CountFragments=True /ExcludeMultiReads=False /UseEffectiveTranscriptLength=False /CountStrandedReads=True /CountReverseStrandedReads=True /AutoTrimUtr=False /OutputFolder="/site/ne/data/bi/omicsoft/FtpRootCR/Users/soka01/Alport_kidney_RNAseq/Study13-04182_April2016/B38_R83_mapped";  Output alport kidney 4.16;  End;
Using Array Studio version 9.0.1.38 transcripts were filtered based on counts as follows: By Variable;  Filter Sum>=0.1;  Options /Group=(all) /ApplyToAllGroups=True /CountingCutoff=5 /FilterByDetection=False;  Output counts_greaterthan0.1;  End;  End;
Using Array Studio version 9.0.1.38, normalized FPKM values were transformed as follows: Data alport.kidney.study13-04182\\alport kidney 4.16.FPKM /Variables=alport.kidney.study13-04182\\counts_greaterthan0.1;  By Observation;  Options /Normalization=ScaleQuantile /Parameter1=75 /Parameter2=10;  Output filteredFPKM_ScaleQuantNorm;  End;
Using Array Studio version 9.0.1.20  expression data were log transformed as follows: Data alport.kidney.study13-04182\\alport kidney 4.16.FPKM;  Options /Transformation=Log2 /Add=1;  Output alport kidney 4.16_log2FPKM;  End;
Genome_build: Omicsoft Mouse.B38

source_name: kidney

extract_protocol:
RNA was isolated by TRIzol and chloroform extraction from homogenized adipose tissue followed by RNeasy purification to remove genomic DNA (Qiagen).
RNA-seq of total RNA samples was conducted on the Illumina HiSeq 2000 platform, producing 100bp paired-end reads

treatment_protocol: Col4a3-/- mice were treated from 5 weeks of age with weekly (QW) Sub-Cutaneous injection of PBS (Vehicle), Lademirsen at 50mg/kg in PBS (Anti-miR-21) or ramipril at 11 mg/L ad libitum in drinking water (ACEi) and sacrificed at 15 weeks of age. Wild type mice (WT) did not receive any treatment.

tag: genotype

value: kidney

value: 129SJ x C57Bl/6J

tag: treatment

value: Ramipril

tag: group name

value: ACEi


title: X360 day 2 after CHMI [X7172528]

description:
360_G3_V06A
BSPZV1-34-031


title: X351 day 2 after CHMI [X4172561]

description:
351_G3_V06A
BSPZV1-34-027


title: X351 day 9 after CHMI [X7172015]

description:
351_G3_V07T0
BSPZV1-34-027


title: A22

value: anti-miR-21 QW


title: X351 before CHMI [X9172485]

description:
351_G3_V05C
BSPZV1-34-027


title: Infected (deltaE) - 2dpi - Rep2 [E2C RNA-seq]


title: A11


title: A15


title: A12


title: X351 day 2 after 1st vac [X2170390]

description:
351_G3_V01A
BSPZV1-34-027


title: A10


title: X351 day 0 [X3169977]

description:
351_G3_PreVAC
BSPZV1-34-027


title: A2


title: X351 day 7 after 2nd vac [X2170561]

description:
351_G3_V02B
BSPZV1-34-027


title: X335 day 9 after CHMI [X1172009]

description:
335_G3_V07T0
BSPZV1-34-020


title: A8


title: wild type

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

country: United Kingdom

institute: University of Edinburgh

library_source: genomic

data_processing:
Fastq reads aligned to S.cerevisiae SK1 using HiC-Pro v2.11.4 , bowtie2 v2.3.4.1 (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder), removing singleton, multi hit, MAPQ<10 and duplicated reads.
Valid interaction pairs were converted into the .cool contact matrix format using cooler v0.7.11 (1 kb resolution)
Matrixes balanced using Iterative correction
Genome_build: S.cerevisiae SK1
Supplementary_files_format_and_content: Cooler .cool matrix 1kb binned, balanced with iterative correction

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: Cells were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA). Cells were grown to for approx. 16 hours to OD(600) of approx. 4. Cells were diluted to OD(600) = 1.8 and sporulated for 2 hours in SPO media (0.3% Kac) to arrest prior to meiotic S phase

extract_protocol:
Lysates were prepared by grinding the frozen pellet in a chilled mortar with a pestle for 15 minutes and 1/10th of the initial pellet weight (~0.5 g) was taken for further processing. Restriction enzyme digestion (DpnII), filling-in, ligation, crosslink reversal, DNA concentration and purification and biotin removal were carried out as described in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038. DNA was then fragmented on a Bioruptor Plus sonication device (Diagenode) for a total of 2x 30 cycles 30 seconds on/off at High setting.
DNA end repair and A-tailing using T4 DNA polymerase, T4 Polynucleotide Kinase and Klenow fragment DNA polymerase I were carried out as in Schalbetter et al., 2018. Hi-C libraries were fractionated using Ampure XP beads as previously described in Belton et al. (2015) DOI: 10.1101/pdb.prot085209. Biotin pull-down, adapter ligation (NextFlex, Bioo Scientific) and sequencing (EMBL Core Genomics Facility, Heidelberg, Germany) were carried as in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038.

treatment_protocol: Cells were fixed and lysed as in Belton & Dekker (2015) DOI: 10.1101/pdb.prot085209. Briefly, 50 ml of cells at OD~1.8 carrying ndt80 deletion were arrested in meiotic prophase I, fixed with 3% formaldehyde for 20 minutes at 25 ˚C at 250 rpm and the reaction was quenched for 5 minutes by the addition of 0.35 M glycine (final concentration). Cells were washed with cold water, resuspended in 5 ml 1x NEBuffer 2 and frozen in liquid nitrogen.

tag: ploidy

value: Diploid

tag: cell cycle stage

value: Prior to meiotic S phase

value: pCUP-IME1 pCUP-IME4


title: A20

value: PBS QW

value: Veh


title: A13


title: X335 before CHMI [X9172494]

description:
335_G3_V05C
BSPZV1-34-020


title: A4


title: A9


title: X335 day 2 after 1st vac [X1170470]

description:
335_G3_V01A
BSPZV1-34-020


title: A18

value: WT


title: A1


title: X306 day 2 after CHMI [X3172533]

description:
306_G3_V06A
BSPZV1-34-005

value: NP


title: A14


title: X351 day 7 after 1st vac [X2170039]

description:
351_G3_V01B
BSPZV1-34-027

value: Whole Blood


title: A17


title: X335 day 7 after 1st vac [X9170415]

description:
335_G3_V01B
BSPZV1-34-020


title: X306 day 7 after 2nd vac [X9170496]

description:
306_G3_V02B
BSPZV1-34-005


title: X306 day 7 after 1st vac [X7170431]

description:
306_G3_V01B
BSPZV1-34-005


title: X335 day 2 after CHMI [X8172529]

description:
335_G3_V06A
BSPZV1-34-020


title: A19


title: A16


title: X335 day 7 after 2nd vac [X4170581]

description:
335_G3_V02B
BSPZV1-34-020


title: X306 day 2 after 1st vac [X4170311]

description:
306_G3_V01A
BSPZV1-34-005


title: X290 day 9 after CHMI [X7172006]

description:
290_G3_V07T0
BSPZV1-34-004

value: NO


title: X306 day 0 [X5169979]

description:
306_G3_PreVAC
BSPZV1-34-005

value: YES


title: X335 day 0 [X4169978]

description:
335_G3_PreVAC
BSPZV1-34-020


title: X306 day 9 after CHMI [X8172007]

description:
306_G3_V07T0
BSPZV1-34-005


title: X290 day 2 after CHMI [X8172556]

description:
290_G3_V06A
BSPZV1-34-004


title: X290 before CHMI [X8172493]

description:
290_G3_V05C
BSPZV1-34-004


title: X281 day 9 after CHMI [X6172005]

description:
281_G3_V07T0
BSPZV1-34-001


title: Control Total 17

city: New York

first: Jacob

last: Stauber

state: NY

address: 1150 Saint Nicholas Ave., Russ Berrie Bldg. Rm.408A

institute: Columbia University

description:
BT105
Barcode: GTTTCG

data_processing:
Illumina RTA was used to perform base calling, and CASAVA (version 1.8.2) was used for converting base call files (.BCL) to FASTQ format and for performing sequence adaptor trimming.
Reads were then trimmed using Trimmomatic version 0.36 (LEADING:10 TRAILING:10 MINLEN:30).
Reads were aligned to the mouse reference genome (mm10) using STAR aligner version 2.5.3a (default settings).
Count tables were generated with HTSeq (version 0.6.1p2) using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix table csv file with the raw counts generated by HTSeq for all samples

source_name: Whole Kidney

extract_protocol:
Total RNA was purified with Trizol. 4-TU tagged RNA was biotinylated by EZ-link Biotin HPDP (1 mg/ml, Pierce Biotechnology) in N,N-dimethylformamide (DMF, Sigma) for 30min and for 3 hours with EZ-link Biotin HPDP (0.2 mg/ml) in 1 ml of 10 M Tris/HCl, pH7.5, 1mM EDTA for every 100μg of total RNA. RNA was mixed with streptavidin beads (100μl, Miltenyi Biotec Inc), and applied to magnetic columns (Miltenyi Biotec Inc). Biotinylated RNA was eluted with 5% (v/v) β-mercaptoethanol. We finally used RNeasy MinElute Cleanup Kit (Qiagen) to concentrate the biotinylated RNA.
Library prepared by using Illumina TruSeq RNA prep kit

treatment_protocol: 4-TU (430 mg/kg body weight; ip) was administered 4 hours prior to kidney dissection and RNA isolation.

value: Control

tag: Sex

value: f

tag: rna tag

value: Untagged

value: 5.5 months


title: Control Total 21

description:
BT109
Barcode: ATTCCT

value: m

tag: age

value: 3 months

value: kidney


title: X306 before CHMI [X7172483]

description:
306_G3_V05C
BSPZV1-34-005


title: Control Total 20

description:
BT108
Barcode: ACTGAT


title: Control Atp6b1v1 Pulldown 16

description:
BT103
Barcode: GTGAAA

source_name: Pulldown of TU tagged Kidney RNA


title: X281 day 2 after CHMI [X7172555]

description:
281_G3_V06A
BSPZV1-34-001


title: Control Total 16

description:
BT104
Barcode: GTGGCC


title: X281 before CHMI [X5172481]

description:
281_G3_V05C
BSPZV1-34-001


title: Control Atp6b1v1 Pulldown 15

description:
BT102
Barcode: GTCCGC


title: A6

tag: strain

value: 129SJ x C57Bl/6J


title: Control Total 18

description:
BT106
Barcode: CGTACG


title: Control Total 19

description:
BT107
Barcode: GAGTGG


title: A3


title: Control Hoxb7 Pulldown 10

description:
BT100
Barcode: ATGTCA


title: Control Atp6b1v1 Pulldown 14

description:
BT101
Barcode: CCGTCC


title: X281 day 7 after 2nd vac [X6170547]

description:
281_G3_V02B
BSPZV1-34-001


title: X281 day 7 after 1st vac [X6170430]

description:
281_G3_V01B
BSPZV1-34-001


title: X281 day 2 after 1st vac [X2170309]

description:
281_G3_V01A
BSPZV1-34-001


title: Control Atp6b1v1 Pulldown 13

description:
BT098
Barcode: AGTCAA


title: X281 day 0 [X4169987]

description:
281_G3_PreVAC
BSPZV1-34-001

value: Screen 3


title: X274 day 9 after CHMI [X8171611]

description:
274_G2_V07T0
BSPZV1-34-076


title: Control Total 15

description:
BT085
Barcode: ATGTCA


title: X274 day 2 after CHMI [X3171399]

description:
274_G2_V06A
BSPZV1-34-076


title: Control Total 14

description:
BT084
Barcode: AGTTCC


title: Control Total 13

description:
BT083
Barcode: AGTCAA


title: X274 before CHMI [X1171271]

description:
274_G2_V05C
BSPZV1-34-076


title: Control Hoxb7 Pulldown 8

description:
BT082
Barcode: CTTGTA


title: Control Hoxb7 Pulldown 7

description:
BT081
Barcode: GGCTAC


title: X274 day 7 after 2nd vac [X2169292]

description:
274_G2_V02B
BSPZV1-34-076


title: Control Total 12

description:
BT079
Barcode: CAGATC


title: Control Total 11

description:
BT078
Barcode: GCCAAT


title: Control Atp6b1v1 Pulldown 12

description:
BT080
Barcode: TAGCTT


title: X274 day 2 after 1st vac [X4169798]

description:
274_G2_V01A
BSPZV1-34-076


title: X274 day 7 after 1st vac [X2169832]

description:
274_G2_V01B
BSPZV1-34-076


title: Control Total 10

description:
BT077
Barcode: ACAGTG


title: X274 day 0 [X6169746]

description:
274_G2_PreVAC
BSPZV1-34-076


title: Control Total 8

description:
BT075
Barcode: TTAGGC


title: X269 day 7 after 1st vac [X3169851]

description:
269_G2_V01B
BSPZV1-34-015

value: P


title: Control Atp6b1v1 Pulldown 11

description:
BT073
Barcode: ATCACG


title: X269 day 2 after 1st vac [X2169778]

description:
269_G2_V01A
BSPZV1-34-015


title: Control Hoxb7 Pulldown 6

description:
BT074
Barcode: CGATGT


title: X269 day 7 after 2nd vac [X4169276]

description:
269_G2_V02B
BSPZV1-34-015


title: X269 day 9 after CHMI [X4171625]

description:
269_G2_V07T0
BSPZV1-34-015


title: Control Total 9

description:
BT076
Barcode: TGACCA


title: X269 before CHMI [X9171270]

description:
269_G2_V05C
BSPZV1-34-015


title: Control Atp6b1v1 Pulldown 10

description:
BT072
Barcode: ATTCCT


title: X269 day 0 [X3169743]

description:
269_G2_PreVAC
BSPZV1-34-015


title: Control Hoxb7 Pulldown 5

description:
BT071
Barcode: ACTGAT


title: X240 day 9 after CHMI [X3171624]

description:
240_G2_V07T0
BSPZV1-34-048


title: Control Hoxb7 Pulldown 4

description:
BT070
Barcode: GAGTGG


title: vAKI Atp6b1v1 Pulldown 7

description:
BT069
Barcode: CGTACG

value: vAKI


title: Control Hoxb7 Pulldown 9

description:
BT099
Barcode: AGTTCC


title: X240 before CHMI [X8171269]

description:
240_G2_V05C
BSPZV1-34-048


title: X239 day 9 after CHMI [X1171613]

description:
239_G2_V07T0
BSPZV1-34-091


title: X269 day 2 after CHMI [X7171394]

description:
269_G2_V06A
BSPZV1-34-015


title: X239 day 2 after CHMI [X3171381]

description:
239_G2_V06A
BSPZV1-34-091


title: iAKI Atp6b1v1 Pulldown 5

description:
BT065
Barcode: GTCCGC

value: iAKI


title: iAKI Atp6b1v1 Pulldown 6

description:
BT066
Barcode: GTGAAA


title: vAKI Atp6b1v1 Pulldown 6

description:
BT068
Barcode: GTTTCG


title: Control Atp6b1v1 Pulldown 9

description:
BT040
Barcode: CCGTCC


title: X239 day 7 after 2nd vac [X5169250]

description:
239_G2_V02B
BSPZV1-34-091


title: vAKI Atp6b1v1 Pulldown 5

description:
BT067
Barcode: GTGGCC


title: X239 before CHMI [X4171283]

description:
239_G2_V05C
BSPZV1-34-091


title: X239 day 2 after 1st vac [X2169796]

description:
239_G2_V01A
BSPZV1-34-091


title: Control Atp6b1v1 Pulldown 8

description:
BT039
Barcode: ATGTCA


title: Control Atp6b1v1 Pulldown 7

description:
BT038
Barcode: AGTTCC


title: vAKI Hoxb7 Pulldown 7

description:
BT034
Barcode: TAGCTT


title: Control Atp6b1v1 Pulldown 6

description:
BT037
Barcode: AGTCAA


title: X198 day 2 after CHMI [X1171397]

description:
198_G2_V06A
BSPZV1-34-040


title: X198 day 9 after CHMI [X9171621]

description:
198_G2_V07T0
BSPZV1-34-040


title: X198 before CHMI [X2171272]

description:
198_G2_V05C
BSPZV1-34-040


title: X239 day 0 [X2169688]

description:
239_G2_PreVAC
BSPZV1-34-091


title: X240 day 2 after CHMI [X6171384]

description:
240_G2_V06A
BSPZV1-34-048


title: Control Total 7

description:
BT032
Barcode: ACTTGA


title: Control Total 6

description:
BT031
Barcode: CAGATC


title: X198 day 7 after 1st vac [X3169860]

description:
198_G2_V01B
BSPZV1-34-040


title: vAKI Hoxb7 Pulldown 6

description:
BT033
Barcode: GATCAG


title: Control Total 5

description:
BT030
Barcode: GCCAAT


title: X198 day 7 after 2nd vac [X3169275]

description:
198_G2_V02B
BSPZV1-34-040


title: Control Total 4

description:
BT029
Barcode: ACAGTG


title: X198 day 0 [X9169686]

description:
198_G2_PreVAC
BSPZV1-34-040


title: Control Total 3

description:
BT028
Barcode: TGACCA


title: PBMCs-8 wpt

city: Beijing

first: Yaqi

last: Wang

state: Beijing

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

description: 8 wpt

data_processing:
The clean single-cell RNA-seq data was mapped to macaca mulatta reference genome Mmul_10 using Cell Ranger v3.1.0.
Cell quality control was performed by R package scater v1.14.0.
The raw UMI counts were then normalized by R package scran v1.14.1 .
Seurat v3.2.3 was used for downstream analysis including identifying cell types.
Genome_build: Mmul_10
Supplementary_files_format_and_content: .tar.gz files containing cellranger output
.csv files containing raw count matrix or cell metadata

molecule: polyA RNA

organism: Macaca mulatta

source_name: monkey peripheral blood mononuclear cells

extract_protocol:
Cells were harvested and resuspended in PBS with 0.04% BSA at 1×10^6 cells per milliliter. Then, cell suspensions were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using ChromiumTM Single Cell 5' Library & Gel Bead Kit V1 (10x Genomics, 1000006). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
Barcoded cDNAs were pooled and underwent cleanup by using DynaBeads MyOne Silane Beads (Invitrogen, 37002D) and then amplified and cleanup for further next generation library construction. Single-cell RNA seq libraries were prepared using ChromiumTM Single Cell 5' Library Construction Kit V1 (10x Genomics, 1000020) following instructions provided by the manufacturer. Sequencing was performed on an Illumina HiSeq X Ten (Illumina, San Diego, CA, USA) with pair end 150bp.
Single-cell RNA sequencing

value: whole blood

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: time

value: 8 weeks post-transplantation (wpt)


title: X239 day 7 after 1st vac [X1169831]

description:
239_G2_V01B
BSPZV1-34-091

tag: visit

value: NP

tag: tissue

value: Whole Blood


title: Control Total 2

description:
BT027
Barcode: TTAGGC

value: Control


title: X179 day 9 after CHMI [X4171616]

description:
179_G2_V07T0
BSPZV1-34-054

tag: day

tag: protection

value: YES


title: PBMCs-4 wpt

description: 4 wpt

value: 4 weeks post-transplantation (wpt)


title: Control Hoxb7 Pulldown 3

description:
BT024
Barcode: GTGGCC

value: 5.5 months


title: Control Total 1

description:
BT025
Barcode: ATCACG

value: f

value: Untagged


title: PBMCs-Post-IS (Pre-Tx)

description: after immunosuppression and before cell transplant

value: before transplantation

value: Post-IS (after immunosuppression)


title: vAKI Atp6b1v1 Pulldown 4

description:
BT020
Barcode: ATGTCA

value: kidney


title: X179 before CHMI [X3171255]

description:
179_G2_V05C
BSPZV1-34-054

value: P

tag: immunization

tag: group


title: Control Hoxb7 Pulldown 2

description:
BT023
Barcode: GTGAAA

value: m

tag: genotype


title: vAKI Atp6b1v1 Pulldown 3

description:
BT019
Barcode: AGTTCC

tag: treatment

value: vAKI


title: Control Hoxb7 Pulldown 1

description:
BT021
Barcode: CCGTCC


title: vAKI Atp6b1v1 Pulldown 1

description:
BT017
Barcode: CTTGTA


title: PBMCs-Pre-IS

description: before immunosuppression

value: whole blood

value: Pre-IS (before immunosuppression)


title: X179 day 7 after 2nd vac [X6169287]

description:
179_G2_V02B
BSPZV1-34-054

tag: sample id


title: vAKI Atp6b1v1 Pulldown 2

description:
BT018
Barcode: AGTCAA


title: X198 day 2 after 1st vac [X6169782]

description:
198_G2_V01A
BSPZV1-34-040


title: vAKI Hoxb7 Pulldown 5

description:
BT016
Barcode: GGCTAC


title: 15_5

city: Düsseldorf

first: Sebastian

last: Fraune

state: North Rhine-Westphalia

address: Universitätsstr. 1, Building: 26.24, Floor/Room: 02.114

department: Institute for Zoology and Organismic Interactions

country: Germany

institute: Heinrich-Heine-University

data_processing:
Sequencing reads were trimmed for adaptor and low-quality bases using Trimmomatic v.0.38
Trimmed reads were mapped to Nematostella vectensis genome using hisat2 v2.1.0
Mapped reads were used for genome guided assemblies using StringTie v2.0 and Scallop v0.10.4. These assemblies were merged using TACO, which was then used to improve the ensembl gene model
FeatureCounts was used to to generate read counts for each gene in each sample
Genome_build: Nemetostella vectensis (Ensembl Metazoa database release 40,)
Supplementary_files_format_and_content: gene model in gff3 format
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Nematostella vectensis

source_name: host tissue

growth_protocol: polyps cultured in 16‰ arificial sea water, at either 15, 20 or 25°C

extract_protocol:
Total RNA and DNA extraction protocol from Qiagen "AllPrep DNA/RNA/miRNA Universal Kit"
TruSeq stranded mRNA (incl. p-A enrichment)

value: F1 offspring of CH2XCH6 (Kimura et al., 2003)

value: mesenteric body portion

tag: life stage

value: adult


title: 20_5


title: X179 day 7 after 1st vac [X8169829]

description:
179_G2_V01B
BSPZV1-34-054

value: Whole Blood


title: vAKI Hoxb7 Pulldown 4

description:
BT015
Barcode: TAGCTT


title: iAKI Atp6b1v1 Pulldown 4

description:
BT014
Barcode: GATCAG

value: iAKI


title: X179 day 2 after 1st vac [X8169793]

description:
179_G2_V01A
BSPZV1-34-054

value: YES


title: iAKI Atp6b1v1 Pulldown 3

description:
BT013
Barcode: ACTTGA

value: 5.5 months


title: 25_4


title: X179 day 0 [X7169594]

description:
179_G2_PreVAC
BSPZV1-34-054

value: Screen 3


title: iAKI Atp6b1v1 Pulldown 2

description:
BT012
Barcode: CAGATC

value: f


title: X179 day 2 after CHMI [X1171388]

description:
179_G2_V06A
BSPZV1-34-054


title: iAKI Atp6b1v1 Pulldown 1

description:
BT011
Barcode: GCCAAT


title: X160 day 9 after CHMI [X1171604]

description:
160_G2_V07T0
BSPZV1-34-053

value: NP

value: NO


title: vAKI Hoxb7 Pulldown 3

description:
BT010
Barcode: GTGAAA

value: kidney


title: 25_5


title: vAKI Hoxb7 Pulldown 1

description:
BT008
Barcode: CCGTCC


title: 15_4


title: iAKI Hoxb7 Pulldown 7

description:
BT007
Barcode: CGTACG


title: X160 day 2 after CHMI [X4171382]

description:
160_G2_V06A
BSPZV1-34-053


title: X160 before CHMI [X3171282]

description:
160_G2_V05C
BSPZV1-34-053


title: iAKI Hoxb7 Pulldown 5

description:
BT005
Barcode: GTGGCC


title: iAKI Hoxb7 Pulldown 6

description:
BT006
Barcode: GTTTCG


title: iAKI Hoxb7 Pulldown 4

description:
BT004
Barcode: GTGAAA


title: iAKI Hoxb7 Pulldown 3

description:
BT003
Barcode: GTCCGC


title: 20_3


title: 15_3


title: X156 day 2 after CHMI [X4171391]

description:
156_G2_V06A
BSPZV1-34-060


title: iAKI Hoxb7 Pulldown 2

description:
BT002
Barcode: CCGTCC


title: 25_2


title: X156 before CHMI [X9171261]

description:
156_G2_V05C
BSPZV1-34-060


title: X156 day 7 after 2nd vac [X2169265]

description:
156_G2_V02B
BSPZV1-34-060


title: iAKI Hoxb7 Pulldown 1

description:
BT001
Barcode: ATGTCA


title: 20_4


title: 20_2


title: vAKI Hoxb7 Pulldown 2

description:
BT009
Barcode: GTCCGC


title: 15_2


title: X156 day 7 after 1st vac [X6169827]

description:
156_G2_V01B
BSPZV1-34-060


title: 25_3


title: 25_1


title: X156 day 9 after CHMI [X6171609]

description:
156_G2_V07T0
BSPZV1-34-060


title: X156 day 2 after 1st vac [X7169792]

description:
156_G2_V01A
BSPZV1-34-060


title: 20_1


title: X156 day 0 [X7169666]

description:
156_G2_PreVAC
BSPZV1-34-060


title: 15_1


title: X144 day 9 after CHMI [X1171622]

description:
144_G2_V07T0
BSPZV1-34-047


title: X144 day 2 after CHMI [X5171383]

description:
144_G2_V06A
BSPZV1-34-047


title: X144 before CHMI [X2171254]

description:
144_G2_V05C
BSPZV1-34-047


title: CA1 cNESCs P22/D10 6F rep1

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

data_processing:
Raw fast5 files were basecalled using Guppy v.4.2.2 with the guppy_basecaller command and the dna_r9.4.1_450bps_fast.cfg configuration file and default settings. Output fast5 files were generated with the --fast5_out argument.
Barcodes were detected and reads were demultiplexed with the guppy_barcoder using the default settings.
The resulting FASTQ reads were aligned to the GRCh38 human reference with Minimap2 using the following parameters: -aLx splice --cs=long.
Raw read counts were obtained with the featureCounts tool from the Subread package v 2.0.0, using the exon counting mode.
EdgeR R-package (v3.12.1) was then used to normalize the data, calculate RNA abundance (as counts per million reads (CPM), and perform statistical analysis. Briefly, a common biological coefficient of variation (BCV) and dispersion (variance) were estimated based on a negative binomial distribution model. This estimated dispersion value was incorporated into the final EdgeR analysis for differential gene expression, and the generalized linear model (GLM) likelihood ratio test was used for statistics, as described in EdgeR user guide. Differential gene expression was established as genes with a fold change ≥ 1.5, p-value ≤0.05 and FDR ≤0.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Varga_et_al_lrRNAseq_DE_CPM.txt contains CPM values for each samples obtained from EdgeR, as well as differential expression comparisons for each sets of replicates. EdgeR output contains the log2(Fold Change of expression between samples), log2(CPM), as well as the Likelihood ratio (LR), P-values and False discovery rates (FDR). For more information, please refer to the EdgeR package manual.

source_name: CA1 hESCs-derived cNESCs

growth_protocol: H1 and CA1 human pluripotent stem cells (hPSCs) were routinely cultured on mitomycin C treated mouse embryonic fibroblast feeder cells in KSR media with 10ng/ml FGF2. KSR media contains 80% DMEM-F12 (GIBCO), 20% Knockout serum replacement (GIBCO), 0.1mM 2-mercaptoethanol, 2mM Glutamax, 0.1mM Non-essential amino acids. Prior to neural differentiation hPSCs were transferred to geltrex (GIBCO) coated surface in the absence of feeders and were cultured in mTESR2 (Stem cell technologies) media. On the day of neural induction, hPSCs were replated on geltrex coated surface in N2B27 media supplemented with 10µM SB431542 and 100nM LDN193189 and 10µM Y27632. Neural cultures were detached from Geltrex first on day 8-10 with Accutase or PBS-EDTA, and replated on laminin (Sigma) coated surface, in neural maintenance media (NES) supplemented with 10µM Y27632 at 3x105 cells per cm2 and 6F : 10ng/ml FGF2, 3μM CHIR99021, 1μM SB431542 (Peprotech), 100nM LDN193189, 100nM K02288 (Selleckchem), 100nM AKTiVIII, 75nM MK2206 (Selleckchem), and 1 μM XAV939 (Selleckchem). NES media contains 50% DMEM-F12, 50% Neurobasal, 0.1mM 2mercaptoethanol, 2mM Glutamax, 1x N2 supplement, 0.05x B27 minus vitamin A supplement (GIBCO).

extract_protocol:
Cell lysates were homogenized in QIAshredder columns (QIAGEN #79654) and total RNA was extracted with Rneasy mini columns (QIAGEN). RNA was DNase treated using TURBO DNase (ThermoFisher Scientific #AM2238). RNA quality was verified on a 2100 Bioanalyzer (Agilent Technologies) and polyadenylated RNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB # E7490L)
Libraries were generated using 100 ng of poly(A)+ RNA and Oxford Nanopore Technologies’ Direct cDNA Sequencing Kit (ONT SQK-DCS109), with each sample barcoded with the Native Barcoding Expansion kits (ONT EXP-NBD104 and ONT EXP-NBD114), according to the manufacturer’s specifications. Barcoded samples were pooled, loaded on a MinION sequencer on R9 Flow Cells (ONT FLO-MIN106D), and sequenced using the MinKNOW software v19.

treatment_protocol: H1JA and CA1 cNESCs were cultured 10 days in either 6F medium (NES supplemented with 6F) or in 4F medium (NES supplemented with only 10ng/ml FGF2, 3μM CHIR99021, 1μM SB431542, 100nM LDN193189)

value: cNESCs

tag: growth conditions

value: Differentiated from hESCs grown in normal growth conditions

value: Grown 10 days in 6F medium


title: X144 day 7 after 2nd vac [X2169283]

description:
144_G2_V02B
BSPZV1-34-047


title: CA1 cNESCs P22/D10 6F rep2


title: CA1 cNESCs P22/D10 6F-2F rep1

value: Grown 10 days in 4F medium


title: CA1 cNESCs P22/D10 6F-2F rep2


title: X144 day 7 after 1st vac [X5169826]

description:
144_G2_V01B
BSPZV1-34-047


title: CA1 hESCs P40 rep2

source_name: CA1 hESCs

value: hESCs

value: Normal hESC growth conditions

value: No treatment


title: X144 day 2 after 1st vac [X6169791]

description:
144_G2_V01A
BSPZV1-34-047


title: CA1 hESCs P40 rep1


title: dnmt1-WT-WT_B3_R2

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

data_processing:
Library strategy: TOP-Seq
Select reads with length >= 80 nt
Select reads with 5' adapter and trim 3' adapter from the remaining reads
Align reads to a human genome (mm10 build), minimum mapping quality 30
Remove PCR duplicates (used an in house script)
Calculate coverage per CG (used an in house script)
Genome_build: mm10
Supplementary_files_format_and_content: "coverage_matrix.txt.gz" text file contains coverage values (i.e., number of reads) for each CpG site within given mm10 genome

source_name: Mouse Embryonic Stem E14tg2a Cells

growth_protocol: Embryonic stem E14tg2a Dnmt1wt/wt and Dnmt1N1580A/N1580A cells were grown on 0.15% gelatin-coated dishes in Dulbecco‘s modified Eagle‘s medium (Gibco) containing 15% fetal bovine serum (Gibco) and 1000 U/ml mouse leukemia inhibitory factor (Millipore).

extract_protocol:
Genomic DNA was purified from cell lysates using the Genomic DNA Clean & Concentrator-10 Kit (Zymo Research).
Libraries were constructed according to the TOP-seq (Tethered Oligonucleotide-Primed sequencing) protocol (Stasevskij et al., 2017). Briefly, 900 ng of sonicated genomic DNA were end-filled, a 3’-dA mononucleotide extension was added and DNA was ligated to adapters. Ligated DNA was then subjected to Cu(I)-catalyzed cycloaddition reaction in which the alkyne-bearing oligodeoxyribonucleotide with biotin was attached to the azide moiety of the modified DNA. Biotinylated DNA was enriched with streptavidin-coupled magnetic beads and subsequently used in a TOP DNA priming reaction from the attached priming oligodeoxyribonucleotide. The products were amplified and subjected to Ion Proton sequencing.

treatment_protocol: E14TG2a Dnmt1wt/wt and Dnmt1N1580A/N1580A cells were inoculated with freshly prepared 1 mM ado-6-azide solution in Opti-MEM by electroporation with NEPA21 system (Nepa Gene) using cell culture plate electrode CUY900. gDNA was isolated 3h following the electroporation. Dnmt1wt/wt and Dnmt1N1580A/N1580A cells were inoculated with freshly prepared 300 µL of 1 mM ado-6-azide solution in Opti-MEM by electroporation with NEPA21 system (Nepa Gene) using cell culture plate electrode CUY900. Cell poring pulse voltage was set up at 200V and pulse length - 5 ms. gDNA was isolated 3h following the electroporation.

value: Wild Type


title: X144 day 0 [X6169665]

description:
144_G2_PreVAC
BSPZV1-34-047

value: Whole Blood


title: X139 day 9 after CHMI [X7171610]

description:
139_G2_V07T0
BSPZV1-34-030


title: dnmt1-WT-WT_B2_R2


title: dnmt1-WT-WT_B3_R1


title: H1JA cNESCs P37/D10 6F rep1

source_name: H1 hESCs-derived cNESCs


title: HPAP Case 28

type: genomic

city: Bethesda

first: Drew

last: Pratt

state: Maryland

address: 10 Center Drive, Building 10, Room 2S235

department: Laboratory of Pathology

institute: National Institutes of Health

description: Tumor

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: R package meffil v1.3.1

label: Cy5 and Cy3

source_name: tumor sample

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was bisulfite-converted with the EZ DNA Methylation Kitm (Zymo Research D5001)

tag: sex predicted

value: M

tag: os months

tag: os status (0=alive, 1=deceased)

tag: material

value: FFPE

value: high-grade glioma with pleomorphic and pseudopapillary features (HPAP)


title: HPAP Case 25

description: Tumor

tag: age

value: F


title: HPAP Case 24

description: Tumor


title: H1JA cNESCs P37/D10 6F rep2

tag: cell type


title: HPAP Case 31

description: Tumor


title: X139 before CHMI [X7171268]

description:
139_G2_V05C
BSPZV1-34-030

tag: visit

value: YES


title: X139 day 2 after CHMI [X3171372]

description:
139_G2_V06A
BSPZV1-34-030

value: NP

tag: tissue


title: H1JA cNESCs P37/D10 6F-2F rep2


title: HPAP Case 29

description: Tumor


title: HPAP Case 21

description: Tumor


title: dnmt1-WT-WT_B1_R1


title: HPAP Case 23

description: Tumor


title: HPAP Case 14

description: Tumor


title: HPAP Case 20

description: Tumor


title: dnmt1-N1580A-N1580A_B3_R2

value: Dnmt1 homozygous  N1580A knock-in


title: dnmt1-WT-WT_B2_R1


title: dnmt1-WT-WT_B1_R2


title: HPAP Case 19

description: Tumor


title: HPAP Case 27

description: Tumor


title: HPAP Case 15

description: Tumor


title: HPAP Case 26

description: Tumor


title: HPAP Case 11

description: Tumor


title: HPAP Case 16

description: Tumor


title: HPAP Case 22

description: Tumor


title: H1 hESCs P40 rep2

source_name: H1 hESCs


title: HPAP Case 12

description: Tumor


title: dnmt1-N1580A-N1580A_B2_R1


title: dnmt1-N1580A-N1580A_B3_R1


title: HPAP Case 3

description: Tumor


title: H1JA cNESCs P37/D10 6F-2F rep1


title: H1 hESCs P40 rep1


title: Krt Ctrl_rep3

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

description: polysomal RNA

data_processing:
Reads were aligned to the transcriptome using Bowtie v1.1.1
Gene abundances were estimated using RSEM v1.2.20
Genome_build: GRCz10,Ensembl 83 annotation
Supplementary_files_format_and_content: The processed data file for each sample is the gene-level abundance output of RSEM and is a tab-delimited text file

organism: Danio rerio

source_name: epithelial

extract_protocol:
Larvae were stored at -80°C in minimal residual media. QIAshredder (Quiagen) was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent (Invitrogen).
RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low, library prep was done with the NuGEN Ovation Single Cell RNA-Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane, following manufacturer’s protocols.

treatment_protocol: Zebrafish larvae were microinjected into one cell stage embryos and screened 3 days post fertilization for transgene expression. Microinjections for TRAP-RNA-sequencing included either control pTol2-krt4-RFP-HRas or oncogenic pTol2-krt4-RFP-HRasG12V constructs injected with pTol2-krt4-GFP-L10a in wildtype larvae, or into Tg(LyzC:EGFP-L10a) or Tg(mpeg1:EGFP-L10a) larvae for keratinocyte, neutrophil, or macrophage-specific expression profiling, respectively.

tag: batch

value: wild type

value: keratinocyte

tag: cell type id


title: X139 day 7 after 1st vac [X8169838]

description:
139_G2_V01B
BSPZV1-34-030

tag: day

tag: protection

tag: immunization


title: dnmt1-N1580A-N1580A_B1_R1

tag: genotype


title: X139 day 2 after 1st vac [X4169789]

description:
139_G2_V01A
BSPZV1-34-030

tag: group

tag: sample id


title: X139 day 0 [X6169566]

description:
139_G2_PreVAC
BSPZV1-34-030

value: Screen 3


title: dnmt1-N1580A-N1580A_B2_R2


title: HPAP Case 10

description: Tumor


title: dnmt1-N1580A-N1580A_B1_R2


title: HPAP Case 9

description: Tumor


title: Smc3 eco1-aa cdc6-mn IP

description:
Reads mapped to SK1 only/calibrated to S.pombe
RPL13A-2xFKBP12 fpr1∆ tor1-1 ndt80∆ Eco1-FRB-GFP pSCC1::3HA-CDC6

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt v3.0 (MAPQ 10, min. length 65)
To obtain reads mapping only to S.cerevisiae SK1;
ChIP-Seq reads were first mapped with MiniMap2 v2.10-r763-dirty (-ax sr) to pombe
Unmapped pombe reads were filtered using samtools v1.9
Unmapped pombe reads were then mapped to SK1
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads) using bedtools v2.27.0
chrMito was excluded with samtools
To obtain reads mapping only to Pombe;
Reads were also mapped to SK1
Unmapped SK1 reads were filtered using samtools
Unmapped SK1 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
Genome_build: S.cerevisiae SK1 + s.pombe ASM294v2.22
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization), To obtain calibrated bigWigs;  samtools flagstat was used to count reads mapping to SK1 and pombe only for each sample  the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (SK1)), calibrated SK1 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiase (strain SK1)/Schizosaccharomyces pombe

growth_protocol: Cells were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA) for approx. 16 hours. Cells were then diluted to OD(600) = 1.8 and sporulated for 6 hours in SPO media (0.3% Kac) to arrest in prophase I.

extract_protocol:
Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 60 seconds four times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/0.1% SDS before sonicating in a Bioruptor (Diagenode) for two times 30 cycles at 30sec on/off intervals at "High" setting. The supernatant was subject to IP with homemade anti-Smc3 antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.
DNA was blunted using NEB Quick Blunting kit followed by Ampure XP bead purification of fragments over 100bp. dA tails were added using Klenow (exo-) and NextFlex adaptors ligated to each sample. This was followed by two Ampure purifications of fragments over 100bp and then fragments over 150-200bp. Libraries were amplified using NextFlex primers and Phusion DNA polymerase. Lastly, double-sided Ampure purification was carried out to obtain fragments between 100-300bp in size.

treatment_protocol: Cells were fixed in 1% formaldehyde for 2hrs before washing twice in TBS and once in FA lysis buffer with 0.1% SDS.

tag: chip antibody

value: Homemade rabbit Smc3 antibody

tag: ploidy

value: Diploid (S.c.) / Haploid (S.p.)

tag: cell cycle stage

value: Meiotic prophase I

value: RPL13A-2xFKBP12 fpr1delta tor1-1 ndt80delta Eco1-FRB-GFP pSCC1::3HA-CDC6


title: HPAP Case 18

description: Tumor

tag: sex predicted

tag: os months

tag: os status (0=alive, 1=deceased)


title: Mpeg Ctrl_rep3

description: polysomal RNA

source_name: macrophage

tag: age

tag: cell type

value: macrophage


title: HPAP Case 17

description: Tumor

tag: material

tag: tissue


title: Lyz Ctrl_rep3

description: polysomal RNA

source_name: neutrophil

tag: batch

value: neutrophil

tag: cell type id


title: Smc3 cdc6-mn IP

description:
Reads mapped to SK1 only/calibrated to S.pombe
RPL13A-2xFKBP12 fpr1∆ tor1-1 ndt80∆ pSCC1::3HA-CDC6

value: RPL13A-2xFKBP12 fpr1delta tor1-1 ndt80delta pSCC1::3HA-CDC6


title: X117 day 9 after CHMI [X8171620]

description:
117_G2_V07T0
BSPZV1-34-011

source_name: Whole Blood

tag: visit

tag: day

tag: protection

value: Whole Blood


title: Krt V12_rep3

description: polysomal RNA

tag: genotype

value: mutant (HRas G12V)


title: Smc3 eco1-aa IP

description:
Reads mapped to SK1 only/calibrated to S.pombe
RPL13A-2xFKBP12 fpr1∆ tor1-1 ndt80∆ Eco1-FRB-GFP

value: RPL13A-2xFKBP12 fpr1delta tor1-1 ndt80delta Eco1-FRB-GFP


title: Lyz V12_rep3

description: polysomal RNA


title: Smc3 eco1-aa cdc6-mn input

description:
Reads mapped to SK1 only
RPL13A-2xFKBP12 fpr1∆ tor1-1 ndt80∆ Eco1-FRB-GFP pSCC1::3HA-CDC6


title: Smc3 WT IP

description:
Reads mapped to SK1 only/calibrated to S.pombe
RPL13A-2xFKBP12 fpr1Δ tor1-1 ndt80Δ

value: RPL13A-2xFKBP12 fpr1delta tor1-1 ndt80delta


title: Mpeg Ctrl_rep2

description: polysomal RNA


title: X117 before CHMI [X4171274]

description:
117_G2_V05C
BSPZV1-34-011

tag: immunization

value: YES

tag: group

tag: sample id


title: X117 day 7 after 2nd vac [X9169281]

description:
117_G2_V02B
BSPZV1-34-011

value: NP


title: Lyz Ctrl_rep2

description: polysomal RNA


title: HPAP Case 13

description: Tumor

value: F

value: FFPE

value: high-grade glioma with pleomorphic and pseudopapillary features (HPAP)


title: Krt V12_rep2

description: polysomal RNA

value: keratinocyte


title: Lyz V12_rep2

description: polysomal RNA


title: X117 day 7 after 1st vac [X7169837]

description:
117_G2_V01B
BSPZV1-34-011


title: Smc3 cdc6-mn input

description:
Reads mapped to SK1 only
RPL13A-2xFKBP12 fpr1∆ tor1-1 ndt80∆ pSCC1::3HA-CDC6

tag: chip antibody

value: Homemade rabbit Smc3 antibody

tag: ploidy

tag: cell cycle stage


title: X117 day 2 after CHMI [X3171390]

description:
117_G2_V06A
BSPZV1-34-011


title: Mpeg V12_rep3

description: polysomal RNA


title: Krt Ctrl_rep1

description: polysomal RNA

value: wild type


title: Smc3 eco1-aa input

description:
Reads mapped to SK1 only
RPL13A-2xFKBP12 fpr1∆ tor1-1 ndt80∆ Eco1-FRB-GFP

value: Diploid (S.c.) / Haploid (S.p.)

value: Meiotic prophase I


title: X117 day 2 after 1st vac [X4169771]

description:
117_G2_V01A
BSPZV1-34-011


title: Krt Ctrl_rep2

description: polysomal RNA


title: Smc3 WT input

description:
Reads mapped to SK1 only
RPL13A-2xFKBP12 fpr1Δ tor1-1 ndt80Δ


title: X117 day 0 [X1169561]

description:
117_G2_PreVAC
BSPZV1-34-011

value: Screen 3


title: control 3 [Control-3]

city: Houston

first: Jason

middle: T

last: Yustein

state: TX

address: 1102 Bates Ave

department: Pediatrics-Oncology

institute: Texas Children's Hospital

data_processing:
Samples were trimmed using TrimGalore
Trimmed samples were aligned to the mm10 genome using STAR
Features were quantified using featurecounts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with feature counscounts for every gene and every sample

source_name: control 3

extract_protocol:
RNA was extracted with Qiagen RNAeasy Plus Mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: gastrocnemius muscle


title: Lyz V12_rep1

description: polysomal RNA

tag: age

value: neutrophil


title: Lyz Ctrl_rep1

description: polysomal RNA

tag: cell type


title: Krt V12_rep1

description: polysomal RNA


title: X093 day 9 after CHMI [X6171618]

description:
093_G2_V07T0
BSPZV1-34-022

value: P

value: Whole Blood


title: Mpeg Ctrl_rep1

description: polysomal RNA

value: macrophage


title: Mpeg V12_rep1

description: polysomal RNA

value: mutant (HRas G12V)


title: X093 day 2 after CHMI [X8171395]

description:
093_G2_V06A
BSPZV1-34-022

value: YES


title: control 1 [Control-1]

source_name: control 1


title: control 2 [Control-2]

source_name: control 2


title: Unfused HypPB Puro WT SRT Rep1

first: Matthew

middle: A

last: Lalli

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Remove transposon bases from each read: cutadapt -g "^"$barcode$Long_PB_LTR -o $out_file".temp.fastq.gz" --minimum-length 1 --discard-untrimmed -e 0.2 --no-indel
Remove any remaining Illumina adpaters: cutadapt -a "CTGTCTCTTATACACATCTCCGAGCCCACGAGACTNNNNNNNNNNTCTCGTATGCCGTCTTCTGCTTG" -o $out_file".fastq --minimum-length 1 $out_file".temp.fastq.gz"
Identify SRT barcode: umi_tools extract --stdin $out_file".temp.fastq.gz" --bc-pattern=CCCCNGTTAA --whitelist=$safelist --stdout $out_file".fastq.gz"
Align reads to reference genome: novoalign -d /novoalign_indexes/$genome/$genome.nvx -f $out_file".fastq.gz"  -n 40 -o SAM -o SoftClip > $out_sam
Convert to sorted bam file: samtools view -bS -h -F 260 $out_sam | samtools sort - -o $out_bam_map
Tag bam file with sequencing indexes: python3 TagBam.py
Tag bam file with SRT barcodes: python3 TagBamWithSrtBC.py
Annotate SRT insertion sites: python3 AnnotateInsertionSites.py
Convert insertion sites to Calling Card Format: python3 BamToCallingCard.py -b XP XJ XQ -i $out_map_sort_prefix"_final.bam" -o $out_map_sort_prefix"_unsorted.ccf"
Sort CCF file: sort -k1V -k2n -k3n $out_map_sort_prefix"_unsorted.ccf" > $out_map_sort_prefix"_final.ccf"
Genome_build: hg38
Supplementary_files_format_and_content: qBED (calling cards format, .ccf) Chromosome start stop number of insertions strand barcode/index

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in Dulbecco’s Modified Eagle Media (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were passaged every 3–4 d by enzymatic dissociation using trypsin.

extract_protocol:
Total RNA is harvested using Direct-zol RNA MiniPrep kit (Zymo Research). RNA concentration and integrity was assessed using Nanodrop.
Calling card libraries were prepared as described. We performed first-strand reverse transcription reactions in 20 μL total volume using 2 μg of RNA from each in vitro sample. RNA mixed with water and dNTPs was hybridized to oligo-dT primers (1 μL of 50 μM SMART_dTVN) by incubation at 65 ˚C for 5 minutes and immediately transferred onto ice. 0.5 μL of Maxima H Minus Reverse Transcriptase, RNasin RNAse inhibitor, and 5X RT buffer were added and samples are incubated at 50 °C for 60 min for reverse transcription. cDNA is then amplified with primers specific to the SRT before tagmentation.

treatment_protocol: Calling card experiments are performed as described with minor modifications. Twenty-four hours before transfection, 250,000 HEK293T cells are plated per well in a 12 well plate. The next day, cells are transfected using PEI (Polysciences) with 1 ug of total DNA comprising 500 ng of piggyBac (fused or unfused) and 500 ng of donor SRT (purified PCR product or miniprepped DNA). Medium is changed 24 hours after transfection. Three days after transfection, each well is trypsinized and replated into a T25 flask. For puromycin-resistance SRTs, puromycin is added 24 hours later (2 ug / mL). RNA is extracted three days after puromycin selection.

tag: transposase

value: unfused-hyper-piggyBac

tag: self-reporting transposon

value: wild-type Puro SRT


title: X093 before CHMI [X3171246]

description:
093_G2_V05C
BSPZV1-34-022

tag: tissue


title: NGN1 mix Puro BC SRT Rep4

value: mixed barcoded Puro SRT


title: Unfused HypPB Puro WT SRT Rep2


title: Mpeg V12_rep2

description: polysomal RNA

tag: batch

tag: cell type id


title: K-Ras G12D mutant [KMR19]

source_name: K-Ras G12D mutant

value: tumor


title: NGN1 mix Puro BC SRT Rep3


title: NGN1 mix Puro BC SRT Rep1


title: K-Ras G12D mutant [KMR46]

value: K-RasG12D p53F/+


title: X093 day 7 after 2nd vac [X9169263]

description:
093_G2_V02B
BSPZV1-34-022

tag: visit

tag: day


title: NGN1 mix Puro BC SRT Rep2


title: K-Ras G12D mutant [KMR72-3]

tag: genotype


title: NEUROD2 tdTomato WT SRT Rep2

value: wild-type tdTomato SRT


title: X093 day 7 after 1st vac [X6169836]

description:
093_G2_V01B
BSPZV1-34-022

tag: protection

tag: immunization


title: NEUROD2 single tdTomato BC SRT Rep3

value: single barcoded tdTomato SRT


title: NEUROD2 tdTomato WT SRT Rep1


title: X093 day 2 after 1st vac [X5169772]

description:
093_G2_V01A
BSPZV1-34-022

tag: group

tag: sample id


title: NEUROD2 single tdTomato BC SRT Rep2


title: K-Ras G12D mutant [KMR78-arm ]


title: NEUROD2 single tdTomato BC SRT Rep1


title: Unfused HypPB Puro WT SRT Rep3


title: K-Ras wild type  [MF21]

source_name: K-Ras wild type

value: K-RasWT p53F/+


title: NEUROD2 mix 5 tdTomato BC SRT Rep3

value: mixed barcoded tdTomato SRT


title: X078 day 9 after CHMI [X5171608]

description:
078_G2_V07T0
BSPZV1-34-021


title: NEUROD2 mix 5 tdTomato BC SRT Rep1


title: NEUROD2 mix 5 tdTomato BC SRT Rep2


title: K-Ras wild type  [MR17]

value: K-RasWT p53R172H/+


title: NEUROD2 mix tdTomato BC SRT Rep1


title: K-Ras wild type  [MR42]


title: NEUROD2 Puro WT SRT Rep4


title: NEUROD2 Puro WT SRT Rep3


title: X078 before CHMI [X7171250]

description:
078_G2_V05C
BSPZV1-34-021


title: islets

data_processing:
The clean single-cell RNA-seq data of hCiPSC-islets_S6D2 and islets were mapped to reference genome hg19 using Cell Ranger v3.1.0, while the data of hCiPSC-islets_10 wpt was mapped to human-mouse mixed reference genome hg19_mm10 using the same version Cell Ranger.
Cell quality control was performed by R package scater v1.14.0.
The raw UMI counts were then normalized by R package scran v1.14.1 .
Seurat v3.2.3 was used for downstream analysis including identifying cell types.
Genome_build: hg19/hg19_mm10
Supplementary_files_format_and_content: .tar.gz files containing cellranger output
.csv files containing raw count matrix or cell metadata

source_name: islets derived from donor pancreas

growth_protocol: islets were cultured in CMRL1066 (Thermo Scientific, Cat# 11530037) containing 10% FBS (Thermo Scientific, Cat# 10099141C) and 1% Pen/Strep (Gibco, Cat# 15140-122). hCiPSC-islets were cultured in DMEM-basic supplied with 0.5x B27.

extract_protocol:
Cells were harvested and resuspended in PBS with 0.04% BSA at 1×10^6 cells per milliliter. Then, cell suspensions were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using ChromiumTM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10x Genomics, 1000075). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
Barcoded cDNAs were pooled and underwent cleanup by using DynaBeads MyOne Silane Beads (Invitrogen, 37002D) and then amplified and cleanup for further next generation library construction. Single-cell RNA seq libraries were prepared using ChromiumTM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10x Genomics, 1000075) following instructions provided by the manufacturer. Sequencing was performed on an Illumina HiSeq X Ten (Illumina, San Diego, CA, USA) with pair end 150bp.
Single-cell RNA sequencing

treatment_protocol: hCiPSC-islets after transplantation under mouse kidney capsule for 10 weeks

value: islets derived from donor pancreas

tag: sample type

value: primary islets


title: NEUROD2 Puro WT SRT Rep1


title: X139 day 7 after 2nd vac [X1169282]

description:
139_G2_V02B
BSPZV1-34-030

value: NP


title: MYOD1 mix tdTomato BC SRT Rep3


title: hCiPSC-islets_10 wpt

source_name: islets derived from pluripotent stem cells

tag: treatment

value: mouse kidney capsule grafts of transplanted islets, which were derived from chemically induced pluripotent stem cells using step-wise differentiation protocol

tag: time

value: sample collected at 10 weeks post transplantation (wpt)


title: MYOD1 mix tdTomato BC SRT Rep2


title: X078 day 7 after 2nd vac [X1169246]

description:
078_G2_V02B
BSPZV1-34-021

value: P

value: Whole Blood


title: X078 day 7 after 1st vac [X5169808]

description:
078_G2_V01B
BSPZV1-34-021

value: YES


title: MYOD1 mix tdTomato BC SRT Rep1


title: X093 day 0 [X3169671]

description:
093_G2_PreVAC
BSPZV1-34-022

value: Screen 3


title: hCiPSC-islets_S6D2

value: islets derived from pluripotent stem cells

value: islets derived from chemically induced pluripotent stem cells using step-wise differentiation protocol

value: sample collected at Stage 6 Day 2


title: X078 day 2 after 1st vac [X8169775]

description:
078_G2_V01A
BSPZV1-34-021


title: Single nucleotide mutagenesis position 4 Rep2

value: unfused-hyper-piggyBac

value: mutant amplicon Puro SRT


title: Single nucleotide mutagenesis position 4 Rep1


title: hCiPSC-#4

data_processing:
Quality control was performed by using FastQC v0.11.8.
The adapter of raw RNA sequencing fastq reads were trimmed using TrimGalore v0.6.6.
The cleaned RNA sequencing fastq reads were aligned to hg19 UCSC human reference genome using STAR v2.7.3 with default parameters.
Output bam files were then sorted by samtools v1.9.
The number of alignments mapped to each gene were counted using htseq-count v0.11.3 with parameters '-f bam -r name -s reverse -a 10 -t exon -i gene_id -m union '.
The count matrix was made by merging htseq-count outputs of every sample.
Genome_build: hg19
Supplementary_files_format_and_content: .csv file containing raw count values of all genes for every sample.

source_name: human induced pluripotent stem cells

growth_protocol: hADFs were cultured in Mesenchymal Stem Cell Growth Medium 2 (Promo Cell, C-28009) with supplement mix (Promo Cell, C-39809). Pluripotent stem cell lines were cultured in mTeSR1 (Stem Cell, Cat# 85850) on 1: 40 diluted Matrigel-coated (BD BioSciences, Cat# 356231) 6-well plate (Corning, Cat# 353046).

extract_protocol:
Cells were harvested and resuspended in PBS with 0.04% BSA at 1×10^6 cells per milliliter.  Cells were lysed and the released RNA for the construction of sequencing libraries.
Sequencing libraries were prepared using  Illumina protocols
Bulk RNA sequencing

value: induced pluripotent stem cells

value: induced pluripotent stem cells derived from adipose derived fibroblasts using pure chemical reprogramming strategy


title: hCiPSC-#3


title: X078 day 0 [X5169565]

description:
078_G2_PreVAC
BSPZV1-34-021


title: Single nucleotide mutagenesis position 3 Rep1


title: Single nucleotide mutagenesis position 2 Rep3


title: X078 day 2 after CHMI [X5171392]

description:
078_G2_V06A
BSPZV1-34-021


title: NEUROD2 Puro WT SRT Rep2

value: wild-type Puro SRT


title: Single nucleotide mutagenesis position 2 Rep1


title: Single nucleotide mutagenesis position 1 Rep3


title: X054 day 9 after CHMI [X3171606]

description:
054_G2_V07T0
BSPZV1-34-010

value: NO


title: Single nucleotide mutagenesis position 2 Rep2


title: hCiPSC-#2


title: hCiPSC-#1


title: X054 before CHMI [X8171251]

description:
054_G2_V05C
BSPZV1-34-010


title: Single nucleotide mutagenesis position 1 Rep2


title: Single nucleotide mutagenesis position 1 Rep1


title: NNN mutagenesis Rep2


title: H9

source_name: human embryonic stem cells

tag: cell line

value: embryonic stem cells


title: NNNN mutagenesis Rep2


title: NNN mutagenesis Rep1


title: H1

tag: cell type


title: rna-seq from Tumor_HDLBP_KO_4

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center

data_processing:
Basecalls were converted to fastq files using Bcl2Fastq (2.16.0.10). Reads were demultiplexed and 3’adapter sequences removed by Flexbar (v2.5). Read counts per gene and TPM values were obtained by RSEM (v.1.2.20) (Li and Dewey, 2011) using default parameters and Bowtie (v.1.1.2) (Langmead et al., 2009) as transcriptome alignment program.
Raw read counts were normalized using DESeq2 (Love et al., 2014) and pairwise comparisons between and within fractions performed using standard parameters.
Genome_build: hg19
Supplementary_files_format_and_content: processed_data_A549_tumor.txt: tab delimited matrix of read counts per mRNA for all samples, log2-transformed fold changes and p-adjusted values from DESeq2 output from pairwise comparisons, as well as normalized read counts per mRNA (norm. prefix).

source_name: A549 tumor

growth_protocol: A549 cells were grown in DMEM + 10%FCS

extract_protocol:
RNA was extracted using Trizol
Next Ultra Directional RNA Library Prep Kit (NEB)
polyA+ RNA-Seq single end

tag: hdlbp

value: HDLBP knockout

tag: replicate

value: replicate 3


title: hiPSC (episomal)-#1

value: induced pluripotent stem cells derived from adipose derived fibroblasts using episomal reprogramming strategy


title: Insertion mutagenesis Rep3

tag: transposase

tag: self-reporting transposon


title: hiPSC (mRNA)-#2

value: induced pluripotent stem cells derived from adipose derived fibroblasts using mRNA reprogramming strategy


title: hiPSC (mRNA)-#1


title: hADF-#3

source_name: human adipose derived fibroblasts

value: adipose derived fibroblasts


title: rna-seq from Tumor_WT_7

value: WT

value: replicate 7


title: hADF-#2


title: ASCL1 mix tdTomato BC SRT Rep2

value: mixed barcoded tdTomato SRT


title: rna-seq from Tumor_WT_8

value: replicate 8


title: X054 day 2 after CHMI [X6171393]

description:
054_G2_V06A
BSPZV1-34-010

value: NP

tag: tissue

value: Whole Blood


title: ASCL1 mix tdTomato BC SRT Rep3


title: rna-seq from Tumor_WT_6

value: replicate 6


title: rna-seq from Tumor_HDLBP_KO_3

value: replicate 2


title: Insertion mutagenesis Rep1

value: unfused-hyper-piggyBac

value: mutant amplicon Puro SRT


title: ASCL1 mix tdTomato BC SRT Rep4


title: 8265 ChIP-Seq Stat5 Pro-B

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: ChIP-Seq Stat5 Pro-B

data_processing:
ChIP-Seq: After sequencing, all reads that passed the Illumina quality filtering were considered for alignment. mm10: The ChIP-seq samples, which were used for generating the data shown in Fig. 5 B and Fig. S5, C, D and I, were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) using the bwa program version 0.7.17. The read coverages, displayed in Fig. 5B and Fig. S5 I, were calculated with the bedtools program version 2.27.1, normalized to reads per millions (RPM) using the SAMtools version 1.9 and Kent tools version 20190507. Peaks were called with the MACS program version 2.2.5, using only one of the two read sequences in case of paired-end read samples, with the input sample 35327 as a control, except for the B-ALL samples 138002 and 138003, where the associated input sample 138001 was used. mm9: The ChIP-seq samples, which were used for generating the data shown in Fig. 7, H, I and L, Fig. S2 A, Fig. S5 A and Fig. S7, F and G, were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program version 1.0.0. Peaks were called with the MACS program version 1.3.6.1. Peaks of samples 29936 and 29938, 38870 and 40031 and 40030 and 46051 were called by using the pro-B cell input GSM2461724 as control.
After sequencing, reads that passed the Illumina quality filtering were considered for alignment. Reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) or human ribosomal RNAs (U13369.1) were removed.  RNA-seq samples for experiment 2&3 which were used to define the gene expression changes between ex vivo sorted Pax5–/– and Pax5+/+ pro-B cells  (Fig. S2A) as well as ex vivo sorted pro-B cells from Vav-Bcl2 Rag1-Cre Stat5fl/fl and control Vav-Bcl2 Rag1-Cre Stat5fl/+ (Fig. S7D), were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Tophat program version 1.4.1a. The number of reads per gene was counted using featureCounts version 1.5.0 with the default settings and the modified refGene gene annotation described in (Schwickert et al. 2019, PMID: 31591571). TPM values were calculated as described (Wagner et al., 2012).  RNA-seq samples for experiments 1 & 4, which were used to define the gene expression changes between Pax5Jak2/+ and Pax5+/+ pro-B cells (Fig. 2A) as well as Pax5Jak2/+ and control Pax5+/– Cdkn2ab+/– B-ALL tumors (Fig. 2C), were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) using the STAR program version 2.4.2a [PMID: 23104886] with the parameters ‘–outSAMStrandField intronMotif’ and ‘–removeNonCannonical RemoveNonCannonicalUnannotated’ in paired-end mode. The number of reads per gene was counted using featureCounts version 1.5.0 with the setting -p and the refGene gene annotation of mm10 downloaded from UCSC on Dec 6th 2018 expanded by Immunoglobulin and T cell receptor gene annotation from Gencode version 29. TPM values were calculated as described (Wagner et al., 2012).
Genome_build: NCBI37/mm9; GRCm38/mm10;
Supplementary_files_format_and_content: bigwig = read coverage (reads per million) in bigWIG format; txt = ASCII text format.

source_name: Pro-B cells

extract_protocol: ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: wild-type

tag: cell preparation

value: Pro-B culture (SB+)

tag: chip antibody

value: STAT5A+B Art.Nr:R&D SystemsPA-ST5A and R&D SystemsPA-ST5B


title: hADF-#1


title: rna-seq from Tumor_WT_5

value: replicate 5


title: OUH_miR_159

type: RNA

city: Odense

first: Ines

last: Block

address: J.B. Winsløws Vej 4

department: Department of Clinical Genetics

country: Denmark

institute: Odense University Hospital

description: Total RNA extracted from fresh frozen primary breast tumour of a female patient with relapse

hyb_protocol: Hybridization, washing, and scanning (Agilent G2565CA Microarray scanner) were performed according to the recommendations provided by Exiqon.

scan_protocol: Scanned images were imported into GenePixPro6.0 software (Molecular Devices) for quality control and raw data extraction.

data_processing: Signals from 3 spots were compiled, only human microRNAs were selected, the R-package limma was used for LOESS normalization and quantile normalization of raw signal intensities, and the ComBat function embedded in the sva R-package was used for adjustment of the normalized intensities and to eliminate potential batch effects

source_name: Primary breast tumour of patient with relapse

label_protocol: The miRCURY Power labeling kit (Exiqon), miRCURY LNA Array hybridization buffer (Exiqon) and miRCURY LNA Array Washing buffer kit (Exiqon) were used for sample labelling, hybridization and washing, respectively.

extract_protocol: Total RNA was isolated from tumor samples with Trizol (Invitrogen) and further purified with the RNeasy micro kit (Qiagen), including DNAse treatment. NanoDrop Spectrophotometer (NanoDrop Technologies) was used for RNA quantification. The quality of extracted RNA was assessed with Bioanalyzer 2100 (Agilent Technologies) using the RNA 6000 Nano Kit (Agilent Technologies).

treatment_protocol: After surgical removal, tumor samples were snap-frozen and stored at -80°C.

tag: pair no.

tag: metastasis (1= yes; 0=no)

tag: tumour type

value: IDC

tag: esr1 expression (1=yes; 0=no)

tag: lymph node status (1=positive; 0=negative)

tag: status at last follow up (1=dead, 0=alive)

source_name: common reference pool of all samples

value: human breast tumour


title: ASCL1 mix tdTomato BC SRT Rep1


title: OUH_miR_158

description: Total RNA extracted from fresh frozen primary breast tumour of a female patient without relapse

source_name: Primary breast tumour of patient without relapse


title: OUH_miR_157


title: OUH_miR_156

value: Papillary carcinoma


title: Resident, MID49, 5O

city: Aachen

first: Oliver

last: Pabst

address: Pauwelsstrasse 30

institute: RWTH Aachen University

data_processing:
Library strategy: TCR-Seq
UMI demultiplexing: migec Checkout with “oute” parameters follow by Histogram command
UMI consensus sequences: migec Assemble with “-m” parameter as found by Histogram step
Alignment: mixcr analyze amplicon --library imgt --species MusMusculus --starting-material rna --5-end v-primers –3-end j-primers --adapters adapters-present --receptor-type TRA --region-of-interest CDR3 --only-productive --align "-OreadsLayout=Collinear" --align "-OsaveOriginalReads=true" --assemble "-OseparateByV=true" --assemble "-OseparateByJ=true" --assemble "-ObadQualityThreshold=20" --assemble "-OmaxBadPointsPercent=0" --assemble "-OcloneClusteringParameters=null" S0_R1.fastq S0_R2.fastq output_directory
Joined all clonotype tables across samples into a matrix (mids_counts.csv)
Genome_build: IMGT 202122 mouse reference
Supplementary_files_format_and_content: MiXCR clonotype table, tab-separated files with the following columns:
Supplementary_files_format_and_content: '- cloneCount: number of unique V-CDR3-J clones identified by MiXCR
Supplementary_files_format_and_content: '- nSeqCDR3: CDR3 nucleotide sequence
Supplementary_files_format_and_content: '- aaSeqCDR3: CDR3 aminoacid sequence
Supplementary_files_format_and_content: '- bestVHit: V gene with highest score
Supplementary_files_format_and_content: '- bestJHit: J gene with highest score
Supplementary_files_format_and_content: '- bestDHit: D gene with highest score
Supplementary_files_format_and_content: '- cloneFraction: relative abundance within this sample

source_name: Mesenteric lymph node

extract_protocol:
RNA was isolated using RNeasy Micro Plus Kit  (Qiagen) according to manufacturer's instructions
Library preparation was performed using the template switch technique and UMI-adaptor incorporation during the TCR-specific cDNA synthesis (Mint-2 cDNA synthesis kit, Evrogen).  This was followed by two nested PCRs and a third amplification for the Illumina adaptor incorporation. DNA was purified using MinElute PCR Purification Kit (Qiagen)
RNA-Seq (RACE)

treatment_protocol: 7 days after photoconversion of the mesenteric lymph node

value: Mesenteric lymph node

value: Resident T cells

tag: cell subtype

value: Treg

tag: organ

value: coMLN-PC (photoconverted colon draining mesenteric lymph node)


title: rna-seq from Tumor_WT_3

value: WT

value: replicate 3


title: OUH_miR_160


title: Insertion mutagenesis Rep2


title: Resident, MID48, 4O

tag: cell type


title: OUH_miR_155


title: rna-seq from Tumor_WT_2

tag: hdlbp


title: rna-seq from Tumor_WT_4

tag: replicate

value: replicate 4


title: Resident, MID47, 3O


title: OUH_miR_153


title: OUH_miR_152


title: rna-seq from Tumor_WT_1

value: replicate 1


title: OUH_miR_150


title: Resident, MID46, 2O


title: rna-seq from A549_HDLBP_KO_3

source_name: A549 cell line

value: HDLBP knockout


title: OUH_miR_149


title: rna-seq from Tumor_HDLBP_KO_2


title: NNNN mutagenesis Rep1

tag: transposase

value: mutant amplicon Puro SRT


title: OUH_miR_148


title: OUH_miR_154


title: Resident, MID45, 1O


title: OUH_miR_147


title: OUH_miR_146


title: Circulating, MID9, 5D

value: Circulating effector/memory T cells

value: Tcell

value: siMLN-PC (photoconverted small intestine draining mesenteric lymph node)


title: OUH_miR_151


title: Circulating, MID8, 4D


title: rna-seq from A549_HDLBP_KO_1


title: Circulating, MID7, 3D


title: rna-seq from A549_WT_3


title: OUH_miR_144


title: OUH_miR_142


title: OUH_miR_143


title: OUH_miR_139


title: OUH_miR_141


title: OUH_miR_140


title: rna-seq from A549_WT_2

value: replicate 2


title: Circulating, MID6, 2D


title: OUH_miR_138

value: IDC


title: rna-seq from A549_WT_1


title: rna-seq from A549_HDLBP_KO_2


title: OUH_miR_136

value: human breast tumour


title: Circulating, MID5, 1D


title: HEK293T ncRNAseq cells 2

description: ncRNA-seq

data_processing:
Basecalls were converted to fastq files using Bcl2Fastq (2.16.0.10). Reads were demultiplexed and adapter sequences removed by Flexbar (2.5). Reads were then collapsed to remove PCR duplicates, followed by removal of random nucleotides (four on both 5’ and 3’ end of the reads) using fastx_trimmer (FASTX Toolkit 0.0.14).
To obtain accurate mapping to transcripts originating from repetitive genomic loci, reads were sequentially mapped to reference transcripts by Bowtie2 (v2.3.2)  in the following order by retaining the unmapped reads from the previous to the next mapping step. We started with human pre-rRNA (GenBank U13369.1), followed by rRNA (GenBank NR_023363.1, NR_003285.2, NR_003287.2, NR_003286.2), snRNA, snoRNA, other ncRNA (all from Ensembl, including RN7SL) and tRNA (GtRNADb).
Initially, we obtained mature tRNA fasta files from GtRNADb (http://gtrnadb.ucsc.edu/, hg19 build) and kept only one fasta sequence per tRNA molecule to avoid mapping non-uniquely due to tRNA gene duplications and pseudogenes. The tRNAs missing from this initial set were obtained from HEK293 Hydro-seq results (Gogakos et al., 2017), resulting in a custom made FASTA tRNA reference that contained 58 unique tRNAs. Reads were mapped to this reference using Bowtie 2 (v.2.3.2) and custom scripts using BedTools (v2.26.0) intersect were used to obtain read counts per tRNA.
3’ adaptor 4N-RA3, rApp-NNNNTGGAATTCTCGGGTGCCAAGG-InvdT; 5’adaptor 4N-SRC-cDNA, /5Phos/NNNNGATCGTCGGACTGTAGAACTCTGAAC-SpC3
Genome_build: GtRNADb hg19
Supplementary_files_format_and_content: processed_data_ncrna_trna.txt: tab delimited matrix of raw and normalized read counts per tRNA for both replicates, as well as codon usage.

source_name: HEK293 Flp-In T-REx embryonic kidney cell line

growth_protocol: HEK293 Flp-In T-REx cells were cultured in standard Dulbeco´s modified Eagle´s medium (DMEM, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich) and 1% 2 mM L-glutamine (Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted from HEK293 cells with Qiagen RNAeasy kit according to the manufacturer’s instruction.
2 µg were fragmented in a total volume of 100 µl fragmentation solution (10mM ZnOAc, 100mM Tris buffer pH 8.0) in a thin-walled PCR tube at 95 °C for 55 s.  Next, the samples were immediately cooled on ice and RNA was purified with RNA Clean and Concentrator kit (Zymo Research) according to the manufacturer’s instruction. RNA was then treated with 10 U of calf intestine alkaline phosphatase in 1x CutSmart buffer (both from New England Biolabs) for 1h at 37 °C. Next, the samples were immediately cooled on ice and RNA was purified with RNA Clean and Concentrator kit (Zymo Research) according to the manufacturer’s instruction. RNA was then treated with 20 U of T4 polynucleotide kinase in 1x T4 PNK reaction buffer (both from New England Biolabs) supplemented with 0.1 % (v/v) Triton-X100 for 30 min at 37 °C. Next, the samples were immediately cooled on ice and RNA was purified with RNA Clean and Concentrator kit (Zymo Research) according to the manufacturer’s instruction. The next step was 3’ adaptor ligation, which was performed for 16 h at 16 °C in a total volume of 20 µl in the presence of 2 U of T4 RNA ligase 2 truncated K227Q, 1x RNA ligase buffer, 25 % PEG-8000 (all from New England Biolabs) and 25 pmol of pre-adenylated 4N-RA3 adapter (see Oligonucleotides). Afterwards, RNA was separated on 10% Novex TBE Urea gels, and fragments in the range of 65-100 nt were excised and eluted in 300 mM NaCl overnight at 4 °C with 900 rpm agitation. RNA was then precipitated by the addition of 0.5 µl GlycoBlue co-precipitant, 3 volumes of absolute ethanol and incubation at -80 °C for at least 2 h. Next, precipitated RNA was reverse transcribed for 30 min at 37 °C in a total volume of 20 µl containing 1x buffer (25 mM Tris, pH 8.6, 30 mM NaCl and 5 mM dithiotreitol), 4.5 pmol RTP primer (see Oligonucleotides), 4 mM each dNTP, 20 mM MgCl2, 7.1 % (v/v) dimethylsulfoxide and 10 U of AMV reverse transcriptase (Promega). Afterwards, RNA was removed by RNase H (5 U) treatment for 30 min at 37 °C (New England Biolabs) and ssDNA was separated on 10% Novex TBE Urea gels. Fragments in the range of 65-100 nt were excised and eluted in 300 mM NaCl overnight at 4 °C with 900 rpm agitation. ssDNA was then precipitated by the addition of 0.5 µl GlycoBlue co-precipitant, 3 volumes of absolute ethanol and incubation at -80 °C for at least 2 h. The next step was 5’adaptor ligation, which was performed for 16 h at 22 °C in a total volume of 20 µl. The reaction contained precipitated ssDNA, 60 U of high concentration T4 RNA ligase 1, 1x RNA ligase buffer, 22.5 % PEG-8000, 1 mM ATP (all from New England Biolabs) and 50 pmol of 4N-SRC-cDNA adapter (see Oligonucleotides). ssDNA was purified with DNA Clean and Concentrator kit (Zymo Research) according to the manufacturer’s ssDNA protocol. PCR amplification for the final library was performed according to the Truseq small RNA protocol (Illumina) using standard indexed PCR primers (RPIx) for multiplexing (Illumina). Typically, 14 cycles of amplification were required to obtain a sufficient amount of the final cDNA library in the size range of 150-220 bp (average size 180 bp). PCR reactions were separated on a 2.5 % agarose gel and the final DNA library of the expected size range was excised.

treatment_protocol: No treatment.

tag: cell line

tag: molecule subtype

value: tRNA


title: HEK293T ncRNAseq cells 1

description: ncRNA-seq


title: Resident, MID37, 3C

tag: tissue

value: Mesenteric lymph node


title: OUH_miR_135


title: HEK293T rna-seq from N_2A15_2

description: RNA-Seq paired end

data_processing:
Basecalls were converted to fastq files using Bcl2Fastq (2.16.0.10). Reads were demultiplexed and 3’adapter sequences removed by Flexbar (v2.5). Read counts per gene and TPM values were obtained by RSEM (v.1.2.20) (Li and Dewey, 2011) using default parameters and Bowtie (v.1.1.2) (Langmead et al., 2009) as transcriptome alignment program.
Raw read counts were normalized using DESeq2 (Love et al., 2014) and pairwise comparisons between and within fractions performed using standard parameters.
Genome_build: hg19
Supplementary_files_format_and_content: processed_data_rnaseq_fractionation.txt: tab delimited matrix of read counts per gene for all samples, log2-transformed fold changes and p-adjusted values from DESeq2 output from pairwise comparisons, as well as normalized read counts per gene (norm. prefix).

growth_protocol: HEK293T cells were grown in DMEM + 10%FCS

extract_protocol:
Cell fractionation by sequential detergent extraction was performed as previously described (Jagannathan et al., 2011, doi: 10.1007/978-1-61779-005-8_19 ) with minor modifications. HEK293 and HEK293 HDLBP knockout cell lines (1 15 cm dish per replicate) were grown to ~90 % confluency. Cells were washed with PBS. All further steps were carried out on ice using ice cold reagents and cells were always pelleted at 3000 g for 5 min at 4°C. First, PBS containing 50 µg/ml cycloheximide was added for 10 min. In the meantime cells were scraped using a rubber policeman. After pelleting, the cells were resuspended with 500 µl permeabilization buffer (110 mM KOAc, 25 mM K-HEPES [pH 7. 2], 2.5 mM Mg(OAc)2, 1 mM EGTA, 0.015 % digitonin, 1 mM DTT, 50 µg/ml cycloheximide, complete EDTA-free protease inhibitor cocktail [Roche], 40 U/mL SUPERaseIn [Thermo Fisher Scientifc]) per sample and incubated for 15 min at 4°C on a rotating wheel. After centrifugation the supernatant was collected as the cytosolic fraction. To wash the pellet, 5 ml of washing buffer (110 mM KOAc, 25 mM K-HEPES [pH 7.2], 2.5 mM Mg(OAc)2, 1mM EGTA, 0.004% digitonin, 1 mM DTT, 50 μg/ml cycloheximide) was used. After pelleting, 500 µl lysis buffer (400 mM KOAc, 25 mM K-HEPES [pH 7.2], 15 mM Mg(OAc)2, 0.5 % IGEPAL CA-630, 1 mM DTT, 50 μg/ml cycloheximide, complete EDTA-free protease inhibitor cocktail, 40 U/mL SUPERase•In) per sample was added for 5 min. After centrifugation, the supernatant was collected as the membrane fraction. The remaining pellet  was resuspended with 500 µl lysis buffer, 200 µl 10 % sucrose in lysis buffer was added and the sample were centrifuged at 14000 rpm for 5 min at 4°C. The supernatant was removed, 200 µl wash buffer was added. After centrifucation the supernantant was remvoed and the pellet was collected as the nucleus fraction. Cytosol and membrane fractions were clarified by centrifugation at 7500 g for 10 min at 4°C. 250 µl of each sample was collected and RNA was isolated using Trizol LS (Thermo Fisher Scientific) in combination with RNA Clean & Concentrator-25 kit (Zymo Research) for RNA sequencing.
Illumina TruSeq Stranded mRNA Kit

tag: genotype/variation

value: HDLBP knockout guide 1

tag: cellular compartment

value: Nucleus


title: OUH_miR_134

tag: pair no.


title: OUH_miR_145

tag: metastasis (1= yes; 0=no)


title: OUH_miR_132

tag: tumour type


title: OUH_miR_133

tag: esr1 expression (1=yes; 0=no)


title: Resident, MID35, 1C

value: Resident T cells


title: OUH_miR_129

tag: lymph node status (1=positive; 0=negative)


title: OUH_miR_128

tag: status at last follow up (1=dead, 0=alive)


title: OUH_miR_125


title: HEK293T rna-seq from N_2A15_1

description: RNA-Seq paired end


title: OUH_miR_126


title: Circulating, MID34, 5B

tag: cell subtype

value: Treg


title: OUH_miR_124

value: Carcinoma with metaplasia


title: Circulating, MID33, 4B

tag: organ


title: OUH_miR_122


title: OUH_miR_123


title: OUH_miR_121


title: HEK293T rna-seq from N_293_1

description: RNA-Seq paired end

value: HDLBP WT


title: Circulating, MID32, 3B

tag: cell type


title: OUH_miR_131


title: HEK293T rna-seq from N_293_2

description: RNA-Seq paired end


title: HEK293T rna-seq from M_3C2_2

description: RNA-Seq paired end

value: HDLBP knockout guide 2

value: Membrane


title: Circulating, MID31, 2B


title: OUH_miR_119


title: OUH_miR_120


title: HEK293T rna-seq from N_3C2_2

description: RNA-Seq paired end


title: OUH_miR_017_2


title: OUH_miR_118


title: OUH_miR_130


title: Circulating, MID30, 1B


title: HEK293T rna-seq from M_2A15_2

description: RNA-Seq paired end


title: HEK293T rna-seq from N_3C2_1

description: RNA-Seq paired end

value: replicate 1


title: HEK293T rna-seq from M_3C2_1

description: RNA-Seq paired end


title: Resident, MID29, 5A


title: Resident, MID36, 2C


title: OUH_miR_018_2

value: Mucinous carcinoma


title: HEK293T rna-seq from M_2A15_1

description: RNA-Seq paired end


title: OUH_miR_116


title: rna-seq from Tumor_HDLBP_KO_5

tag: hdlbp

value: HDLBP knockout

value: replicate 4


title: HEK293T rna-seq from M_293_2

description: RNA-Seq paired end

tag: replicate

value: replicate 2


title: OUH_miR_115

value: IDC


title: Resident, MID27, 3A

value: siMLN-PC (photoconverted small intestine draining mesenteric lymph node)


title: HEK293T rna-seq from M_293_1

description: RNA-Seq paired end


title: IP-Smc3_30310_wpl1

description: Reads mapped to SK1 only/calibrated to S.pombe

source_name: Smc3 wpl1Δ IP

growth_protocol:
Cells were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA) for approx. 16 hours. Cells were then diluted to OD(600) = 1.8 and sporulated for 6 hours in SPO media (0.3% Kac) to arrest in prophase I.
S. pombe culture at OD600=0.4 was fixed in 1% formaldehyde for 2hrs, washed twice in TBS and once in FA lysis buffer with 0.1% SDS, and aliquoted into equal pellets all equivalent to 100ml of the original culture. Each S. cerevisiae pellet (4 pellets per sample, each obtained from 50ml of meiotic culture at about OD600=2) was mixed with one S. pombe pellet, for a total of 4 S. cerevisiae and 4 S. pombe pellets per sample.
Overall, each sample contains S. cerevisiae and S. pombe cells in an approximate ratio of 2:1. Mixed pellets were lysed by beating.

tag: chip antibody

value: Homemade rabbit Smc3 antibody

tag: ploidy

value: Diploid (S.c.) / Haploid (S.p.)

tag: cell cycle stage

value: Meiotic prophase I

tag: calibration genome

value: S. pombe cells

tag: background strain

tag: genotype

value: smc3::pCLB2-3HA-SMC3 SMC3 ndt80-delta wpl1-delta


title: IP-Smc3_30311_smc3-2r_wp1

source_name: Smc3 smc3-2R wpl1Δ IP

value: smc3::pCLB2-3HA-SMC3 SMC3-K112R,K113R ndt80-delta wpl1-delta


title: OUH_miR_113

tag: pair no.

tag: tissue

value: human breast tumour


title: OUH_miR_112

tag: metastasis (1= yes; 0=no)

tag: tumour type


title: OUH_miR_137

tag: esr1 expression (1=yes; 0=no)

tag: lymph node status (1=positive; 0=negative)


title: OUH_miR_111

tag: status at last follow up (1=dead, 0=alive)


title: HEK293T rna-seq from C_3C2_2

description: RNA-Seq paired end

tag: cell line

tag: genotype/variation

tag: cellular compartment

value: Cytosol


title: IP-Smc3_29315_wt

source_name: Smc3 WT IP

value: smc3::pCLB2-3HA-SMC3 SMC3 ndt80-delta


title: Resident, MID26, 2A

value: Mesenteric lymph node

tag: cell type

value: Resident T cells

tag: cell subtype

value: Treg

tag: organ


title: INPUT-Smc3_30311_smc3-2r_wp1

description: Reads mapped to SK1 only

source_name: Smc3 smc3-2R wpl1Δ input

tag: chip antibody

value: none (input)

tag: ploidy

tag: cell cycle stage


title: INPUT-Smc3_30310_wpl1

description: Reads mapped to SK1 only

source_name: Smc3 wpl1Δ input

tag: calibration genome

tag: background strain

tag: genotype


title: INPUT-Smc3_29316_smc3-2r

description: Reads mapped to SK1 only

source_name: Smc3 smc3-2R input


title: U-87MG  Survivor

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Library strategy: CRISPR screen
extraction of sgRNA sequences with cutadapt
sgRNA counting and comparison with MAGeCK and the Brunello CRISPR library
Genome_build: hg38
Supplementary_files_format_and_content: gene-level summary

extract_protocol:
Genomic DNA (gDNA) of cell pellets was isolated using a Quick-DNA Miniprep Plus kit (Zymo Research).
PCR was performed on gDNA to construct Illumina sequencing libraries, each containing 5 μg gDNA, according to the Broad Institute protocol for PCR of sgRNAs for Illumina sequencing.

tag: rounds of infection


title: HEK293T rna-seq from C_3C2_1

description: RNA-Seq paired end

value: HDLBP knockout guide 2

tag: replicate

value: replicate 1


title: INPUT-Smc3_29315_wt

description: Reads mapped to SK1 only

source_name: Smc3 WT input


title: Resident, MID28, 4A

tag: tissue


title: U-87MG  Control


title: IP-Smc3_29781_eco1_wpl1

source_name: Smc3 eco1-aa wpl1-delta IP

growth_protocol:
Cells were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA) for approx. 16 hours. Cells were then diluted to OD(600) = 1.8 and sporulated for 6 hours in SPO media (0.3% Kac) to arrest in prophase I.
Cells were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA) for approx. 16 hours. Cells were then diluted to OD(600) = 1.8 and sporulated for 6 hours in SPO media (0.3% Kac) to arrest in prophase I.
S. pombe culture at OD600=0.4 was fixed in 1% formaldehyde for 2hrs, washed twice in TBS and once in FA lysis buffer with 0.1% SDS, and aliquoted into equal pellets all equivalent to 100ml of the original culture. Each S. cerevisiae pellet (4 pellets per sample, each obtained from 50ml of meiotic culture at about OD600=2) was mixed with one S. pombe pellet, for a total of 4 S. cerevisiae and 4 S. pombe pellets per sample.
Overall, each sample contains S. cerevisiae and S. pombe cells in an approximate ratio of 2:1. Mixed pellets were lysed by beating.

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta Eco1-FRB-GFP wpl1-delta


title: IP-Smc3_29750_wpl1

source_name: Smc3 wpl1-delta IP

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta wpl1-delta


title: HEK293T rna-seq from C_2A15_1

description: RNA-Seq paired end

value: HDLBP knockout guide 1


title: IP-Smc3_29316_smc3-2r

source_name: Smc3 smc3-2R IP

value: Homemade rabbit Smc3 antibody

value: Diploid (S.c.) / Haploid (S.p.)


title: HEK293T rna-seq from C_2A15_2

description: RNA-Seq paired end

value: replicate 2


title: IP-Smc3_28719_wt

value: S. pombe cells

value: Meiotic prophase I

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta


title: HEK293T rna-seq from C_293_2

description: RNA-Seq paired end

value: HDLBP WT

value: Cytosol


title: AN4-S37-d25-1

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

data_processing:
QIAGEN GeneGlobe RNA-seq bioinformatics tool
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: normalised counts

source_name: Cortical neuronal progenitor cells

growth_protocol: hESCs were cultured on Laminin-521 (BioLamina) in StemMACS iPS-Brew XF self-renewal media (Miltenyi).

extract_protocol:
Total RNA was extracted with the QIAGEN RNeasy kit
QIAseq UPX 3' Transcriptome Kit

treatment_protocol: hESCs were differentiated into cortical neuronal progenitor cells for 25 days using a dual-Smad inhibition protocol

tag: differentiation


title: INPUT-Smc3_29781_eco1_wpl1

description: Reads mapped to SK1 only

source_name: Smc3 eco1-aa wpl1-delta input


title: AN5-S37-d25-1


title: IP-Smc3_28720_eco1-aa

source_name: Smc3 eco1-aa IP

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta Eco1-FRB-GFP


title: RNaseH2A_R2

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt v1.13
Mapping to the hg38 genome was performed with STAR v2.6.1d.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1
Mapped reads were de-duplicated with Picard (ChIP-seq and DRIP-seq)
Bigwig files were generated with the Deeptools2 v2.5.0.1 bamCoverage tool
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
RNA were purified from the chromatin fraction. DNA were purified from chromatin IP products.
For Chromatin RNA-seq, libraries were prepared using Illumina's TruSeq Stranded Total RNA library Preparation Kit according to Illumina's instructions. For ChIP-seq and DRIP-seq, libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions.

treatment_protocol: siRNAs were transfected for 72 hours according to Lipofectamine 2000 reagent protocol.

value: HeLa

tag: antibody

value: RNASEH2A Antibody; Proteintech; 16132-1-AP

tag: sirna


title: INPUT-Smc3_28719_wt

first: Daniel

last: Robertson

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

description: Reads mapped to SK1 only

value: none (input)


title: AN6-Shef4-d26-1

tag: cell line


title: INPUT-Smc3_28720_eco1-aa

description: Reads mapped to SK1 only

source_name: Smc3 eco1-aa input


title: INPUT-Smc3_29750_wpl1

description: Reads mapped to SK1 only

source_name: Smc3 wpl1-delta input


title: RNaseH2A_R1


title: OUH_miR_114

source_name: Primary breast tumour of patient without relapse

tag: pair no.

tag: metastasis (1= yes; 0=no)

tag: tumour type

value: IDC

tag: esr1 expression (1=yes; 0=no)

tag: lymph node status (1=positive; 0=negative)

tag: status at last follow up (1=dead, 0=alive)

source_name: common reference pool of all samples

value: human breast tumour


title: AN4-S8-d25-1


title: IP-Rec8_29781_eco1_wpl1

description: Reads mapped to SK1

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt v3.0 (MAPQ 10, min. length 65)
ChIP-Seq reads were mapped with MiniMap2 v2.10-r763-dirty (-ax sr) to S.cerevisiae SK1
Unmapped reads were filtered using samtools v1.9
rDNA regions were removed from chrXII (saturated with reads) using bedtools v2.27.0
chrMito was excluded with samtools
Genome_build: S.cerevisiae SK1
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization)

source_name: Rec8 eco1-aa wpl1Δ IP

extract_protocol:
Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 60 seconds four times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/0.1% SDS before sonicating in a Bioruptor (Diagenode) for two times 30 cycles at 30sec on/off intervals at "High" setting. The supernatant was subject to IP with homemade anti-Rec8 antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.
DNA was blunted using NEB Quick Blunting kit followed by Ampure XP bead purification of fragments over 100bp. dA tails were added using Klenow (exo-) and NextFlex adaptors ligated to each sample. This was followed by two Ampure purifications of fragments over 100bp and then fragments over 150-200bp. Libraries were amplified using NextFlex primers and Phusion DNA polymerase. Lastly, double-sided Ampure purification was carried out to obtain fragments between 100-300bp in size.

treatment_protocol: Cells carrying ndt80Δ deletion were arrested in meiotic prophase I, fixed in 1% formaldehyde for 2hrs before washing twice in TBS and once in FA lysis buffer with 0.1% SDS.

tag: chip antibody

value: Homemade Rec8 antibody

tag: ploidy

value: Diploid

tag: cell cycle stage

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta Eco1-FRB-GFP wpl1-delta


title: IP-Rec8_28720_eco1-aa

description: Reads mapped to SK1

source_name: Rec8 eco1-aa IP

tag: background strain

tag: genotype


title: AN5-S9-d25-1


title: PolII

source_name: PolII

value: RNA Polymerase II/POLR2A Antibody; Novus Biologicals; NBP2-32080


title: IP-Rec8_29750_wpl1

description: Reads mapped to SK1

source_name: Rec8 wpl1Δ IP

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta wpl1-delta


title: HEK293T rna-seq from C_293_1

description: RNA-Seq paired end

source_name: HEK293 Flp-In T-REx embryonic kidney cell line

tag: genotype/variation

tag: cellular compartment

tag: replicate

value: replicate 1


title: OUH_miR_127

source_name: Primary breast tumour of patient with relapse

tag: tissue


title: IP-Rec8_28719_wt

description: Reads mapped to SK1

source_name: Rec8 WT IP


title: AN4-S34-d25-1

tag: differentiation


title: INPUT-Rec8_29781_eco1_wpl1

description: Reads mapped to SK1

source_name: Rec8 eco1-aa wpl1Δ input


title: INPUT-Rec8_29750_wpl1

description: Reads mapped to SK1

source_name: Rec8 wpl1Δ input


title: AN4-S9-d25-1

tag: cell line


title: Resident, MID38, 4C

source_name: Mesenteric lymph node

value: Mesenteric lymph node

tag: cell type

value: Resident T cells

tag: cell subtype

value: Tcell

tag: organ

value: siMLN-PC (photoconverted small intestine draining mesenteric lymph node)


title: INPUT-Rec8_28720_eco1-aa

description: Reads mapped to SK1

source_name: Rec8 eco1-aa input

value: Meiotic prophase I


title: INPUT-Rec8_28719_wt

description: Reads mapped to SK1

source_name: Rec8 WT input

value: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta


title: Input_siLuc_DRIP_R1

data_processing:
Library strategy: DRIP-seq
Adapters were trimmed with Cutadapt v1.13
Mapping to the hg38 genome was performed with STAR v2.6.1d.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1
Mapped reads were de-duplicated with Picard (ChIP-seq and DRIP-seq)
Bigwig files were generated with the Deeptools2 v2.5.0.1 bamCoverage tool
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

value: HeLa

tag: antibody

tag: sirna

value: Scramble siRNA


title: Input_siLuc_DRIP_R2


title: AN6-S8-d0-1

source_name: hESCs